Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold481
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1334154
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 122349 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1215335 original size:21 final size:21
Alignment explanation
Indices: 1215311--1215393 Score: 125
Period size: 21 Copynumber: 4.0 Consensus size: 21
1215301 CAACATACAC
1215311 CATAGCATTGAAATCTCATAG
1 CATAGCATTGAAATCTCATAG
1215332 CATAGCATTGAAATCTCATAG
1 CATAGCATTGAAATCTCATAG
* *
1215353 CATACCATTGGAATCTCATAG
1 CATAGCATTGAAATCTCATAG
1215374 CATAGCA-T-ACAATCTCATAG
1 CATAGCATTGA-AATCTCATAG
1215394 AATCGTATTC
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
20 11 0.19
21 46 0.81
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (21 bp):
CATAGCATTGAAATCTCATAG
Found at i:1215660 original size:21 final size:21
Alignment explanation
Indices: 1215634--1215713 Score: 117
Period size: 21 Copynumber: 3.8 Consensus size: 21
1215624 CATTTCAATT
1215634 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
1215655 TCTCATAGCATAGCATACAAA
1 TCTCATAGCATAGCATACAAA
*
1215676 TCTCATAGCATATCATTA-AAA
1 TCTCATAGCATAGCA-TACAAA
* *
1215697 TCGCATACCATAGCATA
1 TCTCATAGCATAGCATA
1215714 GCATAAATTT
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
20 2 0.04
21 50 0.93
22 2 0.04
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (21 bp):
TCTCATAGCATAGCATACAAA
Found at i:1217402 original size:24 final size:24
Alignment explanation
Indices: 1217370--1217419 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1217360 AATTCCGGAA
1217370 ACTGCAAAATTTCATATTAACATG
1 ACTGCAAAATTTCATATTAACATG
1217394 ACTGCAAAATTTCATATTAACATG
1 ACTGCAAAATTTCATATTAACATG
1217418 AC
1 AC
1217420 AATTGGTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (24 bp):
ACTGCAAAATTTCATATTAACATG
Found at i:1230593 original size:172 final size:170
Alignment explanation
Indices: 1230301--1230744 Score: 728
Period size: 172 Copynumber: 2.6 Consensus size: 170
1230291 GTAAGGCTTT
1230301 AGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATAGCATT
1 AGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATA-C--T
* *
1230366 A-TAACCTTGGTCAAGTTCGAAAATCAGCATTGGTGGATACTTTTTGTTGGAGTTATGGGACTTT
63 ACTATCCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGACTTT
1230430 GACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGTA
128 GACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGTA
* *
1230473 AGCGCTCTCATGCCCACAAATTTTGACGGATTTTCATTAAATTTATGCCAAATGTTTATACTACT
1 AGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACTACT
*
1230538 GACTCCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTTGAGTTATGGGACTTTG
66 -A-TCCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGACTTTG
1230603 ACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGTA
129 ACCACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGTA
* *
1230645 AGTGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACCACT
1 AGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACTACT
** *
1230710 AATACCTTGGTCAAGTTCCTAAATCAGCCTTGGTC
66 -AT-CCTTGGTCAAGTTCGAAAATCAGCATTGGTC
1230745 AATAGACTCT
Statistics
Matches: 255, Mismatches: 13, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
169 2 0.01
170 1 0.00
171 3 0.01
172 249 0.98
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (170 bp):
AGCGCTCTCATGCCTACAAATTTTGACGGATTTTCATTAAATTTATACCAAATGTTTATACTACT
ATCCTTGGTCAAGTTCGAAAATCAGCATTGGTCGATACTTTTTGTTGGAGTTATGGGACTTTGAC
CACAATAATGACTCCGTTTTATCCAAAAATTGACCTTGTA
Found at i:1241065 original size:168 final size:168
Alignment explanation
Indices: 1240718--1241232 Score: 628
Period size: 168 Copynumber: 3.0 Consensus size: 168
1240708 GAACCATAAG
* *
1240718 ACCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAATGTAGATTCAGAA-TTGTGAAAAT
1 ACCAGGAAAGCTGAAACTTGTGTGGAAGCATTCTCAGGTAGTGTAGATTCA-AAGTTGTGAAAAT
* * * * * * *
1240782 CATGATCCCCGGGTGTAGAGTGGGGCCACAAT--GGGGGTGTTAAAGTTTTACAAATGAATATAT
65 CATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGGGGGTGAAGTTTTACATAGGAATATAT
*
1240845 AGAGTAAATCTTTAAAAATCTTCTTCTCTGAAACTAATC
130 AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
* *
1240884 AGCCAGGAAAGCTGAAACTTGTGTGGAAACATTCTCAGGTAGTGTAGATTCAAAGTTGTGGAAAT
1 A-CCAGGAAAGCTGAAACTTGTGTGGAAGCATTCTCAGGTAGTGTAGATTCAAAGTTGTGAAAAT
* * * *
1240949 CATGA-CCCCGGGGGTAGGGGGGGGGCAAAATGGGGGGGGGGCGAAGTTTTACATAGGAATATAT
65 CATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGGGGGTGAAGTTTTACATAGGAATATAT
* * *
1241013 AGAGTAAATATTTAAAAATCTTCTCCTCAGAAACTCATC
130 AGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
*
1241052 TACCAGGAAAGCTGAAACTTGTGTGGAAGTA-TCATCAGGTAGACGTGTAGATTCAAAGTTGTGA
1 -ACCAGGAAAGCTGAAACTTGTGTGGAAGCATTC-TCAGGT--A-GTGTAGATTCAAAGTTGTGA
* * *
1241116 AAATCATGATCCCTGGGGGTAGGGTGAGGCCACATTGGGGGGGGGGGGGGGGTGTTAAAGTTTTA
61 AAATCATGATCCCCGGGGGTAGGGTGGGGCCACAAT------GGGGGGGGGGTG---AAGTTTTA
*
1241181 CATAGGAATATATAGAGTAAATCTTTAAGAATCTTCTTCTCA-AAACTAATC
117 CATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
1241232 A
1 A
1241233 GCAAGATGAT
Statistics
Matches: 297, Mismatches: 33, Indels: 25
0.84 0.09 0.07
Matches are distributed among these distances:
166 24 0.08
167 63 0.21
168 93 0.31
169 1 0.00
170 1 0.00
171 28 0.09
172 20 0.07
178 11 0.04
179 1 0.00
180 8 0.03
181 47 0.16
ACGTcount: A:0.32, C:0.14, G:0.27, T:0.26
Consensus pattern (168 bp):
ACCAGGAAAGCTGAAACTTGTGTGGAAGCATTCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATC
ATGATCCCCGGGGGTAGGGTGGGGCCACAATGGGGGGGGGGTGAAGTTTTACATAGGAATATATA
GAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATC
Found at i:1242752 original size:22 final size:22
Alignment explanation
Indices: 1242727--1242803 Score: 100
Period size: 22 Copynumber: 3.4 Consensus size: 22
1242717 AATACATATA
*
1242727 TTACACATATAAAATATTTGTT
1 TTACACATATAAAATATGTGTT
1242749 TTACACATATAAAATATGTGTT
1 TTACACATATAAAATATGTGTT
* *
1242771 TTACAAATATAAGATATGCTGTGT
1 TTACACATATAAAATATG-TGT-T
1242795 TTAACACAT
1 TT-ACACAT
1242804 GATTAAACAC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
22 37 0.77
23 3 0.06
24 3 0.06
25 5 0.10
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.40
Consensus pattern (22 bp):
TTACACATATAAAATATGTGTT
Found at i:1242814 original size:12 final size:12
Alignment explanation
Indices: 1242797--1242834 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
1242787 TGCTGTGTTT
1242797 AACACATGATTA
1 AACACATGATTA
1242809 AACACAT-ATTA
1 AACACATGATTA
*
1242820 AACACTTG-TTA
1 AACACATGATTA
1242831 AACA
1 AACA
1242835 TGTGTGAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 17 0.71
12 7 0.29
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.26
Consensus pattern (12 bp):
AACACATGATTA
Found at i:1243410 original size:13 final size:12
Alignment explanation
Indices: 1243385--1243420 Score: 56
Period size: 13 Copynumber: 3.0 Consensus size: 12
1243375 TAATCCAAAT
1243385 TTCTTATATTTA
1 TTCTTATATTTA
1243397 TTCTTATAATTTA
1 TTCTTAT-ATTTA
1243410 TTCTT-TATTTA
1 TTCTTATATTTA
1243421 ACTTTCCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 5 0.22
12 8 0.35
13 10 0.43
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (12 bp):
TTCTTATATTTA
Found at i:1245570 original size:186 final size:186
Alignment explanation
Indices: 1245250--1246270 Score: 1580
Period size: 186 Copynumber: 5.5 Consensus size: 186
1245240 TTTATTGCCA
* *
1245250 TTTGGAACTTTGCCAAAAATTGT-ATTTTTCCTGTT-TTTCACAGTTAATTTTGCATTGTTTGGA
1 TTTGGCACTTTGCCAAAAATCGTAATTTTT-CTGTTATTT-ACAGTTAATTTTGCATTGTTTGGA
* *
1245313 AAATAGATATAAGAAATCTAAATATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATG
64 AAATGGATATAAGAAATCTAATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATG
* * *
1245378 AAAACATTTATGGAGAAACATTCAAAAAAAAAAATATCATGACATAGAAATTATATGT
129 AAAACATTTATGGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGT
* *
1245436 TTTGGCACTTTGCCAAAAATCGTAATTTTTCTGTTATTTTCAGTTAATTTTGCATTGATTGGAAA
1 TTTGGCACTTTGCCAAAAATCGTAATTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAA
* *
1245501 ATGGATTTTAGAAATCTAATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAA
66 ATGGATATAAGAAATCTAATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAA
* * *
1245566 AACATTTATGGAGAAACACTCAAGAACAAAAATATTATGACATAAAAATTGTATGT
131 AACATTTATGGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGT
* *
1245622 TTTGGCACCTTGCCAAAAATCGTATTTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAA
1 TTTGGCACTTTGCCAAAAATCGTAATTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAA
* * * *
1245687 TTGGATATAAGAAATTTATTTATAAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAA
66 ATGGATATAAGAAATCTAATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAA
*
1245752 AACATTTTTGGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGTT
131 AACATTTATGGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATG-T
* * * *
1245809 TTTTGCACTTTGCCAAAAATCGTAATTTTTCTGTTATTTTCAGTTAATTTTGCATTGATCGGAAA
1 TTTGGCACTTTGCCAAAAATCGTAATTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAA
1245874 ATGGATATAAGAAATCTAATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAA
66 ATGGATATAAGAAATCTAATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAA
* * * *
1245939 AACATTTATGGAGAAACACTCAAGAACAAAAATATTATGACATAAAAATTTTATGT
131 AACATTTATGGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGT
* *
1245995 TTTGGCACCTTGCCAAAAATCGTATTTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAA
1 TTTGGCACTTTGCCAAAAATCGTAATTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAA
* * * * * *
1246060 TTGGATATAAAAAATTTATTTATAAGCAATAAATTATCAAACATAGAACCTTTAATATAAATGAA
66 ATGGATATAAGAAATCTAATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAA
* * *
1246125 AACATTTATGGAAAAACATTCGAGAAAAAAAATATTATGACATAGAAATTGTATAT
131 AACATTTATGGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGT
* * * *
1246181 TTTGGCACTTTGCCAAAAATCAT-ATTTTCCCTGTTAATCACAGTTAATTTTGCATTGTTTGGAA
1 TTTGGCACTTTGCCAAAAATCGTAATTTT-TCTGTTATTTACAGTTAATTTTGCATTGTTTGGAA
*
1246245 AATGGATAAAAGAAATCTAATTATTA
65 AATGGATATAAGAAATCTAATTATTA
1246271 AGAGTCAAAA
Statistics
Matches: 757, Mismatches: 74, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
185 4 0.01
186 573 0.76
187 180 0.24
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (186 bp):
TTTGGCACTTTGCCAAAAATCGTAATTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAA
ATGGATATAAGAAATCTAATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAA
AACATTTATGGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGT
Found at i:1245961 original size:373 final size:372
Alignment explanation
Indices: 1245259--1246270 Score: 1722
Period size: 373 Copynumber: 2.7 Consensus size: 372
1245249 ATTTGGAACT
* * * *
1245259 TTGCCAAAAATTGTATTTTTCCTGTT-TTTCACAGTTAATTTTGCATTGTTTGGAAAATAGATAT
1 TTGCCAAAAATCGTATTTTTTCTGTTATTT-ACAGTTAATTTTGCATTGTTTGGAAATTGGATAT
* ** *
1245323 AAGAAATCTAAATATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTA
65 AAGAAATTTATTTATAAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTA
* * *
1245388 TGGAGAAACATTCAAAAAAAAAAATATCATGACATAGAAATTATATGTTTTGGCACTTTGCCAAA
130 TGGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGTTTTGGCACTTTGCCAAA
* *
1245453 AATCGTAATTTTTCTGTTATTTTCAGTTAATTTTGCATTGATTGGAAAATGGATTTTAGAAATCT
195 AATCGTAATTTTTCTGTTATTTTCAGTTAATTTTGCATTGATTGGAAAATGGATATAAGAAATCT
1245518 AATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTATGGAGAAAC
260 AATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTATGGAGAAAC
1245583 ACTCAAGAACAAAAATATTATGACATAAAAATTGTATGTTTTGGCACC
325 ACTCAAGAACAAAAATATTATGACATAAAAATTGTATGTTTTGGCACC
1245631 TTGCCAAAAATCGTATTTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAATTGGATATA
1 TTGCCAAAAATCGTATTTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAATTGGATATA
*
1245696 AGAAATTTATTTATAAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTTT
66 AGAAATTTATTTATAAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTAT
*
1245761 GGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGTTTTTTGCACTTTGCCAAA
131 GGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATG-TTTTGGCACTTTGCCAAA
*
1245826 AATCGTAATTTTTCTGTTATTTTCAGTTAATTTTGCATTGATCGGAAAATGGATATAAGAAATCT
195 AATCGTAATTTTTCTGTTATTTTCAGTTAATTTTGCATTGATTGGAAAATGGATATAAGAAATCT
1245891 AATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTATGGAGAAAC
260 AATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTATGGAGAAAC
*
1245956 ACTCAAGAACAAAAATATTATGACATAAAAATTTTATGTTTTGGCACC
325 ACTCAAGAACAAAAATATTATGACATAAAAATTGTATGTTTTGGCACC
1246004 TTGCCAAAAATCGTATTTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAATTGGATATA
1 TTGCCAAAAATCGTATTTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAATTGGATATA
* *
1246069 AAAAATTTATTTATAAGCAATAAATTATCAAACATAGAACCTTTAATATAAATGAAAACATTTAT
66 AGAAATTTATTTATAAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTAT
* * *
1246134 GGAAAAACATTCGAGAAAAAAAATATTATGACATAGAAATTGTATATTTTGGCACTTTGCCAAAA
131 GGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGTTTTGGCACTTTGCCAAAA
* * * ** * *
1246199 ATCAT-ATTTTCCCTGTTAATCACAGTTAATTTTGCATTGTTTGGAAAATGGATAAAAGAAATCT
196 ATCGTAATTTT-TCTGTTATTTTCAGTTAATTTTGCATTGATTGGAAAATGGATATAAGAAATCT
1246263 AATTATTA
260 AATTATTA
1246271 AGAGTCAAAA
Statistics
Matches: 605, Mismatches: 32, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
371 5 0.01
372 236 0.39
373 364 0.60
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (372 bp):
TTGCCAAAAATCGTATTTTTTCTGTTATTTACAGTTAATTTTGCATTGTTTGGAAATTGGATATA
AGAAATTTATTTATAAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTAT
GGAGAAACATTCAAGAAAAAAAATATTATGACATAGAAATTGTATGTTTTGGCACTTTGCCAAAA
ATCGTAATTTTTCTGTTATTTTCAGTTAATTTTGCATTGATTGGAAAATGGATATAAGAAATCTA
ATTATTAGCAATAAATTGTCAAACATAGAACCTTTAATATAAATGAAAACATTTATGGAGAAACA
CTCAAGAACAAAAATATTATGACATAAAAATTGTATGTTTTGGCACC
Found at i:1264278 original size:42 final size:42
Alignment explanation
Indices: 1264221--1264304 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
1264211 ATTTAAAAGA
1264221 AAAAAAACTGCATTAGCCGTCACGATTTTAAAACTTGACTAG
1 AAAAAAACTGCATTAGCCGTCACGATTTTAAAACTTGACTAG
*
1264263 AAAAAAACTGCATTAGCCGTCACGATTTTAAAAGTTGACTAG
1 AAAAAAACTGCATTAGCCGTCACGATTTTAAAACTTGACTAG
1264305 TTATTTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.40, C:0.18, G:0.15, T:0.26
Consensus pattern (42 bp):
AAAAAAACTGCATTAGCCGTCACGATTTTAAAACTTGACTAG
Found at i:1268618 original size:21 final size:21
Alignment explanation
Indices: 1268592--1268661 Score: 90
Period size: 21 Copynumber: 3.3 Consensus size: 21
1268582 AATCCTATCG
1268592 TATCGTGCGTGTATACTGTTC
1 TATCGTGCGTGTATACTGTTC
* *
1268613 TATCGTGCGT-TAATCCT-ATC
1 TATCGTGCGTGT-ATACTGTTC
1268633 GTATCGTGCGTGTATACTGTTC
1 -TATCGTGCGTGTATACTGTTC
1268655 TATCGTG
1 TATCGTG
1268662 TGTTAATCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
20 3 0.07
21 35 0.85
22 3 0.07
ACGTcount: A:0.16, C:0.20, G:0.23, T:0.41
Consensus pattern (21 bp):
TATCGTGCGTGTATACTGTTC
Found at i:1268641 original size:42 final size:42
Alignment explanation
Indices: 1268582--1268671 Score: 171
Period size: 42 Copynumber: 2.1 Consensus size: 42
1268572 ATTGCATATC
1268582 AATCCTATCGTATCGTGCGTGTATACTGTTCTATCGTGCGTT
1 AATCCTATCGTATCGTGCGTGTATACTGTTCTATCGTGCGTT
*
1268624 AATCCTATCGTATCGTGCGTGTATACTGTTCTATCGTGTGTT
1 AATCCTATCGTATCGTGCGTGTATACTGTTCTATCGTGCGTT
1268666 AATCCT
1 AATCCT
1268672 GTCAGATTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.18, C:0.21, G:0.20, T:0.41
Consensus pattern (42 bp):
AATCCTATCGTATCGTGCGTGTATACTGTTCTATCGTGCGTT
Found at i:1268673 original size:21 final size:21
Alignment explanation
Indices: 1268592--1268673 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
1268582 AATCCTATCG
*
1268592 TATCGTGCGTGT-ATACTGTTC
1 TATCGTGCGT-TAATCCTGTTC
*
1268613 TATCGTGCGTTAATCCT-ATC
1 TATCGTGCGTTAATCCTGTTC
*
1268633 GTATCGTGCGTGT-ATACTGTTC
1 -TATCGTGCGT-TAATCCTGTTC
*
1268655 TATCGTGTGTTAATCCTGT
1 TATCGTGCGTTAATCCTGT
1268674 CAGATTTATC
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.08
21 43 0.86
22 3 0.06
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.43
Consensus pattern (21 bp):
TATCGTGCGTTAATCCTGTTC
Found at i:1272967 original size:2 final size:2
Alignment explanation
Indices: 1272962--1273034 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
1272952 ATATATATAT
1272962 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1273004 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1273035 ACTTNNNNNN
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1273102 original size:2 final size:2
Alignment explanation
Indices: 1273097--1273146 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
1273087 NNNTATATAT
*
1273097 AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1273139 AG AG AG AG
1 AG AG AG AG
1273147 GGTGACTGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1274620 original size:2 final size:2
Alignment explanation
Indices: 1274615--1274659 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1274605 GTGTGTGTGT
1274615 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1274657 GA G
1 GA G
1274660 TATAGGGATC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1280384 original size:17 final size:18
Alignment explanation
Indices: 1280362--1280395 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1280352 AACAACGAAA
1280362 TCGATA-TTTGTTTAATT
1 TCGATATTTTGTTTAATT
1280379 TCGATATTTTGTTTAAT
1 TCGATATTTTGTTTAAT
1280396 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.24, C:0.06, G:0.12, T:0.59
Consensus pattern (18 bp):
TCGATATTTTGTTTAATT
Found at i:1292125 original size:8 final size:8
Alignment explanation
Indices: 1292112--1292154 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
1292102 TTTCCTCTGC
*
1292112 GTCCGTCA
1 GTCCGTCT
1292120 GTCCGTCT
1 GTCCGTCT
1292128 GTCCGTCT
1 GTCCGTCT
* *
1292136 GTCTGTCC
1 GTCCGTCT
1292144 GTCCGTCT
1 GTCCGTCT
1292152 GTC
1 GTC
1292155 TGTCCCACTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.02, C:0.37, G:0.26, T:0.35
Consensus pattern (8 bp):
GTCCGTCT
Found at i:1292139 original size:12 final size:12
Alignment explanation
Indices: 1292120--1292159 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1292110 GCGTCCGTCA
1292120 GTCCGTCTGTCC
1 GTCCGTCTGTCC
*
1292132 GTCTGTCTGTCC
1 GTCCGTCTGTCC
*
1292144 GTCCGTCTGTCT
1 GTCCGTCTGTCC
1292156 GTCC
1 GTCC
1292160 CACTTCAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.00, C:0.38, G:0.25, T:0.38
Consensus pattern (12 bp):
GTCCGTCTGTCC
Found at i:1292151 original size:16 final size:16
Alignment explanation
Indices: 1292111--1292159 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
1292101 CTTTCCTCTG
* *
1292111 CGTCCGTCAGTCCGTC
1 CGTCCGTCTGTCTGTC
*
1292127 TGTCCGTCTGTCTGTC
1 CGTCCGTCTGTCTGTC
1292143 CGTCCGTCTGTCTGTC
1 CGTCCGTCTGTCTGTC
1292159 C
1 C
1292160 CACTTCAGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.02, C:0.39, G:0.24, T:0.35
Consensus pattern (16 bp):
CGTCCGTCTGTCTGTC
Found at i:1312283 original size:2 final size:2
Alignment explanation
Indices: 1312276--1312350 Score: 141
Period size: 2 Copynumber: 37.5 Consensus size: 2
1312266 TATTTTTATA
*
1312276 CT CT CT CT CT CT CT CT CT CT CT CT CG CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1312318 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1312351 AAACAACTAC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.00, C:0.51, G:0.01, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1319254 original size:9 final size:9
Alignment explanation
Indices: 1319236--1319268 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1319226 AATTAAATGA
1319236 AAAT-AAAT
1 AAATAAAAT
1319244 AAATAAAAT
1 AAATAAAAT
*
1319253 AAAAAAAAT
1 AAATAAAAT
1319262 AAATAAA
1 AAATAAA
1319269 TATATATACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.18
9 18 0.82
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (9 bp):
AAATAAAAT
Found at i:1319256 original size:18 final size:19
Alignment explanation
Indices: 1319225--1319268 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
1319215 AAAAGAGATA
* *
1319225 AAATTAAATGAAAATAAAT
1 AAATAAAATGAAAAAAAAT
1319244 AAATAAAAT-AAAAAAAAT
1 AAATAAAATGAAAAAAAAT
1319262 AAATAAA
1 AAATAAA
1319269 TATATATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 15 0.65
19 8 0.35
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.20
Consensus pattern (19 bp):
AAATAAAATGAAAAAAAAT
Found at i:1323517 original size:12 final size:12
Alignment explanation
Indices: 1323500--1323526 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1323490 TACATGCATG
1323500 AAAAAATGAAAA
1 AAAAAATGAAAA
1323512 AAAAAATGAAAA
1 AAAAAATGAAAA
1323524 AAA
1 AAA
1323527 GAAAATAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAAATGAAAA
Done.