Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold334
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: 1116604
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.28
Warning! 144470 characters in sequence are not A, C, G, or T
File 7 of 6
Found at i:1068024 original size:39 final size:39
Alignment explanation
Indices: 1067970--1068097 Score: 140
Period size: 39 Copynumber: 3.3 Consensus size: 39
1067960 ATATAGTTTT
*
1067970 TGGACGGGTACATTGATATTAT-AGCTCTCTACAAGTACA
1 TGGACTGGTACATTGATATTATAAGCTCTCTACAAGTA-A
* *
1068009 TGGACTGGTACATTGATATTATAAGAT-TCTACAAGTAT
1 TGGACTGGTACATTGATATTATAAGCTCTCTACAAGTAA
* * *
1068047 TGGA-TAAGTACATTGATATCATAAGC-C-CTGCAAGTAA
1 TGGACT-GGTACATTGATATTATAAGCTCTCTACAAGTAA
1068084 TTGGACTGGTACAT
1 -TGGACTGGTACAT
1068098 ACGTATTTTA
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 9 0.12
38 31 0.41
39 32 0.43
40 3 0.04
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (39 bp):
TGGACTGGTACATTGATATTATAAGCTCTCTACAAGTAA
Found at i:1068096 original size:38 final size:38
Alignment explanation
Indices: 1067969--1068097 Score: 131
Period size: 38 Copynumber: 3.4 Consensus size: 38
1067959 GATATAGTTT
*
1067969 TTGGACGGGTACATTGATATTAT-AGCTCTCTACAAGTACA
1 TTGGACTGGTACATTGATATTATAAGC-C-CTACAAGTA-A
**
1068009 -TGGACTGGTACATTGATATTATAAGATTCTACAAGT-A
1 TTGGACTGGTACATTGATATTATAAG-CCCTACAAGTAA
* * *
1068046 TTGGA-TAAGTACATTGATATCATAAGCCCTGCAAGTAA
1 TTGGACT-GGTACATTGATATTATAAGCCCTACAAGTAA
1068084 TTGGACTGGTACAT
1 TTGGACTGGTACAT
1068098 ACGTATTTTA
Statistics
Matches: 74, Mismatches: 9, Indels: 14
0.76 0.09 0.14
Matches are distributed among these distances:
37 9 0.12
38 33 0.45
39 30 0.41
40 2 0.03
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (38 bp):
TTGGACTGGTACATTGATATTATAAGCCCTACAAGTAA
Found at i:1075540 original size:43 final size:43
Alignment explanation
Indices: 1075454--1075580 Score: 182
Period size: 43 Copynumber: 2.9 Consensus size: 43
1075444 ATAGATCTTT
** ** *
1075454 TCTCGTAATAACGAGAAAATTAACTCGTAATAACGAGAAAATTA
1 TCTCGTAATAACGAG-ATCTTTTCTCGTAATAACGAGATAATTA
1075498 TCTCGTAATAACGAGATCTTTTCTCGTAATAACGAGATAATTA
1 TCTCGTAATAACGAGATCTTTTCTCGTAATAACGAGATAATTA
* *
1075541 ACTCGTAATAACGAGATCTTTTCTCGTAATTACGAGATAA
1 TCTCGTAATAACGAGATCTTTTCTCGTAATAACGAGATAA
1075581 AAATATTTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
43 61 0.80
44 15 0.20
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (43 bp):
TCTCGTAATAACGAGATCTTTTCTCGTAATAACGAGATAATTA
Found at i:1075550 original size:65 final size:64
Alignment explanation
Indices: 1075446--1075578 Score: 212
Period size: 65 Copynumber: 2.1 Consensus size: 64
1075436 CATTTTATAT
1075446 AGATCTTTTCTCGTAATAACGAGAAAATTAACTCGTAATAACGAGAAAATTATCTCGTAATAACG
1 AGATCTTTTCTCGTAATAACGAGAAAATTAACTCGTAATAACGAG-AAATTATCTCGTAATAACG
* ** * *
1075511 AGATCTTTTCTCGTAATAACGAGATAATTAACTCGTAATAACGAGATCTTTTCTCGTAATTACG
1 AGATCTTTTCTCGTAATAACGAGAAAATTAACTCGTAATAACGAGAAATTATCTCGTAATAACG
1075575 AGAT
1 AGAT
1075579 AAAAATATTT
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
64 19 0.30
65 44 0.70
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (64 bp):
AGATCTTTTCTCGTAATAACGAGAAAATTAACTCGTAATAACGAGAAATTATCTCGTAATAACG
Found at i:1075557 original size:22 final size:22
Alignment explanation
Indices: 1075454--1075580 Score: 159
Period size: 22 Copynumber: 5.9 Consensus size: 22
1075444 ATAGATCTTT
*
1075454 TCTCGTAATAACGAGAAAATTA
1 TCTCGTAATAACGAGATAATTA
* *
1075476 ACTCGTAATAACGAGAAAATTA
1 TCTCGTAATAACGAGATAATTA
* *
1075498 TCTCGTAATAACGAGAT-CTTT
1 TCTCGTAATAACGAGATAATTA
1075519 TCTCGTAATAACGAGATAATTA
1 TCTCGTAATAACGAGATAATTA
* * *
1075541 ACTCGTAATAACGAGAT-CTTT
1 TCTCGTAATAACGAGATAATTA
*
1075562 TCTCGTAATTACGAGATAA
1 TCTCGTAATAACGAGATAA
1075581 AAATATTTTT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
21 36 0.40
22 54 0.60
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (22 bp):
TCTCGTAATAACGAGATAATTA
Found at i:1080717 original size:8 final size:8
Alignment explanation
Indices: 1080704--1080729 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1080694 TTCTGCAGAT
1080704 CAATTGTA
1 CAATTGTA
1080712 CAATTGTA
1 CAATTGTA
1080720 CAATTGTA
1 CAATTGTA
1080728 CA
1 CA
1080730 TGTATCCGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (8 bp):
CAATTGTA
Found at i:1082634 original size:25 final size:25
Alignment explanation
Indices: 1082594--1082641 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
1082584 GAAAAAGTGA
*
1082594 TGTTGTACACGAGGTGTATACAACG
1 TGTTGTACAAGAGGTGTATACAACG
*
1082619 TGTTGTACAAGGGGTGTATACAA
1 TGTTGTACAAGAGGTGTATACAA
1082642 TCGGTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (25 bp):
TGTTGTACAAGAGGTGTATACAACG
Found at i:1085857 original size:25 final size:25
Alignment explanation
Indices: 1085823--1085870 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1085813 GAAAAAGCGA
*
1085823 TTGTATACACCCCTTGTACAACACG
1 TTGTATACACCCCGTGTACAACACG
1085848 TTGTATACACCCCGTGTACAACA
1 TTGTATACACCCCGTGTACAACA
1085871 TCACTTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.29, C:0.31, G:0.12, T:0.27
Consensus pattern (25 bp):
TTGTATACACCCCGTGTACAACACG
Found at i:1087123 original size:7 final size:7
Alignment explanation
Indices: 1087111--1087177 Score: 62
Period size: 7 Copynumber: 9.6 Consensus size: 7
1087101 GAGAAGGATC
1087111 ATTCGAG
1 ATTCGAG
1087118 ATTCGAG
1 ATTCGAG
** *
1087125 ATTATAA
1 ATTCGAG
*
1087132 ATACGAG
1 ATTCGAG
*
1087139 ATTCGAA
1 ATTCGAG
*
1087146 ATACGAG
1 ATTCGAG
*
1087153 ATTCAAG
1 ATTCGAG
*
1087160 ATTCGAA
1 ATTCGAG
1087167 ATTCGAG
1 ATTCGAG
1087174 ATTC
1 ATTC
1087178 AATATCTAAA
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.28
Consensus pattern (7 bp):
ATTCGAG
Found at i:1087161 original size:21 final size:21
Alignment explanation
Indices: 1087137--1087179 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1087127 TATAAATACG
1087137 AGATTCGAAATACGAGATTCA
1 AGATTCGAAATACGAGATTCA
*
1087158 AGATTCGAAATTCGAGATTCA
1 AGATTCGAAATACGAGATTCA
1087179 A
1 A
1087180 TATCTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.26
Consensus pattern (21 bp):
AGATTCGAAATACGAGATTCA
Found at i:1087393 original size:53 final size:53
Alignment explanation
Indices: 1087308--1087470 Score: 186
Period size: 53 Copynumber: 3.0 Consensus size: 53
1087298 TAATTATTAA
*
1087308 GGTCTTCCGTTTCCAACGGAAGACCTTATTGTT-TTCGTTCGGTTTCTTTTTAG
1 GGTCTTCCGTTTCCAACGGAAGACCCTATTGTTATTC-TTCGGTTTCTTTTTAG
* * *
1087361 GGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTTTTATTATTAA
1 GGTCTTCCGTTTCCAACGGAAGACCCTATTGTTATTCTTCGGTTTC----T-TT-TTAG
* *
1087420 GGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTT-TGTTTCTTTTT
1 GGTCTTCCGTTTCCAACGGAAGACCCTATTGTTATT-CTTCGGTTTCTTTTT
1087471 CACTATTATT
Statistics
Matches: 94, Mismatches: 8, Indels: 16
0.80 0.07 0.14
Matches are distributed among these distances:
53 41 0.44
54 5 0.05
55 1 0.01
57 1 0.01
58 2 0.02
59 41 0.44
60 3 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (53 bp):
GGTCTTCCGTTTCCAACGGAAGACCCTATTGTTATTCTTCGGTTTCTTTTTAG
Found at i:1087437 original size:59 final size:59
Alignment explanation
Indices: 1087300--1087581 Score: 258
Period size: 63 Copynumber: 4.7 Consensus size: 59
1087290 TAACTTAATA
1087300 ATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTT-TTCGTTCGGTTTC----T
1 ATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTC-TTCGGTTTCTTTTT
* * * *
1087355 -TT-TTAGGGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATTCTTCGGTTTCTTTTT
1 ATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTCTTCGGTTTCTTTTT
*
1087412 ATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTT-TGTTTCTTTTTCACT
1 ATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATT-CTTCGGTTTC-TTTT---T
*** * *
1087475 ATTATTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTT-TGTTTCTTTTCCTCTA
1 ATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATT-CTTCGGTTTC---T--T-T-
1087539 TT
58 TT
***
1087541 ATTATTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTT
1 ATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTT
1087582 TTTGCTTTGT
Statistics
Matches: 196, Mismatches: 13, Indels: 25
0.84 0.06 0.11
Matches are distributed among these distances:
53 42 0.21
54 5 0.03
57 1 0.01
58 2 0.01
59 41 0.21
60 7 0.04
63 51 0.26
65 2 0.01
66 42 0.21
67 1 0.01
68 1 0.01
69 1 0.01
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (59 bp):
ATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTCTTCGGTTTCTTTTT
Found at i:1087503 original size:63 final size:62
Alignment explanation
Indices: 1087361--1087592 Score: 283
Period size: 63 Copynumber: 3.7 Consensus size: 62
1087351 TTCTTTTTAG
*** * * *
1087361 GGTCTTCCGTTTTCAACGGAAGACCCTCTTGTTATT-CTTCGGTTTC-TTTT--TATTATTAA
1 GGTCTTCCGTTGGAAACGGAAGACCTTATTGTTATTGCTT-TGTTTCTTTTTCATATTATTAA
***
1087420 GGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCACTATTATTAA
1 GGTCTTCCGTTGGAAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCA-TATTATTAA
*
1087483 GGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTCCTCTATTATTATTA
1 GGTCTTCCGTTGGAAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTT--TC-A-TATTATTA
1087548 A
62 A
*
1087549 GGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTT
1 GGTCTTCCGTTGGAAACGGAAGACCTTATTGTTATTGCTTTGTT
1087593 NAATTACAGT
Statistics
Matches: 156, Mismatches: 9, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
59 38 0.24
60 7 0.04
63 55 0.35
65 2 0.01
66 54 0.35
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.47
Consensus pattern (62 bp):
GGTCTTCCGTTGGAAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCATATTATTAA
Found at i:1087578 original size:66 final size:63
Alignment explanation
Indices: 1087410--1087592 Score: 294
Period size: 63 Copynumber: 2.9 Consensus size: 63
1087400 CGGTTTCTTT
*** *
1087410 TTATTATTAAGGTCTTCCGTTTCCAACGGAAGACCTTATTGTTATTGCTTTGTTTCTTTTTCA
1 TTATTATTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTTCA
*
1087473 CTATTATTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTCCTCT
1 TTATTATTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTT--TC-
1087538 A
63 A
1087539 TTATTATTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTT
1 TTATTATTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTT
1087593 NAATTACAGT
Statistics
Matches: 111, Mismatches: 6, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
63 55 0.50
65 2 0.02
66 54 0.49
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (63 bp):
TTATTATTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTTCA
Found at i:1087907 original size:66 final size:66
Alignment explanation
Indices: 1087801--1087935 Score: 270
Period size: 66 Copynumber: 2.0 Consensus size: 66
1087791 TTCGTCATTT
1087801 TTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTCCTCTATTATT
1 TTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTCCTCTATTATT
1087866 A
66 A
1087867 TTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTCCTCTATTATT
1 TTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTCCTCTATTATT
1087932 A
66 A
1087933 TTA
1 TTA
1087936 TTATTAATTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.49
Consensus pattern (66 bp):
TTAAGGTCTTCCGTTGGAAACGGAAGACCTTATTGTTTTTGCTTTGTTTCTTTTCCTCTATTATT
A
Found at i:1109757 original size:2 final size:2
Alignment explanation
Indices: 1109750--1109786 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1109740 NNNNNNNNNN
1109750 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1109787 GATGTAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1113996 original size:13 final size:13
Alignment explanation
Indices: 1113978--1114002 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1113968 CCGGCAGCCT
1113978 TGGAAAAACCTAA
1 TGGAAAAACCTAA
1113991 TGGAAAAACCTA
1 TGGAAAAACCTA
1114003 TCAAATTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (13 bp):
TGGAAAAACCTAA
Done.