Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1836
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: 1164857
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.29
Warning! 152653 characters in sequence are not A, C, G, or T
File 5 of 4
Found at i:1117648 original size:18 final size:21
Alignment explanation
Indices: 1117634--1117676 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1117624 GAGGAGGAGA
1117634 ACAGTAAAGAAGAGGATGAAG
1 ACAGTAAAGAAGAGGATGAAG
*
1117655 ACAGTGAAGAAGAGGATGAAG
1 ACAGTAAAGAAGAGGATGAAG
1117676 A
1 A
1117677 AGACAGTGGG
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:0.51, C:0.05, G:0.35, T:0.09
Consensus pattern (21 bp):
ACAGTAAAGAAGAGGATGAAG
Found at i:1117648 original size:21 final size:21
Alignment explanation
Indices: 1117619--1117676 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1117609 GAGGAGGAGG
*
1117619 AAGATGAGGAGG-AGAACAGTA
1 AAGAAGAGGAGGAAG-ACAGTA
* *
1117640 AAGAAGAGGATGAAGACAGTG
1 AAGAAGAGGAGGAAGACAGTA
*
1117661 AAGAAGAGGATGAAGA
1 AAGAAGAGGAGGAAGA
1117677 AGACAGTGGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.38, T:0.09
Consensus pattern (21 bp):
AAGAAGAGGAGGAAGACAGTA
Found at i:1120250 original size:29 final size:29
Alignment explanation
Indices: 1120217--1120281 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
1120207 ACCAAATAAA
* * *
1120217 GACACTGGTACTTATTTATCTGTACTATT
1 GACACAGGTACTGATTTATCTGGACTATT
**
1120246 GACACAGGTACTGATTTATCTGGACTAAC
1 GACACAGGTACTGATTTATCTGGACTATT
1120275 GACACAG
1 GACACAG
1120282 TACCTGTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (29 bp):
GACACAGGTACTGATTTATCTGGACTATT
Found at i:1126953 original size:88 final size:87
Alignment explanation
Indices: 1126814--1126978 Score: 285
Period size: 88 Copynumber: 1.9 Consensus size: 87
1126804 CTAGTACCGA
* * * *
1126814 TAACCAATGTTGTATATATGTAACAGGTTGTGAAAAGTCAAGTCTCAACCAGGACTCGAACCCAG
1 TAACAAATGTTGTATAAATATAACAGATTGTGAAAAGTCAAGTCTCAACCAGGACTCGAACCCAG
1126879 GGCCTCTGGCATNTGACAGCTAG
66 GGCCTCTGGCAT-TGACAGCTAG
1126902 TAACAAATGTTGTATAAATATAACAGATTGTGAAAAGTCAAGTCTCAACCAGGACTCGAACCCAG
1 TAACAAATGTTGTATAAATATAACAGATTGTGAAAAGTCAAGTCTCAACCAGGACTCGAACCCAG
1126967 GGCCTCTGGCAT
66 GGCCTCTGGCAT
1126979 ACCGTGCCAG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 73 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (87 bp):
TAACAAATGTTGTATAAATATAACAGATTGTGAAAAGTCAAGTCTCAACCAGGACTCGAACCCAG
GGCCTCTGGCATTGACAGCTAG
Found at i:1127880 original size:167 final size:166
Alignment explanation
Indices: 1127567--1127917 Score: 492
Period size: 167 Copynumber: 2.1 Consensus size: 166
1127557 CCATAAGACC
* *
1127567 AGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTCATGTAAATTTAACGTTGTGAAAATCATG
1 AGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTCATGTAAATTCAAAGTTGTGAAAATCATG
* * * * * *
1127632 ACCCCTGGGGGTAGGGTGGGGCCACAGTGGGGGTTCAAAGTTTAACATAGGAATATATAGAGTAA
66 ACCCCCGGAGGTAGGGTGGGGCCACAATGGGGGATCAAACTTTAACATAGGAATATACAGAGTAA
1127697 ATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCT
131 ATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCT
* * * *
1127733 AGGAAGGCTGACACTTGTGTGGAAGCATCCTCAGGT-AGTGTAGATTCAAAGTTGTGAAAATCAT
1 AGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTCA-TGTAAATTCAAAGTTGTGAAAATCAT
* *
1127797 GACCCCCCGGAGGTAGGGTGGGGCCACAATGGGGGATCGAACTTTTACATAGGAATATACAGAGT
65 GA-CCCCCGGAGGTAGGGTGGGGCCACAATGGGGGATCAAACTTTAACATAGGAATATACAGAGT
* * *
1127862 AAATCTTTAAAAATCTTCTTCTCATG-AAC-CATAAGAT
129 AAATCTTTAAAAATCTTCTTCTCA-GAAACTAATCAGCT
1127899 CAGGAAAGCTGAAACTTGT
1 -AGGAAAGCTGAAACTTGT
1127918 ATGTTATATA
Statistics
Matches: 162, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
165 1 0.01
166 63 0.39
167 97 0.60
168 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.26
Consensus pattern (166 bp):
AGGAAAGCTGAAACTTGTGTGAAAGCATCCTCAGGTCATGTAAATTCAAAGTTGTGAAAATCATG
ACCCCCGGAGGTAGGGTGGGGCCACAATGGGGGATCAAACTTTAACATAGGAATATACAGAGTAA
ATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCT
Found at i:1127975 original size:72 final size:72
Alignment explanation
Indices: 1127851--1127989 Score: 201
Period size: 72 Copynumber: 1.9 Consensus size: 72
1127841 TTACATAGGA
* *
1127851 ATATACAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACCATAAGATCAGGAAAGCTGAAACTT
1 ATATACAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACAATAAGACCAGGAAAGCTGAAACTT
1127916 GTATGTT
66 GTATGTT
* * *
1127923 ATATATAGAGTAAATCTTTAAAAATCTTCTTCTCA-GAAACTAATCAG-CCAGGAAAGCTGACAC
1 ATATACAGAGTAAATCTTTAAAAATCTTCTTCTCATG-AAC-AATAAGACCAGGAAAGCTGAAAC
1127986 TTGT
64 TTGT
1127990 GTAGAAGCAA
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
71 1 0.02
72 55 0.92
73 4 0.07
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.31
Consensus pattern (72 bp):
ATATACAGAGTAAATCTTTAAAAATCTTCTTCTCATGAACAATAAGACCAGGAAAGCTGAAACTT
GTATGTT
Found at i:1128363 original size:164 final size:168
Alignment explanation
Indices: 1127922--1128376 Score: 659
Period size: 175 Copynumber: 2.7 Consensus size: 168
1127912 ACTTGTATGT
*
1127922 TATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGACACT
1 TATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACT
* * * * *
1127987 TGTGTAGAAGCAACCTCAGGTAGTGTAGATTTAATGTTGTGAAAATCATAACCCCCAGGGGTAGG
66 TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGG
1128052 ATGGGGCCACAATGGGGGGCCGAAGCTTTACATAGGAA
131 ATGGGGCCACAATGGGGGGCCGAAGCTTTACATAGGAA
* *
1128090 TATATACTAGAGTACCAGTAAATCTTTAAAAATCTTCCTCTCAGAAACTAATCAGCCAGGAAAAC
1 TATATA-T--AG----AGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGC
* * *
1128155 TGAAACTTGTGTGAAAGCATCTTCAGGTAGTGTAGATACAAAGTTGTGAAAATCATGACCCCC-G
59 TGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAG
* **
1128219 GGGTAGGGTGGGGCCACAAT-GGGGGTTGAAG-TTTAACATAGG-A
124 GGGTAGGATGGGGCCACAATGGGGGGCCGAAGCTTT-ACATAGGAA
*
1128262 -ATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTTAAACT
1 TATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACT
*
1128326 TGTGTGGAAGCATCCTCAGGTCGTGTAGATTCAAAGTTGTGAAAATCATGA
66 TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGA
1128377 TCAGATAGTT
Statistics
Matches: 258, Mismatches: 21, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
164 100 0.39
168 8 0.03
169 1 0.00
170 1 0.00
171 7 0.03
172 4 0.02
173 16 0.06
174 20 0.08
175 101 0.39
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (168 bp):
TATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACT
TGTGTGGAAGCATCCTCAGGTAGTGTAGATTCAAAGTTGTGAAAATCATGACCCCCAGGGGTAGG
ATGGGGCCACAATGGGGGGCCGAAGCTTTACATAGGAA
Found at i:1130177 original size:16 final size:15
Alignment explanation
Indices: 1130144--1130179 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1130134 AAGTGCTAAT
1130144 TAAGTAAGTCCTATC
1 TAAGTAAGTCCTATC
*
1130159 TAAGTAAGTTCTGATC
1 TAAGTAAGTCCT-ATC
1130175 TAAGT
1 TAAGT
1130180 TCATCTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (15 bp):
TAAGTAAGTCCTATC
Found at i:1130178 original size:27 final size:27
Alignment explanation
Indices: 1130148--1130217 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
1130138 GCTAATTAAG
1130148 TAAGTCCTATCTAAG-TAAGTTCTG-ATC
1 TAAGTCC-ATCTAAGTTAA-TTCTGTATC
* *
1130175 TAAGTTCATCTAAGTTAATTCTGTGTC
1 TAAGTCCATCTAAGTTAATTCTGTATC
* *
1130202 TAAGTACATGTAAGTT
1 TAAGTCCATCTAAGTT
1130218 CTACTATCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 12 0.32
27 25 0.68
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (27 bp):
TAAGTCCATCTAAGTTAATTCTGTATC
Found at i:1130696 original size:20 final size:21
Alignment explanation
Indices: 1130673--1130711 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1130663 AAAGTGTTGG
1130673 CATTTTGTT-TCTTTTTTAAA
1 CATTTTGTTATCTTTTTTAAA
*
1130693 CATTTTTTTATCTTTTTTA
1 CATTTTGTTATCTTTTTTA
1130712 GTTTTCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.18, C:0.10, G:0.03, T:0.69
Consensus pattern (21 bp):
CATTTTGTTATCTTTTTTAAA
Found at i:1131191 original size:62 final size:62
Alignment explanation
Indices: 1131094--1131221 Score: 247
Period size: 62 Copynumber: 2.1 Consensus size: 62
1131084 AGGGTAATAG
*
1131094 AACGGATTATGAACTGCGTCTAAACCAATCAGATTTCAGTATTTAACATGAAAGTATAACAA
1 AACGGATTATGAACTGCGTCTAAACCAATCAGATTTCAGTATTAAACATGAAAGTATAACAA
1131156 AACGGATTATGAACTGCGTCTAAACCAATCAGATTTCAGTATTAAACATGAAAGTATAACAA
1 AACGGATTATGAACTGCGTCTAAACCAATCAGATTTCAGTATTAAACATGAAAGTATAACAA
1131218 AACG
1 AACG
1131222 AATTGTTACA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 65 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (62 bp):
AACGGATTATGAACTGCGTCTAAACCAATCAGATTTCAGTATTAAACATGAAAGTATAACAA
Found at i:1139137 original size:166 final size:163
Alignment explanation
Indices: 1138683--1139222 Score: 762
Period size: 165 Copynumber: 3.3 Consensus size: 163
1138673 CAAAGTCGAC
* * * * * * *
1138683 ATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACAATATGGCATGCCTAAACA
1 ATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTATACA
* * *
1138748 AATAGTGTGTTAAAATTTCAAGCATCTGTGATAAATAGCTGCTGAGAAATCTTTGAGGAAAATTT
66 AATACTGTG-TAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTT
*
1138813 GTTTGAAAATTTTGGATAAAATAAACAAAGTACTT
130 GTTTGAAAATTTTGG-TAAAATAAACAAAGTAATT
*
1138848 ATTTAACAGGAAGTTGACGTCCGAATGGTACAAAAATATATCCCAC-ATATGGCATGCCT-TAAC
1 ATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTAT-AC
* *
1138911 AAACACTGTGTAAGAATTTCAAGCATCTGCGAAAAATAGCTGCTGAGAAATCTTTGACGAAAATT
65 AAATACTGTGTAA-AATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATT
1138976 TGTTTGAAAATTTTGGCTAAAAATAAACAAAGTAATT
129 TGTTTGAAAATTTTGG-T-AAAATAAACAAAGTAATT
* *
1139013 ATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATACCACGATATGGCATGCCTATACA
1 ATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTATACA
* *
1139078 AATATTGTGTACAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTATGACGAAAATTT
66 AATACTGTGTA-AAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTT
1139143 GTTTGAAAATTTTGGT----TAAA-AAA-TAA--
130 GTTTGAAAATTTTGGTAAAATAAACAAAGTAATT
*
1139169 A--TAACAGGAAGTTAACGTCCGATTGGTACAAAAATATATCCCACGATATGGCAT
1 ATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCAT
1139223 ATATATTAAC
Statistics
Matches: 345, Mismatches: 24, Indels: 23
0.88 0.06 0.06
Matches are distributed among these distances:
154 50 0.14
156 1 0.00
158 3 0.01
159 3 0.01
160 4 0.01
163 3 0.01
164 88 0.26
165 101 0.29
166 90 0.26
167 2 0.01
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (163 bp):
ATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACGATATGGCATGCCTATACA
AATACTGTGTAAAATTTCAAGCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTTG
TTTGAAAATTTTGGTAAAATAAACAAAGTAATT
Found at i:1139337 original size:36 final size:36
Alignment explanation
Indices: 1139287--1139382 Score: 113
Period size: 35 Copynumber: 2.7 Consensus size: 36
1139277 CAACGGAAAG
*
1139287 TGCGTTAAATTGCGTGATTGCGGGGGAAAAGGTATA
1 TGCGTTAAAATGCGTGATTGCGGGGGAAAAGGTATA
* * * *
1139323 TGCGTCAAAATGCGTGATTGC-GGAGCAACGGTATA
1 TGCGTTAAAATGCGTGATTGCGGGGGAAAAGGTATA
* * *
1139358 TGCGTTAAAGTGCGTTACTGCGGGG
1 TGCGTTAAAATGCGTGATTGCGGGG
1139383 ATGGGGGTTA
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
35 28 0.57
36 21 0.43
ACGTcount: A:0.25, C:0.14, G:0.35, T:0.26
Consensus pattern (36 bp):
TGCGTTAAAATGCGTGATTGCGGGGGAAAAGGTATA
Found at i:1140013 original size:32 final size:32
Alignment explanation
Indices: 1139970--1140240 Score: 389
Period size: 32 Copynumber: 8.4 Consensus size: 32
1139960 ATGATGAATA
* * *
1139970 AAGAGTTGCTCAATGCATGCATTGGACGATTG
1 AAGAGTCGCTCAATGCAGGCATTGGACGACTG
*
1140002 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGACGACTG
* * *
1140034 AAGAGTCGTTCAATGCAGGCATTGGAACAACAG
1 AAGAGTCGCTCAATGCAGGCATTGG-ACGACTG
* *
1140067 AAGAGACGCTCAATGCAGGCATTGGACGATTG
1 AAGAGTCGCTCAATGCAGGCATTGGACGACTG
* *
1140099 AGGAGTCGCTCAATGCAGGCATTGGGCGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGACGACTG
*
1140131 AAGAGTCGCTCAATGCAGGCATTGGAAGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGACGACTG
* *
1140163 AAGAGTCGCTCAATGCATGCATTGGACGATTG
1 AAGAGTCGCTCAATGCAGGCATTGGACGACTG
*
1140195 AGGAGTCGCTCAATGCAGGCATTGGACGACTG
1 AAGAGTCGCTCAATGCAGGCATTGGACGACTG
*
1140227 AAGAGTCGTTCAAT
1 AAGAGTCGCTCAAT
1140241 AGAACTAAAC
Statistics
Matches: 210, Mismatches: 28, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
32 183 0.87
33 27 0.13
ACGTcount: A:0.30, C:0.19, G:0.31, T:0.21
Consensus pattern (32 bp):
AAGAGTCGCTCAATGCAGGCATTGGACGACTG
Done.