Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold231
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1009718
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 7 of 7
Found at i:992540 original size:28 final size:28
Alignment explanation
Indices: 992482--992540 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
992472 GACAATTTCC
** *
992482 ATACAGTCCATTTTAACTAACAATTTCT
1 ATACAGTCCATTTTAACTAACAAGATAT
* *
992510 ATACAGTCCATTTTAACTCACTAGATAT
1 ATACAGTCCATTTTAACTAACAAGATAT
992538 ATA
1 ATA
992541 GATTGCTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (28 bp):
ATACAGTCCATTTTAACTAACAAGATAT
Found at i:994144 original size:2 final size:2
Alignment explanation
Indices: 994139--994176 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
994129 AATATATATA
* *
994139 TG TG TG TG TG TG TG TG TG TG TG TG TG TC TC TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
994177 ACATTTTACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.05, G:0.45, T:0.50
Consensus pattern (2 bp):
TG
Found at i:994384 original size:2 final size:2
Alignment explanation
Indices: 994379--994404 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
994369 TATATATATA
994379 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
994405 ATGTTCTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:994385 original size:228 final size:222
Alignment explanation
Indices: 993960--994578 Score: 771
Period size: 228 Copynumber: 2.8 Consensus size: 222
993950 TAAATAGATG
* *
993960 TTCTTCCTTCCT-T-AACTC-AAAGTTAAAACATTACACCAGGTAAAAAAAAACATTTTGCAAGT
1 TTCTTCCTT-CTATCAACTCAAAAATTAAAACATTACACTAGGTAAAAAAAAACATTTTGCAAGT
* *
994022 TAAGAACAGTGTTGTCAAGGACACAATGCACTTCGAGGCACTAGAACCTTAATATTGCCTGAGGA
65 TAAGAACAGTGTTGTCAAGGGCACAATGCACTTTGAGGCACTAGAACCTTAATATTGCCTGAGGA
* ** * ** * * * * * *
994087 GAAAGGCACAAAAGGAGTGATTGCCTGAGCAAAGTAAGGTGCAATATATATATGTGTGTGTGTGT
130 GCAAGGCACAAAAAAAGTGATCGCCTGAGCAAAGTAAGGCACAATATATATATATATATATATAT
994152 GTGTGTGTGTGTGTCTCTGTGTGTGACA
195 GTGTGTGTGTGTGTCTCTGTGTGTGACA
* *
994180 TT-TTACCTTCTTTCAACTCAAAAGTTAAAACATTACACTAGGTAAAAAAAAAAAAAAACATTTT
1 TTCTT-CCTTCTATCAACTCAAAAATTAAAACATTACACTAGGT------AAAAAAAAACATTTT
*
994244 GAAAGTTAAGAACAGTGTTGTCAAGGGCACAATGCACTTTGAGGCACTAGAACCTTAATATTGCC
59 GCAAGTTAAGAACAGTGTTGTCAAGGGCACAATGCACTTTGAGGCACTAGAACCTTAATATTGCC
*
994309 TGAGGAGCAAGGCACAAAAAAAGTGATCGCCTGAGCAAAGTAAGGCATAATATATATATATATAT
124 TGAGGAGCAAGGCACAAAAAAAGTGATCGCCTGAGCAAAGTAAGGCACAATATATATATATATAT
* * **
994374 ATATATGTGTGTGTGTGTGTGTGTGTGTGTGATG
189 ATATATGTGTGTGTGTGTGTCTCTGTGTGTGACA
* *
994408 TTCTTCCTTCTATCAACTCAAAAATTAAAACATTACATTAGGTAAAGAAAAACATTTTGCAAGTT
1 TTCTTCCTTCTATCAACTCAAAAATTAAAACATTACACTAGGTAAAAAAAAACATTTTGCAAGTT
* * *
994473 AAGAACAGTGTTGTCAAGGG-----TG--CTCTGAGGCACTAGAACCTTGATATTGCTTGAGGAG
66 AAGAACAGTGTTGTCAAGGGCACAATGCACTTTGAGGCACTAGAACCTTAATATTGCCTGAGGAG
* * *
994531 CAAGGCACAAAGAAAGTGCTCG-C-AAGCAAAGTAA-GCAACAATATATAT
131 CAAGGCACAAAAAAAGTGATCGCCTGAGCAAAGTAAGGC-ACAATATATAT
994579 GTGTCTCTCT
Statistics
Matches: 354, Mismatches: 33, Indels: 31
0.85 0.08 0.07
Matches are distributed among these distances:
212 2 0.01
213 20 0.06
214 1 0.00
215 53 0.15
217 2 0.01
219 4 0.01
220 7 0.02
221 5 0.01
222 62 0.18
228 196 0.55
229 2 0.01
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (222 bp):
TTCTTCCTTCTATCAACTCAAAAATTAAAACATTACACTAGGTAAAAAAAAACATTTTGCAAGTT
AAGAACAGTGTTGTCAAGGGCACAATGCACTTTGAGGCACTAGAACCTTAATATTGCCTGAGGAG
CAAGGCACAAAAAAAGTGATCGCCTGAGCAAAGTAAGGCACAATATATATATATATATATATATG
TGTGTGTGTGTGTCTCTGTGTGTGACA
Found at i:994629 original size:2 final size:2
Alignment explanation
Indices: 994622--994647 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
994612 TATGCACGCG
994622 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
994648 TACCCATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:997622 original size:16 final size:16
Alignment explanation
Indices: 997558--997638 Score: 64
Period size: 16 Copynumber: 5.1 Consensus size: 16
997548 TAATTTATAC
997558 TTATTAATTTTT-AAA
1 TTATTAATTTTTAAAA
997573 TT-TTAATTATTT--AA
1 TTATTAATT-TTTAAAA
*
997587 TGATTAATTTTTATGTAAA
1 TTATTAATTTTTA---AAA
997606 TTATTAATTTTTAAAA
1 TTATTAATTTTTAAAA
*
997622 TTATCAGA-TTTTAAAA
1 TTATTA-ATTTTTAAAA
997638 T
1 T
997639 ATACATATAT
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
14 12 0.22
15 11 0.20
16 17 0.31
17 1 0.02
19 14 0.25
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (16 bp):
TTATTAATTTTTAAAA
Found at i:998420 original size:2 final size:2
Alignment explanation
Indices: 998413--998437 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
998403 AAGCATGGTG
998413 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
998438 TAATATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:999932 original size:2 final size:2
Alignment explanation
Indices: 999917--999951 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
999907 TTAATATGCA
* *
999917 AT AT AT AC AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
999952 AGAGGTTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1000208 original size:17 final size:19
Alignment explanation
Indices: 1000176--1000211 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1000166 TGTAAAACCA
1000176 AAATCAAAATATAAAATTT
1 AAATCAAAATATAAAATTT
1000195 AAAT-AAAA-ATAAAATTT
1 AAATCAAAATATAAAATTT
1000212 TCACTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATCAAAATATAAAATTT
Found at i:1000473 original size:3 final size:3
Alignment explanation
Indices: 1000465--1000499 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1000455 TAAAGAAAAT
1000465 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1000500 TGAAGACCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1001073 original size:33 final size:32
Alignment explanation
Indices: 1001018--1001093 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
1001008 TAAATTTCAG
*
1001018 AATATATTTATATATTTTATATT-TATATTAATTTT
1 AATATA-TTA-ATAATTTATATTATAT-TTAA-TTT
1001053 AATATATTAATAATTTATATTATATTTAATTT
1 AATATATTAATAATTTATATTATATTTAATTT
1001085 AATAT-TTAA
1 AATATATTAA
1001094 GATATATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
31 4 0.10
32 8 0.21
33 15 0.38
34 6 0.15
35 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (32 bp):
AATATATTAATAATTTATATTATATTTAATTT
Found at i:1001080 original size:27 final size:27
Alignment explanation
Indices: 1001020--1001082 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1001010 AATTTCAGAA
*
1001020 TATATTT-ATATATTTTATATTTATAT
1 TATATTTAATATATTATATATTTATAT
1001046 TA-ATTTTAATATATTA-ATAATTTATAT
1 TATA-TTTAATATATTATAT-ATTTATAT
1001073 TATATTTAAT
1 TATATTTAAT
1001083 TTAATATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 1 0.03
26 7 0.22
27 23 0.72
28 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TATATTTAATATATTATATATTTATAT
Found at i:1005297 original size:30 final size:30
Alignment explanation
Indices: 1005261--1005317 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
1005251 ACAGCAGCAA
1005261 GACCTGTGAGCCTTTATCAGTTATGATCAG
1 GACCTGTGAGCCTTTATCAGTTATGATCAG
1005291 GACCTGTGAGCCTTTATCAGTTATGAT
1 GACCTGTGAGCCTTTATCAGTTATGAT
1005318 TTTTATTTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (30 bp):
GACCTGTGAGCCTTTATCAGTTATGATCAG
Found at i:1007190 original size:6 final size:6
Alignment explanation
Indices: 1007179--1007236 Score: 71
Period size: 6 Copynumber: 9.7 Consensus size: 6
1007169 CCTGCCCCTA
* * * * *
1007179 TATGGC TATGGC TATGGC AATTGC TGTCGC TATGGC TATGGC TATGAC
1 TATGGC TATGGC TATGGC TATGGC TATGGC TATGGC TATGGC TATGGC
1007227 TATGGC TATG
1 TATGGC TATG
1007237 AAGTTTATTC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.34
Consensus pattern (6 bp):
TATGGC
Found at i:1007692 original size:3 final size:3
Alignment explanation
Indices: 1007686--1007713 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1007676 ATATACTTAT
1007686 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1007714 CCTTAAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.