Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold355
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: 482196
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.32
Warning! 38188 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:433766 original size:168 final size:167
Alignment explanation
Indices: 433453--433766 Score: 461
Period size: 168 Copynumber: 1.9 Consensus size: 167
433443 TTTAAATAAC
*
433453 AATAACAATAATCATTTACCAAAACAAATTTATGCTAAGGGTATTCTAGTCATTTTAGTTTTTCC
1 AATAACAATAACCATTTACCAAAACAAATTTATGCTAAGGGTATTCTAGTCATTTTAGTTTTTCC
* * * * *
433518 ATTATGCCATTACACTTCTATTCCATTCAACCAAACACAATATTACTATTACGCCTCTATTCCAT
66 ATTATGCCATTACACATCAATTCCATTCAACCAAACACAAGAATACTATTAAGCCTCTATTCCAT
433583 TACATTCAACCAAACAGTTGATTTCTTATTAAAATTT
131 TACATTCAACCAAACAGTTGATTTCTTATTAAAATTT
* * *
433620 AATAACAATAACCATTTACCTAAACAAATTTCTGTTAAGGGTATTCTAGTCATTTTAGTTTTTTC
1 AATAACAATAACCATTTACCAAAACAAATTTATGCTAAGGGTATTCTAGTCATTTTAG-TTTTTC
* * * *
433685 CCTTATGCTATTACAACAT-AATTTCATTCAACCAAACACAAGAATACTATTATAG-TTCTATTC
65 CATTATGCCATTAC-ACATCAATTCCATTCAACCAAACACAAGAATACTATTA-AGCCTCTATTC
*
433748 CATTCCATTCAACCAAACA
128 CATTACATTCAACCAAACA
433767 AAAAGATTAC
Statistics
Matches: 130, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
167 54 0.42
168 72 0.55
169 4 0.03
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (167 bp):
AATAACAATAACCATTTACCAAAACAAATTTATGCTAAGGGTATTCTAGTCATTTTAGTTTTTCC
ATTATGCCATTACACATCAATTCCATTCAACCAAACACAAGAATACTATTAAGCCTCTATTCCAT
TACATTCAACCAAACAGTTGATTTCTTATTAAAATTT
Found at i:433804 original size:16 final size:16
Alignment explanation
Indices: 433779--433834 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
433769 AAGATTACAT
*
433779 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
433795 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
* *
433811 ATTACACTTCTATTCT
1 ATTACACCTCTATTCC
433827 ATTACACC
1 ATTACACC
433835 GAACCAAACG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.25, C:0.34, G:0.02, T:0.39
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:435937 original size:162 final size:162
Alignment explanation
Indices: 435696--436042 Score: 613
Period size: 162 Copynumber: 2.1 Consensus size: 162
435686 TTGGGAACAG
* **
435696 CTCTTTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACATGTTGGGAAGAGAAATTT
1 CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACAAATTGGGAAGAGAAATTT
*
435761 CAACTTATTGCATTCTGTGACTTGTACTTCTCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
*
435826 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAA
* * *
435858 CTCTCTATCTTCAAAGTTTGCAATTTCCCAAGACTATTAGCAACACAAATTGGGAAGAGAAATTT
1 CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACAAATTGGGAAGAGAAATTT
*
435923 CAATTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
435988 AGTCTTGGATTATTTCTTCCATTCCAAAGCAA
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAA
436020 CTCTCTATCCTCAGAGTTTGCAA
1 CTCTCTATCCTCAGAGTTTGCAA
436043 ATTGGGCGCA
Statistics
Matches: 174, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 174 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.36
Consensus pattern (162 bp):
CTCTCTATCCTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACAAATTGGGAAGAGAAATTT
CAACTTATTGCATTCTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
AGTCTTGGATTATTTCTTCCATTCCAAAGCAA
Found at i:439239 original size:210 final size:211
Alignment explanation
Indices: 438867--439287 Score: 810
Period size: 210 Copynumber: 2.0 Consensus size: 211
438857 CTGCAGGCAC
438867 ACGACCTGTGGAATGTTGTTCTCAATGACATTGAGCCACCACCACTAAGAGCTAACCCGACTATA
1 ACGACCTGTGGAATGTTGTTCTCAATGACATTGAGCCACCACCACTAAGAGCTAACCCGACTATA
438932 GCCCAGATTAGGCAGCACAATGAAGACTGTGCCAAGAAGTACAAGGCTATGTCGTGCCTTCAAAG
66 GCCCAGATTAGGCAGCACAATGAAGACTGTGCCAAGAAGTACAAGGCTATGTCGTGCCTTCAAAG
438997 TGGAGTTTCTGATGTTATTTTCACAAGAATAATGGCTTGTGACACTCCAAAGCAGGCCTGGGACA
131 TGGAGTTTCTGATGTTATTTTCACAAGAATAATGGCTTGTGACACTCCAAAGCAGGCCTGGGACA
439062 AACTCAAGGAGGAGTT
196 AACTCAAGGAGGAGTT
*
439078 ACGACCTGT-GAATGTTGTTCTCAATGACATTGAGCCACCACCACTAAGAGCTAATCCGACTATA
1 ACGACCTGTGGAATGTTGTTCTCAATGACATTGAGCCACCACCACTAAGAGCTAACCCGACTATA
439142 GCCCAGATTAGGCAGCACAATGAAGAAC-GTGCCAAGAAGTACAAGGCTATGTCGTGCCTTCAAA
66 GCCCAGATTAGGCAGCACAATGAAG-ACTGTGCCAAGAAGTACAAGGCTATGTCGTGCCTTCAAA
439206 GTGGAGTTTCTGATGTTATTTTCACAAGAATAATGGCTTGTGACACTCCAAAGCAGGCCTGGGAC
130 GTGGAGTTTCTGATGTTATTTTCACAAGAATAATGGCTTGTGACACTCCAAAGCAGGCCTGGGAC
439271 AAACTCAAGGAGGAGTT
195 AAACTCAAGGAGGAGTT
439288 TCAGGGGTCT
Statistics
Matches: 208, Mismatches: 1, Indels: 3
0.98 0.00 0.01
Matches are distributed among these distances:
210 197 0.95
211 11 0.05
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (211 bp):
ACGACCTGTGGAATGTTGTTCTCAATGACATTGAGCCACCACCACTAAGAGCTAACCCGACTATA
GCCCAGATTAGGCAGCACAATGAAGACTGTGCCAAGAAGTACAAGGCTATGTCGTGCCTTCAAAG
TGGAGTTTCTGATGTTATTTTCACAAGAATAATGGCTTGTGACACTCCAAAGCAGGCCTGGGACA
AACTCAAGGAGGAGTT
Found at i:457622 original size:22 final size:22
Alignment explanation
Indices: 457597--457639 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
457587 TATTCTCTTT
457597 AAAT-TAACATTAATATAAAATA
1 AAATGTAA-ATTAATATAAAATA
*
457619 AAATGTAAATTAATTTAAAAT
1 AAATGTAAATTAATATAAAAT
457640 TTTAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
AAATGTAAATTAATATAAAATA
Found at i:458485 original size:23 final size:23
Alignment explanation
Indices: 458458--458503 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
458448 AAGCTTATTG
458458 TTGAGTTTTGAAGAGTAGTGTAC
1 TTGAGTTTTGAAGAGTAGTGTAC
458481 TTGAGTTTTGAAGAGTAGTGTAC
1 TTGAGTTTTGAAGAGTAGTGTAC
458504 CTGCATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.04, G:0.30, T:0.39
Consensus pattern (23 bp):
TTGAGTTTTGAAGAGTAGTGTAC
Found at i:459398 original size:15 final size:15
Alignment explanation
Indices: 459373--459410 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
459363 CATACATTAC
459373 CAAAAAA-AAAATCA
1 CAAAAAATAAAATCA
*
459387 CAAAAAATAAAATCT
1 CAAAAAATAAAATCA
*
459402 CCAAAAATA
1 CAAAAAATA
459411 TGGTGCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (15 bp):
CAAAAAATAAAATCA
Found at i:459471 original size:2 final size:2
Alignment explanation
Indices: 459464--459490 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
459454 AGTGGTTGCA
459464 AT 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 A
459491 AGAAACTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:460190 original size:162 final size:162
Alignment explanation
Indices: 459952--460460 Score: 964
Period size: 162 Copynumber: 3.1 Consensus size: 162
459942 TTGGGAACAA
*
459952 CTCTCTATCGTCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
1 CTCTCTATCATCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
* *
460017 CAACTTATTGCATTCTGTGACTCGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
460082 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
460114 CTCTCTATCATCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
1 CTCTCTATCATCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
460179 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
460244 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
460276 CTCTCTATCATCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
1 CTCTCTATCATCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
460341 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
66 CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
* *
460406 AATCTTGGATTATTTCTTCCATTCTAAAGCAC
131 AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
*
460438 CTCTCTATCCTCAGAGTTTGCAA
1 CTCTCTATCATCAGAGTTTGCAA
460461 ATTGGGCGCG
Statistics
Matches: 341, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
162 341 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (162 bp):
CTCTCTATCATCAGAGTTTGCAATTGCCCAAGACTATTAGCAACACACATTGGGAAGAGAAATTT
CAACTTATTGCATTTTGTGACTTGTACTTCCCTTAGGCATTGGAAGCTTATGGTTGATACTTGTG
AGTCTTGGATTATTTCTTCCATTCCAAAGCAC
Found at i:464403 original size:16 final size:15
Alignment explanation
Indices: 464366--464409 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
464356 AAAACTAGGG
* *
464366 TTTTTAAAACATTTA
1 TTTTTAAAATATTCA
464381 TTTTTAAAATATTCA
1 TTTTTAAAATATTCA
464396 TTTCTTAAAATATT
1 TTT-TTAAAATATT
464410 ATATCACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 16 0.62
16 10 0.38
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTTAAAATATTCA
Found at i:467434 original size:162 final size:162
Alignment explanation
Indices: 467245--467617 Score: 595
Period size: 162 Copynumber: 2.3 Consensus size: 162
467235 TATATTGCGA
* * * * * *
467245 GCAACTCTTTTATCTTCAAATTATGCAATTACCCAAGGCTATTAGCAATAGACATTGGGAAGAGA
1 GCAACTC-TTTATCTTCAAAGTATGCAATTGCTCAAGGCTATTAGCAACAGACAGTGAGAAGAGA
* *
467310 TACTTCAAATTATCACAGTTTT-TAACTTCTATTTCCCTTAAACTTTGGAGGCTTATGCATGGCA
65 TACTTCAAATTATCACA-TTTTGGAACTTCTATTTCCCTTAAACTTTAGAGGCTTATGCATGGCA
467374 CTTGTGAGTCTTGGATTATGCCTTCCAAGCTCCG
129 CTTGTGAGTCTTGGATTATGCCTTCCAAGCTCCG
467408 GCAACTCTTTATCTTCAAAGTATGCAATTGCTCAAGGCTATTAGCAACAGACAGTGAGAAGAGAT
1 GCAACTCTTTATCTTCAAAGTATGCAATTGCTCAAGGCTATTAGCAACAGACAGTGAGAAGAGAT
* * * *
467473 ACTTTAAATTATCGCATTTTGGAACTTCTATTTCCCTTAAACTTTAGAGGCTTATGTATGGCAGT
66 ACTTCAAATTATCACATTTTGGAACTTCTATTTCCCTTAAACTTTAGAGGCTTATGCATGGCACT
467538 TGTGAGTCTTGGATTATGCCTTCCAAGCTCCG
131 TGTGAGTCTTGGATTATGCCTTCCAAGCTCCG
* *
467570 ACAACTTTTTATCTTCAAAGTATGCAATTGCTCAAGGCTATTAGCAAC
1 GCAACTCTTTATCTTCAAAGTATGCAATTGCTCAAGGCTATTAGCAAC
467618 TAGGAAGATA
Statistics
Matches: 195, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
161 4 0.02
162 184 0.94
163 7 0.04
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (162 bp):
GCAACTCTTTATCTTCAAAGTATGCAATTGCTCAAGGCTATTAGCAACAGACAGTGAGAAGAGAT
ACTTCAAATTATCACATTTTGGAACTTCTATTTCCCTTAAACTTTAGAGGCTTATGCATGGCACT
TGTGAGTCTTGGATTATGCCTTCCAAGCTCCG
Found at i:475370 original size:7 final size:7
Alignment explanation
Indices: 475351--475390 Score: 62
Period size: 7 Copynumber: 5.6 Consensus size: 7
475341 CTGTCATATA
475351 TATAGATT
1 TATAGA-T
475359 TATAGAT
1 TATAGAT
475366 TATAGAT
1 TATAGAT
475373 TATAGAT
1 TATAGAT
*
475380 GATAGAT
1 TATAGAT
475387 TATA
1 TATA
475391 TATATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 24 0.80
8 6 0.20
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (7 bp):
TATAGAT
Found at i:481586 original size:6 final size:6
Alignment explanation
Indices: 481575--481602 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
481565 ATTATAGACA
481575 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
481603 TGCTTTCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Done.