Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1777
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: 28641
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:298 original size:132 final size:132
Alignment explanation
Indices: 55--412 Score: 497
Period size: 132 Copynumber: 2.7 Consensus size: 132
45 ACAACAGGGC
* *
55 TAGAGTATCCTCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCAAGGTTAGAGTATCCTCG
1 TAGAGTATCCTCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTAGAGTATCCCCG
* * * *
120 ATTGTGAAAAAATCGATGCTTTAGAAATAAGGCCGGGGTTGGAGTATCCCCGTGAAAATAACGAG
66 ATTGTGAAAAAATTGATGCTTTAGAAATAAGGCCGGGGTCGAAGTATCCCCGTGAAAATAACAAG
185 GT
131 GT
*
187 TAGAGTATCCCCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTAGAGTATCCCCG
1 TAGAGTATCCTCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTAGAGTATCCCCG
252 ATTGTGAAAAAATTGATGCTTTAGAAATAAGGCCGGGGTCGAAGTATCCCCGTGAAAATAACAAG
66 ATTGTGAAAAAATTGATGCTTTAGAAATAAGGCCGGGGTCGAAGTATCCCCGTGAAAATAACAAG
317 GT
131 GT
* * * * * *** * *
319 TGGAGTATCTTCGATTGTGAGAAATTGGGTGTT-TTGGAACTAAAATCG-GAGTTGGAGTATCCC
1 TAGAGTATCCTCGATTATG-GAAAATCGGTGTTCTAAAAAATAAAATCGAG-GTTAGAGTATCCC
* **
382 CGATTGTG-AAAAATTGGTATTTTAGAAATAA
64 CGATTGTGAAAAAATTGATGCTTTAGAAATAA
413 AATTGGGGTT
Statistics
Matches: 203, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
131 21 0.10
132 171 0.84
133 11 0.05
ACGTcount: A:0.35, C:0.13, G:0.25, T:0.28
Consensus pattern (132 bp):
TAGAGTATCCTCGATTATGGAAAATCGGTGTTCTAAAAAATAAAATCGAGGTTAGAGTATCCCCG
ATTGTGAAAAAATTGATGCTTTAGAAATAAGGCCGGGGTCGAAGTATCCCCGTGAAAATAACAAG
GT
Found at i:431 original size:51 final size:52
Alignment explanation
Indices: 316--433 Score: 157
Period size: 51 Copynumber: 2.3 Consensus size: 52
306 AAAATAACAA
** * * * *
316 GGTTGGAGTATCTTCGATTGTGAGAAATTGGGTGTTTTGGAACTAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGGTATTTTAGAAATAAAATCGG
* *
368 AGTTGGAGTATCCCCGATTGTGAAAAATT-GGTATTTTAGAAATAAAATTGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGGTATTTTAGAAATAAAATCGG
419 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
434 TCGGAAATAA
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
51 32 0.56
52 25 0.44
ACGTcount: A:0.28, C:0.10, G:0.29, T:0.33
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGGTATTTTAGAAATAAAATCGG
Found at i:660 original size:51 final size:51
Alignment explanation
Indices: 586--903 Score: 275
Period size: 51 Copynumber: 6.3 Consensus size: 51
576 AATGACAGGG
* * ** * * *
586 TTGGAGTATTCCCAATTGTGAAAAATTGGTATTTTGGAAATAAAATC-AGA
1 TTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAACCGAGA
* * * *
636 GTTGGAGTATCCTCGATTAAGAAAAATTGATGTTGTGGAGATGAAACCGAGA
1 -TTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAACCGAGA
** * * * * *
688 TTGGAGTATCCCCGATTGCGAAAAATCGATGCTTTAGAAACAAAATC-AGA
1 TTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAACCGAGA
* * * * *
738 GTTGGAGTATCTCTGATTAAGAAAAATTGATGTTTTGGAGATGAAACCGGGA
1 -TTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAACCGAGA
* ** * ** * * *
790 TTGGAGTATCCCCGGTTGCGATAAATCAATGCTTTAGAAATAAAATCG-GA
1 TTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAACCGAGA
* *
840 GTTGGAGTAT-CCCGATTAAGAAAAATTGATGTTTTGAAAATGAAACCGAGA
1 -TTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAACCGAGA
891 TTGGAGTATCCCC
1 TTGGAGTATCCCC
904 AAGATGAAAA
Statistics
Matches: 203, Mismatches: 58, Indels: 12
0.74 0.21 0.04
Matches are distributed among these distances:
50 41 0.20
51 157 0.77
52 5 0.02
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (51 bp):
TTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATAAAACCGAGA
Found at i:733 original size:102 final size:102
Alignment explanation
Indices: 586--903 Score: 460
Period size: 102 Copynumber: 3.1 Consensus size: 102
576 AATGACAGGG
* * * * * ** *
586 TTGGAGTATTCCCAATTGTGAAAAATTGGTATTTTGGAAATAAAATCAGAGTTGGAGTATCCTCG
1 TTGGAGTATCCCCGATTGCGAAAAATCGATGCTTTAGAAATAAAATCAGAGTTGGAGTATCCTCG
*
651 ATTAAGAAAAATTGATGTTGTGGAGATGAAACCGAGA
66 ATTAAGAAAAATTGATGTTTTGGAGATGAAACCGAGA
*
688 TTGGAGTATCCCCGATTGCGAAAAATCGATGCTTTAGAAACAAAATCAGAGTTGGAGTAT-CTCT
1 TTGGAGTATCCCCGATTGCGAAAAATCGATGCTTTAGAAATAAAATCAGAGTTGGAGTATCCTC-
*
752 GATTAAGAAAAATTGATGTTTTGGAGATGAAACCGGGA
65 GATTAAGAAAAATTGATGTTTTGGAGATGAAACCGAGA
* * * *
790 TTGGAGTATCCCCGGTTGCGATAAATCAATGCTTTAGAAATAAAATCGGAGTTGGAGTATCC-CG
1 TTGGAGTATCCCCGATTGCGAAAAATCGATGCTTTAGAAATAAAATCAGAGTTGGAGTATCCTCG
* *
854 ATTAAGAAAAATTGATGTTTTGAAAATGAAACCGAGA
66 ATTAAGAAAAATTGATGTTTTGGAGATGAAACCGAGA
891 TTGGAGTATCCCC
1 TTGGAGTATCCCC
904 AAGATGAAAA
Statistics
Matches: 195, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
101 51 0.26
102 143 0.73
103 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (102 bp):
TTGGAGTATCCCCGATTGCGAAAAATCGATGCTTTAGAAATAAAATCAGAGTTGGAGTATCCTCG
ATTAAGAAAAATTGATGTTTTGGAGATGAAACCGAGA
Found at i:3276 original size:53 final size:53
Alignment explanation
Indices: 3214--3321 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 53
3204 AAAATGCCTG
* * *
3214 AATGTATCGATACATTGTA-AAATGTATTGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATG-AGAAATGTATCGATACAATGAACAATGTATCGATAC
* *
3267 AATGTATCGATACAATGAGCAATGTATCGATACAATGAACAATGTATTGATAC
1 AATGTATCGATACAATGAGAAATGTATCGATACAATGAACAATGTATCGATAC
3320 AA
1 AA
3322 ATTGTGAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
52 1 0.02
53 48 0.98
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (53 bp):
AATGTATCGATACAATGAGAAATGTATCGATACAATGAACAATGTATCGATAC
Found at i:3279 original size:33 final size:33
Alignment explanation
Indices: 3234--3303 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
3224 TACATTGTAA
*
3234 AATGTATTGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
3267 AATGTATCGATACAATGAGCAATGTATCGATAC
1 AATGTATCGATACAATGAGCAATGTATCGATAC
3300 AATG
1 AATG
3304 AACAATGTAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.29
Consensus pattern (33 bp):
AATGTATCGATACAATGAGCAATGTATCGATAC
Found at i:3289 original size:20 final size:19
Alignment explanation
Indices: 3214--3321 Score: 102
Period size: 20 Copynumber: 5.8 Consensus size: 19
3204 AAAATGCCTG
* *
3214 AATGTATCGATACATTGTAA
1 AATGTATCGATACAATG-AC
*
3234 AATGTATTGATACAATGAGC
1 AATGTATCGATACAATGA-C
3254 AATGTATCG-----AT-AC
1 AATGTATCGATACAATGAC
3267 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-C
3287 AATGTATCGATACAATGAAC
1 AATGTATCGATACAATG-AC
*
3307 AATGTATTGATACAA
1 AATGTATCGATACAA
3322 ATTGTGAAAA
Statistics
Matches: 74, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
13 10 0.14
14 1 0.01
15 2 0.03
18 2 0.03
19 2 0.03
20 56 0.76
21 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (19 bp):
AATGTATCGATACAATGAC
Found at i:3302 original size:13 final size:13
Alignment explanation
Indices: 3253--3283 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3243 ATACAATGAG
3253 CAATGTATCGATA
1 CAATGTATCGATA
3266 CAATGTATCGATA
1 CAATGTATCGATA
3279 CAATG
1 CAATG
3284 AGCAATGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:9113 original size:20 final size:20
Alignment explanation
Indices: 9088--9141 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
9078 GTTAGAAGCA
9088 ATGTATCGATACAAT-T-CAAC
1 ATGTATCGATACAATGTGC--C
9108 ATGTATCGATACAATGTGCC
1 ATGTATCGATACAATGTGCC
9128 ATGTATCGATACAA
1 ATGTATCGATACAA
9142 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACAATGTGCC
Found at i:9195 original size:20 final size:19
Alignment explanation
Indices: 9170--9262 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 19
9160 CTGCTAGTTT
**
9170 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
9190 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
9209 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
*
9230 -ATGTATCGATACATCTGAA
1 CATGTATCGATACA-ATGAA
**
9249 TGTGTATCGATACA
1 CATGTATCGATACA
9263 TTCAAGGGTT
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
19 19 0.30
20 42 0.67
21 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:13840 original size:90 final size:89
Alignment explanation
Indices: 13683--13853 Score: 315
Period size: 90 Copynumber: 1.9 Consensus size: 89
13673 TAGATGGCAA
13683 TGTTATTCATTATCACCTACATGTACATGATAAATGAAAGTAGAGGTTAGAAGTGTTTCTCTGAG
1 TGTTATTCATTATCACCTACATGTACATGATAAATGAAAGTAGAGGTTAGAAGTGTTTCTCTGAG
*
13748 TAAACCTATTCTCTGGGTTAGAAG
66 TAAACATATTCTCTGGGTTAGAAG
*
13772 TGTTCATTCATTATCACCTACATGTACATGATAAATGAAAGTAGTGGTTAGAAGTGTTTCTCTGA
1 TGTT-ATTCATTATCACCTACATGTACATGATAAATGAAAGTAGAGGTTAGAAGTGTTTCTCTGA
13837 GTAAACATATTCTCTGG
65 GTAAACATATTCTCTGG
13854 TTTATTCTAG
Statistics
Matches: 79, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
89 4 0.05
90 75 0.95
ACGTcount: A:0.31, C:0.14, G:0.19, T:0.36
Consensus pattern (89 bp):
TGTTATTCATTATCACCTACATGTACATGATAAATGAAAGTAGAGGTTAGAAGTGTTTCTCTGAG
TAAACATATTCTCTGGGTTAGAAG
Found at i:15544 original size:97 final size:96
Alignment explanation
Indices: 15352--15547 Score: 225
Period size: 97 Copynumber: 2.0 Consensus size: 96
15342 TTTTTGGTTA
* * * **
15352 AAAAATGAGGTTAGATTATCCCCTCAAAGGAATGAGGTTGGAGTATCCCAACAATAACAATTTGG
1 AAAAATGAGGTTAGAGTATCCCCTCAAAAGAATGAGGTTAGAGTATCCCAACAATAACAATTTAA
*
15417 GAAAAAATAAGATTTAAATCTTGAGAAGTTT
66 GAAAAAATAAAATTTAAATCTTGAGAAGTTT
* * ***
15448 AAAAATGGGGTTAGAGTATCCCCTCAAAAGAAT-AGAGTTAGAGTATCCCCGAGGTTAACAATTT
1 AAAAATGAGGTTAGAGTATCCCCTCAAAAGAATGAG-GTTAGAGTAT-CCCAACAATAACAATTT
* * *
15512 AAGCAAAAATAAAATTTTAGTCTTGACG-AGTTT
64 AAGAAAAAATAAAATTTAAATCTTGA-GAAGTTT
15545 AAA
1 AAA
15548 GAAAACGGAG
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
95 2 0.02
96 39 0.47
97 41 0.49
98 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.27
Consensus pattern (96 bp):
AAAAATGAGGTTAGAGTATCCCCTCAAAAGAATGAGGTTAGAGTATCCCAACAATAACAATTTAA
GAAAAAATAAAATTTAAATCTTGAGAAGTTT
Found at i:17965 original size:18 final size:20
Alignment explanation
Indices: 17925--17976 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
17915 TAACTGGATT
17925 TATCGATACATTAAAAAATA
1 TATCGATACATTAAAAAATA
17945 TATCGATACATTAAAAAATA
1 TATCGATACATTAAAAAATA
*
17965 TATTGATACATT
1 TATCGATACATT
17977 TAAGGTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.50, C:0.10, G:0.06, T:0.35
Consensus pattern (20 bp):
TATCGATACATTAAAAAATA
Found at i:20602 original size:24 final size:25
Alignment explanation
Indices: 20551--20602 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 25
20541 TTTATCGTCG
*
20551 ATATTTATTATAATTGATCATTATA
1 ATATTTATTATAATTGATAATTATA
20576 ATATTTATTAT-ATTCG-TAATTATA
1 ATATTTATTATAATT-GATAATTATA
20600 ATA
1 ATA
20603 AACATGACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (25 bp):
ATATTTATTATAATTGATAATTATA
Found at i:24662 original size:23 final size:23
Alignment explanation
Indices: 24598--24677 Score: 119
Period size: 22 Copynumber: 3.6 Consensus size: 23
24588 TCCTTGTTAA
*
24598 GTGTGTTAGGT-AAACATATTAG
1 GTGTGTTAGGTGAAGCATATTAG
*
24620 GTGTGTTAAGTG-AGCATATTAG
1 GTGTGTTAGGTGAAGCATATTAG
*
24642 GTGTGTTAGGTGAAGCATATTAA
1 GTGTGTTAGGTGAAGCATATTAG
24665 GTGTGTTAGGTGA
1 GTGTGTTAGGTGA
24678 TGTGTTAGGT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
22 30 0.58
23 22 0.42
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.36
Consensus pattern (23 bp):
GTGTGTTAGGTGAAGCATATTAG
Found at i:24686 original size:44 final size:43
Alignment explanation
Indices: 24592--24687 Score: 113
Period size: 44 Copynumber: 2.2 Consensus size: 43
24582 TTAATTTCCT
* *
24592 TGTTAAGTGTGTTAGGTAAACATATTAGGTGTGTTAAGTGAGCA
1 TGTTAGGTGTGTTAGGTAAACATATTAAGTGTGTTAAGTGAG-A
* * *
24636 TATTAGGTGTGTTAGGTGAAGCATATTAAGTGTGTTAGGTGATG-
1 TGTTAGGTGTGTTAGGT-AAACATATTAAGTGTGTTAAGTGA-GA
24680 TGTTAGGT
1 TGTTAGGT
24688 AAGCATATTA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
44 22 0.50
45 21 0.48
46 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.32, T:0.39
Consensus pattern (43 bp):
TGTTAGGTGTGTTAGGTAAACATATTAAGTGTGTTAAGTGAGA
Found at i:24697 original size:34 final size:34
Alignment explanation
Indices: 24643--24726 Score: 132
Period size: 34 Copynumber: 2.4 Consensus size: 34
24633 GCATATTAGG
*
24643 TGTGTTAGGTGAAGCATATTAAGTGTGTTAGGTGA
1 TGTGTTAGGT-AAGCATATTAAGTGTGTTAGGTAA
*
24678 TGTGTTAGGTAAGCATATTACGTGTGTTAGGTAA
1 TGTGTTAGGTAAGCATATTAAGTGTGTTAGGTAA
*
24712 TGTGTTAGGTGAGCA
1 TGTGTTAGGTAAGCA
24727 AGATATTTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
34 36 0.78
35 10 0.22
ACGTcount: A:0.25, C:0.05, G:0.33, T:0.37
Consensus pattern (34 bp):
TGTGTTAGGTAAGCATATTAAGTGTGTTAGGTAA
Done.