Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold388
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: 35805
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Found at i:1388 original size:93 final size:93
Alignment explanation
Indices: 1281--1451 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
1271 GCCCCTAAGT
* *
1281 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1346 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
1374 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1439 CGAGTTCGGATGC
66 CGAGTTCGGATGC
1452 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:1448 original size:46 final size:46
Alignment explanation
Indices: 1276--1448 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
1266 AACCCGCCCC
* * *
1276 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
1322 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
1370 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1415 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1449 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:1903 original size:30 final size:30
Alignment explanation
Indices: 1869--1928 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
1859 ATTTAATACG
1869 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
1899 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
1929 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:8942 original size:92 final size:91
Alignment explanation
Indices: 8829--8996 Score: 291
Period size: 92 Copynumber: 1.8 Consensus size: 91
8819 GCCCCTAAGT
* *
8829 GAACTCGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGACTCAACTCAACG
1 GAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGACTCAACTCAACG
8894 AGTTCGGATGCCTAGTTACATTTCAC
66 AGTTCGGATGCCTAGTTACATTTCAC
* *
8920 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTGGACTCAACTCAAC
1 GAACTC-GACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGACTCAACTCAAC
8985 GAGTTCGGATGC
65 GAGTTCGGATGC
8997 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
91 6 0.08
92 66 0.92
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (91 bp):
GAACTCGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATTTCAC
Found at i:8993 original size:45 final size:45
Alignment explanation
Indices: 8824--8993 Score: 186
Period size: 45 Copynumber: 3.7 Consensus size: 45
8814 AACCCGCCCC
* * *
8824 TAAGTGAACTCGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
8869 TAAGTGAACTCGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
8916 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTC-GACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
8961 TAAGTGAACTGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGACTCAACTCAACGAGTTCGGA
8994 TGCTCAACCA
Statistics
Matches: 103, Mismatches: 12, Indels: 20
0.76 0.09 0.15
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 55 0.53
46 11 0.11
47 24 0.23
48 1 0.01
49 3 0.03
50 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (45 bp):
TAAGTGAACTCGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:9446 original size:30 final size:30
Alignment explanation
Indices: 9412--9471 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
9402 ATTTAATACC
9412 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
9442 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
9472 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:17029 original size:34 final size:34
Alignment explanation
Indices: 16953--17047 Score: 90
Period size: 34 Copynumber: 2.9 Consensus size: 34
16943 TGGGCCATAG
* *
16953 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTAA
1 TGTTATCTGAATAAGGGGCTAAGGCCCAATTCAA
* ** *
16987 TGTAATCTGAA-AAGGGGCTCTGGCCCAATATCAC
1 TGTTATCTGAATAAGGGGCTAAGGCCCAAT-TCAA
*
17021 TGTTATCTGAAT---GGGCTTAGGCCCAAT
1 TGTTATCTGAATAAGGGGCTAAGGCCCAAT
17048 GGGCTTGAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
32 13 0.26
33 15 0.30
34 22 0.44
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.28
Consensus pattern (34 bp):
TGTTATCTGAATAAGGGGCTAAGGCCCAATTCAA
Found at i:18847 original size:27 final size:27
Alignment explanation
Indices: 18817--18994 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
18807 ATATTGAGTC
* * * *
18817 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
18844 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
18871 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
18899 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
18926 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
18953 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
18980 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
18995 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:18956 original size:82 final size:81
Alignment explanation
Indices: 18838--18993 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
18828 TGCTATATAA
* *
18838 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
18903 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
18920 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
18984 CACTTAGTGC
65 CACTTAGTGC
18994 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:19560 original size:13 final size:13
Alignment explanation
Indices: 19542--19566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
19532 TACTAAATTT
19542 TCATGGATTCAAG
1 TCATGGATTCAAG
19555 TCATGGATTCAA
1 TCATGGATTCAA
19567 TATACCATTA
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:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:28336 original size:40 final size:40
Alignment explanation
Indices: 28299--28481 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
28289 GCTACTCGTT
*
28299 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
28339 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
* *
28379 CCAATGCCTTCGGG-CTTAGCCCGG-AATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
* * * * *
28418 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGTTATAGTAAC-TCGCA
28459 CAAA-GCCTTC-GGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
28482 ACATCATTCG
Statistics
Matches: 124, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
38 2 0.02
39 40 0.32
40 71 0.57
41 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:28410 original size:79 final size:80
Alignment explanation
Indices: 28301--28482 Score: 219
Period size: 79 Copynumber: 2.3 Consensus size: 80
28291 TACTCGTTCA
* *
28301 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGG-CTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
28364 ATTTAGTAAC-TCGCACC
64 ATATAGTAACTTAGCA-C
**
28381 AATGCCTTCGGGCTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGAT
1 AATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
* *
28445 ATGGTCACTTAGCAC
66 ATAGTAACTTAGCAC
* *
28460 AAAGCCTTCGGACTTAGCCCGGA
1 AATGCCTTCGGGCTTAGCCCGGA
28483 CATCATTCGA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
78 3 0.03
79 69 0.78
80 17 0.19
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (80 bp):
AATGCCTTCGGGCTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGAT
ATAGTAACTTAGCAC
Found at i:33877 original size:1 final size:1
Alignment explanation
Indices: 33871--34028 Score: 109
Period size: 1 Copynumber: 158.0 Consensus size: 1
33861 CCCACACCAC
* * * * * ** * * *
33871 AAAAAAAAAAAAAAAAAAAAAGAACAAAAAAAGAAAACAACAAAAAAACGAAAAAAAACACAACA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* ** * * ** * * * * *
33936 ATAAAAACCAACACAAAAAACCAAAAAAAAAAAAAATAAAAAAACAAAAAAACAACAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
34001 AACAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
34029 TGGCGGGACC
Statistics
Matches: 116, Mismatches: 41, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 116 1.00
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Found at i:33961 original size:46 final size:45
Alignment explanation
Indices: 33871--34028 Score: 168
Period size: 46 Copynumber: 3.5 Consensus size: 45
33861 CCCACACCAC
*
33871 AAAAAAAAAAAAAAAAA-AAAAGAACA-AAAA-AAGAAAA-CAACAA
1 AAAAAAAAAAAAAAAAACAAAAAAACACAAAACAA-AAAACCAA-AA
* *
33914 AAAAACGAAAAAAAACACAACAATAAAAAC-CAACACAAAAAACCAAAA
1 AAAAA--AAAAAAAA-AAAACAA-AAAAACACAAAACAAAAAACCAAAA
33962 AAAAAAAAAATAAAAAAACAAAAAAACAACAAAACAAAAAA-CAAAA
1 AAAAAAAAAA-AAAAAAACAAAAAAAC-ACAAAACAAAAAACCAAAA
34008 AAAAAAAAAAAAAAAAA-AAAA
1 AAAAAAAAAAAAAAAAACAAAA
34029 TGGCGGGACC
Statistics
Matches: 99, Mismatches: 5, Indels: 21
0.79 0.04 0.17
Matches are distributed among these distances:
43 5 0.05
44 4 0.04
45 21 0.21
46 29 0.29
47 16 0.16
48 19 0.19
49 5 0.05
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.01
Consensus pattern (45 bp):
AAAAAAAAAAAAAAAAACAAAAAAACACAAAACAAAAAACCAAAA
Found at i:33970 original size:54 final size:47
Alignment explanation
Indices: 33871--34026 Score: 172
Period size: 47 Copynumber: 3.3 Consensus size: 47
33861 CCCACACCAC
* *
33871 AAAAAAAAAAAAAA-AAAAAAAGAACAAAAAAAGAAAACAACAAAAAAA
1 AAAAAAAAAAAAAACAAAAAAAAAACAAAACAA-AAAACAA-AAAAAAA
* * * * * * *
33919 CGAAAAAAAACACAAC-AATAAAAACCAACACAAAAAACCAAAAAAAA
1 -AAAAAAAAAAAAAACAAAAAAAAAACAAAACAAAAAACAAAAAAAAA
* *
33966 AAAAAATAAAAAAACAAAAAAACAACAAAACAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAACAAAAAAAAAACAAAACAAAAAACAAAAAAAAA
34013 AAAAAAAAAAAAAA
1 AAAAAAAAAAAAAA
34027 AATGGCGGGA
Statistics
Matches: 86, Mismatches: 19, Indels: 6
0.77 0.17 0.05
Matches are distributed among these distances:
46 11 0.13
47 46 0.53
48 6 0.07
49 23 0.27
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.01
Consensus pattern (47 bp):
AAAAAAAAAAAAAACAAAAAAAAAACAAAACAAAAAACAAAAAAAAA
Done.