Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold986
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: 57763
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:715 original size:16 final size:17
Alignment explanation
Indices: 690--723 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
680 TTCGATTACA
*
690 TAATTTATTC-ACTATT
1 TAATTCATTCTACTATT
706 TAATTCATTCTACTATT
1 TAATTCATTCTACTATT
723 T
1 T
724 TTAATGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (17 bp):
TAATTCATTCTACTATT
Found at i:1541 original size:41 final size:40
Alignment explanation
Indices: 1476--1665 Score: 232
Period size: 38 Copynumber: 4.8 Consensus size: 40
1466 TTGGGATTAG
*
1476 CCGGATATAGCT-ACTACGCTCAAATGCCTGTCGGGA-CTAGC
1 CCGGATATAG-TAACT-CGCACAAATGCCT-TCGGGACCTAGC
*
1517 CCGGTTATAGTAACTCGCAACAAATGCCTTCGGGACCTAGC
1 CCGGATATAGTAACTCGC-ACAAATGCCTTCGGGACCTAGC
1558 GCCGGAT-TAGTAACTCGCACAAATG-CTTCGGGACCTAG-
1 -CCGGATATAGTAACTCGCACAAATGCCTTCGGGACCTAGC
*
1596 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACCTAGC
** *
1636 CC-GAT-TAGTCCCTAGCACAAATGCCTTCGG
1 CCGGATATAGTAACTCGCACAAATGCCTTCGG
1666 CACTTAGACC
Statistics
Matches: 135, Mismatches: 7, Indels: 17
0.85 0.04 0.11
Matches are distributed among these distances:
37 6 0.04
38 40 0.30
39 28 0.21
40 19 0.14
41 37 0.27
42 5 0.04
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACCTAGC
Found at i:1610 original size:79 final size:77
Alignment explanation
Indices: 1496--1665 Score: 236
Period size: 79 Copynumber: 2.2 Consensus size: 77
1486 CTACTACGCT
*
1496 CAAATGCCTGTCGGGACTAGCCCGGTTATAGTAACTCGCAACAAATGCCTTCGGGACCTAGCGCC
1 CAAATGCCT-TCGGGACTAGCCCGGATATAGTAACTCGC-ACAAATGCCTTCGGGACCTAGC-CC
*
1561 GGATTAGTAACTCGCA
63 -GATTAGTAACTAGCA
*
1577 CAAATG-CTTCGGGACCTAG-CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
1 CAAATGCCTTCGGGA-CTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACCTAGCCCGA
**
1640 TTAGTCCCTAGCA
65 TTAGTAACTAGCA
1653 CAAATGCCTTCGG
1 CAAATGCCTTCGG
1666 CACTTAGACC
Statistics
Matches: 82, Mismatches: 5, Indels: 8
0.86 0.05 0.08
Matches are distributed among these distances:
76 18 0.22
77 8 0.10
78 21 0.26
79 23 0.28
80 6 0.07
81 6 0.07
ACGTcount: A:0.26, C:0.29, G:0.24, T:0.22
Consensus pattern (77 bp):
CAAATGCCTTCGGGACTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACCTAGCCCGAT
TAGTAACTAGCA
Found at i:9533 original size:40 final size:40
Alignment explanation
Indices: 9473--9680 Score: 332
Period size: 40 Copynumber: 5.2 Consensus size: 40
9463 TACCTTGGAT
*
9473 TTAG-CCGGATATAGCT-ACTCGCTCAAATGCCTTCGGGAC
1 TTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGAC
*
9512 TTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
*
9552 CTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
9592 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
* *
9632 TTAGCCCGGA-ATTAGTCACTAGCACAAATGCCTTCGGGAC
1 TTAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGAC
9672 TTAGCCCGG
1 TTAGCCCGG
9681 TTATCATCCG
Statistics
Matches: 159, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 6 0.04
40 153 0.96
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
TTAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGAC
Found at i:17794 original size:40 final size:40
Alignment explanation
Indices: 17717--17934 Score: 343
Period size: 40 Copynumber: 5.5 Consensus size: 40
17707 AAACCAAGTA
* *
17717 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
17756 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
17796 CCTTCGGGACCTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
17836 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
17876 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
17916 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
17935 TTATCATCCG
Statistics
Matches: 168, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
39 15 0.09
40 153 0.91
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:23590 original size:60 final size:59
Alignment explanation
Indices: 23465--23596 Score: 133
Period size: 60 Copynumber: 2.2 Consensus size: 59
23455 GTGTTAACTG
* * * *
23465 GGCCTTAGCCCATATCAATATTAATCTGGGCCATAGCCCTTTATAGTAACAGAGTATACTG
1 GGCC-TAGCCCAAATCAATATCAATCTGGGCCATAGCCCTTTAAAGT-ACAGAGTATACTA
* * *
23526 GGCCTAGCCCAAATCAGTATCAATCTGGGCCGTAGCCCTATTACAAGT-C-GAGATATATTA
1 GGCCTAGCCCAAATCAATATCAATCTGGGCCATAGCCCT-TTA-AAGTACAGAG-TATACTA
*
23586 GGCCTTGCCCA
1 GGCCTAGCCCA
23597 TATTGACACA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 3 0.05
60 47 0.78
61 7 0.12
62 3 0.05
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (59 bp):
GGCCTAGCCCAAATCAATATCAATCTGGGCCATAGCCCTTTAAAGTACAGAGTATACTA
Found at i:33644 original size:43 final size:43
Alignment explanation
Indices: 33574--33696 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 43
33564 GTTAGTGGTG
* * * * * * *
33574 TTTTCTCACAAGCGCCACTATAGAACATGGTCTTTAGTAGTGC
1 TTTTATCACAAACGCCGCTAAAAAACATGATCTTTAGCAGTGC
*
33617 TTTTA-CAGCAAACGCCGCTAAAAAACATGATCTTTAGCGGTGC
1 TTTTATCA-CAAACGCCGCTAAAAAACATGATCTTTAGCAGTGC
* * * *
33660 TTTTATTACAAACGCTGCTAAAGAACAAGATCATTTA
1 TTTTATCACAAACGCCGCTAAAAAACATGATC-TTTA
33697 TAGCGTTTGT
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
42 2 0.03
43 58 0.89
44 5 0.08
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (43 bp):
TTTTATCACAAACGCCGCTAAAAAACATGATCTTTAGCAGTGC
Found at i:38487 original size:46 final size:47
Alignment explanation
Indices: 38299--38512 Score: 152
Period size: 46 Copynumber: 4.6 Consensus size: 47
38289 GAGGCTGATT
* * * * *
38299 CCATGTCCCAGACATGGTCTTACACTAGCTCTCACATATCCGTGCCGACG
1 CCATGTCCCAGACATGGTCTTACACTAAC-C-CACATCT-CATACCGATG
* * *
38349 TCATGTCCCAGACATGGTCTTACACTGA--CACATCTCGTAGCCGATG
1 CCATGTCCCAGACATGGTCTTACACTAACCCACATCTCATA-CCGATG
* ** ** * * ** *
38395 -CATGTCCCAGACAT-GTCTTACATTGGCTTACGTCCCGAGGCTGATG
1 CCATGTCCCAGACATGGTCTTACACTAACCCACATCTC-ATACCGATG
*
38441 -CATGTCCCAGACAT-GTCTTACACTAACCCTCATCTCAATACCGATG
1 CCATGTCCCAGACATGGTCTTACACTAACCCACATCTC-ATACCGATG
*
38487 CCATGTCCGAGACATGGTCTTACACT
1 CCATGTCCCAGACATGGTCTTACACT
38513 GGCTCTCATA
Statistics
Matches: 130, Mismatches: 28, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
44 10 0.08
45 17 0.13
46 55 0.42
47 13 0.10
48 10 0.08
50 25 0.19
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.26
Consensus pattern (47 bp):
CCATGTCCCAGACATGGTCTTACACTAACCCACATCTCATACCGATG
Found at i:38503 original size:138 final size:145
Alignment explanation
Indices: 38245--38513 Score: 347
Period size: 138 Copynumber: 1.9 Consensus size: 145
38235 GGTAAGTTTT
*
38245 CGATGCCATGTCCCATACATCGTCTCACACTGGCTATCATCACCGAGGCTGATTCCATGTCCCAG
1 CGATGCCATGTCCCAGACATCGTCTCACACTGGCTATCATCACCGAGGCTGATTCCATGTCCCAG
* ** * *
38310 ACATGGTCTTACACTAGCTCTCACATATCCGTGCCGACGTCATGTCCCAGACATGGTCTTACACT
66 ACATGGTCTTACACTAACTCTCACATATCAATACCGACGCCATGTCCCAGACATGGTCTTACACT
38375 GACACATCTCGTAGC
131 GACACATCTCGTAGC
* * * *
38390 CGATG-CATGTCCCAGACAT-GTCTTACATTGGCT-TACGTC-CCGAGGCTGA-TGCATGTCCCA
1 CGATGCCATGTCCCAGACATCGTCTCACACTGGCTAT-CATCACCGAGGCTGATTCCATGTCCCA
* * * *
38450 GACAT-GTCTTACACTAAC-C-CTCATCTCAATACCGATGCCATGTCCGAGACATGGTCTTACAC
65 GACATGGTCTTACACTAACTCTCACATATCAATACCGACGCCATGTCCCAGACATGGTCTTACAC
38512 TG
130 TG
38514 GCTCTCATAA
Statistics
Matches: 109, Mismatches: 14, Indels: 9
0.83 0.11 0.07
Matches are distributed among these distances:
138 37 0.34
139 1 0.01
140 12 0.11
141 15 0.14
142 11 0.10
143 15 0.14
144 13 0.12
145 5 0.05
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (145 bp):
CGATGCCATGTCCCAGACATCGTCTCACACTGGCTATCATCACCGAGGCTGATTCCATGTCCCAG
ACATGGTCTTACACTAACTCTCACATATCAATACCGACGCCATGTCCCAGACATGGTCTTACACT
GACACATCTCGTAGC
Found at i:38536 original size:94 final size:92
Alignment explanation
Indices: 38299--38559 Score: 255
Period size: 94 Copynumber: 2.8 Consensus size: 92
38289 GAGGCTGATT
* *
38299 CCATGTCCCAGACATGGTCTTACACTAGCTCTCA-CATATCCGTGCCGACGTCATGTCCCAGACA
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATCATAT--G-GCCGATG-CATGTCCCAGACA
* *
38363 TGGTCTTACACTGACACATCTCGTAGCCGATG
62 T-GTCTTACACTAACACATCTCATAGCCGATG
* * ** *
38395 -CATGTCCCAGACAT-GTCTTACATTGGCT-TACGTCCCGA-GGCTGATGCATGTCCCAGACATG
1 CCATGTCCCAGACATGGTCTTACACTGGCTCT-CAT-CATATGGCCGATGCATGTCCCAGACATG
*
38456 TCTTACACTAACCCTCATCTCAATA-CCGATG
64 TCTTACACTAA--CACATCTC-ATAGCCGATG
* * * **
38487 CCATGTCCGAGACATGGTCTTACACTGGCTCTCATAATATGGCCAATGCATGTCCTTGACATGTC
1 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATCATATGGCCGATGCATGTCCCAGACATGTC
38552 TTACACTA
66 TTACACTA
38560 GCCCACAATA
Statistics
Matches: 135, Mismatches: 20, Indels: 22
0.76 0.11 0.12
Matches are distributed among these distances:
90 11 0.08
91 14 0.10
92 18 0.13
93 18 0.13
94 57 0.42
95 15 0.11
96 2 0.01
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (92 bp):
CCATGTCCCAGACATGGTCTTACACTGGCTCTCATCATATGGCCGATGCATGTCCCAGACATGTC
TTACACTAACACATCTCATAGCCGATG
Found at i:38548 original size:140 final size:142
Alignment explanation
Indices: 38251--38556 Score: 327
Period size: 138 Copynumber: 2.2 Consensus size: 142
38241 TTTTCGATGC
* * * *
38251 CATGTCCCATACATCGTCTCACACTGGC-TATCATCACCGAGGCTGATTCCATGTCCCAGACATG
1 CATGTCCCAGACAT-GTCTTACATTGGCTTA-CGTC-CCGAGGCTGATTCCATGTCCCAGACATG
* ** * *
38315 GTCTTACACTAGCTCTCACATATCCGTGCCGACGTCATGTCCCAGACATGGTCTTACACTGACAC
63 GTCTTACACTAACTCTCACATATCAATACCGACGCCATGTCCCAGACATGGTCTTACACTGACAC
** *
38380 ATCTCGTAGCCGATG
128 ATCTAATAGCCAATG
*
38395 CATGTCCCAGACATGTCTTACATTGGCTTACGTCCCGAGGCTGA-TGCATGTCCCAGACAT-GTC
1 CATGTCCCAGACATGTCTTACATTGGCTTACGTCCCGAGGCTGATTCCATGTCCCAGACATGGTC
* * * * * *
38458 TTACACTAAC-C-CTCATCTCAATACCGATGCCATGTCCGAGACATGGTCTTACACTGGCTC-TC
66 TTACACTAACTCTCACATATCAATACCGACGCCATGTCCCAGACATGGTCTTACACTGACACATC
38520 ATAATATGGCCAATG
131 -TAATA--GCCAATG
**
38535 CATGTCCTTGACATGTCTTACA
1 CATGTCCCAGACATGTCTTACA
38557 CTAGCCCACA
Statistics
Matches: 137, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
137 2 0.01
138 42 0.31
139 1 0.01
140 38 0.28
141 15 0.11
142 10 0.07
143 14 0.10
144 15 0.11
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (142 bp):
CATGTCCCAGACATGTCTTACATTGGCTTACGTCCCGAGGCTGATTCCATGTCCCAGACATGGTC
TTACACTAACTCTCACATATCAATACCGACGCCATGTCCCAGACATGGTCTTACACTGACACATC
TAATAGCCAATG
Found at i:38935 original size:30 final size:30
Alignment explanation
Indices: 38899--38956 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
38889 CAATTCACAT
* *
38899 CTTTGGTAAAATGGCCATTTTACCCCTAGA
1 CTTTGGTAAAATGACAATTTTACCCCTAGA
38929 CTTTGGTAAAATGACAATTTTACCCCTA
1 CTTTGGTAAAATGACAATTTTACCCCTA
38957 TGCTAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (30 bp):
CTTTGGTAAAATGACAATTTTACCCCTAGA
Found at i:40075 original size:16 final size:15
Alignment explanation
Indices: 40050--40082 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
40040 TTACTCATAG
40050 TGATTAATATGTATA
1 TGATTAATATGTATA
40065 TGATCTAATATGTATA
1 TGAT-TAATATGTATA
40081 TG
1 TG
40083 TTCCTCATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.36, C:0.03, G:0.15, T:0.45
Consensus pattern (15 bp):
TGATTAATATGTATA
Found at i:55389 original size:79 final size:79
Alignment explanation
Indices: 55172--55395 Score: 272
Period size: 79 Copynumber: 2.8 Consensus size: 79
55162 GCTCCTCGTT
* * * * *
55172 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCGG
*
55237 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * *
55252 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGG
*
55316 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
* ** * *
55331 CAAATGCCTTC-GGATTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCGG
55395 A
65 A
55396 CATCATTCAA
Statistics
Matches: 125, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
78 29 0.23
79 48 0.38
80 45 0.36
81 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGGA
ATTAGTAACTCGCA
Found at i:55395 original size:40 final size:40
Alignment explanation
Indices: 55172--55395 Score: 285
Period size: 40 Copynumber: 5.7 Consensus size: 40
55162 GCTCCTCGTT
* *
55172 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
55212 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
55252 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
55292 CCAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
55331 CAAATGCCTTC-GGATTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAAC-TCGCA
55371 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
55396 CATCATTCAA
Statistics
Matches: 162, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
38 2 0.01
39 50 0.31
40 110 0.68
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Done.