Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold323
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: 764456
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.32
Warning! 36661 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:736684 original size:4 final size:4
Alignment explanation
Indices: 736675--736700 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
736665 TATATCACCA
736675 AATC AATC AATC AATC AATC AATC AA
1 AATC AATC AATC AATC AATC AATC AA
736701 ACCAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.23, G:0.00, T:0.23
Consensus pattern (4 bp):
AATC
Found at i:739537 original size:11 final size:11
Alignment explanation
Indices: 739510--739543 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
739500 TGGGGGTTTT
739510 TACCAAAATAA
1 TACCAAAATAA
*
739521 TA-CAAAAAAA
1 TACCAAAATAA
739531 TACCAAAATAA
1 TACCAAAATAA
739542 TA
1 TA
739544 TAAACTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (11 bp):
TACCAAAATAA
Found at i:740084 original size:11 final size:11
Alignment explanation
Indices: 740065--740098 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
740055 AAAAAGTTTA
740065 TATTATTTTGG
1 TATTATTTTGG
*
740076 TATT-TTTTTG
1 TATTATTTTGG
740086 TATTATTTTGG
1 TATTATTTTGG
740097 TA
1 TA
740099 AAAACCCCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.18, C:0.00, G:0.15, T:0.68
Consensus pattern (11 bp):
TATTATTTTGG
Found at i:742086 original size:27 final size:26
Alignment explanation
Indices: 742036--742096 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
742026 ACCAAAAATT
*
742036 TATTTTAAAAATAAAAAACAAAAAAG
1 TATTTTAAAAATAAAAAACAAAAAAA
*
742062 TATTTTAAAATTAAAAAA-ATTAAAAAA
1 TATTTTAAAAATAAAAAACA--AAAAAA
742089 TATATTTA
1 TAT-TTTA
742097 TTTATTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
25 1 0.03
26 17 0.57
27 8 0.27
28 4 0.13
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (26 bp):
TATTTTAAAAATAAAAAACAAAAAAA
Found at i:743386 original size:31 final size:31
Alignment explanation
Indices: 743351--743415 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
743341 TTAAAAACAT
743351 AGTAACTTAAATAAAAACTTCCAAATAGTTC
1 AGTAACTTAAATAAAAACTTCCAAATAGTTC
* **
743382 AGTAACTTAAATGAAAACTTTTAAATAGTTC
1 AGTAACTTAAATAAAAACTTCCAAATAGTTC
743413 AGT
1 AGT
743416 GACTACTTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (31 bp):
AGTAACTTAAATAAAAACTTCCAAATAGTTC
Found at i:744866 original size:4 final size:4
Alignment explanation
Indices: 744857--744881 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
744847 AAACAAGGGT
744857 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
744882 CCCAATAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:745645 original size:24 final size:24
Alignment explanation
Indices: 745618--745693 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
745608 TCAAATATGG
*
745618 AAAAAGAAAGAAAATAGAATATAT
1 AAAAAGAAAGAAAATAGAATATAA
* **
745642 AAAAA-ATAGAAAATCA-AATATGG
1 AAAAAGAAAGAAAAT-AGAATATAA
*
745665 AAAAAGAAACAAAATAGAATATAA
1 AAAAAGAAAGAAAATAGAATATAA
745689 AAAAA
1 AAAAA
745694 ATAAAGAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
23 19 0.45
24 23 0.55
ACGTcount: A:0.72, C:0.03, G:0.11, T:0.14
Consensus pattern (24 bp):
AAAAAGAAAGAAAATAGAATATAA
Found at i:745650 original size:47 final size:47
Alignment explanation
Indices: 745598--745745 Score: 226
Period size: 47 Copynumber: 3.1 Consensus size: 47
745588 ATTTAATGGG
745598 AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGAATATATAAA
1 AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGAATATATAAA
* * *
745645 AAATAGAAAATCAAATATGGAAAAAGAAACAAAATAGAATATAAAAA
1 AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGAATATATAAA
* * *
745692 AAATAAAGAATCAAATATGGGAAAGGAAAGAAAATA-ACATATATAAA
1 AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGA-ATATATAAA
745739 AAATAGA
1 AAATAGA
745746 TCATATTAAA
Statistics
Matches: 90, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
46 1 0.01
47 89 0.99
ACGTcount: A:0.67, C:0.03, G:0.14, T:0.16
Consensus pattern (47 bp):
AAATAGAGAATCAAATATGGAAAAAGAAAGAAAATAGAATATATAAA
Found at i:745652 original size:23 final size:23
Alignment explanation
Indices: 745618--745696 Score: 74
Period size: 23 Copynumber: 3.4 Consensus size: 23
745608 TCAAATATGG
*
745618 AAAAAGAA-AGAAAATAGAATAT
1 AAAAAAAATAGAAAATAGAATAT
*
745640 ATAAAAAATAGAAAATCA-AATAT
1 AAAAAAAATAGAAAAT-AGAATAT
* *
745663 GGAAAAAGAA-ACAAAATAGAATAT
1 --AAAAAAAATAGAAAATAGAATAT
745687 AAAAAAAATA
1 AAAAAAAATA
745697 AAGAATCAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
22 13 0.29
23 14 0.31
24 12 0.27
25 6 0.13
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (23 bp):
AAAAAAAATAGAAAATAGAATAT
Found at i:745708 original size:23 final size:22
Alignment explanation
Indices: 745635--745709 Score: 64
Period size: 23 Copynumber: 3.2 Consensus size: 22
745625 AAGAAAATAG
*
745635 AATATATAAAAAATAGAAAATCA
1 AATATAAAAAAAATA-AAAATCA
*
745658 AATATGGAAAAAGAAA-CAAAAT-A
1 AATAT--AAAAA-AAATAAAAATCA
745681 GAATATAAAAAAAATAAAGAATCA
1 -AATATAAAAAAAATAAA-AATCA
745705 AATAT
1 AATAT
745710 GGGAAAGGAA
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
21 3 0.07
22 7 0.17
23 14 0.33
24 11 0.26
25 4 0.10
26 3 0.07
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.19
Consensus pattern (22 bp):
AATATAAAAAAAATAAAAATCA
Found at i:757372 original size:18 final size:18
Alignment explanation
Indices: 757346--757385 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
757336 ATAATTTGTG
*
757346 ATAATTATACATTTAAAA-
1 ATAACTATA-ATTTAAAAT
757364 ATAACTATAATTTAAAAT
1 ATAACTATAATTTAAAAT
757382 ATAA
1 ATAA
757386 GAAAAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAACTATAATTTAAAAT
Found at i:758387 original size:243 final size:240
Alignment explanation
Indices: 757946--758470 Score: 560
Period size: 243 Copynumber: 2.2 Consensus size: 240
757936 TTAAAATATT
* *
757946 AATGTGGGTTTAAAAATAACAT-TCAATAAATAATAAAACGTATGATTTGAAACTAATTAATAAT
1 AATGTGTGTTTAAAAATAACATAT-AATAAATAATAAAACGTATGACTTGAAACTAATTAATAAT
* * * *
758010 AACGCATGAAATATGTACGTTATTAAAATGAAAAAAATTAGACTGAAATGTTTATTTTAGTGTTG
65 AACCCATAAAATATGTACGATATTAAAATGAAAAAAATTAGACTGAAATGTTTATATTAGTGTTG
* * *
758075 TCATCATGAGTCAGTGTAAAGTTAACTTGTGACACCAGCTCAATCAAATGCATTATTAATACTAG
130 TCATCATAAGTCAGTGTAAAGTTAACTTGTGACACAAGCTCAATCAAATACATTATTAATAC-AG
* *
758140 AAATCCTATCACACACGTATGCGCGTGGAAACTAAAAATATGGAAAATA
194 AAATCCTATCACACACGTATGCGCGTGGAAACCAAAAATA--GAAAACA
* ** * *
758189 AATGTGTGTTTAAAAATAACATATATTAAATAATTGAATGTATGGCTTGAAACTAATTAATAATA
1 AATGTGTGTTTAAAAATAACATATAATAAATAATAAAACGTATGACTTGAAACTAATTAATAATA
* * ** *
758254 ACCCATAAAATATGTATGATATTAAAAT-TAAAATTTTA-A-TTAAATTGTTTATCATT-GTGTT
66 ACCCATAAAATATGTACGATATTAAAATGAAAAAAATTAGACTGAAA-TGTTTAT-ATTAGTGTT
* * ** * *
758315 GTTATCAATATTAAGTTAGTGTCGAGTTAACTTGTGACACAA-ATCCAATCAAGTACATTATTAA
129 GTCATC---A-TAAGTCAGTGTAAAGTTAACTTGTGACACAAGCT-CAATCAAATACATTATTAA
* ** * * * * *
758379 TA-AGAAATCTTATCACAGGCGTATGTGTGTGGCAACCACAAATAGAACACA
189 TACAGAAATCCTATCACACACGTATGCGCGTGGAAACCAAAAATAGAAAACA
* *
758430 AATGTGTGTTTAAAAATAATATATAATAAAAAATGAAAACG
1 AATGTGTGTTTAAAAATAACATATAATAAATAAT-AAAACG
758471 AGAAACCACG
Statistics
Matches: 232, Mismatches: 41, Indels: 19
0.79 0.14 0.07
Matches are distributed among these distances:
240 4 0.02
241 54 0.23
242 12 0.05
243 114 0.49
244 3 0.01
245 45 0.19
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.32
Consensus pattern (240 bp):
AATGTGTGTTTAAAAATAACATATAATAAATAATAAAACGTATGACTTGAAACTAATTAATAATA
ACCCATAAAATATGTACGATATTAAAATGAAAAAAATTAGACTGAAATGTTTATATTAGTGTTGT
CATCATAAGTCAGTGTAAAGTTAACTTGTGACACAAGCTCAATCAAATACATTATTAATACAGAA
ATCCTATCACACACGTATGCGCGTGGAAACCAAAAATAGAAAACA
Found at i:761731 original size:66 final size:66
Alignment explanation
Indices: 761649--761777 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 66
761639 GAATCGGAAA
* * * *
761649 GAATAAAACAAGCCGAAAAAGAATGATAAAGAT-GGGTGAATAAATCAAAACAGATAAAAAATAG
1 GAATAAAACAAACCGAAAAAGAAT-AAAAAAATGGGGTGAATAAAACAAAACAGATAAAAAATAG
761713 AT
65 AT
761715 GAATAAAACAAACCGAAAAAGAATAAAAAAATGGGGTGAATAAAACAAAACAGATAAAAAATA
1 GAATAAAACAAACCGAAAAAGAATAAAAAAATGGGGTGAATAAAACAAAACAGATAAAAAATA
761778 TGGAGGAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
65 6 0.10
66 52 0.90
ACGTcount: A:0.63, C:0.08, G:0.16, T:0.13
Consensus pattern (66 bp):
GAATAAAACAAACCGAAAAAGAATAAAAAAATGGGGTGAATAAAACAAAACAGATAAAAAATAGA
T
Found at i:763429 original size:18 final size:19
Alignment explanation
Indices: 763406--763441 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
763396 GTTTATTCAA
*
763406 AATTTT-ATGTCAAACAAT
1 AATTTTCATGCCAAACAAT
763424 AATTTTCATGCCAAACAA
1 AATTTTCATGCCAAACAA
763442 GTTCCACTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (19 bp):
AATTTTCATGCCAAACAAT
Done.