Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold553
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: 449280
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
File 4 of 4
Found at i:412148 original size:30 final size:28
Alignment explanation
Indices: 412114--412195 Score: 87
Period size: 27 Copynumber: 2.9 Consensus size: 28
412104 GGTATTTTTG
412114 GAAATAAATCGGAGTTGGAGTATCCCCTCA
1 GAAAT-AA-CGGAGTTGGAGTATCCCCTCA
* *
412144 GAAATAACGGGGTTGGAGTATCCCC-GA
1 GAAATAACGGAGTTGGAGTATCCCCTCA
* *
412171 TG-ATTAACGGGGTTGGAGTATCCCC
1 -GAAATAACGGAGTTGGAGTATCCCC
412196 GATTGTGAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
27 23 0.48
28 18 0.38
29 2 0.04
30 5 0.10
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (28 bp):
GAAATAACGGAGTTGGAGTATCCCCTCA
Found at i:412158 original size:28 final size:27
Alignment explanation
Indices: 412127--412195 Score: 95
Period size: 27 Copynumber: 2.5 Consensus size: 27
412117 ATAAATCGGA
412127 GTTGGAGTATCCCCTCA-GAAATAACGGG
1 GTTGGAGTATCCCC-CATG-AATAACGGG
* *
412155 GTTGGAGTATCCCCGATGATTAACGGG
1 GTTGGAGTATCCCCCATGAATAACGGG
412182 GTTGGAGTATCCCC
1 GTTGGAGTATCCCC
412196 GATTGTGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
27 23 0.61
28 15 0.39
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (27 bp):
GTTGGAGTATCCCCCATGAATAACGGG
Found at i:412249 original size:54 final size:51
Alignment explanation
Indices: 412182--412312 Score: 165
Period size: 51 Copynumber: 2.5 Consensus size: 51
412172 GATTAACGGG
* * *
412182 GTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTG-AGAAATTAGTG--TCTTGAAAATAAAATCGGA
*
412236 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTGTGAG-AAATTAGTGTCTTGAAAATAAAATCGGA
*
412287 GTTGGAATATCCCCGATTGTGGAGAA
1 GTTGGAGTATCCCCGATTGT-GAGAA
412313 TTGAGAAACT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
51 35 0.51
52 4 0.06
53 10 0.15
54 19 0.28
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTGTGAGAAATTAGTGTCTTGAAAATAAAATCGGA
Found at i:414676 original size:20 final size:20
Alignment explanation
Indices: 414649--414703 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
414639 TAAAATTTTC
*
414649 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
414669 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
414689 AAATGTATCGATACA
1 AAATGTATCGATACA
414704 TTTCCTTGGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:414747 original size:19 final size:18
Alignment explanation
Indices: 414723--414790 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
414713 TAGTAGCTAA
414723 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
414742 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
414757 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
414774 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
414791 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:414763 original size:13 final size:13
Alignment explanation
Indices: 414745--414769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
414735 ACAATACTTA
414745 TGTATCGATACAT
1 TGTATCGATACAT
414758 TGTATCGATACA
1 TGTATCGATACA
414770 AAACTTATGT
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:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:414767 original size:32 final size:32
Alignment explanation
Indices: 414726--414788 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
414716 TAGCTAATTA
*
414726 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
414758 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
414789 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:414870 original size:21 final size:21
Alignment explanation
Indices: 414846--414902 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
414836 CATTTGTAGG
*
414846 ATGTATCGATACATTCCACAA
1 ATGTATCGATACATTCAACAA
414867 ATGTATCGATACATTCAACAA
1 ATGTATCGATACATTCAACAA
*
414888 ATGTATCAATACATT
1 ATGTATCGATACATT
414903 TGGATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCAACAA
Found at i:415734 original size:55 final size:55
Alignment explanation
Indices: 415650--416175 Score: 593
Period size: 55 Copynumber: 9.3 Consensus size: 55
415640 ATAAAGTGTA
* * * * ** *
415650 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCATGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
415705 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * * *
415760 CCCTGCTCTTTGAGGACTGGAAA-ATGCCATCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
415815 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGAG-G
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAG-GTG
* * **
415870 TCCTGCTCTTTGGGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
*
415931 TCCTGCTCTTTGAGGACTG-AAGGTGCCACCAACTTAG-GTGGGCTTTAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTT-GTGTGGGCTTT----G-AAAGGTG
* *
415990 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTTAAAAGAAAATGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT----G-AAAGGTG
*
416049 TCCCGCTCTTTGAGGACTG-AAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
416103 TCCTGCTCTCTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
416158 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
416176 AAAAAGCGGA
Statistics
Matches: 422, Mismatches: 28, Indels: 42
0.86 0.06 0.09
Matches are distributed among these distances:
53 2 0.00
54 26 0.06
55 225 0.53
56 15 0.04
58 1 0.00
59 102 0.24
60 27 0.06
61 18 0.04
64 6 0.01
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:417194 original size:18 final size:17
Alignment explanation
Indices: 417142--417217 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
417132 CTTAAGTAGG
*
417142 TTTTTTCTTTTCTCTCTTT
1 TTTTTTTTTTTC-CT-TTT
* * *
417161 TTCTTTGTTTT-GTTTT
1 TTTTTTTTTTTCCTTTT
417177 TTTGTTTTTTTTCC-TTT
1 TTT-TTTTTTTTCCTTTT
* *
417194 TTTTTTCTTTTGCTTTT
1 TTTTTTTTTTTCCTTTT
417211 TTTTTTT
1 TTTTTTT
417218 GAAGAGAAGG
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
16 13 0.29
17 23 0.51
19 9 0.20
ACGTcount: A:0.00, C:0.12, G:0.05, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTTTCCTTTT
Found at i:429845 original size:27 final size:26
Alignment explanation
Indices: 429797--429879 Score: 87
Period size: 27 Copynumber: 3.0 Consensus size: 26
429787 TGGTATTTTT
*
429797 GGAAATAAATCGGAGTTGGAGTATCCCTC
1 GGAAAT-AA-CGGGGTTGGAGTATCCC-C
429826 GGAAATAACGGGGTTGGAGTATCCCC
1 GGAAATAACGGGGTTGGAGTATCCCC
* *
429852 -GATGATTAACAGGGTTGGAGTATCCCC
1 GGA--AATAACGGGGTTGGAGTATCCCC
429879 G
1 G
429880 ATTATGAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
25 2 0.04
26 1 0.02
27 37 0.77
28 2 0.04
29 6 0.12
ACGTcount: A:0.28, C:0.18, G:0.31, T:0.23
Consensus pattern (26 bp):
GGAAATAACGGGGTTGGAGTATCCCC
Found at i:429896 original size:106 final size:106
Alignment explanation
Indices: 429626--429931 Score: 336
Period size: 107 Copynumber: 2.9 Consensus size: 106
429616 AAAATCGAGA
* ***
429626 TTGGAGTATCCCC--TCGAAAATAACGGGGTTGGAGTATCCCCAATTATG-AGAAATCAATATTT
1 TTGGAGTATCCCCGAT-G-AAATAAC-GGGTTGGAGTATCCCCGATTATGAAGAAATTGGTATTT
* * * * *
429688 TAGG-AATAAAGCTGGGGTTGGAGCATCCCCTCGGAAGTAAAAGGG
63 TTGGAAATAAATC-GGAGTTGGAGTAT-CCCTCGGAAATAAAAGGG
* * * *
429733 TTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGACTGTGAA-AATTTGGTATTTTT
1 TTGGAGTATCCCCGATGAAATAACG-GGTTGGAGTATCCCCGATTATGAAGAAATTGGTATTTTT
**
429797 GGAAATAAATCGGAGTTGGAGTATCCCTCGGAAATAACGGGG
65 GGAAATAAATCGGAGTTGGAGTATCCCTCGGAAATAAAAGGG
* *
429839 TTGGAGTATCCCCGATG-ATTAACAGGGTTGGAGTATCCCCGATTATGAAGAAATTGGTGTTTTT
1 TTGGAGTATCCCCGATGAAATAAC-GGGTTGGAGTATCCCCGATTATGAAGAAATTGGTATTTTT
429903 CGGAAATAAAATCGGAGTTGGAGTATCCC
65 -GGAAAT-AAATCGGAGTTGGAGTATCCC
429932 CGATTATAGA
Statistics
Matches: 169, Mismatches: 21, Indels: 17
0.82 0.10 0.08
Matches are distributed among these distances:
105 26 0.15
106 46 0.27
107 66 0.39
108 30 0.18
109 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.27
Consensus pattern (106 bp):
TTGGAGTATCCCCGATGAAATAACGGGTTGGAGTATCCCCGATTATGAAGAAATTGGTATTTTTG
GAAATAAATCGGAGTTGGAGTATCCCTCGGAAATAAAAGGG
Found at i:429981 original size:51 final size:54
Alignment explanation
Indices: 429865--429987 Score: 164
Period size: 51 Copynumber: 2.3 Consensus size: 54
429855 GATTAACAGG
* * *
429865 GTTGGAGTATCCCCGATTATGAAGAAATTGGTGTTTTTCGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTCTTCGAAAATAAAATCGGA
429919 GTTGGAGTATCCCCGATTAT--AGAAAATTAGTG-TCTT-GAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATTAGTGTTCTTCGAAAATAAAATCGGA
* *
429970 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
429988 GTGGAGAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 30 0.48
52 5 0.08
53 8 0.13
54 20 0.32
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.32
Consensus pattern (54 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTAGTGTTCTTCGAAAATAAAATCGGA
Found at i:432361 original size:20 final size:20
Alignment explanation
Indices: 432334--432388 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
432324 TAAAATTTCC
*
432334 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
432354 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
432374 AAATGTATCGATACA
1 AAATGTATCGATACA
432389 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:432432 original size:19 final size:18
Alignment explanation
Indices: 432408--432475 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
432398 CAGTAGCTAA
432408 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
432427 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
432442 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
432459 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
432476 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:432448 original size:13 final size:13
Alignment explanation
Indices: 432430--432454 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
432420 ACAATACTTA
432430 TGTATCGATACAT
1 TGTATCGATACAT
432443 TGTATCGATACA
1 TGTATCGATACA
432455 AAACTTATGT
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:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:432452 original size:32 final size:32
Alignment explanation
Indices: 432411--432473 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
432401 TAGCTAATTA
*
432411 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
432443 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
432474 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:432555 original size:21 final size:21
Alignment explanation
Indices: 432531--432587 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
432521 CATTTGTAGG
* *
432531 ATGTATCAATACATTCCACAA
1 ATGTATCGATACATTCAACAA
432552 ATGTATCGATACATTCAACAA
1 ATGTATCGATACATTCAACAA
432573 ATGTATCGATACATT
1 ATGTATCGATACATT
432588 TGGATAATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.40, C:0.19, G:0.09, T:0.32
Consensus pattern (21 bp):
ATGTATCGATACATTCAACAA
Found at i:435241 original size:84 final size:84
Alignment explanation
Indices: 435088--435284 Score: 229
Period size: 84 Copynumber: 2.3 Consensus size: 84
435078 GAAAGGATAC
* * * **
435088 TCCAACCTCATTCTAACAAAAATCCAAATTTACTTTGTGGAATTTTACCTTTGGGAAAACTCCAT
1 TCCAACCCCGTTCTAACAAAAATTC-AA-TTACTTCATGGAATTTTACCTTTGGGAAAACTCCAT
**
435153 CCCCACTCTTTTGAGGGGACATT
64 CCCCACTCCCTTG-GGGGAC-TT
* * *
435176 T-CAACCCGGTTCTAACAAAAATTCAA-TACTTCATGGAATTTTACCTTTAGGG-ACACTCTATC
1 TCCAACCCCGTTCTAACAAAAATTCAATTACTTCATGGAATTTTACCTTT-GGGAAAACTCCATC
435238 CCCACTCCCTTGGGGGACTT
65 CCCACTCCCTTGGGGGACTT
*
435258 TCCAACCCCGCTCTAACAAAAATTCAA
1 TCCAACCCCGTTCTAACAAAAATTCAA
435285 ATCTTCCTTT
Statistics
Matches: 95, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
82 3 0.03
83 29 0.31
84 38 0.40
85 3 0.03
86 2 0.02
87 19 0.20
88 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (84 bp):
TCCAACCCCGTTCTAACAAAAATTCAATTACTTCATGGAATTTTACCTTTGGGAAAACTCCATCC
CCACTCCCTTGGGGGACTT
Found at i:438336 original size:13 final size:13
Alignment explanation
Indices: 438318--438343 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
438308 CAATTTTTGG
438318 TGTATCGATACAT
1 TGTATCGATACAT
438331 TGTATCGATACAT
1 TGTATCGATACAT
438344 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:438355 original size:32 final size:33
Alignment explanation
Indices: 438298--438361 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
438288 TACAAGCCAA
**
438298 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
438331 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
438362 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:438368 original size:19 final size:18
Alignment explanation
Indices: 438298--438368 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
438288 TACAAGCCAA
438298 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
438318 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
438331 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
438350 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
438369 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:440916 original size:13 final size:13
Alignment explanation
Indices: 440898--440923 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
440888 ATAATCACCC
440898 TGTATCGATACAA
1 TGTATCGATACAA
440911 TGTATCGATACAA
1 TGTATCGATACAA
440924 AGAAAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:444864 original size:21 final size:21
Alignment explanation
Indices: 444835--444879 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
444825 AAGTTTTTAT
*
444835 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
444855 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
444877 TTT
1 TTT
444880 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:447116 original size:13 final size:13
Alignment explanation
Indices: 447098--447123 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
447088 CAATTTTTGG
447098 TGTATCGATACAT
1 TGTATCGATACAT
447111 TGTATCGATACAT
1 TGTATCGATACAT
447124 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:447140 original size:32 final size:33
Alignment explanation
Indices: 447078--447141 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
447068 TACAAGCCAA
**
447078 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
*
447111 TGTATCGATAC-ATACTTGGTGTATTGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
447142 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Done.