Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold4054.1
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: 84572
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:435 original size:24 final size:24
Alignment explanation
Indices: 408--453 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
398 ACCTGAATCA
*
408 TGTAAACCCTAATGACATGTCATT
1 TGTAAACCCTAATGAAATGTCATT
432 TGTAAACCCTAATGAAATGTCA
1 TGTAAACCCTAATGAAATGTCA
454 ATTTAGGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.20, G:0.13, T:0.30
Consensus pattern (24 bp):
TGTAAACCCTAATGAAATGTCATT
Found at i:962 original size:50 final size:50
Alignment explanation
Indices: 793--1177 Score: 393
Period size: 51 Copynumber: 7.6 Consensus size: 50
783 CGATGAACAT
* * * * *** *
793 GTGTGTAGTACTGTGTGAAGGCTCCTACGTGTATCGATAAATGATGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCAC
* * * * * *
844 ATATGTAGTACTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGATCAC
*
895 GTATGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCAC
* * * *
945 GTGTGTAGTACTGTGTGAAGACTACTACGTGAATCG-ACAAA-TGATGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTA-AAACT--TGATCAC
* * * * *
996 ATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCAG-AAAGCTTTTG-TCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACC-GTAAAAC--TTGATCAC
* * * * *
1047 ATGTGTAATAATATGTGAAGGCTACTACGTGAATCGTATAACTTGATCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCAC
1097 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCAC
1147 GTGTGTAGTACTATGTGAAGGCTACTACGTG
1 GTGTGTAGTACTATGTGAAGGCTACTACGTG
1178 TATCGAATGA
Statistics
Matches: 281, Mismatches: 41, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
49 8 0.03
50 123 0.44
51 141 0.50
52 8 0.03
54 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGATCAC
Found at i:1069 original size:152 final size:151
Alignment explanation
Indices: 793--1184 Score: 556
Period size: 152 Copynumber: 2.6 Consensus size: 151
783 CGATGAACAT
* * *
793 GTGTGTAGTACTGTGTGAAGGCTCCTACGTGTATCGATAAATGATGGTCACATATGTAGTACTAA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA-AAATGATGGTCACATGTGTAGTACTAA
* * *
858 GTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTATGTAGTACTATGTGAAGGCTACTAC
65 GTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACATATGTAATAATATGTGAAGGCTACTAC
923 GTGAACCGTAAAACTTGATCAC
130 GTGAACCGTAAAACTTGATCAC
*
945 GTGTGTAGTACTGTGTGAAGACTACTACGTGAATCGACAAATGATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA-AAATGATGGTCACATGTGTAGTACTAA
* *
1010 GTGAAGGCTACTATGTGTACC-AGAAAGCTTTTGTCACATGTGTAATAATATGTGAAGGCTACTA
65 GTGAAGGCTACTATGTGTACCGA-AAAGCTTTGGTCACATATGTAATAATATGTGAAGGCTACTA
* *
1074 CGTGAATCGTATAACTTGATCAC
129 CGTGAACCGTAAAACTTGATCAC
* * * *
1097 GTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACT--TGATCACGTGTGTAGTACTA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCG-AAAA-TGATGGTCACATGTGTAGTACTA
* * *
1160 TGTGAAGGCTACTACGTGTATCGAA
64 AGTGAAGGCTACTATGTGTACCGAA
1185 TGATAAAAGT
Statistics
Matches: 216, Mismatches: 20, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
151 39 0.18
152 175 0.81
153 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.30
Consensus pattern (151 bp):
GTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGAAAATGATGGTCACATGTGTAGTACTAAG
TGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACATATGTAATAATATGTGAAGGCTACTACG
TGAACCGTAAAACTTGATCAC
Found at i:19261 original size:23 final size:23
Alignment explanation
Indices: 19230--19280 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
19220 ACCTACTTTC
*
19230 TTACTGTAGTAATTTTCGAGG-TA
1 TTACAGTAGTAATTTTCG-GGATA
19253 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
19276 TTACA
1 TTACA
19281 TTTCTCTCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:20857 original size:50 final size:50
Alignment explanation
Indices: 20789--21276 Score: 645
Period size: 50 Copynumber: 9.6 Consensus size: 50
20779 TTTCCTGTAC
* * ** * *
20789 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * **
20839 TGCCCATGCCATGTCCCAGACATGGCCTTACGGGGGACCTCTCATC-CTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTC-GG
* * *
20889 TGCCATTGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
20939 TGCCAACGCCATGCCCCAGACGTGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
20989 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
21039 TGCCAACGCCATGTCCCAGACATGGTCGTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
21089 TGCCAACGCCATGTCCCAGAGATGGTCATACATGGGACCTCACATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
21139 TGCCAATGTCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* **
21189 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
21245 TGCCAATGCCATGTCCCAGACATGGTCTTACA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACA
21277 CTAGCTCACA
Statistics
Matches: 385, Mismatches: 45, Indels: 10
0.88 0.10 0.02
Matches are distributed among these distances:
49 1 0.00
50 348 0.90
53 5 0.01
56 31 0.08
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:24355 original size:23 final size:23
Alignment explanation
Indices: 24324--24374 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
24314 ACCTACTTTC
*
24324 TTACTGTAGTAATTTTCGAGG-TA
1 TTACAGTAGTAATTTTCG-GGATA
*
24347 TTACAGTAGTAGTTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
24370 TTACA
1 TTACA
24375 CTTGGCACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:28157 original size:16 final size:15
Alignment explanation
Indices: 28116--28158 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
28106 AAAGATGATA
28116 ATATTAATATATAATT
1 ATATTAAT-TATAATT
**
28132 ATATCCATTATAATAT
1 ATATTAATTATAAT-T
28148 ATATTAATTAT
1 ATATTAATTAT
28159 TATCAGCTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATTAATTATAATT
Found at i:34757 original size:82 final size:81
Alignment explanation
Indices: 34606--34826 Score: 286
Period size: 82 Copynumber: 2.7 Consensus size: 81
34596 GTGTGCGATT
* * * * *
34606 TGAGATAACTTCGGCTATTTATGGCACTTAGTGTGC-GATTAGGAATAGCTTC-GACTACATATG
1 TGAGATAGCTTCGACTATGTAAGGCACTTAGTGTGCGGATTA-TAATAGCTTCAG-CTACATATG
34669 GCACTTAATGTGTGAGAC
64 GCACTTAATGTGTGAGAC
* *
34687 TGAGATAGCTTCGACTATGTAAGGCACTTACTGTGCGGGATTATAATAGCTTCAGCTAGATATGG
1 TGAGATAGCTTCGACTATGTAAGGCACTTAGTGTGC-GGATTATAATAGCTTCAGCTACATATGG
* *
34752 CACTTAGTGTGTTAGAC
65 CACTTAATGTGTGAGAC
*
34769 TAAGATAGCTTC-AGCTATGTAAGGCACTTAGTGTGCGAGATTATAATAGCTTCAGCTA
1 TGAGATAGCTTCGA-CTATGTAAGGCACTTAGTGTGCG-GATTATAATAGCTTCAGCTA
34827 TGCGATGGCA
Statistics
Matches: 124, Mismatches: 11, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
81 33 0.27
82 85 0.69
83 6 0.05
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (81 bp):
TGAGATAGCTTCGACTATGTAAGGCACTTAGTGTGCGGATTATAATAGCTTCAGCTACATATGGC
ACTTAATGTGTGAGAC
Found at i:34781 original size:41 final size:41
Alignment explanation
Indices: 34580--34846 Score: 208
Period size: 41 Copynumber: 6.5 Consensus size: 41
34570 GATTAATCGA
* * * * * *
34580 CTATGTTTTGCACTTAGTGTGCGA-TTTGAGATAACTTCGG
1 CTATGTATGGCACTTAGTGTGCGAGATTAAGATAGCTTCAG
* *
34620 CTATTTATGGCACTTAGTGTGC--GATTAGGAATAGCTTC-G
1 CTATGTATGGCACTTAGTGTGCGAGATTAAG-ATAGCTTCAG
** * * * *
34659 ACTACATATGGCACTTAATGTGTGAGACTGAGATAGCTTC-G
1 -CTATGTATGGCACTTAGTGTGCGAGATTAAGATAGCTTCAG
* * *
34700 ACTATGTAAGGCACTTACTGTGCGGGATTATA-ATAGCTTCAG
1 -CTATGTATGGCACTTAGTGTGCGAGATTA-AGATAGCTTCAG
** *
34742 CTA-GATATGGCACTTAGTGTGTTAGACTAAGATAGCTTCAG
1 CTATG-TATGGCACTTAGTGTGCGAGATTAAGATAGCTTCAG
*
34783 CTATGTAAGGCACTTAGTGTGCGAGATTATA-ATAGCTTCAG
1 CTATGTATGGCACTTAGTGTGCGAGATTA-AGATAGCTTCAG
* *
34824 CTATGCGATGGCATTTAGTGTGC
1 CTATG-TATGGCACTTAGTGTGC
34847 AAAACATTGA
Statistics
Matches: 180, Mismatches: 35, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
39 4 0.02
40 46 0.26
41 108 0.60
42 22 0.12
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (41 bp):
CTATGTATGGCACTTAGTGTGCGAGATTAAGATAGCTTCAG
Found at i:43789 original size:41 final size:40
Alignment explanation
Indices: 43665--43903 Score: 191
Period size: 41 Copynumber: 5.9 Consensus size: 40
43655 ACTATGTTTA
*
43665 GCACTTAGTGTGC-GAATTGAGATAGCTTCGGCTATTTATG
1 GCACTTAGTGTGCGGAA-TGAGATAGCTTCGGCTATATATG
* * * * * *
43705 GCACTTAATGTGC-GATTGGGAATAGCTTTGACTACATATG
1 GCACTTAGTGTGCGGAATGAG-ATAGCTTCGGCTATATATG
* * *
43745 GCACTTAGTGTGCGTGAATGAGATAGCTTTGGCTATGTAAG
1 GCACTTAGTGTGCG-GAATGAGATAGCTTCGGCTATATATG
* * * * *
43786 GCACTTAGTGTGTGGGATTATAATAACTTCAGG-TATATATG
1 GCACTTAGTGTGCGGAATGA-GATAGCTTC-GGCTATATATG
* * * *
43827 GCACTTAGTGTGTGAGACTGAGATAGCTTCGGCTATGTAAG
1 GCACTTAGTGTGCG-GAATGAGATAGCTTCGGCTATATATG
43868 GCACTTAGTGTGCAGGATTAT-A-ATAGCTTCGGCTAT
1 GCACTTAGTGTGC-GGA--ATGAGATAGCTTCGGCTAT
43904 GCGATGACAT
Statistics
Matches: 158, Mismatches: 31, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
39 3 0.02
40 47 0.30
41 95 0.60
42 12 0.08
43 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.28, T:0.33
Consensus pattern (40 bp):
GCACTTAGTGTGCGGAATGAGATAGCTTCGGCTATATATG
Found at i:43852 original size:82 final size:82
Alignment explanation
Indices: 43665--43897 Score: 267
Period size: 82 Copynumber: 2.9 Consensus size: 82
43655 ACTATGTTTA
* * * * **
43665 GCACTTAGTGTGCGA-ATTGAGATAGCTTCGGCTATTTATGGCACTTAATGTGC--GATTGGGAA
1 GCACTTAGTGTGCGAGAATGAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATT-ATAA
* * * *
43727 TAGCTT-TGACTACATATG
65 TAACTTCAG-GTATATATG
* * **
43745 GCACTTAGTGTGCGTGAATGAGATAGCTTTGGCTATGTAAGGCACTTAGTGTGTGGGATTATAAT
1 GCACTTAGTGTGCGAGAATGAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATTATAAT
43810 AACTTCAGGTATATATG
66 AACTTCAGGTATATATG
* *
43827 GCACTTAGTGTGTGAGACTGAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATTATAAT
1 GCACTTAGTGTGCGAGAATGAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATTATAAT
*
43892 AGCTTC
66 AACTTC
43898 GGCTATGCGA
Statistics
Matches: 129, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
80 14 0.11
81 32 0.25
82 78 0.60
83 5 0.04
ACGTcount: A:0.26, C:0.14, G:0.27, T:0.33
Consensus pattern (82 bp):
GCACTTAGTGTGCGAGAATGAGATAGCTTCGGCTATGTAAGGCACTTAGTGTGCAGGATTATAAT
AACTTCAGGTATATATG
Found at i:43904 original size:41 final size:40
Alignment explanation
Indices: 43656--43923 Score: 179
Period size: 41 Copynumber: 6.6 Consensus size: 40
43646 AATTAATCGA
* * * *
43656 CTATGTTTAGCACTTAGTGTGCGAATTGA-GATAGCTTCGG
1 CTATGTATGGCACTTAGTGTGCGGATT-ATAATAGCTTCGG
* * ** * *
43696 CTATTTATGGCACTTAATGTGC-GATTGGGAATAGCTTTGA
1 CTATGTATGGCACTTAGTGTGCGGATT-ATAATAGCTTCGG
** *
43736 CTACATATGGCACTTAGTGTGCGTGA--ATGAGATAGCTTTGG
1 CTATGTATGGCACTTAGTGTGCG-GATTAT-A-ATAGCTTCGG
* * *
43777 CTATGTAAGGCACTTAGTGTGTGGGATTATAATAACTTCAGG
1 CTATGTATGGCACTTAGTGTG-CGGATTATAATAGCTTC-GG
* * * *
43819 -TATATATGGCACTTAGTGTGTGAGACTGA-GATAGCTTCGG
1 CTATGTATGGCACTTAGTGTGCG-GA-TTATAATAGCTTCGG
*
43859 CTATGTAAGGCACTTAGTGTGCAGGATTATAATAGCTTCGG
1 CTATGTATGGCACTTAGTGTGC-GGATTATAATAGCTTCGG
* * *
43900 CTATGCGATGACATTTAGTGTGCG
1 CTATG-TATGGCACTTAGTGTGCG
43924 AAACATTGAG
Statistics
Matches: 177, Mismatches: 36, Indels: 29
0.73 0.15 0.12
Matches are distributed among these distances:
39 4 0.02
40 51 0.29
41 98 0.55
42 22 0.12
43 2 0.01
ACGTcount: A:0.25, C:0.14, G:0.28, T:0.34
Consensus pattern (40 bp):
CTATGTATGGCACTTAGTGTGCGGATTATAATAGCTTCGG
Found at i:51141 original size:51 final size:50
Alignment explanation
Indices: 51081--51219 Score: 190
Period size: 51 Copynumber: 2.7 Consensus size: 50
51071 GATGAACACG
*
51081 TGTGTAGTACTATGTGAAGACTACTACGTGTATCGATAAA-TAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA-AAACT-ATGGTCACA
* * * *
51132 TGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGAAAAGCTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAA-CTATGGTCACA
*
51183 TGTGTAGTACTATGTGAAGGCTACTACATGTATCGAA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAA
51220 TGATAATAGT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
50 3 0.04
51 74 0.95
52 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAAACTATGGTCACA
Found at i:51244 original size:51 final size:51
Alignment explanation
Indices: 51081--51251 Score: 184
Period size: 51 Copynumber: 3.4 Consensus size: 51
51071 GATGAACACG
* *
51081 TGTGTAGTACTATGTGAAGACTACTACGTGTATCG-ATAAATAATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAAT-GATAATGGTCACA
* * * * * *
51132 TGTGTAGTACTAAGTGAAGGCTACTACGTGTACCGAAAAGCT-TTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCG-AATGATAATGGTCACA
* * *
51183 TGTGTAGTACTATGTGAAGGCTACTACATGTATCGAATGATAATAGTAACA
1 TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATAATGGTCACA
* * *
51234 TGGGTGGTACTCTGTGAA
1 TGTGTAGTACTATGTGAA
51252 AACCCCCAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
50 4 0.04
51 91 0.94
52 1 0.01
53 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
TGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATAATGGTCACA
Found at i:53417 original size:17 final size:18
Alignment explanation
Indices: 53392--53434 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
53382 GGAATCTCAC
* *
53392 TCTTCTTCATTTTA-ATT
1 TCTTTTTCATTTGATATT
*
53409 TCTTTTTCATTTGATTTT
1 TCTTTTTCATTTGATATT
53427 TCTTTTTC
1 TCTTTTTC
53435 TTTCCTCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.12, C:0.16, G:0.02, T:0.70
Consensus pattern (18 bp):
TCTTTTTCATTTGATATT
Found at i:53477 original size:27 final size:27
Alignment explanation
Indices: 53447--53510 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
53437 TCCTCTCACA
*
53447 CTTTTTTAATATCTCTTTCATTTT-TTT
1 CTTTTTTAATA-CACTTTCATTTTCTTT
* *
53474 CTTTTTTTATACACTTTCTTTTTCTTT
1 CTTTTTTAATACACTTTCATTTTCTTT
*
53501 CCTTTTTAAT
1 CTTTTTTAAT
53511 TTCCTCACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.14, C:0.17, G:0.00, T:0.69
Consensus pattern (27 bp):
CTTTTTTAATACACTTTCATTTTCTTT
Found at i:53478 original size:26 final size:29
Alignment explanation
Indices: 53449--53510 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 29
53439 CTCTCACACT
*
53449 TTTTTAATAT-CTCTTTCATTTT-TTT-C
1 TTTTTAATATACACTTTCATTTTCTTTCC
* *
53475 TTTTT-TTATACACTTTCTTTTTCTTTCC
1 TTTTTAATATACACTTTCATTTTCTTTCC
53503 TTTTTAAT
1 TTTTTAAT
53511 TTCCTCACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
25 3 0.11
26 15 0.54
27 3 0.11
28 6 0.21
29 1 0.04
ACGTcount: A:0.15, C:0.16, G:0.00, T:0.69
Consensus pattern (29 bp):
TTTTTAATATACACTTTCATTTTCTTTCC
Found at i:54439 original size:21 final size:19
Alignment explanation
Indices: 54404--54459 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
54394 TTTTTGAATA
54404 TTTTTTAATTCGAATTTTAC
1 TTTTTTAATTCGAATTTT-C
*
54424 TTTTTTAACTTTGAATTTTC
1 TTTTTTAA-TTCGAATTTTC
54444 TTATTTT--TTCGAATTT
1 TT-TTTTAATTCGAATTT
54460 GTTTTTCACT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 8 0.25
20 11 0.34
21 13 0.41
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.64
Consensus pattern (19 bp):
TTTTTTAATTCGAATTTTC
Found at i:56012 original size:31 final size:31
Alignment explanation
Indices: 55928--56029 Score: 116
Period size: 31 Copynumber: 3.2 Consensus size: 31
55918 ATGACTTCTC
** *
55928 ATTAAATGCTACTCACATAATGCAAGACAAA
1 ATTAAATGCTAAACACATAATGCAAGACATA
*
55959 ATTTAAAGATGC-AAACACATAATGCAAGTCATA
1 A-TT-AA-ATGCTAAACACATAATGCAAGACATA
* *
55992 ATTAAATGCTAAACATATAATGCAAGGCATA
1 ATTAAATGCTAAACACATAATGCAAGACATA
56023 ATTAAAT
1 ATTAAAT
56030 ATGCAGGTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
30 4 0.07
31 29 0.48
32 4 0.07
33 20 0.33
34 4 0.07
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (31 bp):
ATTAAATGCTAAACACATAATGCAAGACATA
Found at i:56574 original size:49 final size:50
Alignment explanation
Indices: 56476--56591 Score: 135
Period size: 49 Copynumber: 2.3 Consensus size: 50
56466 TACTTAAGCA
* * * **
56476 TAATTAACATATAAGATGCATAAATGCATGGCTTAATTAAAATGCAAACT
1 TAATTAACATATAAGATACATAAATGCATGACATAATTAAAACACAAACT
* * * *
56526 TATTTAACATATGAGTTACAT-AATGCATGACATAATTAAAACATAAACT
1 TAATTAACATATAAGATACATAAATGCATGACATAATTAAAACACAAACT
*
56575 TAATTAACACATAAGAT
1 TAATTAACATATAAGAT
56592 TCTTCTATGC
Statistics
Matches: 53, Mismatches: 13, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
49 36 0.68
50 17 0.32
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (50 bp):
TAATTAACATATAAGATACATAAATGCATGACATAATTAAAACACAAACT
Found at i:61833 original size:32 final size:33
Alignment explanation
Indices: 61791--61854 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
61781 CTAAATGCAA
61791 AACACATAATGTAAGACATAA-TTAAAGATGCT
1 AACACATAATGTAAGACATAATTTAAAGATGCT
*
61823 AACATATAATGTAAGACATAATTTAAAGATGC
1 AACACATAATGTAAGACATAATTTAAAGATGC
61855 AAACTTATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (33 bp):
AACACATAATGTAAGACATAATTTAAAGATGCT
Found at i:74639 original size:28 final size:28
Alignment explanation
Indices: 74597--74657 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
74587 CTATTCAGTA
* *
74597 ACAGT-ACAGTGTGGGCCTTAGCCTAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
74624 ACAGTAACAATGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
74652 ACAGTA
1 ACAGTA
74658 TCAGTATAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:75002 original size:27 final size:27
Alignment explanation
Indices: 74978--75202 Score: 267
Period size: 27 Copynumber: 8.3 Consensus size: 27
74968 AAGGGTATAA
* *
74978 CAGTCATTTTACCCTGTGGGTGTATTT
1 CAGTCATTTTACCCTGTGGGGGTAATT
**
75005 C-GATCATTTTACCCTGTAAGGGTAATT
1 CAG-TCATTTTACCCTGTGGGGGTAATT
* *
75032 CAGTCATTTTACCCTATGGGAGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
*
75059 CGGTCATTTTACCCTGTGGGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
**
75086 C-GATCATTTTACCCTGTGGGCTTAATT
1 CAG-TCATTTTACCCTGTGGGGGTAATT
* *
75113 -TGATCATTTTACCTTGTGGGGGTAATT
1 CAG-TCATTTTACCCTGTGGGGGTAATT
* *
75140 CAATCATCTTACCCTGTGGGGGTAATT
1 CAGTCATTTTACCCTGTGGGGGTAATT
*
75167 CAGTCATTTTACCCTGTGGGGGTAATC
1 CAGTCATTTTACCCTGTGGGGGTAATT
*
75194 CGGTCATTT
1 CAGTCATTT
75203 ATTGACCTCT
Statistics
Matches: 169, Mismatches: 24, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
26 2 0.01
27 166 0.98
28 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.39
Consensus pattern (27 bp):
CAGTCATTTTACCCTGTGGGGGTAATT
Found at i:78281 original size:40 final size:39
Alignment explanation
Indices: 78183--78405 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
78173 TCCTCGTTCA
* * ** * *
78183 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
*
78222 AATGCCTTCGGGACATAACCCGGATTTAACAATTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
*
78261 GAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
**
78301 GAATGCCTTCGGGACTTAACCCGGATTT-AGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAACAAT-TCGCAC
* * * * * *
78341 AAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAATTCGCAC
* *
78382 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
78406 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
39 39 0.25
40 108 0.69
41 8 0.05
42 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAATTCGCAC
Found at i:78339 original size:80 final size:79
Alignment explanation
Indices: 78181--78405 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
78171 GCTCCTCGTT
* * ** * *
78181 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAATGCCTTCGGGACTTAACCCGGA
78246 TTTAACAATTCGCA
66 TTTAACAATTCGCA
*
78260 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACGAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCAC-AATGCCTTCGGGACTTAACCCGG
**
78325 ATTT-AGTATCTCGCA
65 ATTTAACAAT-TCGCA
* * * * * * *
78340 CAAAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACAATGCCTTCGGGACTTAACCC
78403 GGA
63 GGA
78406 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
79 41 0.33
80 77 0.62
81 6 0.05
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACAATGCCTTCGGGACTTAACCCGGA
TTTAACAATTCGCA
Found at i:78405 original size:120 final size:119
Alignment explanation
Indices: 78183--78405 Score: 288
Period size: 120 Copynumber: 1.9 Consensus size: 119
78173 TCCTCGTTCA
* * *
78183 AATGCCTTCGGGACATAGCCCGGATTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
* *
78248 TAACAATTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
66 TAACAATTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
78302 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTC-GGATCTTAATCCGGA
1 AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGA-CATAACCCGGA
* * *
78366 TATATTCACTTAGCAC-AAAGCCTTCGGGACTTAGCCCGGA
64 TATA-ACAATTAGCACGAAAGCCTTCGGGACTTAACCCGGA
78406 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
119 38 0.43
120 42 0.48
121 8 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (119 bp):
AATGCCTTCGGGACATAACCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATA
TAACAATTAGCACGAAAGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Done.