Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 4 of 240
Found at i:1491125 original size:17 final size:18
Alignment explanation
Indices: 1491103--1491142 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1491093 AAAATTTTAT
*
1491103 TAAAAATTAGAAAAAA-A
1 TAAAAATCAGAAAAAATA
*
1491120 TAAAAATCATAAAAAATA
1 TAAAAATCAGAAAAAATA
1491138 TAAAA
1 TAAAA
1491143 TTTTGTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
TAAAAATCAGAAAAAATA
Found at i:1491152 original size:56 final size:55
Alignment explanation
Indices: 1491092--1491264 Score: 149
Period size: 55 Copynumber: 3.1 Consensus size: 55
1491082 TTTCAAATAT
1491092 TAAAATTTTATTAAAAATTAGAAAAAAATA-AAAATCATA-AAAAATATAAAATTTTG
1 TAAAATTTTA-TAAAAA-TAGAAAAAAATATAAAAT-ATATAAAAATATAAAATTTTG
* * * *** *
1491148 TAAAATTTTATAAAAATCGTAAAAAATATAAAATATATAGAAATATAAAAAAGTA
1 TAAAATTTTATAAAAATAGAAAAAAATATAAAATATATAAAAATATAAAATTTTG
* * *
1491203 TAAAATTTTAT-AAAGTCGTAAGAAAATTATATAAAATGTA-AAGAAATAT-AAATTTTG
1 TAAAATTTTATAAAAATAG-AA-AAAA--ATATAAAATATATAA-AAATATAAAATTTTG
1491260 TAAAA
1 TAAAA
1491265 AAATAATAAA
Statistics
Matches: 95, Mismatches: 15, Indels: 13
0.77 0.12 0.11
Matches are distributed among these distances:
54 19 0.20
55 35 0.37
56 14 0.15
57 10 0.11
58 17 0.18
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (55 bp):
TAAAATTTTATAAAAATAGAAAAAAATATAAAATATATAAAAATATAAAATTTTG
Found at i:1491246 original size:21 final size:21
Alignment explanation
Indices: 1491204--1491248 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1491194 AAAAAAGTAT
* *
1491204 AAAATTTTATAAAGTCGTAAG
1 AAAATTATATAAAATCGTAAG
1491225 AAAATTATATAAAAT-GTAAAG
1 AAAATTATATAAAATCGT-AAG
1491246 AAA
1 AAA
1491249 TATAAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.58, C:0.02, G:0.11, T:0.29
Consensus pattern (21 bp):
AAAATTATATAAAATCGTAAG
Found at i:1491249 original size:20 final size:20
Alignment explanation
Indices: 1491173--1491249 Score: 54
Period size: 21 Copynumber: 4.0 Consensus size: 20
1491163 ATCGTAAAAA
* *
1491173 ATATAAAATATATAGAAA-T
1 ATATAAAATGTAAAGAAATT
* *
1491192 ATA-AAAAAGTATA-AAATT
1 ATATAAAATGTAAAGAAATT
* *
1491210 TTATAAAGTCGT-AAGAAAATT
1 ATATAAAAT-GTAAAG-AAATT
1491231 ATATAAAATGTAAAGAAAT
1 ATATAAAATGTAAAGAAAT
1491250 ATAAATTTTG
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
17 3 0.07
18 11 0.25
19 7 0.16
20 8 0.18
21 15 0.34
ACGTcount: A:0.60, C:0.01, G:0.09, T:0.30
Consensus pattern (20 bp):
ATATAAAATGTAAAGAAATT
Found at i:1491683 original size:88 final size:85
Alignment explanation
Indices: 1491579--1491767 Score: 218
Period size: 86 Copynumber: 2.2 Consensus size: 85
1491569 TAAGAGCAAG
* *
1491579 GGCTTAATTGTTTTTTGAAAATTTTTGAGGATCTTTTTGATGCATTTTGAAAGTTCAAGTACCCA
1 GGCTTAATTGATTTTTGAAAA-GTTTGAGGATC-TTTTGATGCATTTTGAAAGTTCAAGTACCCA
*
1491644 ATTGAGTGGAAAAAGAAA-GAAGA
64 ATTGAGTAGAAAAA-AAATG-AGA
* * * * * **
1491667 GGCTTAATTGATTTTTGAGAAGTTTGAGGGTCTTTTGATGGATTTTGAAAGTTTAAGTGCTTAAT
1 GGCTTAATTGATTTTTGAAAAGTTTGAGGATCTTTTGATGCATTTTGAAAGTTCAAGTACCCAAT
* *
1491732 TGAGTATAAAAAAAATGAGG
66 TGAGTAGAAAAAAAATGAGA
*
1491752 GGCTTAATTGCTTTTT
1 GGCTTAATTGATTTTT
1491768 CTTTTTTTAA
Statistics
Matches: 87, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
85 20 0.23
86 39 0.45
87 9 0.10
88 19 0.22
ACGTcount: A:0.31, C:0.06, G:0.23, T:0.39
Consensus pattern (85 bp):
GGCTTAATTGATTTTTGAAAAGTTTGAGGATCTTTTGATGCATTTTGAAAGTTCAAGTACCCAAT
TGAGTAGAAAAAAAATGAGA
Found at i:1491809 original size:91 final size:92
Alignment explanation
Indices: 1491686--1491877 Score: 264
Period size: 91 Copynumber: 2.1 Consensus size: 92
1491676 GATTTTTGAG
* * * *
1491686 AAGTTTGAGGGTCTTTTGATGGATTTTGAAAGTTTAAGTGCTTAATTGAGT-ATAAAAAAAATGA
1 AAGTTTGAGGGCCTTTTGATGGATTTTAAAAGTTTAAGTGCTCAATTGAGTCA-AAAAAAAAAGA
1491750 GGGGCTTAATT-GCTT-TTTCTTTTTTT
65 GGGGCTTAATTAGCTTATTTCTTTTTTT
*
1491776 AAGTTTGAGGGCCTTTTTGATGTATTTTAAAAGTTTAAGTGCTCAATTGAGTGCAAAAAAAAAAG
1 AAGTTTGAGGGCC-TTTTGATGGATTTTAAAAGTTTAAGTGCTCAATTGAGT-CAAAAAAAAAAG
* **
1491841 ATGGGCTTAATTATTTTATTTCTTTTTTT
64 AGGGGCTTAATTAGCTTATTTCTTTTTTT
1491870 AAGTTTGA
1 AAGTTTGA
1491878 AGACTTTTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
90 12 0.13
91 35 0.39
92 20 0.22
93 3 0.03
94 19 0.21
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (92 bp):
AAGTTTGAGGGCCTTTTGATGGATTTTAAAAGTTTAAGTGCTCAATTGAGTCAAAAAAAAAAGAG
GGGCTTAATTAGCTTATTTCTTTTTTT
Found at i:1496510 original size:20 final size:21
Alignment explanation
Indices: 1496466--1496517 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
1496456 AAATCTAAAT
1496466 TTTTTATTT-T-AATATCATA
1 TTTTTATTTCTAAATATCATA
*
1496485 -TGTTATTTCTAAATA-CATA
1 TTTTTATTTCTAAATATCATA
1496504 TTTTTA-TTCTAAAT
1 TTTTTATTTCTAAAT
1496518 TTATGATCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 7 0.25
19 13 0.46
20 8 0.29
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTTATTTCTAAATATCATA
Found at i:1511840 original size:101 final size:100
Alignment explanation
Indices: 1511659--1511840 Score: 224
Period size: 101 Copynumber: 1.8 Consensus size: 100
1511649 TTATCAAACG
* * * * * *
1511659 TTATTAGTCATGGCAAAATCTGAACCATCTATTTATACCCTACTTTTATTAATCATGCTAAAATT
1 TTATTAGTCATGACAAAATCTGAACCATCCATTTACACCCTAATTTAATTAATCATGCTAAAATC
* *
1511724 CAAGCTTAATTCAATAATTATCGAACAAAATAATTA
66 CAAAC-TAATGCAATAATTATCGAACAAAATAATTA
*
1511760 TTATTAGTCATGACAAAATTTGAACCATCCATTTACACCCATAATTATAATTAATCATGAC-AAA
1 TTATTAGTCATGACAAAATCTGAACCATCCATTTACACCC-TAATT-TAATTAATCATG-CTAAA
*
1511824 ATCCAAAC-CATGCAATA
63 ATCCAAACTAATGCAATA
1511841 GATTCTGATT
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
101 43 0.63
102 4 0.06
103 20 0.29
104 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.07, T:0.34
Consensus pattern (100 bp):
TTATTAGTCATGACAAAATCTGAACCATCCATTTACACCCTAATTTAATTAATCATGCTAAAATC
CAAACTAATGCAATAATTATCGAACAAAATAATTA
Found at i:1516463 original size:12 final size:12
Alignment explanation
Indices: 1516446--1516471 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1516436 CGCAAGGATC
1516446 AATGGGAAAACG
1 AATGGGAAAACG
1516458 AATGGGAAAACG
1 AATGGGAAAACG
1516470 AA
1 AA
1516472 GAAAATCAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.31, T:0.08
Consensus pattern (12 bp):
AATGGGAAAACG
Found at i:1530067 original size:121 final size:122
Alignment explanation
Indices: 1529841--1530085 Score: 483
Period size: 121 Copynumber: 2.0 Consensus size: 122
1529831 AACACGGTTG
1529841 CTCAAGCTCTCACCATGTACAAAAGCCCAGTTTTAGTGATGTTTCTGCCAACGGTTCTCGTCTAA
1 CTCAAGCTCTCACCATGTACAAAAGCCCAGTTTTAGTGATGTTTCTGCCAACGGTTCTCGTCTAA
1529906 ACGTCTCTCCACCGAGCTATAAAACAGGCTCCTAGAAGAAAGAGTAGAACTGTATTT
66 ACGTCTCTCCACCGAGCTATAAAACAGGCTCCTAGAAGAAAGAGTAGAACTGTATTT
1529963 CTCAAGCTCTCACCATGTACAAAAGCCCAGTTTTAGTGATGTTTCTGCCAAC-GTTCTCGTCTAA
1 CTCAAGCTCTCACCATGTACAAAAGCCCAGTTTTAGTGATGTTTCTGCCAACGGTTCTCGTCTAA
1530027 ACGTCTCTCCACCGAGCTATAAAACAGGCTCCTAGAAGAAAGAGTAGAACTGTATTT
66 ACGTCTCTCCACCGAGCTATAAAACAGGCTCCTAGAAGAAAGAGTAGAACTGTATTT
1530084 CT
1 CT
1530086 GGGTCATTGT
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
121 71 0.58
122 52 0.42
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (122 bp):
CTCAAGCTCTCACCATGTACAAAAGCCCAGTTTTAGTGATGTTTCTGCCAACGGTTCTCGTCTAA
ACGTCTCTCCACCGAGCTATAAAACAGGCTCCTAGAAGAAAGAGTAGAACTGTATTT
Found at i:1533629 original size:27 final size:27
Alignment explanation
Indices: 1533577--1533630 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
1533567 TATAATCTTT
* *
1533577 TTTTTATTTACCAAAATATTATAAAAA
1 TTTTTATTTACCAAAATATAAAAAAAA
1533604 TTTTTATTTACCAAAATATAAAAAAAA
1 TTTTTATTTACCAAAATATAAAAAAAA
1533631 ACAAAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (27 bp):
TTTTTATTTACCAAAATATAAAAAAAA
Found at i:1533712 original size:27 final size:27
Alignment explanation
Indices: 1533682--1533787 Score: 158
Period size: 27 Copynumber: 3.9 Consensus size: 27
1533672 GGCCAATCAC
1533682 ATTGGCGGCACCAAAGGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
* *
1533709 ATTGGTGGCACCAAATGTGCCAAAGAG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
* * *
1533736 ATTGGCGGCACCAATGGTGCCAATGTG
1 ATTGGCGGCACCAAAGGTGCCAAAGAG
*
1533763 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGTGCCAAAG
1533788 GACTAAAATG
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 71 1.00
ACGTcount: A:0.29, C:0.22, G:0.32, T:0.17
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAGAG
Found at i:1534128 original size:19 final size:19
Alignment explanation
Indices: 1534104--1534167 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
1534094 ATTAAAATAG
1534104 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
1534123 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
1534141 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
1534160 TTTAATTT
1 TTTAATTT
1534168 TAAAAAATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:1534436 original size:37 final size:37
Alignment explanation
Indices: 1534395--1534490 Score: 174
Period size: 37 Copynumber: 2.6 Consensus size: 37
1534385 ATTTTATATT
* *
1534395 TTAAATGAAAATAGAGTTGTTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1534432 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1534469 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
1534491 CTTAATTAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.38
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:1534437 original size:18 final size:19
Alignment explanation
Indices: 1534395--1534490 Score: 115
Period size: 19 Copynumber: 5.2 Consensus size: 19
1534385 ATTTTATATT
*
1534395 TTAAATGAAAATAGAGTTG
1 TTAAATGAAAATAGAGTTA
* *
1534414 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
1534432 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
1534451 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
1534469 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
1534488 TTA
1 TTA
1534491 CTTAATTAGA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
18 29 0.46
19 34 0.54
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.38
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:1535104 original size:27 final size:27
Alignment explanation
Indices: 1535063--1535114 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
1535053 CATTTTAGTC
1535063 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
* *
1535090 CTTTGGCACCTTTGGTGTCGCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
1535115 GTGATTGGCC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.13, C:0.31, G:0.23, T:0.33
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:1535122 original size:27 final size:27
Alignment explanation
Indices: 1535065--1535123 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
1535055 TTTTAGTCCT
*
1535065 TTGGCACCATTGGTGCCGCCAATCTCT
1 TTGGCACCATTGGTGCCGCCAATCTCA
* * * *
1535092 TTGGCACCTTTGGTGTCGCCAATGTGA
1 TTGGCACCATTGGTGCCGCCAATCTCA
1535119 TTGGC
1 TTGGC
1535124 CTGATCAGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.14, C:0.27, G:0.27, T:0.32
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATCTCA
Found at i:1535204 original size:27 final size:27
Alignment explanation
Indices: 1535174--1535237 Score: 110
Period size: 27 Copynumber: 2.4 Consensus size: 27
1535164 TTTTTTTTGT
*
1535174 ATATTTTGGTAAATAAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
*
1535201 ATATTTTGATAAATAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAGTTATA
1535228 ATATTTTGGT
1 ATATTTTGGT
1535238 TATTTTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.42
Consensus pattern (27 bp):
ATATTTTGGTAAATAAAAAAAGTTATA
Found at i:1536726 original size:14 final size:14
Alignment explanation
Indices: 1536690--1536739 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
1536680 ATATCCAAAC
1536690 AATAACAACAA-AA
1 AATAACAACAAGAA
* *
1536703 TAGTAGCAACAATGAA
1 -AATAACAACAA-GAA
1536719 AA-AACAACAAGAA
1 AATAACAACAAGAA
1536732 AATAACAA
1 AATAACAA
1536740 AAAAACAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
13 5 0.17
14 21 0.72
15 1 0.03
16 2 0.07
ACGTcount: A:0.68, C:0.14, G:0.08, T:0.10
Consensus pattern (14 bp):
AATAACAACAAGAA
Found at i:1537435 original size:18 final size:17
Alignment explanation
Indices: 1537412--1537450 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
1537402 AAAGACTTAT
1537412 ATTTTAATTATGTGTTA
1 ATTTTAATTATGTGTTA
1537429 CATTTTAATTATGTGTTA
1 -ATTTTAATTATGTGTTA
1537447 ATTT
1 ATTT
1537451 CAATACTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.28, C:0.03, G:0.10, T:0.59
Consensus pattern (17 bp):
ATTTTAATTATGTGTTA
Found at i:1538673 original size:7 final size:7
Alignment explanation
Indices: 1538661--1538686 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1538651 CTACTAGTCA
1538661 AAATCGC
1 AAATCGC
1538668 AAATCGC
1 AAATCGC
1538675 AAATCGC
1 AAATCGC
1538682 AAATC
1 AAATC
1538687 AATGTGATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (7 bp):
AAATCGC
Found at i:1541220 original size:22 final size:22
Alignment explanation
Indices: 1541195--1541244 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
1541185 AACATGGTAA
*
1541195 GTTAACAGGGTAAACTTAAGCT
1 GTTAACAGAGTAAACTTAAGCT
1541217 GTTAACAGAGTAAACTTAAGCT
1 GTTAACAGAGTAAACTTAAGCT
1541239 GTTAAC
1 GTTAAC
1541245 TTACCATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (22 bp):
GTTAACAGAGTAAACTTAAGCT
Found at i:1550897 original size:6 final size:6
Alignment explanation
Indices: 1550888--1550914 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
1550878 CAAATTTATC
1550888 CGCAGA CGCAGA CGCAGA CGCAGA CGC
1 CGCAGA CGCAGA CGCAGA CGCAGA CGC
1550915 CGATTCATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.37, G:0.33, T:0.00
Consensus pattern (6 bp):
CGCAGA
Found at i:1551203 original size:20 final size:20
Alignment explanation
Indices: 1551178--1551215 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1551168 ATCTTTTTTA
1551178 TAATTTAATTCTTTATAATG
1 TAATTTAATTCTTTATAATG
* *
1551198 TAATTTATTTTTTTATAA
1 TAATTTAATTCTTTATAA
1551216 AAAAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TAATTTAATTCTTTATAATG
Found at i:1555274 original size:14 final size:14
Alignment explanation
Indices: 1555255--1555305 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
1555245 TTTTATCAAT
*
1555255 ATAAAATATAATAA
1 ATAAAATATTATAA
1555269 ATAAAAATATTATAA
1 AT-AAAATATTATAA
*
1555284 ATATAATATTATATA
1 ATAAAATATTATA-A
1555299 A-AAAATA
1 ATAAAATA
1555306 AAAATACTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 17 0.53
15 15 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAATATTATAA
Found at i:1555305 original size:34 final size:34
Alignment explanation
Indices: 1555260--1555327 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
1555250 TCAATATAAA
*
1555260 ATATAATAAATAAAAATA-TTAT-AAATATAATATT
1 ATATAAAAAATAAAAATACTT-TCAAA-ATAATATT
1555294 ATATAAAAAATAAAAATACTTTCAAAATAATATT
1 ATATAAAAAATAAAAATACTTTCAAAATAATATT
1555328 TGTTGTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 26 0.84
35 5 0.16
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (34 bp):
ATATAAAAAATAAAAATACTTTCAAAATAATATT
Found at i:1561435 original size:15 final size:16
Alignment explanation
Indices: 1561415--1561459 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
1561405 GTTTAAATTT
1561415 ATTATAAAATTAAT-A
1 ATTATAAAATTAATAA
1561430 ATTATAAAAATATAATAA
1 ATTAT-AAAAT-TAATAA
1561448 ATT-T-AAATTAAT
1 ATTATAAAATTAAT
1561460 TAACCTATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.15
15 9 0.33
16 5 0.19
17 5 0.19
18 4 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATTATAAAATTAATAA
Found at i:1564541 original size:31 final size:31
Alignment explanation
Indices: 1564480--1564541 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
1564470 TAATATTTTT
* *
1564480 TTAAACTATTAGTAAGTTTATATTTTAGTTA
1 TTAAACTATTAGAAAGTTTATATTTAAGTTA
1564511 TTAAACTATGTA-AAAGTTT-TCATTTAAGTTA
1 TTAAACTAT-TAGAAAGTTTAT-ATTTAAGTTA
1564542 CTGAATTAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 1 0.04
31 24 0.89
32 2 0.07
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (31 bp):
TTAAACTATTAGAAAGTTTATATTTAAGTTA
Found at i:1584326 original size:24 final size:24
Alignment explanation
Indices: 1584269--1584327 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1584259 AGGAGTAGAA
1584269 GATGCTCCAAAAGCAGGACTGCTT
1 GATGCTCCAAAAGCAGGACTGCTT
* **
1584293 GAAG-TGCCAAAAGCAGGTGTGCTT
1 GATGCT-CCAAAAGCAGGACTGCTT
1584317 GATGCTCCAAA
1 GATGCTCCAAA
1584328 TGTGCCTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (24 bp):
GATGCTCCAAAAGCAGGACTGCTT
Found at i:1584441 original size:24 final size:24
Alignment explanation
Indices: 1584409--1584487 Score: 104
Period size: 24 Copynumber: 3.3 Consensus size: 24
1584399 TTCCAGTTGA
* * *
1584409 ACCAAAGGCCGGAGTGCTGGTAGC
1 ACCAAAGGCAGGAGTGCTCGTGGC
* * *
1584433 ACCAAAGGCAGGGGTGCTTGTGGA
1 ACCAAAGGCAGGAGTGCTCGTGGC
1584457 ACCAAAGGCAGGAGTGCTCGTGGC
1 ACCAAAGGCAGGAGTGCTCGTGGC
1584481 ACCAAAG
1 ACCAAAG
1584488 CTACCAAATG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.28, C:0.23, G:0.37, T:0.13
Consensus pattern (24 bp):
ACCAAAGGCAGGAGTGCTCGTGGC
Found at i:1584629 original size:24 final size:24
Alignment explanation
Indices: 1584551--1584630 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
1584541 ACTTGAAGAT
1584551 GCTCCAAAAGCAGGAGTGCTCGAA
1 GCTCCAAAAGCAGGAGTGCTCGAA
* * * *
1584575 CCCCCAAATGCAGGAGTGCTGGAA
1 GCTCCAAAAGCAGGAGTGCTCGAA
* * *
1584599 G-TGCCAAAAGCAGGTGTGCTTGAT
1 GCT-CCAAAAGCAGGAGTGCTCGAA
1584623 GCTCCAAA
1 GCTCCAAA
1584631 TGTGCCACCT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
24 43 0.98
25 1 0.02
ACGTcount: A:0.30, C:0.25, G:0.29, T:0.16
Consensus pattern (24 bp):
GCTCCAAAAGCAGGAGTGCTCGAA
Found at i:1584739 original size:24 final size:24
Alignment explanation
Indices: 1584712--1584897 Score: 201
Period size: 24 Copynumber: 7.8 Consensus size: 24
1584702 TTCCAGTTGA
*
1584712 ACCAAAGGCAGGGGTGCTTGTGGC
1 ACCAAAGGCAGGGGTACTTGTGGC
* * ** *
1584736 ACCAAAGGCTGGAGTACTCATGGA
1 ACCAAAGGCAGGGGTACTTGTGGC
*
1584760 ACCAAAGGCAGGGGTACTTGTGCC
1 ACCAAAGGCAGGGGTACTTGTGGC
* * *
1584784 ACCAAAAGCAGGGGCACTCGTGGC
1 ACCAAAGGCAGGGGTACTTGTGGC
* * * *
1584808 ACCAAAAGCAAGGGCACTCGTGGC
1 ACCAAAGGCAGGGGTACTTGTGGC
1584832 ACCAAAGGCAGGGGTACTTGTGGC
1 ACCAAAGGCAGGGGTACTTGTGGC
* * *
1584856 ACCAAAAGCAGAGGTGCTTGTGGC
1 ACCAAAGGCAGGGGTACTTGTGGC
* *
1584880 ACCGAAGGCAGGAGTACT
1 ACCAAAGGCAGGGGTACT
1584898 GGAACCAAAA
Statistics
Matches: 133, Mismatches: 29, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 133 1.00
ACGTcount: A:0.28, C:0.24, G:0.34, T:0.14
Consensus pattern (24 bp):
ACCAAAGGCAGGGGTACTTGTGGC
Found at i:1584797 original size:72 final size:72
Alignment explanation
Indices: 1584712--1584897 Score: 248
Period size: 72 Copynumber: 2.6 Consensus size: 72
1584702 TTCCAGTTGA
* *
1584712 ACCAAAGGCAGGGGTGCTTGTGGCACCAAAGGCTGGAGTACTCATGGAACCAAAGGCAGGGGTAC
1 ACCAAAAGCAGGGGTGCTTGTGGCACCAAAGGCAGGAGTACTCATGGAACCAAAGGCAGGGGTAC
1584777 TTGTGCC
66 TTGTGCC
** * * * * *
1584784 ACCAAAAGCAGGGGCACTCGTGGCACCAAAAGCAAGG-GCACTCGTGGCACCAAAGGCAGGGGTA
1 ACCAAAAGCAGGGGTGCTTGTGGCACCAAAGGC-AGGAGTACTCATGGAACCAAAGGCAGGGGTA
*
1584848 CTTGTGGC
65 CTTGTGCC
* *
1584856 ACCAAAAGCAGAGGTGCTTGTGGCACCGAAGGCAGGAGTACT
1 ACCAAAAGCAGGGGTGCTTGTGGCACCAAAGGCAGGAGTACT
1584898 GGAACCAAAA
Statistics
Matches: 95, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
71 3 0.03
72 90 0.95
73 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.34, T:0.14
Consensus pattern (72 bp):
ACCAAAAGCAGGGGTGCTTGTGGCACCAAAGGCAGGAGTACTCATGGAACCAAAGGCAGGGGTAC
TTGTGCC
Found at i:1587205 original size:16 final size:17
Alignment explanation
Indices: 1587131--1587209 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
1587121 GATTAAATAA
*
1587131 ATTTATAAATAATTATA
1 ATTTATAAATAATTATG
1587148 ATTTATAAATAATT-TG
1 ATTTATAAATAATTATG
* **
1587164 ATTT-TCAATTTTTATCG
1 ATTTATAAATAATTAT-G
1587181 ATTTATAAATAATT-TG
1 ATTTATAAATAATTATG
*
1587197 ATCTATAAATAAT
1 ATTTATAAATAAT
1587210 CTTACATCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
15 6 0.12
16 19 0.37
17 20 0.39
18 6 0.12
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (17 bp):
ATTTATAAATAATTATG
Found at i:1593662 original size:23 final size:20
Alignment explanation
Indices: 1593618--1593677 Score: 50
Period size: 23 Copynumber: 2.9 Consensus size: 20
1593608 ACATATATTT
* **
1593618 AAAA-AATAAATAAATACGA
1 AAAATAATAAAAAAATAATA
1593637 AAAATATATAAATAATAATAATA
1 AAAATA-ATAAA-AA-AATAATA
*
1593660 AAATTAATAAAAAAATAA
1 AAAATAATAAAAAAATAA
1593678 AGAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 4 0.12
20 6 0.18
21 7 0.21
22 6 0.18
23 10 0.30
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (20 bp):
AAAATAATAAAAAAATAATA
Found at i:1593843 original size:20 final size:21
Alignment explanation
Indices: 1593808--1593847 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
1593798 GCAATTTATC
1593808 CCTCCACTTAAAAACACGCGT
1 CCTCCACTTAAAAACACGCGT
1593829 CCTCCACTT-AAAACACGCG
1 CCTCCACTTAAAAACACGCG
1593848 GATCCTAGGC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.33, C:0.40, G:0.10, T:0.17
Consensus pattern (21 bp):
CCTCCACTTAAAAACACGCGT
Found at i:1598304 original size:24 final size:25
Alignment explanation
Indices: 1598277--1598323 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
1598267 GACTAATTGA
1598277 AAAAAAAGATTG-AA-TTTTAACAAT
1 AAAAAAAGA-TGAAATTTTTAACAAT
*
1598301 AAAAAACGATGAAATTTTTAACA
1 AAAAAAAGATGAAATTTTTAACA
1598324 GAATGATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 10 0.50
25 8 0.40
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (25 bp):
AAAAAAAGATGAAATTTTTAACAAT
Found at i:1601972 original size:21 final size:19
Alignment explanation
Indices: 1601934--1601973 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
1601924 GCATTAATTT
*
1601934 TATTTTCTTTTTTTAAAAA
1 TATTTTCTTTTATTAAAAA
1601953 TATTTTCTATTTAATTAAAAA
1 TATTTTCT-TTT-ATTAAAAA
1601974 CATTATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 3 0.17
21 7 0.39
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTCTTTTATTAAAAA
Found at i:1602034 original size:56 final size:55
Alignment explanation
Indices: 1601955--1602063 Score: 182
Period size: 56 Copynumber: 2.0 Consensus size: 55
1601945 TTTAAAAATA
* * *
1601955 TTTTCTATTTAATTAAAAACATTATAATATAAAAAAATACAACATCATGTATTTAT
1 TTTTCTATTTAAATAAAAACATTATAATAT-AAAAAATACAACATAATCTATTTAT
1602011 TTTTCTATTTAAATAAAAACATTATAATATAAAAAATACAACATAATCTATTT
1 TTTTCTATTTAAATAAAAACATTATAATATAAAAAATACAACATAATCTATTT
1602064 CATATTTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
55 21 0.42
56 29 0.58
ACGTcount: A:0.50, C:0.09, G:0.01, T:0.40
Consensus pattern (55 bp):
TTTTCTATTTAAATAAAAACATTATAATATAAAAAATACAACATAATCTATTTAT
Found at i:1602383 original size:16 final size:17
Alignment explanation
Indices: 1602359--1602394 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1602349 ATATTATTTA
*
1602359 TTTATAAATAAATAAGT
1 TTTATAAATAAATAAAT
1602376 TTTA-AAATAAATAAAT
1 TTTATAAATAAATAAAT
1602392 TTT
1 TTT
1602395 TGACAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTATAAATAAATAAAT
Found at i:1614313 original size:11 final size:11
Alignment explanation
Indices: 1614294--1614328 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
1614284 AACACCGAAC
*
1614294 TTTTTGGGTAA
1 TTTTCGGGTAA
1614305 TTTTCGGGTAA
1 TTTTCGGGTAA
1614316 TTTTCGGGTAA
1 TTTTCGGGTAA
1614327 TT
1 TT
1614329 CGGTTAATCG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.17, C:0.06, G:0.26, T:0.51
Consensus pattern (11 bp):
TTTTCGGGTAA
Found at i:1614336 original size:9 final size:9
Alignment explanation
Indices: 1614307--1614354 Score: 62
Period size: 9 Copynumber: 5.2 Consensus size: 9
1614297 TTGGGTAATT
1614307 TTCGGGTAA
1 TTCGGGTAA
1614316 TTTTCGGGTAA
1 --TTCGGGTAA
*
1614327 TTCGGTTAA
1 TTCGGGTAA
1614336 -TCGGGTAA
1 TTCGGGTAA
1614344 TTCGGGTAA
1 TTCGGGTAA
1614353 TT
1 TT
1614355 TTTAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 7 0.21
9 18 0.53
11 9 0.26
ACGTcount: A:0.21, C:0.10, G:0.29, T:0.40
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:1614341 original size:17 final size:17
Alignment explanation
Indices: 1614319--1614353 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1614309 CGGGTAATTT
*
1614319 TCGGGTAATTCGGTTAA
1 TCGGGTAATTCGGGTAA
1614336 TCGGGTAATTCGGGTAA
1 TCGGGTAATTCGGGTAA
1614353 T
1 T
1614354 TTTTAACCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.31, T:0.34
Consensus pattern (17 bp):
TCGGGTAATTCGGGTAA
Found at i:1615889 original size:21 final size:21
Alignment explanation
Indices: 1615863--1615903 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1615853 TCTCTTTTGC
* *
1615863 TTCTCCCTCTATTTTCCTTCA
1 TTCTCCATATATTTTCCTTCA
*
1615884 TTCTCCATATTTTTTCCTTC
1 TTCTCCATATATTTTCCTTC
1615904 TATGTGTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.34, G:0.00, T:0.56
Consensus pattern (21 bp):
TTCTCCATATATTTTCCTTCA
Found at i:1616220 original size:29 final size:29
Alignment explanation
Indices: 1616151--1616212 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1616141 AAATTGCATC
* *
1616151 TTAA-CCCTAAAGTTTCCTAAAATTATGTT
1 TTAACCCCTAAA-ATTCCTAAAATTATATT
*
1616180 TTGACCCCTAAAATTCCTAAAATTATATT
1 TTAACCCCTAAAATTCCTAAAATTATATT
1616209 TTAA
1 TTAA
1616213 TCCTTAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (29 bp):
TTAACCCCTAAAATTCCTAAAATTATATT
Found at i:1616602 original size:11 final size:11
Alignment explanation
Indices: 1616583--1616654 Score: 64
Period size: 11 Copynumber: 6.9 Consensus size: 11
1616573 CCGAGAGAAG
*
1616583 AAGAGGAAAAA
1 AAGAAGAAAAA
1616594 AAGAAGAAAAA
1 AAGAAGAAAAA
1616605 AAG-AG-AAAA
1 AAGAAGAAAAA
*
1616614 AA-AA-AAAGA
1 AAGAAGAAAAA
*
1616623 AGGAAGAAGAAA
1 AAGAAGAA-AAA
*
1616635 AAGAAAAAAAA
1 AAGAAGAAAAA
1616646 AAGAA-AAAA
1 AAGAAGAAAA
1616655 GAAAAATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
9 11 0.22
10 8 0.16
11 23 0.46
12 8 0.16
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAGAAGAAAAA
Found at i:1616635 original size:16 final size:17
Alignment explanation
Indices: 1616594--1616653 Score: 61
Period size: 16 Copynumber: 3.6 Consensus size: 17
1616584 AGAGGAAAAA
1616594 AAGAAGAAAAA-AAGAG
1 AAGAAGAAAAAGAAGAG
* *
1616610 AAAAAAAAAAAGAAG-G
1 AAGAAGAAAAAGAAGAG
* *
1616626 AAGAAGAAAAAGAAAAA
1 AAGAAGAAAAAGAAGAG
*
1616643 AAAAAGAAAAA
1 AAGAAGAAAAA
1616654 AGAAAAATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
16 22 0.63
17 13 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAGAAGAAAAAGAAGAG
Found at i:1616635 original size:29 final size:26
Alignment explanation
Indices: 1616589--1616660 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 26
1616579 GAAGAAGAGG
1616589 AAAAAAAGAAGAAAAAAAGAGAAAAAA
1 AAAAAAAGAAGAAAAAAA-AGAAAAAA
*
1616616 AAAAAGAAGGAAGAAGAAAAAGAAAAAA
1 AAAAA-AA-GAAGAAAAAAAAGAAAAAA
*
1616644 AAAAGAAAAAAGAAAAA
1 AAAA-AAAGAAGAAAAA
1616661 TAAATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 12 0.31
28 16 0.41
29 11 0.28
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (26 bp):
AAAAAAAGAAGAAAAAAAAGAAAAAA
Found at i:1616847 original size:24 final size:25
Alignment explanation
Indices: 1616810--1616870 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 25
1616800 GGAAAAAAAA
1616810 CCAACAGGCCCAACAGCCTAGCAGG
1 CCAACAGGCCCAACAGCCTAGCAGG
* *
1616835 CCAACA-GCCCAACAGCTTGGCAGG
1 CCAACAGGCCCAACAGCCTAGCAGG
*
1616859 CCAGCAGGCCCA
1 CCAACAGGCCCA
1616871 TCACAGCAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 21 0.66
25 11 0.34
ACGTcount: A:0.30, C:0.41, G:0.25, T:0.05
Consensus pattern (25 bp):
CCAACAGGCCCAACAGCCTAGCAGG
Found at i:1616974 original size:9 final size:9
Alignment explanation
Indices: 1616960--1616992 Score: 52
Period size: 8 Copynumber: 3.9 Consensus size: 9
1616950 CAGTCTAGGA
1616960 AAAAAAGAG
1 AAAAAAGAG
1616969 -AAAAA-AG
1 AAAAAAGAG
1616976 AAAAAAGAG
1 AAAAAAGAG
1616985 AAAAAAGA
1 AAAAAAGA
1616993 AAAGGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 2 0.09
8 10 0.45
9 10 0.45
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AAAAAAGAG
Found at i:1616977 original size:7 final size:7
Alignment explanation
Indices: 1616961--1617014 Score: 56
Period size: 7 Copynumber: 7.3 Consensus size: 7
1616951 AGTCTAGGAA
1616961 AAAAAGAG
1 AAAAA-AG
1616969 AAAAAAG
1 AAAAAAG
1616976 AAAAAAG
1 AAAAAAG
1616983 AGAAAAA-
1 A-AAAAAG
*
1616990 AGAAAAGG
1 A-AAAAAG
1616998 AAAAAAAG
1 -AAAAAAG
1617006 AAAAAAG
1 AAAAAAG
1617013 AA
1 AA
1617015 GTCCGAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
7 25 0.61
8 15 0.37
9 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1616981 original size:16 final size:16
Alignment explanation
Indices: 1616960--1617013 Score: 85
Period size: 16 Copynumber: 3.5 Consensus size: 16
1616950 CAGTCTAGGA
1616960 AAAAAAGAGAAAAAAG
1 AAAAAAGAGAAAAAAG
1616976 AAAAAAGAGAAAAAAG
1 AAAAAAGAGAAAAAAG
*
1616992 -AAAAGGA-AAAAAAG
1 AAAAAAGAGAAAAAAG
1617006 AAAAAAGA
1 AAAAAAGA
1617014 AGTCCGAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
14 7 0.20
15 12 0.34
16 16 0.46
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAAGAGAAAAAAG
Found at i:1617001 original size:21 final size:21
Alignment explanation
Indices: 1616971--1617014 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1616961 AAAAAGAGAA
*
1616971 AAAAGAAAAAAGAGAAAAAAG
1 AAAAGAAAAAAAAGAAAAAAG
*
1616992 AAAAGGAAAAAAAGAAAAAAG
1 AAAAGAAAAAAAAGAAAAAAG
1617013 AA
1 AA
1617015 GTCCGAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAAAAGAAAAAAG
Found at i:1617004 original size:9 final size:8
Alignment explanation
Indices: 1616958--1617011 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 8
1616948 CCCAGTCTAG
1616958 GAAAAAAA
1 GAAAAAAA
1616966 GAGAAAAAA
1 GA-AAAAAA
1616975 G-AAAAAA
1 GAAAAAAA
1616982 GAGAAAAAA
1 GA-AAAAAA
*
1616991 G--AAAAG
1 GAAAAAAA
1616997 GAAAAAAA
1 GAAAAAAA
1617005 GAAAAAA
1 GAAAAAA
1617012 GAAGTCCGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
6 5 0.13
7 7 0.18
8 13 0.33
9 14 0.36
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (8 bp):
GAAAAAAA
Found at i:1617470 original size:41 final size:39
Alignment explanation
Indices: 1617401--1617492 Score: 96
Period size: 41 Copynumber: 2.3 Consensus size: 39
1617391 AATTAATAAT
*
1617401 TGTTTCAAAAATCTTTGTGTTTAAAAAAATAAAAATTCTCG
1 TGTTTCAAAAATCTTTATGTTT-AAAAAA-AAAAATTCTCG
** * *
1617442 TGTTTCAAAAAT-TTTAATGTTTTCAAAAAACAATTTTCG
1 TGTTTCAAAAATCTTT-ATGTTTAAAAAAAAAAATTCTCG
1617481 TGTTTTCAAAAA
1 TG-TTTCAAAAA
1617493 AAATTTATCG
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 11 0.25
40 16 0.36
41 17 0.39
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (39 bp):
TGTTTCAAAAATCTTTATGTTTAAAAAAAAAAATTCTCG
Found at i:1617477 original size:22 final size:21
Alignment explanation
Indices: 1617448--1617498 Score: 75
Period size: 22 Copynumber: 2.4 Consensus size: 21
1617438 CTCGTGTTTC
1617448 AAAAATTTTAATGTTTTCAAA
1 AAAAATTTTAATGTTTTCAAA
**
1617469 AAACAATTTTCGTGTTTTCAAA
1 AAA-AATTTTAATGTTTTCAAA
1617491 AAAAATTT
1 AAAAATTT
1617499 ATCGTATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (21 bp):
AAAAATTTTAATGTTTTCAAA
Found at i:1617503 original size:22 final size:22
Alignment explanation
Indices: 1617459--1617508 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1617449 AAAATTTTAA
1617459 TGTTTTCAAAAAACAATTTTCG
1 TGTTTTCAAAAAACAATTTTCG
1617481 TGTTTTCAAAAAA-AATTTATCG
1 TGTTTTCAAAAAACAATTT-TCG
*
1617503 TATTTT
1 TGTTTT
1617509 ATAGATTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.46
Consensus pattern (22 bp):
TGTTTTCAAAAAACAATTTTCG
Found at i:1617517 original size:39 final size:37
Alignment explanation
Indices: 1617474--1617581 Score: 118
Period size: 35 Copynumber: 2.9 Consensus size: 37
1617464 TCAAAAAACA
1617474 ATTTTCGTGTTTTCAAAAAAAATTTATCGTATTTTATAG
1 ATTTTCGTGTTTTCAAAAAAAATTT-TCGTATTTTA-AG
1617513 ATTTTCGTGTTTT--AAAAAAA-TTTCGTATTTCTAAG
1 ATTTTCGTGTTTTCAAAAAAAATTTTCGTATTT-TAAG
* *
1617548 ATTCTT-GT-ATTTCTAAAAAAAATTTTCGTGTTTT
1 ATT-TTCGTGTTTTC-AAAAAAAATTTTCGTATTTT
1617582 CAAAAAAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
34 3 0.05
35 15 0.25
36 6 0.10
37 15 0.25
38 9 0.15
39 13 0.21
ACGTcount: A:0.31, C:0.08, G:0.10, T:0.50
Consensus pattern (37 bp):
ATTTTCGTGTTTTCAAAAAAAATTTTCGTATTTTAAG
Found at i:1617602 original size:20 final size:20
Alignment explanation
Indices: 1617548--1617604 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
1617538 TATTTCTAAG
*
1617548 ATTCTTGTATTTCTAAAAAAA
1 ATTCTTGTGTTTC-AAAAAAA
1617569 ATT-TTCGTGTTTTCAAAAAAA
1 ATTCTT-GTG-TTTCAAAAAAA
1617590 ATTCTTGTGTTTCAA
1 ATTCTTGTGTTTCAA
1617605 TCGGATCACG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
20 8 0.25
21 18 0.56
22 6 0.19
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.46
Consensus pattern (20 bp):
ATTCTTGTGTTTCAAAAAAA
Found at i:1623727 original size:23 final size:22
Alignment explanation
Indices: 1623695--1623738 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
1623685 GAAAAATAAA
*
1623695 GTATAATAATTGTAATATCTAT
1 GTATAATAATTATAATATCTAT
1623717 GTATAAATAATTATAATATCTA
1 GTAT-AATAATTATAATATCTA
1623739 ATACAAATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (22 bp):
GTATAATAATTATAATATCTAT
Found at i:1634304 original size:30 final size:28
Alignment explanation
Indices: 1634251--1634321 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 28
1634241 AAATATTTAT
1634251 AAAAATTATAAAAATTCTAAAAATTCTA
1 AAAAATTATAAAAATTCTAAAAATTCTA
*
1634279 AAAAATATATAAAGAAATT-TAAAAATTTTA
1 AAAAAT-TAT-AA-AAATTCTAAAAATTCTA
* *
1634309 AAAATTTCTAAAA
1 AAAAATTATAAAA
1634322 TAAAAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
27 2 0.05
28 8 0.22
29 5 0.14
30 17 0.46
31 5 0.14
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.32
Consensus pattern (28 bp):
AAAAATTATAAAAATTCTAAAAATTCTA
Found at i:1634320 original size:10 final size:10
Alignment explanation
Indices: 1634239--1634321 Score: 68
Period size: 9 Copynumber: 8.6 Consensus size: 10
1634229 AATAATTGGA
*
1634239 ATAAATATTT
1 ATAAAAATTT
1634249 ATAAAAA-TT
1 ATAAAAATTT
1634258 ATAAAAA-TT
1 ATAAAAATTT
*
1634267 CTAAAAATTCT
1 ATAAAAATT-T
*
1634278 A-AAAAATAT
1 ATAAAAATTT
*
1634287 ATAAAGAAATT
1 ATAAA-AATTT
1634298 -TAAAAATTT
1 ATAAAAATTT
1634307 -TAAAAATTT
1 ATAAAAATTT
*
1634316 CTAAAA
1 ATAAAA
1634322 TAAAAATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
9 32 0.52
10 25 0.41
11 4 0.07
ACGTcount: A:0.60, C:0.04, G:0.01, T:0.35
Consensus pattern (10 bp):
ATAAAAATTT
Found at i:1639177 original size:69 final size:69
Alignment explanation
Indices: 1639101--1639237 Score: 256
Period size: 69 Copynumber: 2.0 Consensus size: 69
1639091 AAGGTTAAAT
*
1639101 TAAATAATGTGTAAAAGTTGAATGTTAATTTTTAGAATCAAAACTAAACTAACACAATATATAAA
1 TAAATAATGTGTAAAAGTTGAATGTTAATTTTTAGAATAAAAACTAAACTAACACAATATATAAA
1639166 TATA
66 TATA
*
1639170 TAAATAATGTGTAAAAGTTGAATGTTAATTTTTAGAATAAAAACTAAACTAACATAATATATAAA
1 TAAATAATGTGTAAAAGTTGAATGTTAATTTTTAGAATAAAAACTAAACTAACACAATATATAAA
1639235 TAT
66 TAT
1639238 TTGAGGATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (69 bp):
TAAATAATGTGTAAAAGTTGAATGTTAATTTTTAGAATAAAAACTAAACTAACACAATATATAAA
TATA
Found at i:1639717 original size:3 final size:3
Alignment explanation
Indices: 1639711--1639753 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1639701 AATGATGATA
* *
1639711 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ACC ATC ACC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1639754 CCTTCTCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (3 bp):
ATC
Found at i:1646846 original size:6 final size:6
Alignment explanation
Indices: 1646835--1646859 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1646825 ACATCATCAG
1646835 CCTCTT CCTCTT CCTCTT CCTCTT C
1 CCTCTT CCTCTT CCTCTT CCTCTT C
1646860 ATCATCGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCTCTT
Found at i:1652742 original size:18 final size:18
Alignment explanation
Indices: 1652719--1652811 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
1652709 CCCAACTACT
*
1652719 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* *
1652737 GTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACC
1652755 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
*
1652773 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
1652791 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
1652809 GTA
1 GTA
1652812 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:1652771 original size:36 final size:36
Alignment explanation
Indices: 1652719--1652811 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
1652709 CCCAACTACT
*
1652719 GTATACGTGAACAGTACCGTATACGTAAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
*
1652755 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
1652791 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
1652812 AACGGTCGTA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
Found at i:1658701 original size:32 final size:33
Alignment explanation
Indices: 1658660--1658728 Score: 122
Period size: 32 Copynumber: 2.1 Consensus size: 33
1658650 GTGAGCCGAT
*
1658660 TGTTTAGTTCTTACGAAATAATATATTTGCAC-
1 TGTTTAGTTCTTAAGAAATAATATATTTGCACG
1658692 TGTTTAGTTCTTAAGAAATAATATATTTGCACG
1 TGTTTAGTTCTTAAGAAATAATATATTTGCACG
1658725 TGTT
1 TGTT
1658729 ATTTATTACA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 31 0.89
33 4 0.11
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.45
Consensus pattern (33 bp):
TGTTTAGTTCTTAAGAAATAATATATTTGCACG
Found at i:1662988 original size:16 final size:16
Alignment explanation
Indices: 1662960--1662999 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1662950 GGAATCAGTT
1662960 ATATT-AATGTTATTTA
1 ATATTAAAT-TTATTTA
*
1662976 ATTTTAAATTTATTTA
1 ATATTAAATTTATTTA
1662992 ATATTAAA
1 ATATTAAA
1663000 ATAATATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
ATATTAAATTTATTTA
Found at i:1663009 original size:26 final size:26
Alignment explanation
Indices: 1662986--1663036 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
1662976 ATTTTAAATT
1662986 TATTTAATATTAAAATAATATAAAAA
1 TATTTAATATTAAAATAATATAAAAA
*
1663012 TATTTAATATTAAAATAATACAAAA
1 TATTTAATATTAAAATAATATAAAA
1663037 TTCATCATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TATTTAATATTAAAATAATATAAAAA
Found at i:1663676 original size:14 final size:16
Alignment explanation
Indices: 1663645--1663679 Score: 56
Period size: 14 Copynumber: 2.3 Consensus size: 16
1663635 AGCTTAACAA
1663645 TTTAATATTTATTAAT
1 TTTAATATTTATTAAT
1663661 TTTAATA-TTA-TAAT
1 TTTAATATTTATTAAT
1663675 TTTAA
1 TTTAA
1663680 AAGTTAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 3 0.16
16 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAATATTTATTAAT
Found at i:1670864 original size:14 final size:14
Alignment explanation
Indices: 1670845--1670871 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1670835 AAATAAACAT
1670845 AATAAATAAATTTA
1 AATAAATAAATTTA
1670859 AATAAATAAATTT
1 AATAAATAAATTT
1670872 CTCAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AATAAATAAATTTA
Found at i:1675265 original size:40 final size:39
Alignment explanation
Indices: 1675149--1675277 Score: 102
Period size: 40 Copynumber: 3.3 Consensus size: 39
1675139 CGAGTCAATT
* * *
1675149 AGACACTGGGTGTGAATCTATTACTTCGGATTAATTCGATG
1 AGACACTGGGTGTCAAT-TATTACTTCGAATT-ATCCGATG
* * * * * *
1675190 AGGCACTGGGTGCCAA-T-GTACTT-TAGTTTAGCCGATG
1 AGACACTGGGTGTCAATTATTACTTCGA-ATTATCCGATG
1675227 AGACACTGGGTGTCAACTTATTACTTCGAATTATCCGATG
1 AGACACTGGGTGTCAA-TTATTACTTCGAATTATCCGATG
**
1675267 AGGTACTGGGT
1 AGACACTGGGT
1675278 ACCAATTTGG
Statistics
Matches: 66, Mismatches: 17, Indels: 11
0.70 0.18 0.12
Matches are distributed among these distances:
37 20 0.30
38 7 0.11
39 2 0.03
40 23 0.35
41 14 0.21
ACGTcount: A:0.25, C:0.17, G:0.26, T:0.32
Consensus pattern (39 bp):
AGACACTGGGTGTCAATTATTACTTCGAATTATCCGATG
Found at i:1677041 original size:60 final size:58
Alignment explanation
Indices: 1676958--1677073 Score: 142
Period size: 60 Copynumber: 2.0 Consensus size: 58
1676948 AAATAGTTAG
* * * * *
1676958 GTGATCATTTTGTAACTTATCATATTTGAGTGACAAAACAAGAAATTTACTAATAATTGA
1 GTGACCATTTCGTAACTTATCATAATTAAGTGACAAAA-AA-AAATTTACAAATAATTGA
* * *
1677018 GTGACCATTTCGTAATTTTTCATAATTAAGTGACAAAAAATAATTTACAAATAATT
1 GTGACCATTTCGTAACTTATCATAATTAAGTGACAAAAAAAAATTTACAAATAATT
1677074 AGGTGATTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 14 0.29
59 2 0.04
60 32 0.67
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.37
Consensus pattern (58 bp):
GTGACCATTTCGTAACTTATCATAATTAAGTGACAAAAAAAAATTTACAAATAATTGA
Found at i:1677791 original size:6 final size:6
Alignment explanation
Indices: 1677780--1677804 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1677770 TATATTCAGG
1677780 CCGGGC CCGGGC CCGGGC CCGGGC C
1 CCGGGC CCGGGC CCGGGC CCGGGC C
1677805 AAAAAAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.52, G:0.48, T:0.00
Consensus pattern (6 bp):
CCGGGC
Found at i:1679957 original size:41 final size:41
Alignment explanation
Indices: 1679876--1679977 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 41
1679866 AATGACGAAT
* * *
1679876 CCCCCAAAATGGAAAATTTTAGGATCTAGCAAGGACCTCAA
1 CCCCTAAAATGAAAAATTTTAGGATCTAGCAAAGACCTCAA
* * *
1679917 CCCCTAAAATGAAAAATTTTTGGGTCT-GACAAAGATCTCAA
1 CCCCTAAAATGAAAAATTTTAGGATCTAG-CAAAGACCTCAA
*
1679958 CTCCTAAAATGAAAAATTTT
1 CCCCTAAAATGAAAAATTTT
1679978 CATTCAAGCT
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
40 1 0.02
41 52 0.98
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.25
Consensus pattern (41 bp):
CCCCTAAAATGAAAAATTTTAGGATCTAGCAAAGACCTCAA
Found at i:1683334 original size:17 final size:18
Alignment explanation
Indices: 1683312--1683345 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1683302 AAATTTAAAT
*
1683312 TTAAATTTAT-ATAAAAA
1 TTAAATTAATCATAAAAA
1683329 TTAAATTAATCATAAAA
1 TTAAATTAATCATAAAA
1683346 TAATTACGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TTAAATTAATCATAAAAA
Found at i:1684633 original size:16 final size:17
Alignment explanation
Indices: 1684607--1684644 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1684597 GATGGGAGGA
*
1684607 TTCTCTTCTTCTTCTTT
1 TTCTCTTCTTCATCTTT
1684624 TTCT-TTCTTCATCTTT
1 TTCTCTTCTTCATCTTT
*
1684640 CTCTC
1 TTCTC
1684645 CTTTTATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.66
Consensus pattern (17 bp):
TTCTCTTCTTCATCTTT
Found at i:1691189 original size:19 final size:20
Alignment explanation
Indices: 1691165--1691208 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1691155 ATATAACTTT
*
1691165 AAAAAA-TAGTAATATTATA
1 AAAAAACTAATAATATTATA
*
1691184 AAAAAACCTAATGATATTATA
1 AAAAAA-CTAATAATATTATA
1691205 AAAA
1 AAAA
1691209 TTATAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
21 15 0.71
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (20 bp):
AAAAAACTAATAATATTATA
Found at i:1693023 original size:13 final size:14
Alignment explanation
Indices: 1693005--1693036 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1692995 TTAAATTAAG
1693005 ATTAAAATATC-AA
1 ATTAAAATATCAAA
1693018 ATT-AAATATCAAA
1 ATTAAAATATCAAA
1693031 ATTAAA
1 ATTAAA
1693037 CTAAAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.41
13 8 0.47
14 2 0.12
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTAAAATATCAAA
Found at i:1695328 original size:44 final size:45
Alignment explanation
Indices: 1695233--1695353 Score: 154
Period size: 44 Copynumber: 2.7 Consensus size: 45
1695223 ACAGGACAGA
* *
1695233 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
1695279 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** *
1695323 ACAGGAATAATTCATGTAAGTCCATGTTAAA
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA
1695354 GACGTGGCAT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
44 37 0.58
45 1 0.02
46 26 0.41
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:1701688 original size:44 final size:45
Alignment explanation
Indices: 1701593--1701726 Score: 162
Period size: 44 Copynumber: 3.0 Consensus size: 45
1701583 ACAGGACAGA
* *
1701593 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
1701639 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * *
1701683 ACAGGAATAATTCATGTAAGTCCATGTTAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
1701727 CAGGATATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 37 0.49
45 1 0.01
46 37 0.49
ACGTcount: A:0.35, C:0.13, G:0.24, T:0.28
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:1706767 original size:150 final size:150
Alignment explanation
Indices: 1706496--1706948 Score: 818
Period size: 150 Copynumber: 3.0 Consensus size: 150
1706486 TTAAACGTAT
*
1706496 TGAGAATAGCTCTACA-GTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTA
1 TGAGAATAGCTC-AAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTA
*
1706560 GGTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTGGAAGGTCAACTGAGGGAGA
65 AGTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTGGAAGGTCAACTGAGGGAGA
1706625 AAGTCCCATGGTTGATGATTC
130 AAGTCCCATGGTTGATGATTC
1706646 TGAGAATAGCTCAAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
1 TGAGAATAGCTCAAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
1706711 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTGGAAGGTCAACTGAGGGAGAA
66 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTGGAAGGTCAACTGAGGGAGAA
1706776 AGTCCCATGGTTGATGATTC
131 AGTCCCATGGTTGATGATTC
*
1706796 TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
1 TGAGAATAGCTCAAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
* * * *
1706861 GTCAAGTTGTTGATTCTTTAGGCTTAGAGGATGTGGTTAGTGATAGAAGGTCAACTAAGGGAGAA
66 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTGGAAGGTCAACTGAGGGAGAA
*
1706926 AATCCCATGGTTGATGATTC
131 AGTCCCATGGTTGATGATTC
1706946 TGA
1 TGA
1706949 TCGCCCTCCG
Statistics
Matches: 294, Mismatches: 8, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
149 2 0.01
150 292 0.99
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.27
Consensus pattern (150 bp):
TGAGAATAGCTCAAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTGGAAGGTCAACTGAGGGAGAA
AGTCCCATGGTTGATGATTC
Found at i:1713164 original size:10 final size:10
Alignment explanation
Indices: 1713149--1713173 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1713139 TCTTTCTTTA
1713149 TTTTTTTATT
1 TTTTTTTATT
1713159 TTTTTTTATT
1 TTTTTTTATT
1713169 TTTTT
1 TTTTT
1713174 AAATTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:1713180 original size:18 final size:18
Alignment explanation
Indices: 1713145--1713180 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1713135 GTTTTCTTTC
**
1713145 TTTATTTTTTTATTTTTT
1 TTTATTTTTTTAAATTTT
1713163 TTTATTTTTTTAAATTTT
1 TTTATTTTTTTAAATTTT
1713181 CATGGTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTATTTTTTTAAATTTT
Found at i:1716572 original size:22 final size:20
Alignment explanation
Indices: 1716546--1716586 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1716536 CAAATATAAA
*
1716546 TTCATCTCATCTTGTATGTGGC
1 TTCATCT-ATCTGGTA-GTGGC
1716568 TTCATCTATCTGGTAGTGG
1 TTCATCTATCTGGTAGTGG
1716587 AACATGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.15, C:0.20, G:0.22, T:0.44
Consensus pattern (20 bp):
TTCATCTATCTGGTAGTGGC
Found at i:1724778 original size:162 final size:162
Alignment explanation
Indices: 1724511--1724835 Score: 596
Period size: 162 Copynumber: 2.0 Consensus size: 162
1724501 TGATTGTCAC
*
1724511 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTGCCAATTCGAGTATAAGAAC
1 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
*
1724576 CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCGGTCTG
66 CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
1724641 GTTTTAAACACATACATGTCTTTGAACACTCA
131 GTTTTAAACACATACATGTCTTTGAACACTCA
*
1724673 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTATGGGTTACCAATTCGAGTATAAGAAC
1 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
*
1724738 CTCTCCGTCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
66 CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
* *
1724803 GTTTTAAGCACATGCATGTCTTTGAACACTCA
131 GTTTTAAACACATACATGTCTTTGAACACTCA
1724835 T
1 T
1724836 TTTCGAATTC
Statistics
Matches: 157, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
162 157 1.00
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (162 bp):
TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
GTTTTAAACACATACATGTCTTTGAACACTCA
Found at i:1735781 original size:11 final size:11
Alignment explanation
Indices: 1735765--1735790 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1735755 TCAATTATTT
1735765 ATATATTTTTA
1 ATATATTTTTA
1735776 ATATATTTTTA
1 ATATATTTTTA
1735787 ATAT
1 ATAT
1735791 TTAAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATATATTTTTA
Found at i:1735800 original size:18 final size:18
Alignment explanation
Indices: 1735752--1735803 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1735742 CATACTAATT
*
1735752 TTTTCAATTATTTATATA
1 TTTTAAATTATTTATATA
* *
1735770 TTTTTAATATATTTTTA-A
1 TTTTAAAT-TATTTATATA
1735788 TATTTAAATTATTTAT
1 T-TTTAAATTATTTAT
1735804 TGACATGACA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.54
19 13 0.46
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTAAATTATTTATATA
Found at i:1741487 original size:21 final size:21
Alignment explanation
Indices: 1741461--1741501 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1741451 AGACGAGCAA
*
1741461 TACTCCACAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1741482 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1741502 TTGAGCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1744313 original size:17 final size:18
Alignment explanation
Indices: 1744288--1744321 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1744278 GCATTTGTAC
*
1744288 AAGT-TTTTTTAATAATG
1 AAGTATTTTATAATAATG
1744305 AAGTATTTTATAATAAT
1 AAGTATTTTATAATAAT
1744322 TTAACTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
AAGTATTTTATAATAATG
Found at i:1745041 original size:22 final size:22
Alignment explanation
Indices: 1745010--1745052 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1745000 CCTACTCTTT
*
1745010 TTGTTGTTTTCCCACTGTTTTC
1 TTGTTATTTTCCCACTGTTTTC
* *
1745032 TTGTTATTTTTCTACTGTTTT
1 TTGTTATTTTCCCACTGTTTT
1745053 GTTGACTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.07, C:0.16, G:0.12, T:0.65
Consensus pattern (22 bp):
TTGTTATTTTCCCACTGTTTTC
Found at i:1746133 original size:20 final size:19
Alignment explanation
Indices: 1746093--1746128 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1746083 ATTCAACTTA
1746093 AAAAAAACAATAAAATTAT
1 AAAAAAACAATAAAATTAT
*
1746112 AAAAAAA-AATTAAATTA
1 AAAAAAACAATAAAATTA
1746129 CATAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAAAAACAATAAAATTAT
Found at i:1750286 original size:33 final size:33
Alignment explanation
Indices: 1750249--1750314 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1750239 AGCCGCCATT
*
1750249 GGAGGTCTCTCTGATAGTAGTGAAAGTAGGTGA
1 GGAGGTCTCTCCGATAGTAGTGAAAGTAGGTGA
*
1750282 GGAGGTCTCTCCGATAGTAGTTAAAGTAGGTGA
1 GGAGGTCTCTCCGATAGTAGTGAAAGTAGGTGA
1750315 TAGATGACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (33 bp):
GGAGGTCTCTCCGATAGTAGTGAAAGTAGGTGA
Found at i:1768562 original size:9 final size:8
Alignment explanation
Indices: 1768547--1768571 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1768537 ATTTATATTT
1768547 TAAAAAAA
1 TAAAAAAA
1768555 TAAAAAAA
1 TAAAAAAA
1768563 TAAAAAAA
1 TAAAAAAA
1768571 T
1 T
1768572 TCTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
TAAAAAAA
Found at i:1774779 original size:33 final size:33
Alignment explanation
Indices: 1774737--1774805 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
1774727 AAAGGAAAAG
1774737 TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
1 TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
1774770 TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
1 TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
1774803 TTG
1 TTG
1774806 AAGGAGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (33 bp):
TTGGTGCCAAAAAGCCTAGTCTTCGCCATGTAT
Found at i:1779980 original size:16 final size:17
Alignment explanation
Indices: 1779959--1779992 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1779949 TACTACTAAA
1779959 AATTTA-TTTTTACTTT
1 AATTTAGTTTTTACTTT
*
1779975 AATTTAGTTTTTATTTT
1 AATTTAGTTTTTACTTT
1779992 A
1 A
1779993 TTTTGGGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
AATTTAGTTTTTACTTT
Found at i:1783853 original size:12 final size:12
Alignment explanation
Indices: 1783836--1783860 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1783826 ATAATTGAAA
1783836 AAAATATTTTTT
1 AAAATATTTTTT
1783848 AAAATATTTTTT
1 AAAATATTTTTT
1783860 A
1 A
1783861 TACAACAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAAATATTTTTT
Found at i:1784106 original size:110 final size:110
Alignment explanation
Indices: 1783947--1784167 Score: 424
Period size: 110 Copynumber: 2.0 Consensus size: 110
1783937 TTAATAATAC
*
1783947 AGGGACTTCTCAAGTGTATTAACTCTAGTTTATTTTCTTTTCGGTTCCATGCACCTATATCGTGT
1 AGGGACTTCTCAAGTGTATTAACTCTAGTTTATTTTCTTTTCGGTTCCATGCACCTAGATCGTGT
*
1784012 GTAATAGTTAAAATATATTATATTATATATGTAAAACATGTATTA
66 GTAATAGTTAAAATATATTATATTATATATGTAAAACATGCATTA
1784057 AGGGACTTCTCAAGTGTATTAACTCTAGTTTATTTTCTTTTCGGTTCCATGCACCTAGATCGTGT
1 AGGGACTTCTCAAGTGTATTAACTCTAGTTTATTTTCTTTTCGGTTCCATGCACCTAGATCGTGT
1784122 GTAATAGTTAAAATATATTATATTATATATGTAAAACATGCATTA
66 GTAATAGTTAAAATATATTATATTATATATGTAAAACATGCATTA
1784167 A
1 A
1784168 AGTATCAGTT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
110 109 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.42
Consensus pattern (110 bp):
AGGGACTTCTCAAGTGTATTAACTCTAGTTTATTTTCTTTTCGGTTCCATGCACCTAGATCGTGT
GTAATAGTTAAAATATATTATATTATATATGTAAAACATGCATTA
Found at i:1794504 original size:33 final size:33
Alignment explanation
Indices: 1794462--1794529 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
1794452 ACAAAACATA
* *
1794462 TACGAAGTTCTCGAATCCTAACTGTTGACCTAG
1 TACGAAGTTCTCGAATCCTAACTCTTGACCAAG
*
1794495 TACGAAGTTCTCGAATTCTAACTCTTGACCAAG
1 TACGAAGTTCTCGAATCCTAACTCTTGACCAAG
1794528 TA
1 TA
1794530 GCATTGGGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (33 bp):
TACGAAGTTCTCGAATCCTAACTCTTGACCAAG
Found at i:1797487 original size:18 final size:18
Alignment explanation
Indices: 1797464--1797499 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1797454 TTCTATTTCA
1797464 GTGAACCAAACTTTGCTT
1 GTGAACCAAACTTTGCTT
1797482 GTGAACCAAACTTTGCTT
1 GTGAACCAAACTTTGCTT
1797500 ACTCAACACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (18 bp):
GTGAACCAAACTTTGCTT
Found at i:1799330 original size:15 final size:15
Alignment explanation
Indices: 1799310--1799360 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
1799300 AGCCCCCAGA
1799310 ACCACCGAAGGGGTC
1 ACCACCGAAGGGGTC
*
1799325 ACCACCGAAGAGGTC
1 ACCACCGAAGGGGTC
1799340 ACCACCGAAGGGGTC
1 ACCACCGAAGGGGTC
1799355 ACCACC
1 ACCACC
1799361 AAAATTGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.29, C:0.37, G:0.27, T:0.06
Consensus pattern (15 bp):
ACCACCGAAGGGGTC
Found at i:1802756 original size:3 final size:3
Alignment explanation
Indices: 1802748--1802779 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
1802738 TTACACATAA
*
1802748 AAC AAC AAC AAC AGC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1802780 TGACAACTAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.31, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1817428 original size:124 final size:123
Alignment explanation
Indices: 1817073--1817435 Score: 464
Period size: 124 Copynumber: 2.9 Consensus size: 123
1817063 GGTCCGGGAA
* * *
1817073 GAAATAAATTTTTTTGACCTTTCTGAGCAAATAGTATAAAATCGCATATAGCAGGATGCTATTTG
1 GAAATAAA-TTTTTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTG
** * *
1817138 AGAAGAAATTT-TG-AAATCGCGCCCTCGTTAACGCGCTCTTGCTACAGTAGGTCATGGAT
65 AGAA-AAATTTGTGAAAATCGCGCCCTCGTGGACGC-TTATTGCTACAGTAGGTCATGGAT
** * * * *
1817197 GAAATATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAATTCGCTCCTAGCAGGATTCTATTTG
1 GAAATA-AATTTTTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTG
* *
1817262 AGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCTAAATTGCTACAGTAGGTCATGGAT
65 AGAAAAATTTGTGAAAATCGCGCCCTCGTGGACGCT-TATTGCTACAGTAGGTCATGGAT
*
1817321 GAAATAAATTTTTTGACATTTCTAAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGA
1 GAAATAAATTTTTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGA
* * *
1817386 GAACAATTTGTGAAAATCGCACCCTCAG-GGACGCATTTTTGCTACAGTAG
66 GAAAAATTTGTGAAAATCGCGCCCTC-GTGGACGC-TTATTGCTACAGTAG
1817436 CATGTTTGGG
Statistics
Matches: 207, Mismatches: 25, Indels: 14
0.84 0.10 0.06
Matches are distributed among these distances:
123 67 0.32
124 138 0.67
125 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (123 bp):
GAAATAAATTTTTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGA
GAAAAATTTGTGAAAATCGCGCCCTCGTGGACGCTTATTGCTACAGTAGGTCATGGAT
Found at i:1820593 original size:44 final size:44
Alignment explanation
Indices: 1820543--1820775 Score: 256
Period size: 44 Copynumber: 5.2 Consensus size: 44
1820533 GAATGTTAAG
1820543 GGTTAGGGTTTTTAAGTTTAGAGTTAGGGTTTTCAACTTAATTA
1 GGTTAGGGTTTTTAAGTTTAGAGTTAGGGTTTTCAACTTAATTA
* * * *
1820587 GGTTAGGGTTTTCAACTTAATTAG-GTTAGGGTTTTTAATTTAATTA
1 GGTTAGGGTTTTTAA-GT--TTAGAGTTAGGGTTTTCAACTTAATTA
* * ** *
1820633 GGTTAGGG--TTTAGGATTTAATTAGTTAGGGTTTAGAATTTAATTA
1 GGTTAGGGTTTTTAAG-TTT-A-GAGTTAGGGTTTTCAACTTAATTA
* * *
1820678 GGTTATGGTTTTTAAGTTTAGGGTTAGGATTTTCAACTTAATTA
1 GGTTAGGGTTTTTAAGTTTAGAGTTAGGGTTTTCAACTTAATTA
* * *
1820722 GGTTAGGGGTTTTAAGTTTAGGGTTAGAGTTTTCAACTTAATTA
1 GGTTAGGGTTTTTAAGTTTAGAGTTAGGGTTTTCAACTTAATTA
1820766 GGTTAGGGTT
1 GGTTAGGGTT
1820776 GTCAACTTAA
Statistics
Matches: 157, Mismatches: 23, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
42 2 0.01
43 1 0.01
44 85 0.54
45 29 0.18
46 31 0.20
47 9 0.06
ACGTcount: A:0.25, C:0.03, G:0.26, T:0.45
Consensus pattern (44 bp):
GGTTAGGGTTTTTAAGTTTAGAGTTAGGGTTTTCAACTTAATTA
Found at i:1820595 original size:23 final size:23
Alignment explanation
Indices: 1820560--1820891 Score: 305
Period size: 23 Copynumber: 14.8 Consensus size: 23
1820550 GTTTTTAAGT
1820560 TTAGAGTTAGGGTTTTCAACTTAA
1 TTAG-GTTAGGGTTTTCAACTTAA
1820584 TTAGGTTAGGGTTTTCAACTTAA
1 TTAGGTTAGGGTTTTCAACTTAA
* *
1820607 TTAGGTTAGGGTTTTTAATTTAA
1 TTAGGTTAGGGTTTTCAACTTAA
*** *
1820630 TTAGGTTAGGGTTTAGGATTTAA
1 TTAGGTTAGGGTTTTCAACTTAA
** *
1820653 TTA-GTTAGGGTTTAGAATTTAA
1 TTAGGTTAGGGTTTTCAACTTAA
* * *
1820675 TTAGGTTATGGTTTTTAA-GT--
1 TTAGGTTAGGGTTTTCAACTTAA
*
1820695 TTAGGGTTAGGATTTTCAACTTAA
1 TTA-GGTTAGGGTTTTCAACTTAA
*
1820719 TTAGGTTAGGGGTTTT-AA-GT--
1 TTAGGTTA-GGGTTTTCAACTTAA
*
1820739 TTAGGGTTAGAGTTTTCAACTTAA
1 TTA-GGTTAGGGTTTTCAACTTAA
*
1820763 TTAGGTTAGGGTTGTCAACTTAA
1 TTAGGTTAGGGTTTTCAACTTAA
* *
1820786 TTAGGTTAGGGTTTTTAA-GT--
1 TTAGGTTAGGGTTTTCAACTTAA
1820806 TTAGGGTTAGGGTTTTCAACTTAA
1 TTA-GGTTAGGGTTTTCAACTTAA
* * * *
1820830 TTAGGTTATGATTTTTAA-GT--
1 TTAGGTTAGGGTTTTCAACTTAA
*
1820850 TTAGGGTTAAGGTTTTCAACTTAA
1 TTA-GGTTAGGGTTTTCAACTTAA
1820874 TTAGGTTAGGGTTTTCAA
1 TTAGGTTAGGGTTTTCAA
1820892 TTTTTATCAC
Statistics
Matches: 255, Mismatches: 34, Indels: 39
0.78 0.10 0.12
Matches are distributed among these distances:
20 18 0.07
21 45 0.18
22 29 0.11
23 141 0.55
24 22 0.09
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (23 bp):
TTAGGTTAGGGTTTTCAACTTAA
Found at i:1820675 original size:45 final size:45
Alignment explanation
Indices: 1820564--1820894 Score: 223
Period size: 44 Copynumber: 7.4 Consensus size: 45
1820554 TTAAGTTTAG
* *
1820564 AGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTCAACTTAATT
1 AGTTAGGGTTTTCAATTTAATTAGGTTAGGGTTTACAACTTAATT
* ** *
1820609 AGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTAGGATTTAATT
1 A-GTTAGGGTTTTCAATTTAATTAGGTTAGGGTTTACAACTTAATT
** * ** * * *
1820655 AGTTAGGGTTTAGAATTTAATTAGGTTATGGTTTTTAAGTTTA-G
1 AGTTAGGGTTTTCAATTTAATTAGGTTAGGGTTTACAACTTAATT
* * * * * * *
1820699 GGTTAGGATTTTCAACTTAATTAGGTTAGGGGTTT-TAAGTTTA-G
1 AGTTAGGGTTTTCAATTTAATTAGGTTA-GGGTTTACAACTTAATT
* * *
1820743 GGTTAGAGTTTTCAACTTAATTAGGTTAGGGTTGT-CAACTTAATT
1 AGTTAGGGTTTTCAATTTAATTAGGTTAGGGTT-TACAACTTAATT
* * *
1820788 AGGTTAGGGTTTTTAAGTTT-A--GGGTTAGGGTTTTCAACTTAATT
1 A-GTTAGGGTTTTCAA-TTTAATTAGGTTAGGGTTTACAACTTAATT
* * * * * *
1820832 AGGTTATGATTTTTAAGTTT-A--GGGTTAAGGTTTTCAACTTAATT
1 A-GTTAGGGTTTTCAA-TTTAATTAGGTTAGGGTTTACAACTTAATT
1820876 AGGTTAGGGTTTTCAATTT
1 A-GTTAGGGTTTTCAATTT
1820895 TTATCACATC
Statistics
Matches: 241, Mismatches: 38, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
43 9 0.04
44 138 0.57
45 40 0.17
46 52 0.22
47 2 0.01
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.46
Consensus pattern (45 bp):
AGTTAGGGTTTTCAATTTAATTAGGTTAGGGTTTACAACTTAATT
Found at i:1820781 original size:67 final size:67
Alignment explanation
Indices: 1820699--1820842 Score: 243
Period size: 67 Copynumber: 2.1 Consensus size: 67
1820689 TTAAGTTTAG
*
1820699 GGTTAGGATTTTCAACTTAATTAGGTTAGGGGTTTTAAGTTTAGGGTTAGAGTTTTCAACTTAAT
1 GGTTAGGATTGTCAACTTAATTAGGTTAGGGGTTTTAAGTTTAGGGTTAGAGTTTTCAACTTAAT
1820764 TA
66 TA
* * *
1820766 GGTTAGGGTTGTCAACTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTCAACTTAAT
1 GGTTAGGATTGTCAACTTAATTAGGTTAGGGGTTTTAAGTTTAGGGTTAGAGTTTTCAACTTAAT
1820831 TA
66 TA
*
1820833 GGTTATGATT
1 GGTTAGGATT
1820843 TTTAAGTTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 71 1.00
ACGTcount: A:0.25, C:0.06, G:0.26, T:0.44
Consensus pattern (67 bp):
GGTTAGGATTGTCAACTTAATTAGGTTAGGGGTTTTAAGTTTAGGGTTAGAGTTTTCAACTTAAT
TA
Found at i:1820804 original size:111 final size:110
Alignment explanation
Indices: 1820587--1820887 Score: 410
Period size: 111 Copynumber: 2.7 Consensus size: 110
1820577 AACTTAATTA
* * *** *
1820587 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTTAA-TTTAATTAGGTTAGGGTTTAGGATTT
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTTAAGTTT-A--GGGTTAGAGTTTTCAACTT
* * *
1820651 AATTA-GTTAGGGTTTAGAATTTAATTAGGTTATGGTTTTTAAGTTTAG
63 AATTAGGTTAGGGTTT-CAACTTAATTAGGTTAGGGTTTTTAAGTTTAG
* *
1820699 GGTTAGGATTTTCAACTTAATTAGGTTAGGGGTTTTAAGTTTAGGGTTAGAGTTTTCAACTTAAT
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTAGAGTTTTCAACTTAAT
1820764 TAGGTTAGGGTTGTCAACTTAATTAGGTTAGGGTTTTTAAGTTTAG
66 TAGGTTAGGGTT-TCAACTTAATTAGGTTAGGGTTTTTAAGTTTAG
* *
1820810 GGTTAGGGTTTTCAACTTAATTAGGTTATGATTTTTAAGTTTAGGGTTA-AGGTTTTCAACTTAA
1 GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTAGA-GTTTTCAACTTAA
1820874 TTAGGTTAGGGTTT
65 TTAGGTTAGGGTTT
1820888 TCAATTTTTA
Statistics
Matches: 170, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
110 20 0.12
111 109 0.64
112 38 0.22
113 3 0.02
ACGTcount: A:0.25, C:0.04, G:0.25, T:0.46
Consensus pattern (110 bp):
GGTTAGGGTTTTCAACTTAATTAGGTTAGGGTTTTTAAGTTTAGGGTTAGAGTTTTCAACTTAAT
TAGGTTAGGGTTTCAACTTAATTAGGTTAGGGTTTTTAAGTTTAG
Found at i:1820928 original size:25 final size:25
Alignment explanation
Indices: 1820893--1821060 Score: 181
Period size: 25 Copynumber: 6.9 Consensus size: 25
1820883 GGTTTTCAAT
*
1820893 TTTTATCACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
1820918 TTTTATTACATCATATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
1820943 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
1820968 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * * *
1820991 --AAATAAC-TCAAA-AAAATTCAA
1 TTTTATTACATCAAATAAACTTCTA
1821012 TTTTTATTACATC-AATAAAACTTCTA
1 -TTTTATTACATCAAAT-AAACTTCTA
*
1821038 TTTTATTACATCAAACAAACTTC
1 TTTTATTACATCAAATAAACTTC
1821061 AAAATATTCA
Statistics
Matches: 120, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
20 9 0.08
21 6 0.05
23 2 0.02
24 10 0.08
25 84 0.70
26 9 0.08
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:1821509 original size:18 final size:18
Alignment explanation
Indices: 1821486--1821523 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1821476 CTCGGAAAAT
*
1821486 GATACATATAAGGGTTAG
1 GATACATATAAGGGATAG
*
1821504 GATACATGTAAGGGATAG
1 GATACATATAAGGGATAG
1821522 GA
1 GA
1821524 AACGCACCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.05, G:0.32, T:0.24
Consensus pattern (18 bp):
GATACATATAAGGGATAG
Found at i:1822184 original size:7 final size:7
Alignment explanation
Indices: 1822174--1822205 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1822164 TTATATACAT
1822174 AATACTA
1 AATACTA
1822181 AATACTA
1 AATACTA
1822188 AATACTA
1 AATACTA
*
1822195 AATACAA
1 AATACTA
1822202 AATA
1 AATA
1822206 TTTATTTGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (7 bp):
AATACTA
Found at i:1822191 original size:14 final size:14
Alignment explanation
Indices: 1822168--1822205 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1822158 TGTTAGTTAT
*
1822168 ATACATAATACTAA
1 ATACAAAATACTAA
*
1822182 ATACTAAATACTAA
1 ATACAAAATACTAA
1822196 ATACAAAATA
1 ATACAAAATA
1822206 TTTATTTGCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (14 bp):
ATACAAAATACTAA
Found at i:1822373 original size:20 final size:20
Alignment explanation
Indices: 1822348--1822385 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1822338 TTTATTTTTA
1822348 AAAATCT-ATATAATAATTGT
1 AAAATCTAATATAA-AATTGT
1822368 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
1822386 TACCTCGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:1823379 original size:51 final size:51
Alignment explanation
Indices: 1823320--1823443 Score: 180
Period size: 51 Copynumber: 2.4 Consensus size: 51
1823310 TATTTTAAAA
* *
1823320 AAGGAAATTGAGAGCAAATTGAAAATAAATATGG-GTT-TGAGAGATTTTTGG
1 AAGGAAATTGAGAGAAAATTGAAAATAAATATGGATTTATGAGA-ATTTTT-G
* *
1823371 AATGAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTTG
1 AAGGAAATTGAGAGAAAATTGAAAATAAATATGGATTTATGAGAATTTTTG
1823422 AAGGAAATTGAGAGAAAATTGA
1 AAGGAAATTGAGAGAAAATTGA
1823444 GAGGAAATTG
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
51 53 0.80
52 8 0.12
53 5 0.08
ACGTcount: A:0.45, C:0.01, G:0.24, T:0.30
Consensus pattern (51 bp):
AAGGAAATTGAGAGAAAATTGAAAATAAATATGGATTTATGAGAATTTTTG
Found at i:1823432 original size:10 final size:11
Alignment explanation
Indices: 1823419--1823469 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
1823409 ATGAGAATTT
1823419 TTGA-AGGAAA
1 TTGAGAGGAAA
*
1823429 TTGAGAGAAAA
1 TTGAGAGGAAA
1823440 TTGAGAGGAAA
1 TTGAGAGGAAA
*
1823451 TTGAGAGAAAA
1 TTGAGAGGAAA
1823462 TATGAGAG
1 T-TGAGAG
1823470 AGGATTTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 4 0.11
11 26 0.72
12 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.20
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:1823437 original size:22 final size:22
Alignment explanation
Indices: 1823419--1823469 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 22
1823409 ATGAGAATTT
1823419 TTGA-AGGAAATTGAGAGAAAA
1 TTGAGAGGAAATTGAGAGAAAA
1823440 TTGAGAGGAAATTGAGAGAAAA
1 TTGAGAGGAAATTGAGAGAAAA
1823462 TATGAGAG
1 T-TGAGAG
1823470 AGGATTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 4 0.14
22 18 0.64
23 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.31, T:0.20
Consensus pattern (22 bp):
TTGAGAGGAAATTGAGAGAAAA
Found at i:1823442 original size:11 final size:11
Alignment explanation
Indices: 1823426--1823470 Score: 72
Period size: 11 Copynumber: 4.0 Consensus size: 11
1823416 TTTTTGAAGG
1823426 AAATTGAGAGA
1 AAATTGAGAGA
*
1823437 AAATTGAGAGG
1 AAATTGAGAGA
1823448 AAATTGAGAGA
1 AAATTGAGAGA
1823459 AAATATGAGAGA
1 AAAT-TGAGAGA
1823471 GGATTTGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 24 0.77
12 7 0.23
ACGTcount: A:0.53, C:0.00, G:0.29, T:0.18
Consensus pattern (11 bp):
AAATTGAGAGA
Found at i:1837333 original size:24 final size:25
Alignment explanation
Indices: 1837301--1837347 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1837291 ACCCTAAATA
1837301 TGTCAGTATTAATTCTT-TTGAAGG
1 TGTCAGTATTAATTCTTGTTGAAGG
*
1837325 TGTCAGTATTAATTTTTGTTGAA
1 TGTCAGTATTAATTCTTGTTGAA
1837348 CCTACAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (25 bp):
TGTCAGTATTAATTCTTGTTGAAGG
Found at i:1837748 original size:14 final size:14
Alignment explanation
Indices: 1837713--1837742 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1837703 TTAGATTATC
1837713 ATACATTAATCAAA
1 ATACATTAATCAAA
1837727 ATACATTAATCAAA
1 ATACATTAATCAAA
1837741 AT
1 AT
1837743 TGATTAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (14 bp):
ATACATTAATCAAA
Done.