Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 5 of 198
Found at i:1585216 original size:21 final size:20
Alignment explanation
Indices: 1585170--1585256 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 20
1585160 CCTGATCAGT
* *
1585170 ATACGACACATAAGTGCTTG
1 ATACGACACAAAAGTGCCTG
* * *
1585190 AAACGACACACGAGGTGCCTG
1 ATACGACACA-AAAGTGCCTG
1585211 ATACGACACATAAAGTGCCTGAG
1 ATACGACACA-AAAGTGCCT--G
1585234 ATACGACACATAAAGTGCCTG
1 ATACGACACA-AAAGTGCCTG
1585255 AT
1 AT
1585257 CGGCAAAGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.16
21 26 0.46
23 21 0.38
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (20 bp):
ATACGACACAAAAGTGCCTG
Found at i:1585240 original size:23 final size:23
Alignment explanation
Indices: 1585170--1585255 Score: 101
Period size: 23 Copynumber: 4.0 Consensus size: 23
1585160 CCTGATCAGT
*
1585170 ATACGACACAT-AAGTGCTTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
1585191 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
1585211 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
1585234 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
1585256 TCGGCAAAGC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
20 9 0.17
21 22 0.41
23 23 0.43
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.17
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:1585252 original size:44 final size:41
Alignment explanation
Indices: 1585170--1585256 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 41
1585160 CCTGATCAGT
* * *
1585170 ATACGACACATAAGTGCTTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
1585211 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
1585255 AT
1 AT
1585257 CGGCAAAGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
41 11 0.28
42 9 0.23
43 1 0.03
44 18 0.46
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.18
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:1586092 original size:39 final size:39
Alignment explanation
Indices: 1586038--1586116 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
1586028 ACTTAAATCC
*
1586038 ATGAGTATTTCACTCTAGGGTTCCAAAAACATCGAATTT
1 ATGAGTATTTCACTCTAGGGTTCCAAAAACATCAAATTT
1586077 ATGAGTATTTCACTCTAGGGTTCCAAAAACATCAAATTT
1 ATGAGTATTTCACTCTAGGGTTCCAAAAACATCAAATTT
1586116 A
1 A
1586117 AACTTCAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (39 bp):
ATGAGTATTTCACTCTAGGGTTCCAAAAACATCAAATTT
Found at i:1587095 original size:22 final size:22
Alignment explanation
Indices: 1587065--1587126 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
1587055 AATTTTAAAA
* *
1587065 TTAATAATTTATGAAAATTATAT
1 TTAA-AATTTATAAAAAATATAT
1587088 TTAAAATTT-TAAAAAATATAT
1 TTAAAATTTATAAAAAATATAT
1587109 TTAAAATATTATAAAAAA
1 TTAAAAT-TTATAAAAAA
1587127 AACAATAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 17 0.49
22 7 0.20
23 11 0.31
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TTAAAATTTATAAAAAATATAT
Found at i:1587191 original size:13 final size:13
Alignment explanation
Indices: 1587173--1587215 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 13
1587163 TATATTTTAA
1587173 ATAATTTAAAATC
1 ATAATTTAAAATC
1587186 ATAATTT-AAA--
1 ATAATTTAAAATC
1587196 ATAATTTAAAAATC
1 ATAATTT-AAAATC
1587210 ATAATT
1 ATAATT
1587216 ATAGAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 7 0.27
12 6 0.23
13 7 0.27
14 6 0.23
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (13 bp):
ATAATTTAAAATC
Found at i:1587207 original size:24 final size:24
Alignment explanation
Indices: 1587152--1587215 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
1587142 AGGTCATATC
* *
1587152 TTTAAAAATAATATATTTTAAATAA
1 TTTAAAAATCATA-ATTTAAAATAA
1587177 TTT-AAAATCATAATTTAAAATAA
1 TTTAAAAATCATAATTTAAAATAA
1587200 TTTAAAAATCATAATT
1 TTTAAAAATCATAATT
1587216 ATAGAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 13 0.36
24 20 0.56
25 3 0.08
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTAAAAATCATAATTTAAAATAA
Found at i:1587229 original size:24 final size:23
Alignment explanation
Indices: 1587154--1587231 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 23
1587144 GTCATATCTT
* *
1587154 TAAAAATAATATATTTTAAATA-A
1 TAAAAATCATA-ATTTAAAATATA
* *
1587177 TTTAAAATCATAATTTAAAATAATT
1 -TAAAAATCATAATTTAAAAT-ATA
1587202 TAAAAATCATAATTATAGAAAT-TA
1 TAAAAATCATAATT-TA-AAATATA
1587226 TAAAAA
1 TAAAAA
1587232 AAATTAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
23 8 0.18
24 30 0.68
25 2 0.05
26 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.01, T:0.37
Consensus pattern (23 bp):
TAAAAATCATAATTTAAAATATA
Found at i:1587259 original size:33 final size:35
Alignment explanation
Indices: 1587222--1587290 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 35
1587212 AATTATAGAA
1587222 ATTATAAAA-AA-AATTAAAAT-ATACATTTAAAAT
1 ATTATAAAACAATAA-TAAAATAATACATTTAAAAT
*
1587255 ATTATAAAACTAATAATAAATTAATACATTTAAAAT
1 ATTATAAAAC-AATAATAAAATAATACATTTAAAAT
1587291 CGTTCTTATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
33 9 0.29
35 7 0.23
36 15 0.48
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (35 bp):
ATTATAAAACAATAATAAAATAATACATTTAAAAT
Found at i:1601065 original size:11 final size:11
Alignment explanation
Indices: 1601042--1601074 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1601032 GAATGAAAAT
*
1601042 TTTTA-AATAA
1 TTTTATAATTA
1601052 TTTTATAATTA
1 TTTTATAATTA
1601063 TTTTATAATTA
1 TTTTATAATTA
1601074 T
1 T
1601075 GTGATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTATAATTA
Found at i:1604032 original size:2 final size:2
Alignment explanation
Indices: 1604025--1604072 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1604015 GGATGCAATG
1604025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1604067 AT AT AT
1 AT AT AT
1604073 GTTAATGGTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1622147 original size:44 final size:44
Alignment explanation
Indices: 1622093--1622538 Score: 190
Period size: 44 Copynumber: 9.7 Consensus size: 44
1622083 GATTGAAGTT
*
1622093 ACAAAACTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
1 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
* * **
1622137 ACAAATCTTATCTTCC-TGAAGTTGCAGTGGAATAGATTGAAGAT
1 ACAAATCTTATC-TCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
* * * * * * *
1622181 AGCAAATCTTATCT-CTCTGAAATTGTAGTAGAGCAAATTAAAACT
1 A-CAAATCTTATCTCCT-TGAAGTTGCAGTGGAGTAGATTAAAGCC
* * ** *
1622226 ACAAATCTTATTTTCC-TAAAGTTGCAGTGGAACATATTAAAGCTAC
1 ACAAATCTTA-TCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGC--C
1622272 AAATTACAAATCTTATCT-CTCTGAAGTTGCAGTGGAGTAGATTGAAA--C
1 -----ACAAATCTTATCTCCT-TGAAGTTGCAGTGGAGTAGATT-AAAGCC
* * * * * * * *
1622320 ATAAGTCCTAT-ACCTCTGAATTTGTAGTTG-GTCAGATTAAATCC
1 ACAAATCTTATCTCCT-TGAAGTTGCAGTGGAGT-AGATTAAAGCC
* * *
1622364 ACCATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAATAGACTAAAGCTACAAGCT
1 A-C--A--AA-TCTTATCTCCTTGAAGTTGCAGTGGAGTAGA-T-----TA-AAGCC
* * * * * *
1622421 ACAAATCTTATCTCCCTGAAGTTGCAATAGAGCAAATTAAAGCT
1 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
* * * * *
1622465 ACAAGTCTAATCTCCTTGAAGTTGTAGTGGAGTAGATTGAAGCA
1 ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
* * *
1622509 ACAAATCATATAC-CTTTAAAGTTGCAGTGG
1 ACAAATCTTAT-CTCCTTGAAGTTGCAGTGG
1622539 GTTAGAATGA
Statistics
Matches: 299, Mismatches: 67, Indels: 72
0.68 0.15 0.16
Matches are distributed among these distances:
42 5 0.02
43 28 0.09
44 129 0.43
45 39 0.13
46 1 0.00
47 1 0.00
48 1 0.00
49 2 0.01
50 22 0.07
51 58 0.19
52 5 0.02
54 1 0.00
56 3 0.01
57 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (44 bp):
ACAAATCTTATCTCCTTGAAGTTGCAGTGGAGTAGATTAAAGCC
Found at i:1622221 original size:89 final size:88
Alignment explanation
Indices: 1622064--1622257 Score: 228
Period size: 89 Copynumber: 2.2 Consensus size: 88
1622054 TCTCTACCCT
* * * * * * *
1622064 TGAAGTTGCAATGAAAAAAGATTGAAGTTACAAAACTTATCTCCTTGAAGTTGCAGTGGAGTAGA
1 TGAAGTTGCAGTG-GAAAAGATTGAAGATACAAAACTTATCTCCTTGAAATTGCAGTAGAGCAAA
*
1622129 TTAAAGCCACAAATCTTATCTTCC
65 TTAAAACCACAAATCTTATCTTCC
* * *
1622153 TGAAGTTGCAGTGGAATAGATTGAAGATAGCAAATCTTATCT-CTCTGAAATTGTAGTAGAGCAA
1 TGAAGTTGCAGTGGAAAAGATTGAAGATA-CAAAACTTATCTCCT-TGAAATTGCAGTAGAGCAA
* *
1622217 ATTAAAACTACAAATCTTATTTTCC
64 ATTAAAACCACAAATCTTATCTTCC
*
1622242 TAAAGTTGCAGTGGAA
1 TGAAGTTGCAGTGGAA
1622258 CATATTAAAG
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
88 15 0.17
89 74 0.83
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (88 bp):
TGAAGTTGCAGTGGAAAAGATTGAAGATACAAAACTTATCTCCTTGAAATTGCAGTAGAGCAAAT
TAAAACCACAAATCTTATCTTCC
Found at i:1622313 original size:140 final size:142
Alignment explanation
Indices: 1622137--1622446 Score: 346
Period size: 144 Copynumber: 2.2 Consensus size: 142
1622127 GATTAAAGCC
* *
1622137 ACAAATCTTATCT-TCCTGAAGTTGCAGTGGAATAGATTGAAGATAGCAAATCTTAT-CTCTCTG
1 ACAAATCTTATCTCT-CTGAAGTTGCAGTGGAATAGATTGAA-ACA-CAAATCCTATAC-CTCTG
* *
1622200 AAATTGTAGTAGAG-CAAATTAAA-A-C-TA-CAAATCTTATTTTCCTAAAGTTGCAGTGGAACA
62 AAATTGTAGTAG-GTCAAATTAAACACCATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAACA
* * *
1622260 TATTAAAGCTACAAATT
126 GACTAAAGCTACAAACT
* * * *
1622277 ACAAATCTTATCTCTCTGAAGTTGCAGTGGAGTAGATTGAAACATAAGTCCTATACCTCTGAATT
1 ACAAATCTTATCTCTCTGAAGTTGCAGTGGAATAGATTGAAACACAAATCCTATACCTCTGAAAT
* * * * *
1622342 TGTAGTTGGTCAGATTAAATCCACCATAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAATAGAC
66 TGTAGTAGGTCAAATTAAA--CACCATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAACAGAC
*
1622407 TAAAGCTACAAGCT
129 TAAAGCTACAAACT
*
1622421 ACAAATCTTATCTCCCTGAAGTTGCA
1 ACAAATCTTATCTCTCTGAAGTTGCA
1622447 ATAGAGCAAA
Statistics
Matches: 143, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
137 1 0.01
138 30 0.21
139 3 0.02
140 38 0.27
141 2 0.01
142 1 0.01
143 2 0.01
144 66 0.46
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (142 bp):
ACAAATCTTATCTCTCTGAAGTTGCAGTGGAATAGATTGAAACACAAATCCTATACCTCTGAAAT
TGTAGTAGGTCAAATTAAACACCATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAACAGACTA
AAGCTACAAACT
Found at i:1622770 original size:7 final size:7
Alignment explanation
Indices: 1622758--1622784 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1622748 TATCATTCCT
1622758 TTATTTA
1 TTATTTA
1622765 TTATTTA
1 TTATTTA
1622772 TTATTTA
1 TTATTTA
1622779 TTATTT
1 TTATTT
1622785 TAGTATTCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTATTTA
Found at i:1633165 original size:105 final size:108
Alignment explanation
Indices: 1633033--1633239 Score: 323
Period size: 110 Copynumber: 1.9 Consensus size: 108
1633023 GGTTGTAACT
1633033 AATTCCAATTAATGGAAGAATTGGTTT-G-G-TTTGATTTGATAATATATTATTGGTTTT-TATG
1 AATTCCAATTAATGGAAGAATTGGTTTGGTGATTTGATTTGATAATATATTATTGGTTTTAT-TG
*
1633094 TTATTAGGTAATGTTTTTAGAACCGGATCAATAGTCATGCCATC
65 TTATTAGGTAATGTCTTTAGAACCGGATCAATAGTCATGCCATC
* *
1633138 AATTTCAATTAATGGAAGAATTGGTTTGGTTTGATTTGATTTGATAATATTTTATTGGTTTTATT
1 AATTCCAATTAATGGAAGAATTGGTTTGG--TGATTTGATTTGATAATATATTATTGGTTTTATT
*
1633203 GTTATTAGGTAATGTCTTTAGAACCGGATTAATAGTC
64 GTTATTAGGTAATGTCTTTAGAACCGGATCAATAGTC
1633240 GAACCAATCA
Statistics
Matches: 92, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
105 26 0.28
106 1 0.01
109 1 0.01
110 63 0.68
111 1 0.01
ACGTcount: A:0.29, C:0.07, G:0.19, T:0.45
Consensus pattern (108 bp):
AATTCCAATTAATGGAAGAATTGGTTTGGTGATTTGATTTGATAATATATTATTGGTTTTATTGT
TATTAGGTAATGTCTTTAGAACCGGATCAATAGTCATGCCATC
Found at i:1639720 original size:4 final size:4
Alignment explanation
Indices: 1639711--1639743 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1639701 ACAAATTATG
1639711 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1639744 CTAAGTTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:1640834 original size:43 final size:44
Alignment explanation
Indices: 1640782--1640865 Score: 118
Period size: 43 Copynumber: 1.9 Consensus size: 44
1640772 CTCTAATTCA
1640782 TGTAGGTTTAACCCAAA-AGGGTAACCAAACACTATA-TTTCTCG
1 TGTAGGTTTAACCCAAATA-GGTAACCAAACACTATACTTTCTCG
* * *
1640825 TGTAGGTTTATCTCAAATAGGTAACCAGACACTATACTTTC
1 TGTAGGTTTAACCCAAATAGGTAACCAAACACTATACTTTC
1640866 ACCTATATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
43 31 0.86
44 5 0.14
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.31
Consensus pattern (44 bp):
TGTAGGTTTAACCCAAATAGGTAACCAAACACTATACTTTCTCG
Found at i:1641978 original size:13 final size:13
Alignment explanation
Indices: 1641960--1641994 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
1641950 CTCAGTCTGT
1641960 CACACGGCTTGGC
1 CACACGGCTTGGC
1641973 CACACGGCTTGGC
1 CACACGGCTTGGC
1641986 CACACGGCT
1 CACACGGCT
1641995 ATATGATCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (13 bp):
CACACGGCTTGGC
Found at i:1642786 original size:12 final size:12
Alignment explanation
Indices: 1642769--1642795 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1642759 AATAATTTTA
1642769 ATATATACATAT
1 ATATATACATAT
1642781 ATATATACATAT
1 ATATATACATAT
1642793 ATA
1 ATA
1642796 AAAATGTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATATACATAT
Found at i:1642945 original size:27 final size:27
Alignment explanation
Indices: 1642915--1642998 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 27
1642905 ATTGGTTCTT
1642915 TGAAACTGCACAAGTCCATCTATGACC
1 TGAAACTGCACAAGTCCATCTATGACC
* * * * * *
1642942 TGAAACAAGCGCCA--CAAGCT-TG-GC
1 TGAAAC-TGCACAAGTCCATCTATGACC
1642966 TGAAACTGCACAAGTCCATCTATGACC
1 TGAAACTGCACAAGTCCATCTATGACC
1642993 TGAAAC
1 TGAAAC
1642999 AAGCACCACA
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
23 4 0.10
24 7 0.17
25 6 0.15
26 6 0.15
27 13 0.32
28 4 0.10
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.19
Consensus pattern (27 bp):
TGAAACTGCACAAGTCCATCTATGACC
Found at i:1642991 original size:51 final size:51
Alignment explanation
Indices: 1642915--1643017 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
1642905 ATTGGTTCTT
*
1642915 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCGCCACAAGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1642966 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1 TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
1643017 T
1 T
1643018 AGAGCTATGT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.18
Consensus pattern (51 bp):
TGAAACTGCACAAGTCCATCTATGACCTGAAACAAGCACCACAAGCTTGGC
Found at i:1648769 original size:26 final size:26
Alignment explanation
Indices: 1648728--1648778 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1648718 CAGTTTGCAT
*
1648728 ATTGAGCTTGTATATCGAGCTCGCAC
1 ATTGAGCTCGTATATCGAGCTCGCAC
* *
1648754 ATTGAGCTCGTGTATCGGGCTCGCA
1 ATTGAGCTCGTATATCGAGCTCGCA
1648779 TGATACTAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (26 bp):
ATTGAGCTCGTATATCGAGCTCGCAC
Found at i:1651364 original size:29 final size:30
Alignment explanation
Indices: 1651305--1651362 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
1651295 TCCGAGCCTT
*
1651305 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
1651335 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
1651363 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:1651590 original size:13 final size:13
Alignment explanation
Indices: 1651572--1651603 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1651562 TTTCCAGTAA
1651572 TTATGAATTTATT
1 TTATGAATTTATT
1651585 TTATGAATTTATT
1 TTATGAATTTATT
*
1651598 TGATGA
1 TTATGA
1651604 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1651812 original size:50 final size:50
Alignment explanation
Indices: 1651698--1651939 Score: 295
Period size: 50 Copynumber: 4.7 Consensus size: 50
1651688 ATTTGGGTAA
* * * *
1651698 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
1651754 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
1651804 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
** * *
1651854 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
**
1651904 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
1651940 TTTGGCATGT
Statistics
Matches: 167, Mismatches: 18, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
50 93 0.56
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1651890 original size:100 final size:103
Alignment explanation
Indices: 1651698--1651947 Score: 362
Period size: 100 Copynumber: 2.4 Consensus size: 103
1651688 ATTTGGGTAA
1651698 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATAAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATAAGAGGTCCC
*
1651763 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
63 CCGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * * *
1651804 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCCG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCCG
* *
1651866 TAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* *
1651904 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
1651948 GTTATTATCA
Statistics
Matches: 132, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
100 51 0.39
101 39 0.30
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATAAGAGGTCCCCCG
TAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:1656830 original size:189 final size:190
Alignment explanation
Indices: 1656508--1656866 Score: 551
Period size: 189 Copynumber: 1.9 Consensus size: 190
1656498 GACCGATAAT
** *** *
1656508 GAGGATGAATTTTGATGTTTCCGGTATGATCATGTCCGCGAGGGCTTAATTTAAGCACTCATGAA
1 GAGGATGAATTTCAATGTTTCCAACATGAGCATGTCCGCGAGGGCTTAATTTAAGCACTCATGAA
* *
1656573 TATGATCGTATCAGTTTCATGCTTAGAAAACCAGAGGAATCATGACAATTAGCTGAATGAACAGA
66 TATGATCATATCAGTTTCATGCTTAGAAAACCAGAGGAATCATGAAAATTAGCTGAATGAACAGA
1656638 GTTTAAACAAGCTAGAACTAGTGAACT-AGACTGATTTCCGGTCATGCCTTATGTGACCG
131 GTTTAAACAAGCTAGAACTAGTGAACTGAGACTGATTTCCGGTCATGCCTTATGTGACCG
* ** *
1656697 GAGGATGAATTTCAATGTTTCCAACATGAGCATGTTCGCGAGGGCTTAATTTAAGCGTTCTTGAA
1 GAGGATGAATTTCAATGTTTCCAACATGAGCATGTCCGCGAGGGCTTAATTTAAGCACTCATGAA
* * *
1656762 TATGATCATATCAGTTTCATGCTTAGAAAACTAGAGGAATCATGAAAAATT-GTTGAATGAATAG
66 TATGATCATATCAGTTTCATGCTTAGAAAACCAGAGGAATCATG-AAAATTAGCTGAATGAACAG
*
1656826 AGTTTGAACAAGCTAGAACTAGTGAACTGAGACTGATTTCC
130 AGTTTAAACAAGCTAGAACTAGTGAACTGAGACTGATTTCC
1656867 CATTCTGCCT
Statistics
Matches: 152, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
189 135 0.89
190 17 0.11
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (190 bp):
GAGGATGAATTTCAATGTTTCCAACATGAGCATGTCCGCGAGGGCTTAATTTAAGCACTCATGAA
TATGATCATATCAGTTTCATGCTTAGAAAACCAGAGGAATCATGAAAATTAGCTGAATGAACAGA
GTTTAAACAAGCTAGAACTAGTGAACTGAGACTGATTTCCGGTCATGCCTTATGTGACCG
Found at i:1671632 original size:25 final size:24
Alignment explanation
Indices: 1671601--1671662 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
1671591 TTTTTAAAAA
1671601 ATATTTGAAATGGTTTTTGTTGGT
1 ATATTTGAAATGGTTTTTGTTGGT
* *
1671625 ATGATTTGAAAT--TATTTGTTTGT
1 AT-ATTTGAAATGGTTTTTGTTGGT
*
1671648 ATATTTCAAATGGTT
1 ATATTTGAAATGGTT
1671663 CTAAATGCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
22 8 0.26
23 11 0.35
24 3 0.10
25 9 0.29
ACGTcount: A:0.26, C:0.02, G:0.19, T:0.53
Consensus pattern (24 bp):
ATATTTGAAATGGTTTTTGTTGGT
Found at i:1675465 original size:24 final size:21
Alignment explanation
Indices: 1675421--1675466 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 21
1675411 CCGCCCATAT
1675421 TATTTTTAATTTTTTTAAAAA
1 TATTTTTAATTTTTTTAAAAA
*
1675442 TATTTGTTATATTTTATTTTAAAA
1 TATTT-TTA-ATTTT-TTTAAAAA
1675466 T
1 T
1675467 TTCATACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 3 0.14
23 5 0.24
24 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TATTTTTAATTTTTTTAAAAA
Found at i:1685342 original size:391 final size:392
Alignment explanation
Indices: 1684494--1685351 Score: 1603
Period size: 392 Copynumber: 2.2 Consensus size: 392
1684484 ATTAGTTTTA
*
1684494 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACAACTCTTTTTTTGTCGTTATGGATATAATAGC
1 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAATAGC
1684559 AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTCAATCGTCATATTTTACATTTCATTCA
66 AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTCAATCGTCATATTTTACATTTCATTCA
1684624 TATAGATATTGCATGTCAAAATTATTATAAATTTTAAATTTTAAATTATTTATTTATATAAAAAA
131 TATAGATATTGCATGTCAAAATTATTATAAATTTTAAATTTTAAATTATTTATTTATATAAAAAA
*
1684689 TTTAATTATTCAATTAAGTATTAATGTATAGTGTGTTTTAAATCGATAAGATACATATATGTATT
196 TTTAATTATTCAATTAAGTATTAATGTATAGAGTGTTTTAAATCGATAAGATACATATATGTATT
* *
1684754 AGATTGTTTCAAAAATTTATATATATGATAAGTATAATTATATCAATAAATTTAATACAGATAAA
261 AGATTGGTTCAAAAATTTATATATATGATAAATATAATTATATCAATAAATTTAATACAGATAAA
1684819 GCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAGA
326 GCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAGA
1684884 AT
391 AT
*
1684886 AAAGTCAATGCAAAATAAGGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAATAGC
1 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAATAGC
*
1684951 AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTTAATCGTCATATTTTACATTTCATTCA
66 AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTCAATCGTCATATTTTACATTTCATTCA
* * *
1685016 TATAGATATTGCATGTCAAAATTATTATAAATTTTTAATTTTTAATTTTTTATTTATATAAAAAA
131 TATAGATATTGCATGTCAAAATTATTATAAATTTTAAATTTTAAATTATTTATTTATATAAAAAA
1685081 TTTAATTATTCAA-TAAGTATTAATGTATAGAGTGTTTTAAATCGATAAGATACATATATGTATT
196 TTTAATTATTCAATTAAGTATTAATGTATAGAGTGTTTTAAATCGATAAGATACATATATGTATT
1685145 AGATTGGTTCAAAAATTTATATATATGATAAATATAATTATATCAATAAATTTAATACAGATAAA
261 AGATTGGTTCAAAAATTTATATATATGATAAATATAATTATATCAATAAATTTAATACAGATAAA
*
1685210 TCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAG-
326 GCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAGA
1685274 AT
391 AT
1685276 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAAATAG
1 AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATAT-AATAG
1685341 CAATTGACAAC
65 CAATTGACAAC
1685352 AAAACATTTA
Statistics
Matches: 454, Mismatches: 11, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
390 60 0.13
391 192 0.42
392 202 0.44
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (392 bp):
AAAGTCAATGCAAAATAAAGAGGAGTTAGTAACTACTCTTTTTTTGTCGTTATGGATATAATAGC
AATTGACAACCATAAATGAACCAACTGGAGAAGCGATTCAATCGTCATATTTTACATTTCATTCA
TATAGATATTGCATGTCAAAATTATTATAAATTTTAAATTTTAAATTATTTATTTATATAAAAAA
TTTAATTATTCAATTAAGTATTAATGTATAGAGTGTTTTAAATCGATAAGATACATATATGTATT
AGATTGGTTCAAAAATTTATATATATGATAAATATAATTATATCAATAAATTTAATACAGATAAA
GCTTTAAAATAAAATATTATTAGTTGTACCAAAAAAAGGTCTTTAGACTTGTACACACAAGAAGA
AT
Found at i:1697004 original size:2 final size:2
Alignment explanation
Indices: 1696999--1697031 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1696989 CACACATTTT
1696999 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1697032 GTACCATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1698617 original size:4 final size:4
Alignment explanation
Indices: 1698603--1698669 Score: 125
Period size: 4 Copynumber: 16.8 Consensus size: 4
1698593 AGAAAATTGA
*
1698603 TATG CATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1698651 TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TAT
1698670 AATATTTATT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 61 1.00
ACGTcount: A:0.25, C:0.01, G:0.24, T:0.49
Consensus pattern (4 bp):
TATG
Found at i:1705137 original size:23 final size:23
Alignment explanation
Indices: 1705110--1705161 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
1705100 CCAAACAATT
1705110 ATATGCAATATTCGCTTCAGGGA
1 ATATGCAATATTCGCTTCAGGGA
*
1705133 ATATGCCATATTCGCTTCAGGGA
1 ATATGCAATATTCGCTTCAGGGA
1705156 ATATGC
1 ATATGC
1705162 TAAAATCTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (23 bp):
ATATGCAATATTCGCTTCAGGGA
Found at i:1727470 original size:17 final size:17
Alignment explanation
Indices: 1727448--1727483 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1727438 TAAAAACACT
1727448 AAAAATGAAAATCCAAC
1 AAAAATGAAAATCCAAC
1727465 AAAAATGAAAATCCAAC
1 AAAAATGAAAATCCAAC
1727482 AA
1 AA
1727484 TTTGACTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.11
Consensus pattern (17 bp):
AAAAATGAAAATCCAAC
Found at i:1729980 original size:3 final size:3
Alignment explanation
Indices: 1729972--1729999 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1729962 TAGATTCATG
1729972 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1730000 TTTTCCACTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1732528 original size:19 final size:19
Alignment explanation
Indices: 1732482--1732529 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1732472 GTATATATTT
1732482 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
1732500 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
1732519 TAAATTTTATT
1 TAAATTTTATT
1732530 CATATTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 4 0.15
19 23 0.85
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:1732578 original size:42 final size:42
Alignment explanation
Indices: 1732532--1732621 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
1732522 ATTTTATTCA
* *
1732532 TATTTTATT-TTATCTTTTAGTAGTTTATTAGAATAAGGGAAT
1 TATTTT-TTCTTATCTTTTAGTAGTTGATTAGAATAAAGGAAT
* *
1732574 TATTTTTTCTTATGTTTTAGTAGTTGATTAGAATAAATGAAT
1 TATTTTTTCTTATCTTTTAGTAGTTGATTAGAATAAAGGAAT
1732616 TATTTT
1 TATTTT
1732622 CCCAATTTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 2 0.05
42 41 0.95
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.54
Consensus pattern (42 bp):
TATTTTTTCTTATCTTTTAGTAGTTGATTAGAATAAAGGAAT
Found at i:1737212 original size:19 final size:19
Alignment explanation
Indices: 1737166--1737213 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1737156 AGGGAGGGTT
1737166 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
1737184 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
1737203 TAAGTTTTATT
1 TAAATTTTATT
1737214 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:1741955 original size:9 final size:9
Alignment explanation
Indices: 1741941--1741977 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
1741931 TATAGTTTGA
1741941 TATTCGAAT
1 TATTCGAAT
1741950 TATTCGAAT
1 TATTCGAAT
*
1741959 TATTCGAGT
1 TATTCGAAT
1741968 TATTCGAAT
1 TATTCGAAT
1741977 T
1 T
1741978 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:1742048 original size:9 final size:9
Alignment explanation
Indices: 1742031--1742061 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1742021 TCGAGTTGAT
1742031 TCGAATAAC
1 TCGAATAAC
*
1742040 TCGATTAAC
1 TCGAATAAC
1742049 TCGAATAAC
1 TCGAATAAC
1742058 TCGA
1 TCGA
1742062 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:1742501 original size:29 final size:29
Alignment explanation
Indices: 1742452--1742508 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1742442 CAATGGTACC
* *
1742452 TTTGAACCAATAACTCAGATATCACTTGG
1 TTTGAACCAACAACTCAGATACCACTTGG
* *
1742481 TTTGAACCAACAGCTCGGATACCACTTG
1 TTTGAACCAACAACTCAGATACCACTTG
1742509 TCATGGGGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (29 bp):
TTTGAACCAACAACTCAGATACCACTTGG
Found at i:1748805 original size:48 final size:48
Alignment explanation
Indices: 1748712--1749208 Score: 338
Period size: 48 Copynumber: 10.4 Consensus size: 48
1748702 AATTGGAGCA
* * * **
1748712 CCAATAGGTGCACCACCCCCCAGTGCATCAGCTGCAGTACCAGGCACT-
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCA-TG
* * * **
1748760 CCAATAGGAGCACCAACTCCAAGTGCACCAGCTGCAACACAAGGCACA
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
** * ** * * * * * * **
1748808 CCGGTAGGAGCAGCACCTCCTGGGGAAGCAGTTGCAAAACAAGGCACA
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* * * ***
1748856 CCAATAGGAGCGCCATCT-CCAGGTGCAACAGCTGCAACATTGGGCATG
1 CCAATAGGAGCACCACCTCCCA-GTGCACCAGCTGCAACACCAGGCATG
* **
1748904 CCAATAGGAGCACCACCT-CCTG-GCACAGCAGCTGCAACACCAGGCACA
1 CCAATAGGAGCACCACCTCCCAGTGCAC--CAGCTGCAACACCAGGCATG
* ** *
1748952 CCAGTAGGAGCACCACCTCCC-GACACACCAACTGCAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCCAG-TGCACCAGCTGCAACACCAGGCATG
* ** **
1749000 GCAATAGGAGCACCACCTCCTGGCACACCAGCTGCAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* * * *** * * *
1749048 GCAATAGGCGCACCATCTCTTGGTACATCAGCTGGAACACCAGGCATG
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* * * * *
1749096 CCAATAGGAGCACCACCTCCCAGTACATCAGTTGCAACACCTGACATG
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* * * * * **
1749144 CCAATTGGAGCAACTCCTCCCAGTGCAGCAGCTGCAGCACCAGGCACA
1 CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
* *
1749192 CCTATAGAAGCACCACC
1 CCAATAGGAGCACCACC
1749209 ACCTGGCACT
Statistics
Matches: 354, Mismatches: 87, Indels: 16
0.77 0.19 0.04
Matches are distributed among these distances:
46 3 0.01
47 2 0.01
48 343 0.97
49 3 0.01
50 3 0.01
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.12
Consensus pattern (48 bp):
CCAATAGGAGCACCACCTCCCAGTGCACCAGCTGCAACACCAGGCATG
Found at i:1748921 original size:96 final size:96
Alignment explanation
Indices: 1748740--1749217 Score: 395
Period size: 96 Copynumber: 5.0 Consensus size: 96
1748730 CCCAGTGCAT
** * * * * *
1748740 CAGCTGCAGTACCAGGCACTCCAATAGGAGCACCAACTCCAAGTGCACCAGCTGCAACACAAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
** ** * *
1748805 ACACCGGTAGGAGCAGCACCTCCTGGGGA-AG
66 ATGCCAATAGGAGCACCACCTCCT-GGCACAG
* * * * * * ***
1748836 CAGTTGCAAAACAAGGCACACCAATAGGAGCGCCATCTCCAGGTGCAACAGCTGCAACATTGGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
1748901 ATGCCAATAGGAGCACCACCTCCTGGCACAG
66 ATGCCAATAGGAGCACCACCTCCTGGCACAG
* * * ** *
1748932 CAGCTGCAACACCAGGCACACCAGTAGGAGCACCACCTCCCGACACACCAACTGCAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
* *
1748997 ATGGCAATAGGAGCACCACCTCCTGGCACAC
66 ATGCCAATAGGAGCACCACCTCCTGGCACAG
*** * ** * *
1749028 CAGCTGCAACACCAGGCATGGCAATAGGCGCACCATCTCTTGGTACATCAGCTGGAACACCAGGC
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
** * *
1749093 ATGCCAATAGGAGCACCACCTCCCAGTACAT
66 ATGCCAATAGGAGCACCACCTCCTGGCACAG
* * * ** * * * * *
1749124 CAGTTGCAACACCTGACATGCCAATTGGAGCAAC-TCCTCCCA-GTGCAGCAGCTGCAGCACCAG
1 CAGCTGCAACACCAGGCACACCAATAGGAGCACCAT-CT-CCAGGTACACCAGCTGCAACACCAG
** * * *
1749187 GCACACCTATAGAAGCACCACCACCTGGCAC
64 GCATGCCAATAGGAGCACCACCTCCTGGCAC
1749218 TCAAGCTGAA
Statistics
Matches: 305, Mismatches: 74, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
95 4 0.01
96 300 0.98
97 1 0.00
ACGTcount: A:0.30, C:0.35, G:0.22, T:0.12
Consensus pattern (96 bp):
CAGCTGCAACACCAGGCACACCAATAGGAGCACCATCTCCAGGTACACCAGCTGCAACACCAGGC
ATGCCAATAGGAGCACCACCTCCTGGCACAG
Found at i:1749450 original size:48 final size:48
Alignment explanation
Indices: 1749373--1749527 Score: 157
Period size: 48 Copynumber: 3.2 Consensus size: 48
1749363 ATGACAACAA
* * *
1749373 GAGCACCAACTCCTGATGCACCAGATGCAACACCTGGCAAGCCAATAG
1 GAGCACCACCTCCTGATGCACCAGCTGCAACACCAGGCAAGCCAATAG
* * * * *
1749421 AAGCACCACCTCCTGGTGCACCAGCTGCAAGACCAGGTACGCCAATAG
1 GAGCACCACCTCCTGATGCACCAGCTGCAACACCAGGCAAGCCAATAG
** * * * * * * *
1749469 GTTCACCATCTCTTGCTGCGCCAGCTGCAACAACAGGCATGCCAGTAG
1 GAGCACCACCTCCTGATGCACCAGCTGCAACACCAGGCAAGCCAATAG
1749517 GAGCACCACCT
1 GAGCACCACCT
1749528 ACCAGTGCAC
Statistics
Matches: 84, Mismatches: 23, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
48 84 1.00
ACGTcount: A:0.28, C:0.35, G:0.22, T:0.15
Consensus pattern (48 bp):
GAGCACCACCTCCTGATGCACCAGCTGCAACACCAGGCAAGCCAATAG
Found at i:1749676 original size:33 final size:33
Alignment explanation
Indices: 1749607--1749677 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1749597 CAAGGCTCAC
* **
1749607 CAATAGGAGCACCAGCAGCAACACCAGGAATGT
1 CAATAGGAGCACCAGCAGCAACACCAAGAACAT
* * *
1749640 CAATTGGAGCACCAGCTGCAACACCAAGCACAT
1 CAATAGGAGCACCAGCAGCAACACCAAGAACAT
1749673 CAATA
1 CAATA
1749678 AGAACGCCAC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.30, G:0.20, T:0.11
Consensus pattern (33 bp):
CAATAGGAGCACCAGCAGCAACACCAAGAACAT
Found at i:1749725 original size:48 final size:48
Alignment explanation
Indices: 1749648--1749884 Score: 136
Period size: 48 Copynumber: 4.9 Consensus size: 48
1749638 GTCAATTGGA
* * *
1749648 GCACCAGCTGCAACACCAAGCACATCAATAAGAACGCCACCTCCTGGT
1 GCACCAGCCGCAACACCAAGCACACCAATAAGAACACCACCTCCTGGT
* * * * ***
1749696 GCACCGGCCGCAACACCAAGCACGCCAATAGGAGCACCACCTCCCAAT
1 GCACCAGCCGCAACACCAAGCACACCAATAAGAACACCACCTCCTGGT
* * * * ** *
1749744 GCACCAGCTGCAACA-CTAGGAAAGCCAATTGGAGCACCACCTCCTGGT
1 GCACCAGCCGCAACACCAAGCACA-CCAATAAGAACACCACCTCCTGGT
* * * * * * * * * *
1749792 GCACCTGCTGTAGCATCAGGGACACCAATAGGATCACCACCTCATGGT
1 GCACCAGCCGCAACACCAAGCACACCAATAAGAACACCACCTCCTGGT
* ** * * * *
1749840 GCACAAGATGCAACACCACA-CACATCTATAGGAGCACCACCTCCT
1 GCACCAGCCGCAACACCA-AGCACACCAATAAGAACACCACCTCCT
1749885 CTTGCACCCG
Statistics
Matches: 145, Mismatches: 41, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
47 4 0.03
48 136 0.94
49 5 0.03
ACGTcount: A:0.31, C:0.37, G:0.19, T:0.13
Consensus pattern (48 bp):
GCACCAGCCGCAACACCAAGCACACCAATAAGAACACCACCTCCTGGT
Found at i:1759045 original size:2 final size:2
Alignment explanation
Indices: 1759038--1759090 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1759028 AACATGATAC
1759038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1759080 AT AT AT AT AT A
1 AT AT AT AT AT A
1759091 CACATTTACC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1763586 original size:28 final size:28
Alignment explanation
Indices: 1763555--1763656 Score: 89
Period size: 28 Copynumber: 3.7 Consensus size: 28
1763545 AAGTCATTTT
* * * *
1763555 GCAGTTCGCCACTTCGTGGTGTCATCTC
1 GCAGTTCTCCACTTCGCGGAGACATCTC
* *
1763583 GCAGCTCTCCACTTCGCAGAGACATCTC
1 GCAGTTCTCCACTTCGCGGAGACATCTC
* * *
1763611 GTAGTTCTCCACTT-GTGGAGACAGCTC
1 GCAGTTCTCCACTTCGCGGAGACATCTC
* * *
1763638 GCACTTCACTACTTCGCGG
1 GCAGTTCTCCACTTCGCGG
1763657 TGTCAACTCG
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
27 20 0.35
28 37 0.65
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.27
Consensus pattern (28 bp):
GCAGTTCTCCACTTCGCGGAGACATCTC
Found at i:1763837 original size:5 final size:5
Alignment explanation
Indices: 1763827--1763876 Score: 100
Period size: 5 Copynumber: 10.0 Consensus size: 5
1763817 TTACTCATTT
1763827 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
1763877 CAATCAAGTT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 45 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:1766317 original size:72 final size:72
Alignment explanation
Indices: 1766227--1766447 Score: 408
Period size: 72 Copynumber: 3.1 Consensus size: 72
1766217 ACTTGATCAC
*
1766227 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCACG-AAGGTTCACAAGATCAAAAATGGAATAC
1 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCA-GTAAGGTTCACAAGATAAAAAATGGAATAC
1766291 GGTATGGG
65 GGTATGGG
1766299 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCAGTAAGGTTCACAAGATAAAAAATGGAATACG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCAGTAAGGTTCACAAGATAAAAAATGGAATACG
1766364 GTATGGG
66 GTATGGG
1766371 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCAGTAAGGTTCACAAGATAAAAAATGGAATACG
1 ACCACTCAAGTTGTTTGATGACAAATCAAGCTCAGTAAGGTTCACAAGATAAAAAATGGAATACG
*
1766436 GTATTGG
66 GTATGGG
1766443 ACCAC
1 ACCAC
1766448 CAATGTCATT
Statistics
Matches: 146, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
71 1 0.01
72 145 0.99
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.23
Consensus pattern (72 bp):
ACCACTCAAGTTGTTTGATGACAAATCAAGCTCAGTAAGGTTCACAAGATAAAAAATGGAATACG
GTATGGG
Found at i:1768677 original size:54 final size:54
Alignment explanation
Indices: 1768591--1768695 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
1768581 TCTCAGTTTA
* *
1768591 CAAATTAATAAAATCTCAATTATATCACATAAAAGTCTATCCCATTTTATACGG
1 CAAATTAATAAAATCTCAATTATACCACATAAAAGTCTATCCCACTTTATACGG
* * * *
1768645 CAAATTAATAAAATCTTAGTTGTACCATATAAAAGTCTATCCCACTTTATA
1 CAAATTAATAAAATCTCAATTATACCACATAAAAGTCTATCCCACTTTATA
1768696 TATGAATCCG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 45 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.34
Consensus pattern (54 bp):
CAAATTAATAAAATCTCAATTATACCACATAAAAGTCTATCCCACTTTATACGG
Found at i:1768922 original size:2 final size:2
Alignment explanation
Indices: 1768884--1768909 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1768874 ACCCAGTGAC
1768884 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1768910 TTTTGAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1780114 original size:21 final size:20
Alignment explanation
Indices: 1780083--1780124 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
1780073 ACTTTAGTTA
1780083 AAAATAATTTAT-CATATTTT
1 AAAATAATTTATACAT-TTTT
1780103 AAAATAATTTTATACATTTTT
1 AAAATAA-TTTATACATTTTT
1780124 A
1 A
1780125 TTTATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 10 0.50
22 3 0.15
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATAATTTATACATTTTT
Found at i:1780121 original size:20 final size:20
Alignment explanation
Indices: 1780083--1780122 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1780073 ACTTTAGTTA
*
1780083 AAAATAATTTATCATATTTT
1 AAAATAATTTATCACATTTT
1780103 AAAATAATTTTAT-ACATTTT
1 AAAATAA-TTTATCACATTTT
1780123 TATTTATTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATAATTTATCACATTTT
Found at i:1782971 original size:3 final size:3
Alignment explanation
Indices: 1782963--1783009 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
1782953 ATTTTATTGT
1782963 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1783010 TTGATTTCTC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1784292 original size:145 final size:145
Alignment explanation
Indices: 1784040--1784311 Score: 485
Period size: 145 Copynumber: 1.9 Consensus size: 145
1784030 TGTCAAAAAT
1784040 ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCACCGATC
1 ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCACCGATC
*
1784105 CTTTATTGAGGTGTGATCGGCTCACAAAAAAAAACAATTCTGGTCTACGAAATTTGAGAAAACAG
66 CTTTATTGAGGTGTGATCGGCCCACAAAAAAAAACAATTCTGGTCTACGAAATTTGAGAAAACAG
1784170 GAAGTTGTCGAAACC
131 GAAGTTGTCGAAACC
1784185 ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCA-CGATC
1 ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCACCGATC
* *
1784249 CTTTATTGAGGTGTGATCGGCCCACCTTAAAAAAAA-TATTCTGGTCTACGAAATTTGAGAAAA
66 CTTTATTGAGGTGTGATCGGCCCA-C-AAAAAAAAACAATTCTGGTCTACGAAATTTGAGAAAA
1784312 TGAGTTCGGG
Statistics
Matches: 122, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
144 28 0.23
145 86 0.70
146 8 0.07
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (145 bp):
ATTTTTTTGAAAACAAAAATAAGTTATCGACTTAAAAAAAACAAAAATTGGAGTCGCCACCGATC
CTTTATTGAGGTGTGATCGGCCCACAAAAAAAAACAATTCTGGTCTACGAAATTTGAGAAAACAG
GAAGTTGTCGAAACC
Found at i:1785154 original size:19 final size:18
Alignment explanation
Indices: 1785117--1785161 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1785107 ATAAAACATG
1785117 AAAATATAAATATTATAA
1 AAAATATAAATATTATAA
* *
1785135 AAAATATGAATGTATATAA
1 AAAATATAAATAT-TATAA
*
1785154 AATATATA
1 AAAATATA
1785162 TAAAAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.33
Consensus pattern (18 bp):
AAAATATAAATATTATAA
Found at i:1785193 original size:30 final size:30
Alignment explanation
Indices: 1785120--1785195 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 30
1785110 AAACATGAAA
*
1785120 ATAT-AAATAT-TATAAAAAATATGAATGT
1 ATATAAAATATATATAAAAAATATAAATGT
1785148 ATATAAAATATATATAAAAAATA-AAATGAT
1 ATATAAAATATATATAAAAAATATAAATG-T
*
1785178 ATGATAATAAAATATATA
1 AT-ATAA-AATATATATA
1785196 CGTACTACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 4 0.10
29 10 0.24
30 14 0.34
31 4 0.10
32 9 0.22
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (30 bp):
ATATAAAATATATATAAAAAATATAAATGT
Found at i:1785291 original size:14 final size:15
Alignment explanation
Indices: 1785274--1785307 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
1785264 ATTTACGTGC
1785274 AATAATAATTATA-T
1 AATAATAATTATACT
1785288 AATAATAATTATACT
1 AATAATAATTATACT
1785303 AATAA
1 AATAA
1785308 ACAATATAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATAATTATACT
Found at i:1786856 original size:106 final size:106
Alignment explanation
Indices: 1786686--1786883 Score: 290
Period size: 106 Copynumber: 1.9 Consensus size: 106
1786676 ATTTTCGGGA
* * * * **
1786686 ATTCGAGACTTCGTGCCCTAACTTACGGGGCATGTTTTTCTTCACAATTAACTTGAAATACGAAG
1 ATTCGAGACTTCGTACCCTAACTTACGAGACATGATTTTCTTCACAATTAACTCAAAATACGAAG
1786751 ACATTCTTCATAAAATTTGATTTAATTTCTTGTTTTTGGAG
66 ACATTCTTCATAAAATTTGATTTAATTTCTTGTTTTTGGAG
* *
1786792 ATTCGAGACATT-GTACCCTAACTTACGAGACATGATTTTCTTCCCTATTAACTCAAAATACGAA
1 ATTCGAGAC-TTCGTACCCTAACTTACGAGACATGATTTTCTTCACAATTAACTCAAAATACGAA
* *
1786856 GATATTTTTCATAAAATTTGATTTAATT
65 GACATTCTTCATAAAATTTGATTTAATT
1786884 AGCGATATTT
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
106 79 0.98
107 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (106 bp):
ATTCGAGACTTCGTACCCTAACTTACGAGACATGATTTTCTTCACAATTAACTCAAAATACGAAG
ACATTCTTCATAAAATTTGATTTAATTTCTTGTTTTTGGAG
Found at i:1790365 original size:21 final size:22
Alignment explanation
Indices: 1790343--1790382 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1790333 AATTTTATTA
1790343 AAATA-ATTTAT-CATATTTTT
1 AAATACATTTATGCATATTTTT
*
1790363 AAATACTTTTATGCATATTT
1 AAATACATTTATGCATATTT
1790383 ATTTATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 5 0.29
22 7 0.41
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.53
Consensus pattern (22 bp):
AAATACATTTATGCATATTTTT
Found at i:1795648 original size:72 final size:72
Alignment explanation
Indices: 1795529--1795669 Score: 176
Period size: 72 Copynumber: 2.0 Consensus size: 72
1795519 TTGATCACAC
* * ** * **
1795529 CACTCAAGTTGTTTGATGACAAATCAAGATAACTAATGTTCGTAAGATCAAAAAGGGAATCGGGT
1 CACTCAAGTTGTTTGAAGACAAATCAAGATAACTAAGGTTCACAAGATAAAAAAGGGAATAAGGT
1795594 ATTGGAT
66 ATTGGAT
* * *
1795601 CACTCAAGTTGTTTGAAGACAAGTCAAG-TAAAGTAAGGTTCACAAGATAAAAAATGGAATAAGG
1 CACTCAAGTTGTTTGAAGACAAATCAAGAT-AACTAAGGTTCACAAGATAAAAAAGGGAATAAGG
1795665 TATTG
65 TATTG
1795670 AACCACCGAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 1 0.02
72 57 0.98
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.26
Consensus pattern (72 bp):
CACTCAAGTTGTTTGAAGACAAATCAAGATAACTAAGGTTCACAAGATAAAAAAGGGAATAAGGT
ATTGGAT
Found at i:1801880 original size:44 final size:42
Alignment explanation
Indices: 1801808--1801905 Score: 108
Period size: 44 Copynumber: 2.3 Consensus size: 42
1801798 ATATAAGTTA
* ** *
1801808 TCGTGTAAGACCATGTATGGGACGTCGGCATC-AATTTGAGATT
1 TCGTGTAAGACCATATATGAAACATCGGCATCGAATTT--GATT
* *
1801851 TACGTGTAAGACCATATCTGAAACATCGGCATCGTATTTGATT
1 T-CGTGTAAGACCATATATGAAACATCGGCATCGAATTTGATT
1801894 TCGTGTAAGACC
1 TCGTGTAAGACC
1801906 CTATTTGGGA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
42 11 0.23
43 6 0.13
44 26 0.55
45 4 0.09
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (42 bp):
TCGTGTAAGACCATATATGAAACATCGGCATCGAATTTGATT
Found at i:1816289 original size:72 final size:72
Alignment explanation
Indices: 1816149--1816307 Score: 214
Period size: 72 Copynumber: 2.2 Consensus size: 72
1816139 ACTTGATCAC
* *
1816149 ACCACTCAAGTTATTTGATGACAAATCAAGATAACTAAGGTACACAAGATCAAAAATGAAATATG
1 ACCACTCAAGTTATTTGATGACAAATCAAGATAACTAAGGTACACAAGATCAAAAATGAAACACG
1816214 GTATTGG
66 GTATTGG
* * * *
1816221 ACCACTCAAGTTGTTTGATGACAAATCAAG-TGAAGTAAGGTTCACAAGATCAAAAATGGAACAC
1 ACCACTCAAGTTATTTGATGACAAATCAAGAT-AACTAAGGTACACAAGATCAAAAATGAAACAC
* *
1816285 GGTATCGA
65 GGTATTGG
1816293 ACCAC-CAATGTTATT
1 ACCACTCAA-GTTATT
1816308 ATAACTCAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
71 4 0.05
72 72 0.95
ACGTcount: A:0.42, C:0.16, G:0.18, T:0.25
Consensus pattern (72 bp):
ACCACTCAAGTTATTTGATGACAAATCAAGATAACTAAGGTACACAAGATCAAAAATGAAACACG
GTATTGG
Found at i:1818671 original size:28 final size:29
Alignment explanation
Indices: 1818631--1818685 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
1818621 ATAATTTTAA
1818631 AAAATAAAGATAAAAAATTC-TAAATTCT
1 AAAATAAAGATAAAAAATTCATAAATTCT
** *
1818659 AAAATAATTATAAAAAGTTCATAAATT
1 AAAATAAAGATAAAAAATTCATAAATT
1818686 TTCAAAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.60, C:0.05, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAATAAAGATAAAAAATTCATAAATTCT
Found at i:1818868 original size:43 final size:43
Alignment explanation
Indices: 1818807--1818893 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
1818797 CAAAAGATTG
1818807 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1818850 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1 AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
1818893 A
1 A
1818894 CTCAAAAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (43 bp):
AGGTTCAATTTAACTCCTATTAAAATGCCAAAAGATAAATTTA
Found at i:1826193 original size:42 final size:42
Alignment explanation
Indices: 1826129--1826223 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
1826119 TAGTTGGATT
* * *
1826129 TTAATCATGGATTATGAGTGTTAAATAAAATTTGATGGTATC
1 TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATC
*
1826171 TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATT
1 TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATC
*
1826213 TTAATAATGAA
1 TTAATCATGAA
1826224 AATACTGATT
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (42 bp):
TTAATCATGAATTATGAATGTTAAATAAAAGTTGATGGTATC
Found at i:1830048 original size:21 final size:21
Alignment explanation
Indices: 1830024--1830076 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
1830014 CATTGTTTCT
**
1830024 AATCTCACCGCTACAGTGTCC
1 AATCTCACCGCTACAGTAACC
*
1830045 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
1830066 AATCTCACCGC
1 AATCTCACCGC
1830077 CACCGCTGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.38, G:0.11, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:1831862 original size:12 final size:12
Alignment explanation
Indices: 1831847--1831872 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1831837 TTTTGTTTCG
1831847 TTTTTTATTTAT
1 TTTTTTATTTAT
1831859 TTTTTTATTTAT
1 TTTTTTATTTAT
1831871 TT
1 TT
1831873 CGAAATACAA
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTATTTAT
Found at i:1832687 original size:22 final size:23
Alignment explanation
Indices: 1832604--1832687 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 23
1832594 TAATTGCTCT
* *
1832604 TATATATATGTATATTTTTTGTA
1 TATATATATATATACTTTTTGTA
* *
1832627 TATATATACATATA-TTTTTTTA
1 TATATATATATATACTTTTTGTA
* *
1832649 TATACTTACATACATACTTTTTGTA
1 TATA--TATATATATACTTTTTGTA
*
1832674 -ATATATATGTATAC
1 TATATATATATATAC
1832688 ATATACACTT
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
22 19 0.40
23 12 0.25
24 10 0.21
25 7 0.15
ACGTcount: A:0.35, C:0.07, G:0.05, T:0.54
Consensus pattern (23 bp):
TATATATATATATACTTTTTGTA
Found at i:1834672 original size:25 final size:25
Alignment explanation
Indices: 1834605--1834672 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 25
1834595 TAGGACATGA
* *
1834605 TATGATAT-AATAAGATATGCTATGC
1 TATGAT-TCAATATGATATGATATGC
* * *
1834630 TATGATTGAATGTAATATGATATGC
1 TATGATTCAATATGATATGATATGC
*
1834655 TATGATTCAGTATGATAT
1 TATGATTCAATATGATAT
1834673 TGTACGTTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
24 1 0.03
25 33 0.97
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.40
Consensus pattern (25 bp):
TATGATTCAATATGATATGATATGC
Found at i:1838377 original size:72 final size:71
Alignment explanation
Indices: 1838244--1838380 Score: 170
Period size: 72 Copynumber: 1.9 Consensus size: 71
1838234 AAAGTGAACA
* * *
1838244 AAGGTTCACAAGATCAAAAATGGAACCTGGTATTGGACCACTCAAGTTGTTTGATGACAAATCAA
1 AAGGTTCAAAAGATCAAAAATGGAACCTGGTATTGGACCACTCAAGTTATTTAAT-ACAAATCAA
1838309 GCCTAGT
65 GCCTAGT
* **
1838316 AAGGTTCAAAAGATTAAAAATGGAATTTGGTATTGGACCAC-CAATGTTATTATAACT-CAAATC
1 AAGGTTCAAAAGATCAAAAATGGAACCTGGTATTGGACCACTCAA-GTTATT-TAA-TACAAATC
1838379 AA
63 AA
1838381 CCTCTTGGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
71 3 0.05
72 50 0.89
73 2 0.04
74 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.27
Consensus pattern (71 bp):
AAGGTTCAAAAGATCAAAAATGGAACCTGGTATTGGACCACTCAAGTTATTTAATACAAATCAAG
CCTAGT
Found at i:1849223 original size:39 final size:39
Alignment explanation
Indices: 1849174--1849253 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
1849164 AGCACCGGCA
* *
1849174 GTCATTGAATTTATACCAAAGGCCTATCCATCATAACAT
1 GTCATAGAATTTATACCAAAGGCCCATCCATCATAACAT
* *
1849213 GTCATAGAATTTATACCATAGGCCCATGCATCATAACAT
1 GTCATAGAATTTATACCAAAGGCCCATCCATCATAACAT
1849252 GT
1 GT
1849254 TTGCATTTAG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (39 bp):
GTCATAGAATTTATACCAAAGGCCCATCCATCATAACAT
Found at i:1853289 original size:54 final size:54
Alignment explanation
Indices: 1853207--1853314 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
1853197 AAAACAACAA
1853207 ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
1 ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
1853261 ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
1 ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
1853315 TTACAGTCTG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (54 bp):
ATAAAGCCTATTCAAGCACCCAACTAAGATACTCAGCAGTGGAAATGTGCTAAG
Found at i:1855838 original size:14 final size:14
Alignment explanation
Indices: 1855800--1855838 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1855790 AAGGTTCGAG
* *
1855800 GTTTATGATTCGAA
1 GTTTAGGATTTGAA
*
1855814 GTTTAGGATTTGAT
1 GTTTAGGATTTGAA
1855828 GTTTAGGATTT
1 GTTTAGGATTT
1855839 AAGGTTCATG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.26, T:0.49
Consensus pattern (14 bp):
GTTTAGGATTTGAA
Found at i:1855851 original size:14 final size:14
Alignment explanation
Indices: 1855834--1855878 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
1855824 TGATGTTTAG
*
1855834 GATTTAAGGTTCAT
1 GATTTAAGGTTCAA
*
1855848 GATTTGA-GTTCAA
1 GATTTAAGGTTCAA
*
1855861 GATTTAAGGTTCGA
1 GATTTAAGGTTCAA
1855875 GATT
1 GATT
1855879 CAAGATTTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (14 bp):
GATTTAAGGTTCAA
Found at i:1855878 original size:27 final size:28
Alignment explanation
Indices: 1855820--1855872 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1855810 CGAAGTTTAG
* *
1855820 GATTTGATGTTTAGGATTTAAGGTTCAT
1 GATTTGATGTTCAAGATTTAAGGTTCAT
1855848 GATTTGA-GTTCAAGATTTAAGGTTC
1 GATTTGATGTTCAAGATTTAAGGTTC
1855873 GAGATTCAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.26, C:0.06, G:0.25, T:0.43
Consensus pattern (28 bp):
GATTTGATGTTCAAGATTTAAGGTTCAT
Found at i:1856514 original size:2 final size:2
Alignment explanation
Indices: 1856507--1856535 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1856497 ATAACATAGA
1856507 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1856536 AATTGTCCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1878590 original size:13 final size:13
Alignment explanation
Indices: 1878572--1878599 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1878562 AGAGAGAGAA
1878572 GAGGAGGGGAGGG
1 GAGGAGGGGAGGG
1878585 GAGGAGGGGAGGG
1 GAGGAGGGGAGGG
1878598 GA
1 GA
1878600 AGGGAAGGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (13 bp):
GAGGAGGGGAGGG
Found at i:1884165 original size:16 final size:18
Alignment explanation
Indices: 1884131--1884165 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1884121 TGTATCCATT
1884131 TATTTTCCTATATATGTA
1 TATTTTCCTATATATGTA
1884149 TATTTT-CTATA-ATGTA
1 TATTTTCCTATATATGTA
1884165 T
1 T
1884166 TATTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 5 0.29
18 6 0.35
ACGTcount: A:0.29, C:0.09, G:0.06, T:0.57
Consensus pattern (18 bp):
TATTTTCCTATATATGTA
Found at i:1884169 original size:17 final size:19
Alignment explanation
Indices: 1884130--1884169 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
1884120 ATGTATCCAT
1884130 TTATTTTCCTATATATGTA
1 TTATTTTCCTATATATGTA
1884149 -TATTTT-CTATA-ATGTA
1 TTATTTTCCTATATATGTA
1884165 TTATT
1 TTATT
1884170 ATTATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 9 0.45
18 6 0.30
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (19 bp):
TTATTTTCCTATATATGTA
Found at i:1886493 original size:39 final size:39
Alignment explanation
Indices: 1886439--1886513 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
1886429 ATTATTGCTT
* * *
1886439 CCACGTCAGCAATCGCGCTTACGTGGACGCGATTTGTTG
1 CCACGTAAGCAATCGCGCTGACATGGACGCGATTTGTTG
*
1886478 CCACGTAAGTAATCGCGCTGACATGGACGCGATTTG
1 CCACGTAAGCAATCGCGCTGACATGGACGCGATTTG
1886514 CTGACACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.21, C:0.27, G:0.28, T:0.24
Consensus pattern (39 bp):
CCACGTAAGCAATCGCGCTGACATGGACGCGATTTGTTG
Found at i:1891677 original size:36 final size:37
Alignment explanation
Indices: 1891611--1891690 Score: 94
Period size: 36 Copynumber: 2.2 Consensus size: 37
1891601 TCTCCACCTT
*
1891611 CCCCT-CCCACAACCCAATCCTCCGCCCCTTCACCC-G
1 CCCCTCCCCACAACCCAATCCCCCGCCCCTTC-CCCTG
** *
1891647 -CCCTCCCCACAACCCCTTCCCCCGCTCCTTCCCCTG
1 CCCCTCCCCACAACCCAATCCCCCGCCCCTTCCCCTG
1891683 CCCCTCCC
1 CCCCTCCC
1891691 AAAACACCCG
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
35 7 0.19
36 23 0.62
37 7 0.19
ACGTcount: A:0.11, C:0.68, G:0.05, T:0.16
Consensus pattern (37 bp):
CCCCTCCCCACAACCCAATCCCCCGCCCCTTCCCCTG
Found at i:1894159 original size:24 final size:22
Alignment explanation
Indices: 1894132--1894177 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
1894122 ATCAAATACA
*
1894132 CTAAAAATATTGAAAGAAATGTTT
1 CTAAAAACATT-AAA-AAATGTTT
*
1894156 CTAAATACATTAAAAAATGTTT
1 CTAAAAACATTAAAAAATGTTT
1894178 AATACTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.40
23 3 0.15
24 9 0.45
ACGTcount: A:0.50, C:0.07, G:0.09, T:0.35
Consensus pattern (22 bp):
CTAAAAACATTAAAAAATGTTT
Found at i:1895562 original size:36 final size:36
Alignment explanation
Indices: 1895515--1895587 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
1895505 ATACTCCCTT
*
1895515 CCTAGCATTGATACCAATATTTACACAGTCACACAG
1 CCTAGCATTGATACCAATATTTACACAATCACACAG
* *
1895551 CCTAGCATTGATACCAATGTTTACATAATCACACAG
1 CCTAGCATTGATACCAATATTTACACAATCACACAG
1895587 C
1 C
1895588 TTGGCGGCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.36, C:0.27, G:0.11, T:0.26
Consensus pattern (36 bp):
CCTAGCATTGATACCAATATTTACACAATCACACAG
Found at i:1897360 original size:3 final size:3
Alignment explanation
Indices: 1897352--1897379 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1897342 AGTAAAATCT
1897352 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1897380 AAGATTAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1898512 original size:9 final size:9
Alignment explanation
Indices: 1898471--1898519 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
1898461 AAATTAATCA
1898471 AATTAA-CG
1 AATTAACCG
*
1898479 TAATTACCCG
1 -AATTAACCG
*
1898489 AATTACCCG
1 AATTAACCG
1898498 AATTAACCG
1 AATTAACCG
*
1898507 AATTAATCG
1 AATTAACCG
1898516 AATT
1 AATT
1898520 GAATCACTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
9 34 0.94
10 2 0.06
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:1898570 original size:6 final size:6
Alignment explanation
Indices: 1898559--1898587 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1898549 ACTTTTAGAC
1898559 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1898588 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:1898611 original size:20 final size:20
Alignment explanation
Indices: 1898543--1898600 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
1898533 ATTAAATTAT
* *
1898543 TTTTAGACTTTTAGACTTTAG
1 TTTTAGAATTTTAG-TTTTAG
1898564 TTTTAG--TTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
1898582 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
1898601 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 10 0.30
21 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:1898668 original size:18 final size:18
Alignment explanation
Indices: 1898628--1898671 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
1898618 AATTTTTATG
*
1898628 ATTGGGTTGAGTTTGATA
1 ATTGGGTTGAGGTTGATA
1898646 ATTGGGTTG-GGTTGAATA
1 ATTGGGTTGAGGTTG-ATA
*
1898664 CTTGGGTT
1 ATTGGGTT
1898672 TGGATTGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.18, C:0.02, G:0.36, T:0.43
Consensus pattern (18 bp):
ATTGGGTTGAGGTTGATA
Found at i:1906824 original size:19 final size:21
Alignment explanation
Indices: 1906800--1906848 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
1906790 AAAAAACTAC
*
1906800 AAATTATAAG-ATT-TTTTTG
1 AAATTATAAGAATTAATTTTG
*
1906819 AAATTACAAGAATTAATTTTG
1 AAATTATAAGAATTAATTTTG
*
1906840 AAATCATAA
1 AAATTATAA
1906849 TTTGTGAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 9 0.38
20 3 0.12
21 12 0.50
ACGTcount: A:0.47, C:0.04, G:0.08, T:0.41
Consensus pattern (21 bp):
AAATTATAAGAATTAATTTTG
Found at i:1920742 original size:10 final size:11
Alignment explanation
Indices: 1920717--1920745 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1920707 TTAAAAATAA
1920717 AAAAATATTTT
1 AAAAATATTTT
1920728 AAAAATATTTT
1 AAAAATATTTT
1920739 AAAAATA
1 AAAAATA
1920746 AAAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1938635 original size:16 final size:15
Alignment explanation
Indices: 1938609--1938640 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
1938599 CGTGCGTTTA
1938609 CTGAAAAGAACAATG
1 CTGAAAAGAACAATG
1938624 CTGAAGAAGAACAATG
1 CTGAA-AAGAACAATG
1938640 C
1 C
1938641 AATGAAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.16, G:0.22, T:0.12
Consensus pattern (15 bp):
CTGAAAAGAACAATG
Found at i:1942007 original size:11 final size:11
Alignment explanation
Indices: 1941991--1942019 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1941981 AAAAAACTTG
1941991 TATATAAATTT
1 TATATAAATTT
1942002 TATATAAATTT
1 TATATAAATTT
1942013 TAT-TAAA
1 TATATAAA
1942020 CATGTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATAAATTT
Found at i:1953971 original size:122 final size:123
Alignment explanation
Indices: 1953753--1953996 Score: 463
Period size: 122 Copynumber: 2.0 Consensus size: 123
1953743 GGCAAACTTG
1953753 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAAGGGCAAAACTAAAATACTGAA
1 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAAGGGCAAAACTAAAATACTGAA
1953818 AAGATAGTGCTAACGACAAGCCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGC
66 AAGATAGTGCTAACGACAAGCCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGC
*
1953876 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAA-GGCAAAAGTAAAATACTGAA
1 AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAAGGGCAAAACTAAAATACTGAA
*
1953940 AAGATAGTGCTAACGACAAGTCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTG
66 AAGATAGTGCTAACGACAAGCCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTG
1953997 ATGTGGTTAA
Statistics
Matches: 119, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
122 75 0.63
123 44 0.37
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.23
Consensus pattern (123 bp):
AAGAAGCTTGTACTCAAGGCTATACTAATGGTTTGAAGGGGTAAGGGCAAAACTAAAATACTGAA
AAGATAGTGCTAACGACAAGCCTAAGTGCTTTAAAGTTGCATTGGAACCAAAAGGTGC
Found at i:1961573 original size:9 final size:9
Alignment explanation
Indices: 1961561--1961590 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1961551 CTGTGTTGTT
1961561 ATTCGGTTA
1 ATTCGGTTA
*
1961570 ATTCGGGTA
1 ATTCGGTTA
1961579 ATTCGGTTA
1 ATTCGGTTA
1961588 ATT
1 ATT
1961591 TTTTACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (9 bp):
ATTCGGTTA
Found at i:1964480 original size:9 final size:9
Alignment explanation
Indices: 1964462--1964507 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
1964452 TTGGGTAATT
1964462 TTCGGGTAA
1 TTCGGGTAA
*
1964471 TTCGGTTAA
1 TTCGGGTAA
*
1964480 TTCGGTTAA
1 TTCGGGTAA
1964489 -TCGGGTAA
1 TTCGGGTAA
1964497 TTCGGGTAA
1 TTCGGGTAA
1964506 TT
1 TT
1964508 TTTAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
8 7 0.21
9 27 0.79
ACGTcount: A:0.22, C:0.11, G:0.28, T:0.39
Consensus pattern (9 bp):
TTCGGGTAA
Found at i:1964497 original size:17 final size:17
Alignment explanation
Indices: 1964462--1964506 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1964452 TTGGGTAATT
*
1964462 TTCGGGTAATTCGGTTAA
1 TTCGGGTAA-TCGGGTAA
*
1964480 TTCGGTTAATCGGGTAA
1 TTCGGGTAATCGGGTAA
1964497 TTCGGGTAAT
1 TTCGGGTAAT
1964507 TTTTAACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.22, C:0.11, G:0.29, T:0.38
Consensus pattern (17 bp):
TTCGGGTAATCGGGTAA
Found at i:1967649 original size:157 final size:158
Alignment explanation
Indices: 1967445--1967764 Score: 579
Period size: 157 Copynumber: 2.0 Consensus size: 158
1967435 GCAATCACTA
* * * *
1967445 TAAGGATCTTATCACAAAGGGATCAATTAAACACAAATCATACCGAGCTAAGGAAAAATTTGCAA
1 TAAGAATCTTATCACAAAGAGATCAACTAAACACAAATCAAACCGAGCTAAGGAAAAATTTGCAA
1967510 TAGGTAGATTAAAAAGAAAAAACATAAGACTCAAGTACCGAAAGTACCTAAAATTACTCAAGTAA
66 TAGGTAGATTAAAAAGAAAAAACATAAGACTCAAGTACCGAAAGTACCTAAAATTACTCAAGTAA
1967575 CAAGTTTACCAA-CCTAGTTACATACCG
131 CAAGTTTACCAACCCTAGTTACATACCG
*
1967602 TAAGAATCTTATCACAAAGAGATCAACTAAACACAAATCAAACCGAGCTAAGGGAAAATTTGCAA
1 TAAGAATCTTATCACAAAGAGATCAACTAAACACAAATCAAACCGAGCTAAGGAAAAATTTGCAA
*
1967667 TAGGTAGATTAAAAAGAAAAAACATAAGACTCGAGTACCGAAAGTACCTAAAATTACTCAAGTAA
66 TAGGTAGATTAAAAAGAAAAAACATAAGACTCAAGTACCGAAAGTACCTAAAATTACTCAAGTAA
1967732 CAAGTTTACCAACCCTAGTTACATACCG
131 CAAGTTTACCAACCCTAGTTACATACCG
1967760 TAAGA
1 TAAGA
1967765 CTCAACATAC
Statistics
Matches: 156, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
157 136 0.87
158 20 0.13
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (158 bp):
TAAGAATCTTATCACAAAGAGATCAACTAAACACAAATCAAACCGAGCTAAGGAAAAATTTGCAA
TAGGTAGATTAAAAAGAAAAAACATAAGACTCAAGTACCGAAAGTACCTAAAATTACTCAAGTAA
CAAGTTTACCAACCCTAGTTACATACCG
Found at i:1969401 original size:32 final size:32
Alignment explanation
Indices: 1969360--1969422 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
1969350 TAATAAGGTA
1969360 AGATTTCTATCCTTAATTATAGGGATTCCAAT
1 AGATTTCTATCCTTAATTATAGGGATTCCAAT
1969392 AGATTTCTATCCTTAATTATAGGGATTCCAA
1 AGATTTCTATCCTTAATTATAGGGATTCCAA
1969423 CACTCCCCCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.40
Consensus pattern (32 bp):
AGATTTCTATCCTTAATTATAGGGATTCCAAT
Found at i:1976998 original size:2 final size:2
Alignment explanation
Indices: 1976993--1977031 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1976983 TTTTTCTTTT
1976993 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1977032 TGATTGAAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1977236 original size:60 final size:60
Alignment explanation
Indices: 1977172--1977312 Score: 210
Period size: 60 Copynumber: 2.4 Consensus size: 60
1977162 GTTATCTAAT
* * * * *
1977172 TATGAAAAGTTACAAAATGGTCACTCAACTATTAGTACATTTCTTTTTTGGTCACCCAAA
1 TATGAAAAGTTACAAAATGGTCACCCAACTATCAGTAAATTTCCTTTTTGATCACCCAAA
* *
1977232 TATGAAAAGTTACAAAATGGTCACCCAACTATCAGTAAATTTCCTTTTTGATCATCTAAA
1 TATGAAAAGTTACAAAATGGTCACCCAACTATCAGTAAATTTCCTTTTTGATCACCCAAA
*
1977292 TATGAAAAGTTACAATATGGT
1 TATGAAAAGTTACAAAATGGT
1977313 TACCTAGCTA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (60 bp):
TATGAAAAGTTACAAAATGGTCACCCAACTATCAGTAAATTTCCTTTTTGATCACCCAAA
Found at i:1979879 original size:33 final size:36
Alignment explanation
Indices: 1979842--1979915 Score: 84
Period size: 35 Copynumber: 2.2 Consensus size: 36
1979832 TAAAAAATAA
*
1979842 TATTTTAA-AATTTAATATCT-C-AATAATATTTTT
1 TATTTTAAGAATTTAATATCTCCAAAAAATATTTTT
* * *
1979875 TA-TTTAAGTATTTATTTTCTCCAAAAAATATTTTT
1 TATTTTAAGAATTTAATATCTCCAAAAAATATTTTT
1979910 TATTTT
1 TATTTT
1979916 TAATTAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
32 5 0.15
33 11 0.33
34 1 0.03
35 13 0.39
36 3 0.09
ACGTcount: A:0.35, C:0.07, G:0.01, T:0.57
Consensus pattern (36 bp):
TATTTTAAGAATTTAATATCTCCAAAAAATATTTTT
Found at i:1985588 original size:10 final size:10
Alignment explanation
Indices: 1985573--1985601 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
1985563 ATTTTGTTAC
1985573 AAGTTAAAAA
1 AAGTTAAAAA
1985583 AAGTTAAAAA
1 AAGTTAAAAA
1985593 AAGTTAAAA
1 AAGTTAAAA
1985602 GACTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (10 bp):
AAGTTAAAAA
Found at i:2004299 original size:58 final size:60
Alignment explanation
Indices: 2004189--2004309 Score: 165
Period size: 58 Copynumber: 2.0 Consensus size: 60
2004179 TACAAAACCA
2004189 ATTCAATCAATAAATTCCGAAAAAAAAACATAATCAAACAAGAACACCTATATTACTC-G
1 ATTCAATCAATAAATTCCGAAAAAAAAACATAATCAAACAAGAACACCTATATTACTCTG
* * * * ** *
2004248 ATTCAATTAATAAATTTCG-AAGAAAAACATGATCAAACAAGAGTACTTATATTACTCTG
1 ATTCAATCAATAAATTCCGAAAAAAAAACATAATCAAACAAGAACACCTATATTACTCTG
2004307 ATT
1 ATT
2004310 TGGGTGTGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 33 0.61
59 21 0.39
ACGTcount: A:0.49, C:0.17, G:0.07, T:0.27
Consensus pattern (60 bp):
ATTCAATCAATAAATTCCGAAAAAAAAACATAATCAAACAAGAACACCTATATTACTCTG
Found at i:2009240 original size:31 final size:32
Alignment explanation
Indices: 2009205--2009264 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2009195 TTTTAGCTAA
*
2009205 ATTTGA-CACTCAA-CTTTTTAAAAAGAGTCGG
1 ATTTGACCA-TCAACCTTTTGAAAAAGAGTCGG
2009236 ATTTGACCATCAACCTTTTGAAAAAGAGT
1 ATTTGACCATCAACCTTTTGAAAAAGAGT
2009265 TGAAATGATG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 10 0.38
32 16 0.62
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (32 bp):
ATTTGACCATCAACCTTTTGAAAAAGAGTCGG
Found at i:2011606 original size:19 final size:18
Alignment explanation
Indices: 2011551--2011606 Score: 51
Period size: 19 Copynumber: 3.0 Consensus size: 18
2011541 AACTTGTCTA
*
2011551 AAAAAAATTGTAATTTTTT
1 AAAATAATT-TAATTTTTT
*
2011570 AAATTAATTT-ATATTTTT
1 AAAATAATTTAAT-TTTTT
*
2011588 AAAATATTTTTAATTTTTT
1 AAAATA-ATTTAATTTTTT
2011607 TAGTTTATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 2 0.07
18 11 0.37
19 15 0.50
20 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
AAAATAATTTAATTTTTT
Found at i:2016053 original size:3 final size:3
Alignment explanation
Indices: 2016045--2016080 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
2016035 TTAGACTTCT
2016045 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2016081 GAGCAATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2024317 original size:72 final size:73
Alignment explanation
Indices: 2024229--2024373 Score: 247
Period size: 72 Copynumber: 2.0 Consensus size: 73
2024219 AAAGAAAATA
2024229 ACTCTTAAATTTTATCAAACAGTCCATGCCATAAGTACACAAGTACTT-AGACTTCAGAGTTCGA
1 ACTCTTAAATTTTATCAAACAGTCCATGCCATAAGTACACAAGTACTTAAGACTTCAGAGTTCGA
2024293 TTCACGTG
66 TTCACGTG
* * * *
2024301 ACTCTTAAATTTTATCAAACTGTCCGTGCCATAAGTACACAAGTACTTAAGACTTTAGAGTTTGA
1 ACTCTTAAATTTTATCAAACAGTCCATGCCATAAGTACACAAGTACTTAAGACTTCAGAGTTCGA
2024366 TTCACGTG
66 TTCACGTG
2024374 CTTCAAGTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
72 46 0.68
73 22 0.32
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.32
Consensus pattern (73 bp):
ACTCTTAAATTTTATCAAACAGTCCATGCCATAAGTACACAAGTACTTAAGACTTCAGAGTTCGA
TTCACGTG
Found at i:2032870 original size:12 final size:11
Alignment explanation
Indices: 2032833--2032885 Score: 61
Period size: 11 Copynumber: 4.6 Consensus size: 11
2032823 TAAACACCAA
2032833 AAAAATATTTT
1 AAAAATATTTT
***
2032844 AAAAATAAAAAT
1 AAAAAT-ATTTT
2032856 AAAAAGTATTTT
1 AAAAA-TATTTT
2032868 AAAAATATTTT
1 AAAAATATTTT
2032879 AAAAATA
1 AAAAATA
2032886 AAAATAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
11 19 0.56
12 14 0.41
13 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:2034568 original size:18 final size:18
Alignment explanation
Indices: 2034545--2034581 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2034535 AAACTACGTT
*
2034545 AAAAAAATGAAAAAAAGA
1 AAAAAAATCAAAAAAAGA
*
2034563 AAAAAAATCAAAGAAAGA
1 AAAAAAATCAAAAAAAGA
2034581 A
1 A
2034582 GCAGAAGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.81, C:0.03, G:0.11, T:0.05
Consensus pattern (18 bp):
AAAAAAATCAAAAAAAGA
Found at i:2043697 original size:28 final size:28
Alignment explanation
Indices: 2043666--2043736 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
2043656 ATATTGATTT
* * *
2043666 TTAAATCTATTAAATCAAATTAGTTCGA
1 TTAAATCTATTAAATCAAAGTAATTAGA
* *
2043694 TTAAATTTATTAAATCAAAGTAATTATA
1 TTAAATCTATTAAATCAAAGTAATTAGA
*
2043722 TTAAATCTATAAAAT
1 TTAAATCTATTAAAT
2043737 AGGTTTAAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (28 bp):
TTAAATCTATTAAATCAAAGTAATTAGA
Found at i:2048233 original size:30 final size:31
Alignment explanation
Indices: 2048197--2048254 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
2048187 TAGCAAATTT
*
2048197 AACAATAA-AACAAGAATGATA-CAATATCGA
1 AACAATAACAACAA-AATAATAGCAATATCGA
2048227 AACAATAACAACAAAATAATAGCAATAT
1 AACAATAACAACAAAATAATAGCAATAT
2048255 AATAGCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (31 bp):
AACAATAACAACAAAATAATAGCAATATCGA
Found at i:2051478 original size:3 final size:3
Alignment explanation
Indices: 2051470--2051523 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
2051460 GTAGTTTACC
2051470 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2051518 ATA ATA
1 ATA ATA
2051524 CCTGAGGTGG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2052475 original size:19 final size:19
Alignment explanation
Indices: 2052428--2052479 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
2052418 AAAATGATAA
2052428 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAAT-GTTTC
**
2052448 AATTGAGTTAAACAT-TTTC
1 AATCAAGTTAAA-ATGTTTC
2052467 AATCAAGTTAAAA
1 AATCAAGTTAAAA
2052480 CTAAATTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.52
20 10 0.37
21 2 0.07
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.35
Consensus pattern (19 bp):
AATCAAGTTAAAATGTTTC
Found at i:2053988 original size:30 final size:28
Alignment explanation
Indices: 2053940--2054006 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 28
2053930 TTTGGTTAAA
*
2053940 TCTATTTTATATCAAATTACTATTTTATAT
1 TCTATTTTATATCAAATTAAT-TTTTAT-T
*
2053970 TCTATTTTACTTTC-AATTAATTTTTATT
1 TCTATTTTA-TATCAAATTAATTTTTATT
2053998 TACTATTTT
1 T-CTATTTT
2054007 CTCATCAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 2 0.06
29 13 0.39
30 15 0.45
31 3 0.09
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.61
Consensus pattern (28 bp):
TCTATTTTATATCAAATTAATTTTTATT
Found at i:2056924 original size:18 final size:19
Alignment explanation
Indices: 2056901--2056941 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2056891 GTTTATGTGC
* *
2056901 TATAAATTATATAATAT-A
1 TATAAATAACATAATATGA
2056919 TATAAATAACATAATATGA
1 TATAAATAACATAATATGA
2056938 TATA
1 TATA
2056942 TTAAAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TATAAATAACATAATATGA
Found at i:2056935 original size:23 final size:21
Alignment explanation
Indices: 2056909--2056953 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
2056899 GCTATAAATT
2056909 ATATAATATATATAAATAACATA
1 ATATAATATAT-TAAA-AACATA
*
2056932 ATATGATATATTAAAAACATA
1 ATATAATATATTAAAAACATA
2056953 A
1 A
2056954 AAAATGAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.33
22 4 0.19
23 10 0.48
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATAATATATTAAAAACATA
Found at i:2061469 original size:9 final size:9
Alignment explanation
Indices: 2061455--2061482 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2061445 TGAGTTTTCG
2061455 AATTCGAAT
1 AATTCGAAT
2061464 AATTCGAAT
1 AATTCGAAT
2061473 AATTCGAAT
1 AATTCGAAT
2061482 A
1 A
2061483 TCAAACTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Done.