Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 4 of 145
Found at i:1476432 original size:13 final size:13
Alignment explanation
Indices: 1476414--1476438 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1476404 TAATTTATGT
1476414 GTGTGAAAATTTC
1 GTGTGAAAATTTC
1476427 GTGTGAAAATTT
1 GTGTGAAAATTT
1476439 TATCGTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:1478369 original size:103 final size:103
Alignment explanation
Indices: 1478190--1478448 Score: 509
Period size: 103 Copynumber: 2.5 Consensus size: 103
1478180 CTAGCAGGCT
1478190 AAATGATTATGGGATATATATAATGGATAATTACATGAGCATTTGTCTATATGAATATGTTAAAT
1 AAATGATTATGGGATATATATAATGGATAATTACATGAGCATTTGTCTATATGAATATGTTAAAT
1478255 TAAGTGATTATATGCATTTGATATATATATATATATAA
66 TAAGTGATTATATGCATTTGATATATATATATATATAA
1478293 AAATGATTATGGGATATATATAATGGATAATTACATGAGCATTTGTCTATATGAATATGTTAAAT
1 AAATGATTATGGGATATATATAATGGATAATTACATGAGCATTTGTCTATATGAATATGTTAAAT
*
1478358 TAAGTGATTATATGCATTTGATATATATATATATATAT
66 TAAGTGATTATATGCATTTGATATATATATATATATAA
1478396 AAATGATTATGGGATATATATAATGGATAATTACATGAGCATTTGTCTATATG
1 AAATGATTATGGGATATATATAATGGATAATTACATGAGCATTTGTCTATATG
1478449 TATTTGATGA
Statistics
Matches: 155, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
103 155 1.00
ACGTcount: A:0.40, C:0.04, G:0.15, T:0.41
Consensus pattern (103 bp):
AAATGATTATGGGATATATATAATGGATAATTACATGAGCATTTGTCTATATGAATATGTTAAAT
TAAGTGATTATATGCATTTGATATATATATATATATAA
Found at i:1480276 original size:18 final size:18
Alignment explanation
Indices: 1480252--1480294 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1480242 TTCGTTTCCA
1480252 AAACATTATTC-ATTTAC
1 AAACATTATTCAATTTAC
*
1480269 AAATCATTATTCAATTTCC
1 AAA-CATTATTCAATTTAC
1480288 AAACATT
1 AAACATT
1480295 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 8 0.35
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.40
Consensus pattern (18 bp):
AAACATTATTCAATTTAC
Found at i:1484074 original size:17 final size:17
Alignment explanation
Indices: 1484031--1484081 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
1484021 TTAGCCATTT
*
1484031 ATTTTTATTTC-ATTTTA
1 ATTTTT-TTTCAATTTAA
*
1484048 TTTTTCTTTTCAATTTAA
1 ATTTT-TTTTCAATTTAA
1484066 ATTTTTTTTCTAATTT
1 ATTTTTTTTC-AATTT
1484082 TTTCTTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTTTTCAATTTAA
Found at i:1490311 original size:119 final size:119
Alignment explanation
Indices: 1490100--1490338 Score: 433
Period size: 119 Copynumber: 2.0 Consensus size: 119
1490090 TGTATGGCAT
*
1490100 TACACATTACATCAAAATTCATGTATAGCTTTGATATTTATATCATTAGTAATGATATAAAATGA
1 TACACATTACATCAAAATTCATGTATAGCTTTGATATTTATACCATTAGTAATGATATAAAATGA
* *
1490165 AATTAGTTTTATCTATTTTTGGCCATTCTAATAATTAACGTTCACCAAACCTAA
66 AACTAGTTTTATCTATTTTTGGCCATTCTAATAATTAACATTCACCAAACCTAA
*
1490219 TACACATTAGATCAAAATTCATGTATAGCTTTGATATTTATACCATTAGTAATGATATAAAATGA
1 TACACATTACATCAAAATTCATGTATAGCTTTGATATTTATACCATTAGTAATGATATAAAATGA
*
1490284 AACTAGTTTTATCTATTTTTGGCCATTCTAATAATTACCATTCACCAAACCTAA
66 AACTAGTTTTATCTATTTTTGGCCATTCTAATAATTAACATTCACCAAACCTAA
1490338 T
1 T
1490339 TTTCAATAAT
Statistics
Matches: 115, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
119 115 1.00
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (119 bp):
TACACATTACATCAAAATTCATGTATAGCTTTGATATTTATACCATTAGTAATGATATAAAATGA
AACTAGTTTTATCTATTTTTGGCCATTCTAATAATTAACATTCACCAAACCTAA
Found at i:1490598 original size:12 final size:12
Alignment explanation
Indices: 1490581--1490605 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1490571 CGCCAACTTG
1490581 TTGTTCTTGCTT
1 TTGTTCTTGCTT
1490593 TTGTTCTTGCTT
1 TTGTTCTTGCTT
1490605 T
1 T
1490606 GGTTTTGATT
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:0.00, C:0.16, G:0.16, T:0.68
Consensus pattern (12 bp):
TTGTTCTTGCTT
Found at i:1499796 original size:111 final size:111
Alignment explanation
Indices: 1499670--1499894 Score: 441
Period size: 111 Copynumber: 2.0 Consensus size: 111
1499660 CATTTTATCA
1499670 AATCCAGTGCGGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
1 AATCCAGTGCGGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
1499735 AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
66 AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
*
1499781 AATCCAGTGCTGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
1 AATCCAGTGCGGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
1499846 AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
66 AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
1499892 AAT
1 AAT
1499895 AAAAATTTGA
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
111 113 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (111 bp):
AATCCAGTGCGGATCTAAGGGGCCCTAAAATAGAATTCTTTTCATTTAAGTCCTTTATAATTTAT
AAAACTTAAATTAGTAATGATAAAATTGTACTTTGGCCCTTAAAAT
Found at i:1525509 original size:18 final size:17
Alignment explanation
Indices: 1525486--1525520 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
1525476 ATATATCATT
1525486 AAAAATTAATTAAAAATA
1 AAAAATT-ATTAAAAATA
1525504 AAAAATTATTAAAAATA
1 AAAAATTATTAAAAATA
1525521 GATTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATTATTAAAAATA
Found at i:1527345 original size:3 final size:3
Alignment explanation
Indices: 1527337--1527368 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1527327 TGTGAGCTGC
1527337 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1527369 TTGGGTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1530762 original size:32 final size:34
Alignment explanation
Indices: 1530723--1530812 Score: 121
Period size: 32 Copynumber: 2.6 Consensus size: 34
1530713 CCTATATAAA
1530723 AAATAGTTTGATACCCTGTGCATTTGGATATA-T
1 AAATAGTTTGATACCCTGTGCATTTGGATATATT
* *
1530756 -AATAGTTTGATACCTTGTGCAATTTGGTTATATT
1 AAATAGTTTGATACCCTGTGC-ATTTGGATATATT
*
1530790 AAACTAGTTCGATACCCTGTGCA
1 AAA-TAGTTTGATACCCTGTGCA
1530813 CTGCTCAGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 19 0.39
33 10 0.20
34 1 0.02
35 3 0.06
36 16 0.33
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (34 bp):
AAATAGTTTGATACCCTGTGCATTTGGATATATT
Found at i:1531030 original size:112 final size:108
Alignment explanation
Indices: 1530852--1531072 Score: 320
Period size: 112 Copynumber: 2.0 Consensus size: 108
1530842 GTATTTTATA
* * *
1530852 AAAATACTGAAATCACATGACAAGAATATTTAAAACCTATATAAAAATTGAATTTTCATAATCAC
1 AAAATACTGAAATCACATGACAAGAATAATAAAAACCCATATAAAAATTGAATTTTCATAATCAC
1530917 ATGTTAATAACAATTAATAAAAAATTATTTATAATTTTAAATT
66 ATGTTAATAACAATTAATAAAAAATTATTTATAATTTTAAATT
*
1530960 AAAATATTGAAATCACATGACAA-AATAAAAATAAAAACCACATATAAAAAATT-AATTTTTCAT
1 AAAATACTGAAATCACATGACAAGAAT---AATAAAAACC-CATAT-AAAAATTGAA-TTTTCAT
**
1531023 AATCACATGTTAATAACAATTAATAAAATTTTATTTATAATTTTAAATT
60 AATCACATGTTAATAACAATTAATAAAAAATTATTTATAATTTTAAATT
1531072 A
1 A
1531073 TTTTTTATTC
Statistics
Matches: 101, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
107 3 0.03
108 22 0.22
110 8 0.08
111 6 0.06
112 62 0.61
ACGTcount: A:0.52, C:0.09, G:0.04, T:0.35
Consensus pattern (108 bp):
AAAATACTGAAATCACATGACAAGAATAATAAAAACCCATATAAAAATTGAATTTTCATAATCAC
ATGTTAATAACAATTAATAAAAAATTATTTATAATTTTAAATT
Found at i:1535964 original size:519 final size:520
Alignment explanation
Indices: 1535091--1536133 Score: 1926
Period size: 519 Copynumber: 2.0 Consensus size: 520
1535081 TGGACAAAAA
* *
1535091 GAGCTATTTTCAAGATCCACACGGCCTGGGGCCTGGGCATTTCCACATGGGCTGGCCACACGCAT
1 GAGCTATTTTCAAGATCCACACGGCCTGGGACCTGGGCATTTCCACATGGGCTGGCCACACGCAC
1535156 ATGTGCCAGCCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
66 ATGTGCCAGCCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
1535221 CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCAAAGAA
131 CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCAAAGAA
*
1535286 GAACGAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAATATTG
196 GAACGAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
1535351 AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTAAC
261 AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTAAC
1535416 TTTGAGATGATTTTATTTCAAATTATGAACTAAATTCCCTAGATACCTAGGGAAGA-GAAACCTA
326 TTTGAGATGATTTTATTTCAAATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
1535480 AGATGAATCTTATTATTTGATTTCTAAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
391 AGATGAATCTTATTATTTGATTTCTAAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
*
1535545 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTACTTCATGTTTAATGTGCTTATTTCAGTG
456 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAGTG
* * *
1535610 GAGCTGTTTTCAGGATCCACACGGCCTGGGACCTGGGCATTTCCACATGGGCTGGCCACACGCCC
1 GAGCTATTTTCAAGATCCACACGGCCTGGGACCTGGGCATTTCCACATGGGCTGGCCACACGCAC
* *
1535675 ATGTGCCAGTCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCATAAAAACTCAATTTTTAGG
66 ATGTGCCAGCCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
* **
1535740 TTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCGGAGAA
131 CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCAAAGAA
*
1535805 GAACGAAGAAAATACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
196 GAACGAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
* *
1535870 AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTTTTGTTGTTATCCTAAT
261 AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTAAC
*
1535935 TTTGAGATGATTTTATTTCAGATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
326 TTTGAGATGATTTTATTTCAAATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
*
1536000 AGATGAATCTTATTATTTGATTTCTGAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
391 AGATGAATCTTATTATTTGATTTCTAAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
1536065 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAGTG
456 TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAGTG
1536130 GAGC
1 GAGC
1536134 AAAAGTCCCT
Statistics
Matches: 506, Mismatches: 17, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
519 366 0.72
520 140 0.28
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (520 bp):
GAGCTATTTTCAAGATCCACACGGCCTGGGACCTGGGCATTTCCACATGGGCTGGCCACACGCAC
ATGTGCCAGCCCGTGTCGATTTCGCACCCTGATTCCCAAACACGCAGAAAAACTCAATTTTTAGG
CTTTCTGAGCATTCTAAAGTCTATAAATACATATTAGGAGAGGACCTAAGGGAGCACGCAAAGAA
GAACGAAGAAAAGACTCGAAGAACGCCACCGAATTCAACTCAGAAGCGAATCTCCTCCAAGATTG
AAGATCTCCATTCAATTTCCTTAGAAGTTTTATTGAGTTTCTTTATGTCTTGTTGTTATCCTAAC
TTTGAGATGATTTTATTTCAAATTATGAACTAAATTCCCTAGATACCTAGGGAAGATGAAACCTA
AGATGAATCTTATTATTTGATTTCTAAATTACATGATAAATACTTGATTCTTGTTCTCAGTTATG
TATGCTTATTTCGTGTTTTAATATTTTCAAGATATTAATTCATGTTTAATGTGCTTATTTCAGTG
Found at i:1540819 original size:28 final size:29
Alignment explanation
Indices: 1540770--1540834 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
1540760 TTCGTAAATT
* *
1540770 TAAAATTTAATCATTATCCTTTT-ATTTC
1 TAAAATTTAATCACTATACTTTTAATTTC
* * *
1540798 TAAAATTTAGTCCCTATACTTTTCAATTTT
1 TAAAATTTAATCACTATACTTTT-AATTTC
1540828 TAAAATT
1 TAAAATT
1540835 CAGGTCTAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 19 0.63
30 11 0.37
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.51
Consensus pattern (29 bp):
TAAAATTTAATCACTATACTTTTAATTTC
Found at i:1546934 original size:31 final size:31
Alignment explanation
Indices: 1546896--1546958 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
1546886 GTACTATGGA
1546896 GGTTACTGCACTAAGAGTCAGATTGTATTTT
1 GGTTACTGCACTAAGAGTCAGATTGTATTTT
1546927 GGTTACTGCACTAAGAGTCAGATTGTATTTT
1 GGTTACTGCACTAAGAGTCAGATTGTATTTT
1546958 G
1 G
1546959 CTTTCTCTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.25, C:0.13, G:0.24, T:0.38
Consensus pattern (31 bp):
GGTTACTGCACTAAGAGTCAGATTGTATTTT
Found at i:1554654 original size:13 final size:13
Alignment explanation
Indices: 1554633--1554663 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1554623 TATAAACGCG
*
1554633 TGTACTTTTTGCA
1 TGTATTTTTTGCA
1554646 TGTATTTTTTGCA
1 TGTATTTTTTGCA
1554659 TGTAT
1 TGTAT
1554664 ACTTAAACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.10, G:0.16, T:0.58
Consensus pattern (13 bp):
TGTATTTTTTGCA
Found at i:1556040 original size:32 final size:32
Alignment explanation
Indices: 1555977--1556036 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
1555967 TCCGAAATCA
*
1555977 AAATTGAACCAAACCTTAAATAACTTGAATTT
1 AAATTGAACCAAACCTAAAATAACTTGAATTT
*
1556009 AAATTG-ACCATAACC-AAAATGACTTGAA
1 AAATTGAACCA-AACCTAAAATAACTTGAA
1556037 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 15 0.60
32 10 0.40
ACGTcount: A:0.48, C:0.17, G:0.08, T:0.27
Consensus pattern (32 bp):
AAATTGAACCAAACCTAAAATAACTTGAATTT
Found at i:1557747 original size:31 final size:31
Alignment explanation
Indices: 1557711--1557769 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
1557701 ATCAACTCAG
*
1557711 TGACTTAAATAAAAACTTTTAAATAGTTCAA
1 TGACTTAAATAAAAACTTTCAAATAGTTCAA
** *
1557742 TGACTTAAATGGAAACTTTCGAATAGTT
1 TGACTTAAATAAAAACTTTCAAATAGTT
1557770 TAGTGACCAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTCAAATAGTTCAA
Found at i:1570298 original size:16 final size:16
Alignment explanation
Indices: 1570248--1570321 Score: 51
Period size: 16 Copynumber: 4.6 Consensus size: 16
1570238 AATCGAATTA
*
1570248 ATTTTAATTTTG-ATC
1 ATTTTAAATTTGAATC
** * *
1570263 ATTTTAAAGATAAATT
1 ATTTTAAATTTGAATC
*
1570279 ATTTTAAATTTGACTC
1 ATTTTAAATTTGAATC
* *
1570295 ATTTCAAAATTCGAATC
1 ATTT-TAAATTTGAATC
1570312 GATTTTAAAT
1 -ATTTTAAAT
1570322 ATCAATCCGA
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
15 8 0.19
16 17 0.40
17 13 0.31
18 4 0.10
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.47
Consensus pattern (16 bp):
ATTTTAAATTTGAATC
Found at i:1573877 original size:29 final size:28
Alignment explanation
Indices: 1573822--1573877 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
1573812 AAAATTTAAG
*
1573822 ATTTAATCCTTTATTTTAATTATATATA
1 ATTTAATCCTTTATTTTAATAATATATA
* *
1573850 ATTTGATCCTTTATTTTTATAATGATAT
1 ATTTAATCCTTTATTTTAATAAT-ATAT
1573878 TAGTTAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (28 bp):
ATTTAATCCTTTATTTTAATAATATATA
Found at i:1588187 original size:3 final size:3
Alignment explanation
Indices: 1588181--1588209 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1588171 AAAAAAAAAA
1588181 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1588210 AGGAAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1591123 original size:13 final size:13
Alignment explanation
Indices: 1591105--1591170 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
1591095 TAGATTTTTC
1591105 CTAAATATTATCA
1 CTAAATATTATCA
1591118 CTAAATAATT-T--
1 CTAAAT-ATTATCA
1591129 -TAAATATTATCA
1 CTAAATATTATCA
*
1591141 CTAAATAGT-T--
1 CTAAATATTATCA
1591151 CTAAATATTATCA
1 CTAAATATTATCA
1591164 CTAAATA
1 CTAAATA
1591171 ACTAAAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
9 3 0.07
10 14 0.33
11 1 0.02
12 1 0.02
13 21 0.49
14 3 0.07
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:1591133 original size:23 final size:23
Alignment explanation
Indices: 1591105--1591171 Score: 116
Period size: 23 Copynumber: 2.9 Consensus size: 23
1591095 TAGATTTTTC
1591105 CTAAATATTATCACTAAATAATT
1 CTAAATATTATCACTAAATAATT
* *
1591128 TTAAATATTATCACTAAATAGTT
1 CTAAATATTATCACTAAATAATT
1591151 CTAAATATTATCACTAAATAA
1 CTAAATATTATCACTAAATAA
1591172 CTAAAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (23 bp):
CTAAATATTATCACTAAATAATT
Found at i:1594072 original size:31 final size:32
Alignment explanation
Indices: 1594037--1594106 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 32
1594027 GTCACAAAAT
* *
1594037 AATCACTGAATC-ATTCAAAAG-TTTTCATTTA
1 AATCACTGAAACTATGCAAAAGCTTTT-ATTTA
* *
1594068 AATCA-TTAAACTATGCAAACGCTTTTATTTA
1 AATCACTGAAACTATGCAAAAGCTTTTATTTA
1594099 AATCACTG
1 AATCACTG
1594107 GACTATTAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
30 4 0.13
31 22 0.71
32 5 0.16
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (32 bp):
AATCACTGAAACTATGCAAAAGCTTTTATTTA
Found at i:1598151 original size:18 final size:19
Alignment explanation
Indices: 1598128--1598163 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1598118 TTTTGATATT
1598128 TGAACAAGAAA-AAAATTA
1 TGAACAAGAAATAAAATTA
*
1598146 TGAACAATAAATAAAATT
1 TGAACAAGAAATAAAATT
1598164 TTACAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.06, G:0.08, T:0.22
Consensus pattern (19 bp):
TGAACAAGAAATAAAATTA
Found at i:1620457 original size:31 final size:31
Alignment explanation
Indices: 1620414--1620472 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1620404 AAATGGTTAT
1620414 TGAACTATTCGAAAGCTTTCATTTAAGTCAC
1 TGAACTATTCGAAAGCTTTCATTTAAGTCAC
* * *
1620445 TGAATTATTCGAAAGTTTTTATTTAAGT
1 TGAACTATTCGAAAGCTTTCATTTAAGT
1620473 AATTGAGTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (31 bp):
TGAACTATTCGAAAGCTTTCATTTAAGTCAC
Found at i:1632912 original size:22 final size:22
Alignment explanation
Indices: 1632875--1632924 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
1632865 TGAAGTTTAC
*
1632875 AATTATTTTTATATTAAGATTTT
1 AATT-TTTTTAAATTAAGATTTT
*
1632898 AATTTTTTTAAATTAAGTTTTT
1 AATTTTTTTAAATTAAGATTTT
1632920 AATTT
1 AATTT
1632925 GATAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (22 bp):
AATTTTTTTAAATTAAGATTTT
Found at i:1642538 original size:13 final size:13
Alignment explanation
Indices: 1642520--1642544 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1642510 TTTTAAAAAT
1642520 ATTTTCTATTTTA
1 ATTTTCTATTTTA
1642533 ATTTTCTATTTT
1 ATTTTCTATTTT
1642545 TTAAAATTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTCTATTTTA
Found at i:1643552 original size:3 final size:3
Alignment explanation
Indices: 1643539--1643571 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
1643529 GATCATTAAA
1643539 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AA
1643572 AATTCGATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1656512 original size:416 final size:415
Alignment explanation
Indices: 1655741--1656571 Score: 1628
Period size: 416 Copynumber: 2.0 Consensus size: 415
1655731 ATTATAAAAT
1655741 TTTGGAGAGGCAATGCTAAAAAATTGTATTAAAAAAACTTGGATTAAATTGTTAACTTTTCACTG
1 TTTGGAGAGGCAATGCTAAAAAATTGTATTAAAAAAACTTGGATTAAATTGTTAACTTTTCACTG
1655806 GATCAAAAATGCAATAATTTCATTTAATGAAAGGCTAAAAAGATTTAAATTTAATGTCTTAATTT
66 GATCAAAAATGCAATAATTTCATTTAATGAAAGGCTAAAAAGATTTAAATTTAATGTCTTAATTT
1655871 ATGGGAGGACCTAAAAGAAATTTTCTTTCCTAGGAAATTATTCAAACTTATAATTACTCGATTTA
131 ATGGGAGGACCTAAAAGAAATTTTCTTTCCTAGGAAATTATTCAAACTTATAATTACTCGATTTA
1655936 TATGCTAACTCAACTTGCCCAATATGTACTTCACTACTTGTATCGTATTAAAAGTTTAACGTAGA
196 TATGCTAACTCAACTTGCCCAATATGTACTTCACTACTTGTATCGTATTAAAAGTTTAACGTAGA
1656001 GAACTTTATTTTTAAGCAATTACAACTGAAAAAGGATTACCTCAAAGGGTGATATATGAACAAGT
261 GAACTTTATTTTTAAGCAATTACAACTGAAAAAGGATTACCTCAAAGGGTGATATATGAACAAGT
1656066 AGGGCAATATACTCTCCACCATGTTCTCTCAAGGAATAAAAGCAACAACAAAAGGGGGGGGGGGA
326 AGGGCAATATACTCTCCACCATGTTCTCTCAAGGAATAAAAGCAACAACAAAA-GGGGGGGGGGA
1656131 TGGAGATGG-GGAGATAAGAGACAGTC
390 TGGAGATGGTGG-GATAAGAGACAGTC
1656157 TTTGGAGAGGCAATGCTAAAAAATTGTATTAAAAAAACTTGGATTAAATTGTTAACTTTTCACTG
1 TTTGGAGAGGCAATGCTAAAAAATTGTATTAAAAAAACTTGGATTAAATTGTTAACTTTTCACTG
1656222 GATCAAAAATGCAATAATTTCATTTAATGAAAGGCTAAAAAGATTTAAATTTAATGTCTTAATTT
66 GATCAAAAATGCAATAATTTCATTTAATGAAAGGCTAAAAAGATTTAAATTTAATGTCTTAATTT
1656287 ATGGGAGGACCTAAAAGAAATTTTCTTTCCTAGGAAATTATTCAAACTTATAATTACTCGATTTA
131 ATGGGAGGACCTAAAAGAAATTTTCTTTCCTAGGAAATTATTCAAACTTATAATTACTCGATTTA
1656352 TATGCTAACTCAACTTGCCCAATATGTACTTCACTACTTGTATCGTATTAAAAGTTTAACGTAGA
196 TATGCTAACTCAACTTGCCCAATATGTACTTCACTACTTGTATCGTATTAAAAGTTTAACGTAGA
1656417 GAACTTTATTTTTAAGCAATTACAACTGAAAAAGGATTACCTCAAAGGGTGATATATGAACAAGT
261 GAACTTTATTTTTAAGCAATTACAACTGAAAAAGGATTACCTCAAAGGGTGATATATGAACAAGT
1656482 AGGGCAATATACTCTCCACCATGTTCTCTCAAGGAATAAAAGCAACAACAAAAGGGGGGGGGGAT
326 AGGGCAATATACTCTCCACCATGTTCTCTCAAGGAATAAAAGCAACAACAAAAGGGGGGGGGGAT
*
1656547 GGGGATGGTGGGATAAGAGACAGTC
391 GGAGATGGTGGGATAAGAGACAGTC
1656572 AAACTTAATT
Statistics
Matches: 413, Mismatches: 1, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
415 33 0.08
416 380 0.92
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.30
Consensus pattern (415 bp):
TTTGGAGAGGCAATGCTAAAAAATTGTATTAAAAAAACTTGGATTAAATTGTTAACTTTTCACTG
GATCAAAAATGCAATAATTTCATTTAATGAAAGGCTAAAAAGATTTAAATTTAATGTCTTAATTT
ATGGGAGGACCTAAAAGAAATTTTCTTTCCTAGGAAATTATTCAAACTTATAATTACTCGATTTA
TATGCTAACTCAACTTGCCCAATATGTACTTCACTACTTGTATCGTATTAAAAGTTTAACGTAGA
GAACTTTATTTTTAAGCAATTACAACTGAAAAAGGATTACCTCAAAGGGTGATATATGAACAAGT
AGGGCAATATACTCTCCACCATGTTCTCTCAAGGAATAAAAGCAACAACAAAAGGGGGGGGGGAT
GGAGATGGTGGGATAAGAGACAGTC
Found at i:1659694 original size:19 final size:21
Alignment explanation
Indices: 1659648--1659703 Score: 73
Period size: 19 Copynumber: 2.8 Consensus size: 21
1659638 GAAAAATTAT
1659648 AATTTTTATAATTTTCTTTAC
1 AATTTTTATAATTTTCTTTAC
*
1659669 AAATTTTAT-A-TTTCTTTAC
1 AATTTTTATAATTTTCTTTAC
*
1659688 -ATTTTTTTAATTTTCT
1 AATTTTTATAATTTTCT
1659704 CACAACTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 6 0.20
19 10 0.33
20 6 0.20
21 8 0.27
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (21 bp):
AATTTTTATAATTTTCTTTAC
Found at i:1661919 original size:15 final size:16
Alignment explanation
Indices: 1661894--1661926 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1661884 TCGATTCCCA
*
1661894 AAGATTTTATTGGTTT
1 AAGATTTTATTAGTTT
1661910 AAGA-TTTATTAGTTT
1 AAGATTTTATTAGTTT
1661925 AA
1 AA
1661927 TATACGAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (16 bp):
AAGATTTTATTAGTTT
Found at i:1671544 original size:16 final size:17
Alignment explanation
Indices: 1671512--1671543 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1671502 CATTTCACGA
1671512 ATAATGGGATTCTTTTT
1 ATAATGGGATTCTTTTT
1671529 ATAA-GGGATT-TTTTT
1 ATAATGGGATTCTTTTT
1671544 TTAACGTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 5 0.33
16 6 0.40
17 4 0.27
ACGTcount: A:0.25, C:0.03, G:0.19, T:0.53
Consensus pattern (17 bp):
ATAATGGGATTCTTTTT
Found at i:1671897 original size:21 final size:21
Alignment explanation
Indices: 1671837--1671902 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
1671827 GATTTTTATT
*
1671837 ATTAT-TATATTTTATTAATTTA
1 ATTATATAT-TTTTATT-ATTCA
* * *
1671859 ATTTTATATTGTGATTATTCA
1 ATTATATATTTTTATTATTCA
1671880 ATTATATATTTTTATTATCTCA
1 ATTATATATTTTTATTAT-TCA
1671902 A
1 A
1671903 GTTTTTATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
21 19 0.54
22 13 0.37
23 3 0.09
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (21 bp):
ATTATATATTTTTATTATTCA
Found at i:1674704 original size:2 final size:2
Alignment explanation
Indices: 1674658--1674687 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1674648 AATAAAATTA
1674658 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
1674688 TTGAATGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1676535 original size:17 final size:17
Alignment explanation
Indices: 1676513--1676568 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
1676503 AAAAAATATT
1676513 AATTTTTTTATAAAATA
1 AATTTTTTTATAAAATA
1676530 AATTTTATTATCATGAAAAT-
1 AATTTT-TT-T-AT-AAAATA
*
1676550 -ATTTTTATATAAAATA
1 AATTTTTTTATAAAATA
1676566 AAT
1 AAT
1676569 AAAAATCCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
15 5 0.16
16 2 0.06
17 9 0.28
18 3 0.09
19 6 0.19
20 2 0.06
21 5 0.16
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (17 bp):
AATTTTTTTATAAAATA
Found at i:1677686 original size:31 final size:31
Alignment explanation
Indices: 1677650--1677731 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
1677640 TAAATTAGGC
* *
1677650 CTTGAACTTTGTAATTGA-TCCCACATTGGGG
1 CTTGAACTTTATAATT-ATTCCCACATTGGGA
* *
1677681 CTTGAA-TTAAATAATTATTCCCATATTGGGA
1 CTTGAACTT-TATAATTATTCCCACATTGGGA
*
1677712 CTTGAACTTTTATTATTATT
1 CTTGAAC-TTTATAATTATT
1677732 ATAAAAGTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
30 3 0.07
31 28 0.68
32 8 0.20
33 2 0.05
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (31 bp):
CTTGAACTTTATAATTATTCCCACATTGGGA
Found at i:1697732 original size:23 final size:23
Alignment explanation
Indices: 1697705--1697754 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1697695 CACTCAAATT
* * *
1697705 TTAAAAATTATAAAATATAAAAA
1 TTAAAAACTACAAAATAAAAAAA
*
1697728 TTAAAAACTACCAAATAAAAAAA
1 TTAAAAACTACAAAATAAAAAAA
1697751 TTAA
1 TTAA
1697755 TCCATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (23 bp):
TTAAAAACTACAAAATAAAAAAA
Found at i:1698244 original size:22 final size:22
Alignment explanation
Indices: 1698219--1698261 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1698209 ATTGGAAGGA
*
1698219 AAAACTC-AGCTATCAAATTGAC
1 AAAACTCAAG-TACCAAATTGAC
1698241 AAAACTCAAGTACCAAATTGA
1 AAAACTCAAGTACCAAATTGA
1698262 GAATTGAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.49, C:0.21, G:0.09, T:0.21
Consensus pattern (22 bp):
AAAACTCAAGTACCAAATTGAC
Found at i:1703615 original size:5 final size:5
Alignment explanation
Indices: 1703607--1703631 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1703597 CAAAGCAACC
1703607 GGCAA GGCAA GGCAA GGCAA GGCAA
1 GGCAA GGCAA GGCAA GGCAA GGCAA
1703632 TGGCTATCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
GGCAA
Found at i:1711149 original size:23 final size:23
Alignment explanation
Indices: 1711119--1711164 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1711109 GGCCAGTTCG
1711119 AATTCAACTCATTTTTGGGTTGT
1 AATTCAACTCATTTTTGGGTTGT
1711142 AATTCAACTCATTTTTGGGTTGT
1 AATTCAACTCATTTTTGGGTTGT
1711165 TTTAGGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (23 bp):
AATTCAACTCATTTTTGGGTTGT
Found at i:1714323 original size:2 final size:2
Alignment explanation
Indices: 1714316--1714341 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1714306 TCAGCTCACT
1714316 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1714342 ATAATAACAT
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):
TA
Found at i:1714452 original size:78 final size:79
Alignment explanation
Indices: 1714322--1714478 Score: 307
Period size: 78 Copynumber: 2.0 Consensus size: 79
1714312 CACTTATATA
1714322 TATATATATATATATATATAATAATAACATCGAAAGATATCGAGTTTCCGACCATTCTTCCAGAT
1 TATATATATATATATATATAATAATAACATCGAAAGATATCGAGTTTCCGACCATTCTTCCAGAT
1714387 GAAACACGTTACAT
66 GAAACACGTTACAT
1714401 TATATATATA-ATATATATAATAATAACATCGAAAGATATCGAGTTTCCGACCATTCTTCCAGAT
1 TATATATATATATATATATAATAATAACATCGAAAGATATCGAGTTTCCGACCATTCTTCCAGAT
1714465 GAAACACGTTACAT
66 GAAACACGTTACAT
1714479 GAAAAGATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 68 0.87
79 10 0.13
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (79 bp):
TATATATATATATATATATAATAATAACATCGAAAGATATCGAGTTTCCGACCATTCTTCCAGAT
GAAACACGTTACAT
Found at i:1715238 original size:23 final size:23
Alignment explanation
Indices: 1715211--1715256 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
1715201 TGAACAAGAG
1715211 GTTCTCGTCCCATCAGGTATCAA
1 GTTCTCGTCCCATCAGGTATCAA
*
1715234 GTTCTCGTCCTATCAGGTATCAA
1 GTTCTCGTCCCATCAGGTATCAA
1715257 AATCCAGCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.28, G:0.17, T:0.33
Consensus pattern (23 bp):
GTTCTCGTCCCATCAGGTATCAA
Found at i:1718988 original size:3 final size:3
Alignment explanation
Indices: 1718980--1719009 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1718970 TTGCTTAGAT
1718980 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1719010 TCTTTGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1730410 original size:13 final size:13
Alignment explanation
Indices: 1730392--1730416 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1730382 TTAATGTTTA
1730392 ATATTTTAAATAT
1 ATATTTTAAATAT
1730405 ATATTTTAAATA
1 ATATTTTAAATA
1730417 AGTTGGTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTTAAATAT
Found at i:1752873 original size:18 final size:18
Alignment explanation
Indices: 1752850--1752891 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1752840 CATTAATACA
*
1752850 AGAACCTGAAACAGAACC
1 AGAACCGGAAACAGAACC
* *
1752868 AGAACCGGAAGCCGAACC
1 AGAACCGGAAACAGAACC
1752886 AGAACC
1 AGAACC
1752892 AGAGCATGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.31, G:0.21, T:0.02
Consensus pattern (18 bp):
AGAACCGGAAACAGAACC
Found at i:1752988 original size:3 final size:3
Alignment explanation
Indices: 1752980--1753012 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1752970 GTCACCCTTT
1752980 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1753013 AAATCACTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:1755202 original size:106 final size:106
Alignment explanation
Indices: 1755084--1755302 Score: 429
Period size: 106 Copynumber: 2.1 Consensus size: 106
1755074 GTCTAATAAG
1755084 AATATATTATGTGTCACACCATTATCGGATCGTATTGTGTTTTGAAGATAAAATGAGATAAAATT
1 AATATATTATGTGTCACACCATTATCGGATCGTATTGTGTTTTGAAGATAAAATGAGATAAAATT
*
1755149 TATAATTTATATATTATTTTTTTTTAAAAAATAAAACTTTA
66 TATAATTTATATATTATTTTTTTATAAAAAATAAAACTTTA
1755190 AATATATTATGTGTCACACCATTATCGGATCGTATTGTGTTTTGAAGATAAAATGAGATAAAATT
1 AATATATTATGTGTCACACCATTATCGGATCGTATTGTGTTTTGAAGATAAAATGAGATAAAATT
1755255 TATAATTTATATATTATTTTTTTATAAAAAATAAAACTTTA
66 TATAATTTATATATTATTTTTTTATAAAAAATAAAACTTTA
1755296 AATATAT
1 AATATAT
1755303 CTATATAGAA
Statistics
Matches: 112, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 112 1.00
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (106 bp):
AATATATTATGTGTCACACCATTATCGGATCGTATTGTGTTTTGAAGATAAAATGAGATAAAATT
TATAATTTATATATTATTTTTTTATAAAAAATAAAACTTTA
Found at i:1758868 original size:26 final size:28
Alignment explanation
Indices: 1758832--1758884 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
1758822 TCACAAGTTC
1758832 AGTTCTAATGTATATTTT-TC-TCGAAG
1 AGTTCTAATGTATATTTTCTCTTCGAAG
*
1758858 AGTTTTAATGTATATTTTCTCTTCGAA
1 AGTTCTAATGTATATTTTCTCTTCGAA
1758885 TTTGATTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 17 0.71
27 2 0.08
28 5 0.21
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.49
Consensus pattern (28 bp):
AGTTCTAATGTATATTTTCTCTTCGAAG
Found at i:1760103 original size:213 final size:214
Alignment explanation
Indices: 1759772--1760180 Score: 633
Period size: 213 Copynumber: 1.9 Consensus size: 214
1759762 TTTTTGTTGG
* * * ** *
1759772 TTATGGTTTCTTATTGTATATATATTGGGGATGTTTAGTTCTTCTAGGACCTAGGTTAATGCTTA
1 TTATGGTTTCTTATTATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTA
*
1759837 TTTCATGTTTATCCTGCATATTTGATGGTTCGTTGTAGTTCAAATTGTTGCTTCATTGTGGCAGC
66 TTTCATGTTTATCCTGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGC
* *
1759902 TATGACCAGTCCAATTTGTGCTGGTTTTTACTCC-ATTTTTGTGAATT-GGGTTCTTGAGATAAT
131 TATGACCAATCCAATTTGTGCTGGTTTTTAATCCTATTTTTGTGAATTGGGGTTCTTGAGATAAT
1759965 GGTGTTTTTTCATTTGTTT
196 GGTGTTTTTTCATTTGTTT
* * *
1759984 TTATCGGTTTCTTATTATATATTTGTTGGGTATATTTAGTTCCTCTAGGACCTAGCCTAACGCTT
1 TTAT-GGTTTCTTATTATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTT
* * * *
1760049 CTTTCATGTTTATTCTGCATATTTGGTGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGGAG
65 ATTTCATGTTTATCCTGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAG
*
1760114 CTATGACCAATCCAATTTGTGCTGGTTTTTAATCCTTTTTTTTGTGAATTGGGGTTCTTGAGATA
130 CTATGACCAATCCAATTTGTGCTGGTTTTTAATCC-TATTTTTGTGAATTGGGGTTCTTGAGATA
1760179 AT
194 AT
1760181 TCTGCTTTTC
Statistics
Matches: 176, Mismatches: 17, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
212 4 0.02
213 144 0.82
215 12 0.07
216 16 0.09
ACGTcount: A:0.19, C:0.13, G:0.21, T:0.47
Consensus pattern (214 bp):
TTATGGTTTCTTATTATATATATATTGGGGATATTTAGTTCCTCTAGGACCTAGCCTAACGCTTA
TTTCATGTTTATCCTGCATATTTGATGGTTCATTGTAGTTCAAATTGTTGCTTCATTGTGGCAGC
TATGACCAATCCAATTTGTGCTGGTTTTTAATCCTATTTTTGTGAATTGGGGTTCTTGAGATAAT
GGTGTTTTTTCATTTGTTT
Found at i:1768438 original size:26 final size:27
Alignment explanation
Indices: 1768390--1768441 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1768380 TCATATAAAT
*
1768390 AAAATAAATTATTATTTTAATATATTA
1 AAAATAAATTATTAGTTTAATATATTA
*
1768417 AAAATAAATTATT-GTTTCATATATT
1 AAAATAAATTATTAGTTTAATATATT
1768442 TACGGTGGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAATAAATTATTAGTTTAATATATTA
Found at i:1768623 original size:25 final size:25
Alignment explanation
Indices: 1768560--1768623 Score: 58
Period size: 26 Copynumber: 2.5 Consensus size: 25
1768550 AAATATTTTA
*
1768560 ATATATAATTTATACACATACAAGT
1 ATATATAATATATACACATACAAGT
* * *
1768585 ATATCTTAATTATATACATATA-AATT
1 ATAT-ATAA-TATATACACATACAAGT
1768611 ATATATGAATATA
1 ATATAT-AATATA
1768624 ATTTTTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
25 9 0.29
26 12 0.39
27 10 0.32
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATATATAATATATACACATACAAGT
Found at i:1772184 original size:20 final size:20
Alignment explanation
Indices: 1772159--1772198 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1772149 AATATTTTCC
* *
1772159 AGTAAATCATTTTGCAGAAA
1 AGTAAAACATTTTCCAGAAA
1772179 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTCCAGAAA
1772199 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTCCAGAAA
Found at i:1772213 original size:34 final size:35
Alignment explanation
Indices: 1772147--1772213 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1772137 CAAACACTGG
* *
1772147 AAAATATTTTCCAGTAAATCATTTTGCAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
1772182 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
1772214 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.45, C:0.13, G:0.10, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:1780105 original size:186 final size:183
Alignment explanation
Indices: 1779778--1780123 Score: 453
Period size: 186 Copynumber: 1.9 Consensus size: 183
1779768 ATCACATAAA
* * * *
1779778 CCAACCAACATTATGTAACTAGTTCAAATGGCAAACCCTTTGCGGGTACGAACATTGGGTCATTC
1 CCAACCAACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGTACGAACATTGGATCATTC
* * * *
1779843 TTATCAAACATTAGGACAAGTTTATGCTCTAACAACGATTGAAGTTGCAAAACATCATTCACAGT
66 TTATCAAACATTAGGACAAGCTTATACTCTAACAACGATTGAAATTG-AAAACATCATTCACAGC
*
1779908 GACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCACGAG
130 AACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCACGAG
* ** * * * **
1779962 CCAACCTACATTACGTGGCTAGTGCAAAAGGCAAACCCTTTGGGGGATTCGAACTTTGGATTGTT
1 CCAACCAACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGG-TACGAACATTGGATCATT
*
1780027 CTTATCAAACGTTAGGACAAGCTTATACATCTAACAATC-ATTGAAATCATG-AAACATCATTCA
65 CTTATCAAACATTAGGACAAGCTTATAC-TCTAACAA-CGATTGAAAT--TGAAAACATCATTCA
*
1780090 CAGCAACATCAAGAATTGTCGGAATACTAATAAA
126 CAGCAACATCAAGAATTGTCGAAATACTAATAAA
1780124 CACTGTACAG
Statistics
Matches: 138, Mismatches: 19, Indels: 8
0.84 0.12 0.05
Matches are distributed among these distances:
184 39 0.28
185 38 0.28
186 58 0.42
187 1 0.01
188 2 0.01
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (183 bp):
CCAACCAACATTACGTAACTAGTGCAAAAGGCAAACCCTTTGCGGGTACGAACATTGGATCATTC
TTATCAAACATTAGGACAAGCTTATACTCTAACAACGATTGAAATTGAAAACATCATTCACAGCA
ACATCAAGAATTGTCGAAATACTAATAAAGACCGTACGTAAACGTTGCACGAG
Found at i:1780273 original size:155 final size:155
Alignment explanation
Indices: 1779991--1780278 Score: 418
Period size: 155 Copynumber: 1.9 Consensus size: 155
1779981 TAGTGCAAAA
** * * *
1779991 GGCAAACCCTTTGGGGGATTCGAACTTTGGATTGTTCTTATCAAACGTTAGGACAAGCTTATACA
1 GGCAAACCCTTTGCAGGATTCGAACTTTGCATTGATCTTATCAAACATTAGGACAAGCTTATACA
* *
1780056 TCTAACAATCATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
66 TCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
1780121 AAACACTGTACAGAAACGCCGCAAC
131 AAACACTGTACAGAAACGCCGCAAC
1780146 GGCAAACCCTTTGCAGGATTCGAAC-TT-CATCTCGATCTTATCAAACATTAGGACAAGCTTATA
1 GGCAAACCCTTTGCAGGATTCGAACTTTGCAT-T-GATCTTATCAAACATTAGGACAAGCTTATA
* * ** * **
1780209 CGTCCAACAATAATTGAAGTTGTGAAACATCATTCACAGCGATGTCAAGAATTGTCGGAATACTA
64 CATCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTA
1780274 ATAAA
129 ATAAA
1780279 GACCGTACGT
Statistics
Matches: 117, Mismatches: 14, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
153 2 0.02
154 3 0.03
155 112 0.96
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (155 bp):
GGCAAACCCTTTGCAGGATTCGAACTTTGCATTGATCTTATCAAACATTAGGACAAGCTTATACA
TCCAACAATAATTGAAATCATGAAACATCATTCACAGCAACATCAAGAATTGTCGGAATACTAAT
AAACACTGTACAGAAACGCCGCAAC
Found at i:1782867 original size:25 final size:27
Alignment explanation
Indices: 1782839--1782889 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1782829 GGTACTACTA
*
1782839 CTTGTT-ATA-AACATTTTTATAAAGG
1 CTTGTTAATAGAACATATTTATAAAGG
*
1782864 CTTGTTAATAGAATATATTTATAAAG
1 CTTGTTAATAGAACATATTTATAAAG
1782890 TTTATGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.39, C:0.06, G:0.12, T:0.43
Consensus pattern (27 bp):
CTTGTTAATAGAACATATTTATAAAGG
Found at i:1785744 original size:54 final size:53
Alignment explanation
Indices: 1785632--1785915 Score: 145
Period size: 54 Copynumber: 5.3 Consensus size: 53
1785622 GCAGAGTTTG
* * * * * * *
1785632 ATTCTCTTCTAGAAATTCGGTTTCCAGTAATGATCC-TCTCAGGGGTTATG-GTTG
1 ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGA-CCTTATCA-GGATT-GGAGTTA
* *
1785686 ATTCCTTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGACATTA
1 ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGA-GTTA
* ** * * * * *
1785740 ATTCCGC-TCTAGGAAG-TTGATCCCCAGTAACGATCC-CA-CCGGAAGTGGGAGTTG
1 ATTCC-CTTCTA-GAAGTTTGGTTTCCAGTAATGA-CCTTATCAGG-A-TTGGAGTTA
* *
1785794 ATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGATGTTA
1 ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGA-GTTA
* ** * * * *
1785848 ATTCCGC-TCTAGGAAG-TTGATCGCCAGTAATGAGCC-CATCAGAAGTGGGAGTTG
1 ATTCC-CTTCTA-GAAGTTTGGTTTCCAGTAATGA-CCTTATCAGGA-TTGGAGTTA
1785902 ATTCCCTTCTAGAA
1 ATTCCCTTCTAGAA
1785916 ATCTGAATTC
Statistics
Matches: 174, Mismatches: 38, Indels: 37
0.70 0.15 0.15
Matches are distributed among these distances:
52 1 0.01
53 23 0.13
54 127 0.73
55 23 0.13
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (53 bp):
ATTCCCTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGAGTTA
Found at i:1785751 original size:108 final size:107
Alignment explanation
Indices: 1785682--1785915 Score: 317
Period size: 108 Copynumber: 2.2 Consensus size: 107
1785672 AGGGGTTATG
* * *
1785682 GTTGATTCCTTTCTAGAAGTTTGGTTTCCAGTAATGACCTTATCAGGATTGGACATTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGACATTAATTCCGC
* * *
1785747 TCTAGGAAGTTGATCCCCAGTAACGATCCCACCGGAAGTGGGA
66 TCTA-GAAATTGATCCCCAGTAACGATCCCACAGGAAGTAGGA
**
1785790 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGATGTTAATTCCGC
1 GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGACATTAATTCCGC
* * * * *
1785855 TCTAGGAAGTTGATCGCCAGTAATGAGCCCATCA-GAAGTGGGA
66 TCTA-GAAATTGATCCCCAGTAACGATCCCA-CAGGAAGTAGGA
1785898 GTTGATTCCCTTCTAGAA
1 GTTGATTCCCTTCTAGAA
1785916 ATCTGAATTC
Statistics
Matches: 116, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
108 115 0.99
109 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (107 bp):
GTTGATTCCCTTCTAGAAGTTTGGTTTCCAATAATGACCTTATCAGGAGTGGACATTAATTCCGC
TCTAGAAATTGATCCCCAGTAACGATCCCACAGGAAGTAGGA
Found at i:1789823 original size:1 final size:1
Alignment explanation
Indices: 1789817--1789862 Score: 92
Period size: 1 Copynumber: 46.0 Consensus size: 1
1789807 AATCAAATAC
1789817 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1789863 GAGCAACAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1790996 original size:21 final size:21
Alignment explanation
Indices: 1790972--1791020 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1790962 TTTTGAGAAC
*
1790972 ATTATTTTTTTTTAAAAATTT
1 ATTATTTATTTTTAAAAATTT
* ***
1790993 ATTAATTATTTTTATTTATTT
1 ATTATTTATTTTTAAAAATTT
1791014 ATTATTT
1 ATTATTT
1791021 GGAGAATGAT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTATTTATTTTTAAAAATTT
Found at i:1793433 original size:24 final size:23
Alignment explanation
Indices: 1793388--1793433 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1793378 ATATAGGTAG
*
1793388 AAAAAATATAAAAGTAATTTTTA
1 AAAAAATATAAAAGAAATTTTTA
1793411 AAAAAATTATAAAA-AAATATTTT
1 AAAAAA-TATAAAAGAAAT-TTTT
1793434 CATAATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AAAAAATATAAAAGAAATTTTTA
Found at i:1795296 original size:17 final size:17
Alignment explanation
Indices: 1795276--1795322 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
1795266 CAATAATTAC
*
1795276 ATAAATAATAAAATTTT
1 ATAAAAAATAAAATTTT
1795293 ATAAAAAATAAAATTTT
1 ATAAAAAATAAAATTTT
1795310 ATAAAAAATAAAA
1 ATAAAAAATAAAA
1795323 AAAAGTTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAAATAAAATTTT
Found at i:1802767 original size:275 final size:275
Alignment explanation
Indices: 1802274--1802794 Score: 864
Period size: 275 Copynumber: 1.9 Consensus size: 275
1802264 AAAAAAACCA
* *
1802274 AAGAAACAATCACTAAAAGTTTCATATGACTTTGCTTAAATTAAATTTCTTCAAAAAAAATTTTA
1 AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTC--AAAAAATTTTA
* * * *
1802339 AATTGAAATAAAACTTATGCTTCTCATTACATTTGGTTGAATACAATGAGTGTTACAAGCTCAAC
64 AAATGAAATAAAACTTATGCTTCTCATGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAAC
*
1802404 CTTGCAAATCATGTAAGCTAAAAAAGTTAATAAACTCCATTTTTCTTGTATTTTCTATAACTTTC
129 CTTGCAAATCATGTAAGCTAAAAAAGTTAACAAACTCCATTTTTCTTGTATTTTCTATAACTTTC
* *
1802469 CTCGAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAATAACTAAATTTCCAAAAAAAG
194 CTCAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAAATTTCCAAAAAAAG
1802534 TGACGCAAACATGAGCT
259 TGACGCAAACATGAGCT
* * *
1802551 AAGAAACAATTACTACAGGTTTAATACGACTTTGCTTAAATTAAATTTCTTC-AAAAATTTTAAA
1 AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTCAAAAAATTTTAAA
*
1802615 ATGAAATAAAACTTATGCTTCTCACTGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAGCC
66 ATGAAATAAAACTTATGCTTCTCA-TGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAACC
* *
1802680 TTGCAAATCATGTAAGCTAAAAAAGTTAACGAACTCCATTTTTCTTGTATTTTCTATCACTTTCC
130 TTGCAAATCATGTAAGCTAAAAAAGTTAACAAACTCCATTTTTCTTGTATTTTCTATAACTTTCC
*
1802745 TCAAACTTTCTCGACACCCAAACAGAGCTTCATCATTCAACAAGAACTAA
195 TCAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAA
1802795 GTCCCCCCCC
Statistics
Matches: 227, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
274 35 0.15
275 145 0.64
277 47 0.21
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (275 bp):
AAGAAACAATCACTAAAAGTTTAATACGACTTTGCTTAAATTAAATTTCTTCAAAAAATTTTAAA
ATGAAATAAAACTTATGCTTCTCATGACACTTGGTTGAACACAATGAGTGTTACAAGCTCAACCT
TGCAAATCATGTAAGCTAAAAAAGTTAACAAACTCCATTTTTCTTGTATTTTCTATAACTTTCCT
CAAACTTTCTCGACACCCAAACAGACCTTCATCATTCAACAAGAACTAAATTTCCAAAAAAAGTG
ACGCAAACATGAGCT
Found at i:1835817 original size:6 final size:6
Alignment explanation
Indices: 1835802--1835869 Score: 129
Period size: 6 Copynumber: 11.5 Consensus size: 6
1835792 AGGTAGCCAA
1835802 TATT-G TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG
1 TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG TATTGG
1835849 TATTGG TATTGG TATTGG TAT
1 TATTGG TATTGG TATTGG TAT
1835870 CAGTACTGGC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 4 0.06
6 58 0.94
ACGTcount: A:0.18, C:0.00, G:0.31, T:0.51
Consensus pattern (6 bp):
TATTGG
Found at i:1852420 original size:30 final size:29
Alignment explanation
Indices: 1852384--1852451 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
1852374 ATAGTTGGAC
* *
1852384 CTAAATT-TTGAAAATTGAAAAGTAGAGGGA
1 CTAAATTCCTGAAAA-T-AAAAGTACAGGGA
*
1852414 CTAAATTCCTGGAAATAAAAGTACAGGGA
1 CTAAATTCCTGAAAATAAAAGTACAGGGA
1852443 CTAAATTCC
1 CTAAATTCC
1852452 AAATTTTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 21 0.62
30 8 0.24
31 5 0.15
ACGTcount: A:0.44, C:0.12, G:0.19, T:0.25
Consensus pattern (29 bp):
CTAAATTCCTGAAAATAAAAGTACAGGGA
Found at i:1855135 original size:31 final size:30
Alignment explanation
Indices: 1855080--1855144 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 30
1855070 TAATCAATTT
1855080 AAAAGTTGGAACTTCTGTACAATTAACCAA
1 AAAAGTTGGAACTTCTGTACAATTAACCAA
* *
1855110 AAAAGTTGAGAACTTTTTGTA-AATTAACCCA
1 AAAAGTTG-GAAC-TTCTGTACAATTAACCAA
1855141 AAAA
1 AAAA
1855145 TAACATTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 8 0.26
31 17 0.55
32 6 0.19
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (30 bp):
AAAAGTTGGAACTTCTGTACAATTAACCAA
Found at i:1863539 original size:13 final size:13
Alignment explanation
Indices: 1863523--1863571 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
1863513 TAAACCAAAT
*
1863523 TTTTCAAAAGTAC
1 TTTTCAAAAGCAC
*
1863536 TTTTTC-ACAGCAC
1 -TTTTCAAAAGCAC
1863549 -TTT-AAAAGCAC
1 TTTTCAAAAGCAC
1863560 TTTTCAAAAGCA
1 TTTTCAAAAGCA
1863572 TTGAAAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
11 9 0.31
12 3 0.10
13 12 0.41
14 5 0.17
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:1869415 original size:2 final size:2
Alignment explanation
Indices: 1869408--1869438 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1869398 ATTGATGTAC
1869408 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 T
1869439 GAGCAGTGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1871926 original size:29 final size:29
Alignment explanation
Indices: 1871884--1871941 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1871874 GCAACCCATT
*
1871884 TTTATTATCATATCGAAACGATATTCCTA
1 TTTATTATCATATCAAAACGATATTCCTA
*
1871913 TTTATTATCATATCAAAACGCTATTCCTA
1 TTTATTATCATATCAAAACGATATTCCTA
1871942 ATAGAAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.41
Consensus pattern (29 bp):
TTTATTATCATATCAAAACGATATTCCTA
Found at i:1873538 original size:15 final size:16
Alignment explanation
Indices: 1873518--1873549 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1873508 ATTATTTAAA
1873518 TTTTAAAA-TTATTAT
1 TTTTAAAATTTATTAT
1873533 TTTTAAAATTTATTAT
1 TTTTAAAATTTATTAT
1873549 T
1 T
1873550 AAAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAAATTTATTAT
Found at i:1878277 original size:197 final size:196
Alignment explanation
Indices: 1877865--1878447 Score: 672
Period size: 197 Copynumber: 2.9 Consensus size: 196
1877855 ATGTTGTTCG
** * *
1877865 GACTCTTCATTTTTCTTGAAGCAC-CAGTGTTTGACAGATGGATATTACATGGAAAACCTTTGAA
1 GACTCTTCATTTTTCTTGAAGCACTC-GTGTCGGACACATGGATATTACATAGAAAACCTTTG-A
* * * * * * *
1877929 AAATGAAAATTCTTACGATACTCGTGTCAAATGCACACCCGTATTTGACACTCACACCCAAGTCC
64 AAA-G-----CCTAACGATACTCGTATTAAATACAAACCCATATTTGACACTCACACCCAAGTCC
* * *
1877994 GAATAACATAGGGCAAAATTCACTATGCCAACTAACAATTGACAGCTAGGGATCACACAATGATA
123 GAGTAACATAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGGGATCACACAATGATA
1878059 AGTTGCTCA
188 AGTTGCTCA
*
1878068 GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACGCATGGATATTACATAGAAAACCTTTGAAA
1 GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACACATGGATATTACATAGAAAACCTTTGAAA
* * * *
1878133 AGCCTAATGATACTC-TCATTAAATACAAACCCATATTTGACACTTACA-TCAGAGTCTGAGTAA
66 AGCCTAACGATACTCGT-ATTAAATACAAACCCATATTTGACACTCACACCCA-AGTCCGAGTAA
* * * * * *
1878196 CGTAAGGGCAAAATTAACTGTGTCAACTGACAATTGACAGCAAGCGG-TCACACAATGCTATGTT
129 CAT-AGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAG-GGATCACACAATGATAAGTT
1878260 GCTCA
192 GCTCA
** * * * *
1878265 TG-CTCTTCATTTTTCTTGAAGCACTCGTGTTTGATATATGTATATTACATGGAAAACCTTTGAA
1 -GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACACATGGATATTACATAGAAAACCTTTGAA
* * * *
1878329 AAGTCTAACGATACTCGTGTTAAATACATACCCATTTTTGACACTCACACCCAAGTCCGAGTAAC
65 AAGCCTAACGATACTCGTATTAAATACAAACCCATATTTGACACTCACACCCAAGTCCGAGTAAC
*
1878394 ATAGGGCAAAATTCACTATGTCAACTAACAAATCGACAGCAAGGGATCATCACA
130 ATAGGGCAAAATTCACTATGTCAACTAAC-AATTGACAGCAAGGGATCA-CACA
1878448 CAAGATTTTT
Statistics
Matches: 324, Mismatches: 45, Indels: 27
0.82 0.11 0.07
Matches are distributed among these distances:
195 3 0.01
196 72 0.22
197 178 0.55
198 10 0.03
201 1 0.00
202 4 0.01
203 55 0.17
204 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (196 bp):
GACTCTTCATTTTTCTTGAAGCACTCGTGTCGGACACATGGATATTACATAGAAAACCTTTGAAA
AGCCTAACGATACTCGTATTAAATACAAACCCATATTTGACACTCACACCCAAGTCCGAGTAACA
TAGGGCAAAATTCACTATGTCAACTAACAATTGACAGCAAGGGATCACACAATGATAAGTTGCTC
A
Found at i:1885279 original size:20 final size:20
Alignment explanation
Indices: 1885254--1885295 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
1885244 AGTTTGACGT
1885254 AATCTAATATTAAATAAATA
1 AATCTAATATTAAATAAATA
1885274 AATCTAATATTAAATAAATA
1 AATCTAATATTAAATAAATA
1885294 AA
1 AA
1885296 GGGTTAAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AATCTAATATTAAATAAATA
Found at i:1889587 original size:15 final size:15
Alignment explanation
Indices: 1889564--1889600 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1889554 TTGCCTCATA
*
1889564 TTACATTTTAGTCAC
1 TTACGTTTTAGTCAC
*
1889579 TTACGTTTTAGTGAC
1 TTACGTTTTAGTCAC
1889594 TTACGTT
1 TTACGTT
1889601 ATCGTTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.22, C:0.16, G:0.14, T:0.49
Consensus pattern (15 bp):
TTACGTTTTAGTCAC
Found at i:1891998 original size:9 final size:9
Alignment explanation
Indices: 1891984--1892013 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1891974 TTGGTCCTGA
1891984 TTTTATTTT
1 TTTTATTTT
1891993 TTTTA-TTT
1 TTTTATTTT
1892001 TTTTATTTT
1 TTTTATTTT
1892010 TTTT
1 TTTT
1892014 TCTAAATTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTATTTT
Found at i:1893675 original size:23 final size:23
Alignment explanation
Indices: 1893649--1893769 Score: 217
Period size: 23 Copynumber: 5.3 Consensus size: 23
1893639 ATAAGTGCCA
1893649 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1893672 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1893695 CACTGA-ATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1893717 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
1893740 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1893763 CACTGAT
1 CACTGAT
1893770 CAATAACACT
Statistics
Matches: 96, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
22 22 0.23
23 74 0.77
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1893714 original size:45 final size:45
Alignment explanation
Indices: 1893649--1893769 Score: 215
Period size: 45 Copynumber: 2.6 Consensus size: 45
1893639 ATAAGTGCCA
1893649 CACTGATATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTAC
1 CACTGA-ATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTAC
*
1893695 CACTGAATGTAGCCGAAGCTACCACTGAAATGTAGCCGAAGCTAC
1 CACTGAATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTAC
1893740 CACTGAAATGTAGCCGAAGCTACCACTGAT
1 CACTG-AATGTAGCCGAAGCTACCACTGAT
1893770 CAATAACACT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
45 43 0.60
46 29 0.40
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.20
Consensus pattern (45 bp):
CACTGAATGTAGCCGAAGCTACCACTGATATGTAGCCGAAGCTAC
Found at i:1903840 original size:18 final size:16
Alignment explanation
Indices: 1903791--1903844 Score: 56
Period size: 18 Copynumber: 3.2 Consensus size: 16
1903781 TTAATAACAA
1903791 AAAATAAATAAACAATAT
1 AAAATAAA-AAA-AATAT
*
1903809 AAAATAAGAAAAATAT
1 AAAATAAAAAAAATAT
1903825 AAAACTTAAAAAAAAT-T
1 AAAA--TAAAAAAAATAT
1903842 AAA
1 AAA
1903845 GAAAAAGACA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 9 0.28
17 7 0.22
18 16 0.50
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAATAAAAAAAATAT
Found at i:1903846 original size:29 final size:30
Alignment explanation
Indices: 1903814--1903880 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
1903804 AATATAAAAT
* * *
1903814 AAGAAAAATATAAAACTTAA-AAAAAATTA
1 AAGAAAAAGACAAAACTTAATAAAAAAGTA
*
1903843 AAGAAAAAGACAAAAGTTAATAAAAAAGTA
1 AAGAAAAAGACAAAACTTAATAAAAAAGTA
*
1903873 AAAAAAAA
1 AAGAAAAA
1903881 AAGTAAACGA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (30 bp):
AAGAAAAAGACAAAACTTAATAAAAAAGTA
Found at i:1904552 original size:55 final size:55
Alignment explanation
Indices: 1904484--1904593 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
1904474 GTTTCAACAG
*
1904484 AAAGAAAAGGAAAAAGTTGATGGTCTTTTAAATAGGTTTTATATCCTCTCCAGAC
1 AAAGAAAAGGAAAAAGTTGATGGTCTTTTAAATAGGCTTTATATCCTCTCCAGAC
*
1904539 AAAGAAAAGGAAAAAGTTGATGGTCTTTTCAATAGGCTTTATATCCTCTCCAGAC
1 AAAGAAAAGGAAAAAGTTGATGGTCTTTTAAATAGGCTTTATATCCTCTCCAGAC
1904594 TCCTTATACA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (55 bp):
AAAGAAAAGGAAAAAGTTGATGGTCTTTTAAATAGGCTTTATATCCTCTCCAGAC
Found at i:1905457 original size:12 final size:12
Alignment explanation
Indices: 1905440--1905496 Score: 87
Period size: 12 Copynumber: 4.8 Consensus size: 12
1905430 GATATCGCAA
1905440 AGTGGCGGCTGC
1 AGTGGCGGCTGC
1905452 AGTGGCGGCTGC
1 AGTGGCGGCTGC
* *
1905464 AGTGACAGCTGC
1 AGTGGCGGCTGC
*
1905476 AATGGCGGCTGC
1 AGTGGCGGCTGC
1905488 AGTGGCGGC
1 AGTGGCGGC
1905497 GTAGGTGGAG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.14, C:0.25, G:0.46, T:0.16
Consensus pattern (12 bp):
AGTGGCGGCTGC
Found at i:1909861 original size:99 final size:100
Alignment explanation
Indices: 1909729--1909928 Score: 393
Period size: 99 Copynumber: 2.0 Consensus size: 100
1909719 ACACGGTTTG
1909729 AACCCGTACCAAACAAGTGTCTGACAAAAGATTTAACCACCGCTTTACACAAGTCAATACAAGTT
1 AACCCGTACCAAACAAGTGTCTGACAAAAGATTTAACCACCGCTTTACACAAGTCAATACAAGTT
1909794 TTAAAATATTTTCATTTAAATGT-ATTATAAAAAT
66 TTAAAATATTTTCATTTAAATGTAATTATAAAAAT
1909828 AACCCGTACCAAACAAGTGTCTGACAAAAGATTTAACCACCGCTTTACACAAGTCAATACAAGTT
1 AACCCGTACCAAACAAGTGTCTGACAAAAGATTTAACCACCGCTTTACACAAGTCAATACAAGTT
1909893 TTAAAATATTTTCATTTAAATGTAATTATAAAAAT
66 TTAAAATATTTTCATTTAAATGTAATTATAAAAAT
1909928 A
1 A
1909929 TAATAAATAC
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
99 88 0.88
100 12 0.12
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (100 bp):
AACCCGTACCAAACAAGTGTCTGACAAAAGATTTAACCACCGCTTTACACAAGTCAATACAAGTT
TTAAAATATTTTCATTTAAATGTAATTATAAAAAT
Found at i:1910395 original size:29 final size:28
Alignment explanation
Indices: 1910365--1910427 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
1910355 TGTTTGTTAT
*
1910365 TTTTTATATTT-AGAATTTAGTCCTTCTA
1 TTTTTA-ATTTAAGAATTTAGTCCCTCTA
1910393 TTTTTAATTTAAAGAATTTAGTCCCTCTA
1 TTTTTAATTT-AAGAATTTAGTCCCTCTA
1910422 CTTTTT
1 -TTTTT
1910428 GGATTTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 4 0.13
28 6 0.19
29 16 0.52
30 5 0.16
ACGTcount: A:0.25, C:0.13, G:0.06, T:0.56
Consensus pattern (28 bp):
TTTTTAATTTAAGAATTTAGTCCCTCTA
Found at i:1913402 original size:30 final size:30
Alignment explanation
Indices: 1913366--1913533 Score: 179
Period size: 30 Copynumber: 5.8 Consensus size: 30
1913356 CATCACCACT
*
1913366 ATCAGCATCCCTATTGCCGTCACCGTCACC
1 ATCAGCATCCCTATTGCCATCACCGTCACC
* * * *
1913396 ATCAGCATCACAATTGTCATCA-C--CACT
1 ATCAGCATCCCTATTGCCATCACCGTCACC
*
1913423 ATCAACATCCCTATTGCCATCACCGTCACC
1 ATCAGCATCCCTATTGCCATCACCGTCACC
* * *
1913453 ATCAGCATCACAATTGCCATCA-C--CACT
1 ATCAGCATCCCTATTGCCATCACCGTCACC
*
1913480 ATCAACATCCCTATTGCCATCACCGTCACC
1 ATCAGCATCCCTATTGCCATCACCGTCACC
*
1913510 TTCAGCATCACC-ATTGCCATCACC
1 ATCAGCATC-CCTATTGCCATCACC
1913534 ATCAGCGTCA
Statistics
Matches: 111, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
27 43 0.39
28 2 0.02
29 2 0.02
30 62 0.56
31 2 0.02
ACGTcount: A:0.27, C:0.40, G:0.08, T:0.24
Consensus pattern (30 bp):
ATCAGCATCCCTATTGCCATCACCGTCACC
Found at i:1913432 original size:57 final size:57
Alignment explanation
Indices: 1913355--1913534 Score: 315
Period size: 57 Copynumber: 3.2 Consensus size: 57
1913345 ATCACCATCA
* *
1913355 CCATCACCACTATCAGCATCCCTATTGCCGTCACCGTCACCATCAGCATCACAATTG
1 CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
*
1913412 TCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
1 CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
* *
1913469 CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCTTCAGCATCACCATTG
1 CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
1913526 CCATCACCA
1 CCATCACCA
1913535 TCAGCGTCAC
Statistics
Matches: 117, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 117 1.00
ACGTcount: A:0.28, C:0.41, G:0.08, T:0.23
Consensus pattern (57 bp):
CCATCACCACTATCAACATCCCTATTGCCATCACCGTCACCATCAGCATCACAATTG
Found at i:1913475 original size:24 final size:24
Alignment explanation
Indices: 1913448--1913557 Score: 85
Period size: 27 Copynumber: 4.2 Consensus size: 24
1913438 GCCATCACCG
1913448 TCACCATCAGCATCACAATTGCCA
1 TCACCATCAGCATCACAATTGCCA
* * *
1913472 TCACCACTATCAACATCCCTATTGCCA
1 TCA-C-C-ATCAGCATCACAATTGCCA
*
1913499 TCACCGTCACCTTCAGCATCACCATTGCCA
1 TCA-C--CA---TCAGCATCACAATTGCCA
* *
1913529 TCACCATCAGCGTCACAATTACCA
1 TCACCATCAGCATCACAATTGCCA
1913553 TCACC
1 TCACC
1913558 GTCACCACTA
Statistics
Matches: 69, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
24 23 0.33
25 1 0.01
26 1 0.01
27 24 0.35
28 1 0.01
29 1 0.01
30 18 0.26
ACGTcount: A:0.29, C:0.41, G:0.07, T:0.23
Consensus pattern (24 bp):
TCACCATCAGCATCACAATTGCCA
Found at i:1916276 original size:2 final size:2
Alignment explanation
Indices: 1916269--1916299 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1916259 AATAATTCAT
*
1916269 TA TA TA TA TA AA 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 T
1916300 GTCTTGAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
TA
Found at i:1919611 original size:31 final size:31
Alignment explanation
Indices: 1919571--1919633 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
1919561 TTCTATTACA
* *
1919571 TTTAGTTTAAT-TTATTAAATTCATTTTATTT
1 TTTAATTTAATATAATTAAATTC-TTTTATTT
*
1919602 TTTAATTTAATATAATTAATTTCTTTTATTT
1 TTTAATTTAATATAATTAAATTCTTTTATTT
1919633 T
1 T
1919634 GATTATTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.30, C:0.03, G:0.02, T:0.65
Consensus pattern (31 bp):
TTTAATTTAATATAATTAAATTCTTTTATTT
Found at i:1919628 original size:26 final size:26
Alignment explanation
Indices: 1919576--1919628 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
1919566 TTACATTTAG
* *
1919576 TTTAATTTATTAAATTCATTTTATTT
1 TTTAATTTAATAAATTCAATTTATTT
*
1919602 TTTAATTTAATATAATT-AATTTCTTT
1 TTTAATTTAATA-AATTCAATTTATTT
1919628 T
1 T
1919629 ATTTTGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (26 bp):
TTTAATTTAATAAATTCAATTTATTT
Found at i:1926706 original size:30 final size:31
Alignment explanation
Indices: 1926672--1926729 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
1926662 AGATGATACT
*
1926672 TGTGATGATG-ATCTTATGGGCC-TATGTACA
1 TGTGATGATGCA-CCTATGGGCCTTATGTACA
*
1926702 TGTGATTATGCACCTATGGGCCTTATGT
1 TGTGATGATGCACCTATGGGCCTTATGT
1926730 GTGAAGATCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 18 0.75
31 6 0.25
ACGTcount: A:0.21, C:0.16, G:0.26, T:0.38
Consensus pattern (31 bp):
TGTGATGATGCACCTATGGGCCTTATGTACA
Found at i:1934569 original size:7 final size:7
Alignment explanation
Indices: 1934557--1934585 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1934547 ATAATGATTG
1934557 ATTTATA
1 ATTTATA
1934564 ATTTATA
1 ATTTATA
1934571 ATTTATA
1 ATTTATA
1934578 ATTTATA
1 ATTTATA
1934585 A
1 A
1934586 ATAATAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
ATTTATA
Found at i:1935644 original size:22 final size:23
Alignment explanation
Indices: 1935607--1935655 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
1935597 AAATTTAAAA
1935607 TTATTTAAATAATAAAAAATAATT
1 TTATTTAAAT-ATAAAAAATAATT
* *
1935631 TTATTTAAAT-TAAATAATATTT
1 TTATTTAAATATAAAAAATAATT
1935653 TTA
1 TTA
1935656 ATTATTCCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 13 0.57
24 10 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TTATTTAAATATAAAAAATAATT
Found at i:1937714 original size:29 final size:29
Alignment explanation
Indices: 1937656--1937718 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
1937646 TATTCGATAA
*
1937656 TTTTTATTTAAGTCACTGAACTATTCAAG
1 TTTTTATTTAAATCACTGAACTATTCAAG
* * *
1937685 TTTTTCATTTAAATCATTGAATTGTT-AAG
1 TTTTT-ATTTAAATCACTGAACTATTCAAG
1937714 TTTTT
1 TTTTT
1937719 TTTCTTAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.45
30 16 0.55
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (29 bp):
TTTTTATTTAAATCACTGAACTATTCAAG
Found at i:1939385 original size:31 final size:31
Alignment explanation
Indices: 1939337--1939405 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
1939327 TTAAACTTTT
*
1939337 TTTATCC-ATGTTAATCCTCAAACTTATAAC
1 TTTATCCAATATTAATCCTCAAACTTATAAC
1939367 TTTATCCAATATTAATCCTCAAACTTATAAC
1 TTTATCCAATATTAATCCTCAAACTTATAAC
1939398 TTTATCCA
1 TTTATCCA
1939406 GTTTTGATCC
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 7 0.19
31 30 0.81
ACGTcount: A:0.35, C:0.23, G:0.01, T:0.41
Consensus pattern (31 bp):
TTTATCCAATATTAATCCTCAAACTTATAAC
Found at i:1943588 original size:20 final size:20
Alignment explanation
Indices: 1943553--1943591 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1943543 TCTTAAGAAC
*
1943553 AATATTCCAACCGAAAAAAA
1 AATATTCCAACAGAAAAAAA
*
1943573 AATATTCCAATAGAAAAAA
1 AATATTCCAACAGAAAAAA
1943592 TGATTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.15, G:0.05, T:0.18
Consensus pattern (20 bp):
AATATTCCAACAGAAAAAAA
Found at i:1944150 original size:28 final size:28
Alignment explanation
Indices: 1944101--1944156 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
1944091 TTTAATTAAA
*
1944101 AAAATTAAAGTTGATCGGAAAATTCAAT
1 AAAATTAAAGTTGATCGCAAAATTCAAT
*
1944129 AAAATTAAAGTTTAGT-GCAAAATTCAAT
1 AAAATTAAAGTTGA-TCGCAAAATTCAAT
1944157 CACATAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 24 0.96
29 1 0.04
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (28 bp):
AAAATTAAAGTTGATCGCAAAATTCAAT
Found at i:1944655 original size:70 final size:70
Alignment explanation
Indices: 1944577--1944711 Score: 243
Period size: 70 Copynumber: 1.9 Consensus size: 70
1944567 GTGAAGAGTA
* * *
1944577 ATGAATGATTCATCAAAAAGAATACATTGACCGTACGTGGATGTACGATCGTTCATTAAAAAGTA
1 ATGAATGATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACGATCGCTCACTAAAAAGTA
1944642 CTGTT
66 CTGTT
1944647 ATGAATGATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACGATCGCTCACTAAAAAGTA
1 ATGAATGATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACGATCGCTCACTAAAAAGTA
1944712 ATGTGAGCGT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (70 bp):
ATGAATGATTCATAAAAAAGAATACATTGACCGTACGTGGATGTACGATCGCTCACTAAAAAGTA
CTGTT
Found at i:1956580 original size:18 final size:18
Alignment explanation
Indices: 1956557--1956595 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1956547 CCGCTCCAGC
1956557 AAAGGACACTAAAGATGG
1 AAAGGACACTAAAGATGG
**
1956575 AAAGGATGCTAAAGATGG
1 AAAGGACACTAAAGATGG
1956593 AAA
1 AAA
1956596 AGACTCGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.28, T:0.13
Consensus pattern (18 bp):
AAAGGACACTAAAGATGG
Found at i:1957106 original size:38 final size:38
Alignment explanation
Indices: 1957064--1957145 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
1957054 TTTGCTTATT
* * *
1957064 ATCAT-TTTCGTGGTTTTATCTATGATTGTGTTTAAAAC
1 ATCATATTT-GTGGTTATATCGATGATTGTGCTTAAAAC
* *
1957102 ATCATATTTGTGGTTATATCGATGATTGTGCTTAACAT
1 ATCATATTTGTGGTTATATCGATGATTGTGCTTAAAAC
1957140 ATCATA
1 ATCATA
1957146 AAAATGACCT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 35 0.92
39 3 0.08
ACGTcount: A:0.27, C:0.11, G:0.16, T:0.46
Consensus pattern (38 bp):
ATCATATTTGTGGTTATATCGATGATTGTGCTTAAAAC
Found at i:1966443 original size:30 final size:31
Alignment explanation
Indices: 1966405--1966472 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
1966395 TACAAAATGA
*
1966405 TCATTAAATTA-TTGAAAAGTTTAATTTAAG
1 TCATTAAATTATTTAAAAAGTTTAATTTAAG
* * *
1966435 TTATTAAATTATTTAAAAATTTTTATTTAAG
1 TCATTAAATTATTTAAAAAGTTTAATTTAAG
1966466 TCATTAA
1 TCATTAA
1966473 GTTGTGTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.31
31 22 0.69
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (31 bp):
TCATTAAATTATTTAAAAAGTTTAATTTAAG
Found at i:1970086 original size:9 final size:10
Alignment explanation
Indices: 1970074--1970152 Score: 60
Period size: 9 Copynumber: 8.2 Consensus size: 10
1970064 AAATATTTTA
1970074 AATATAAT-T
1 AATATAATAT
1970083 AATATAATAT
1 AATATAATAT
1970093 AAT-TAATAT
1 AATATAATAT
*
1970102 TATATTATATAT
1 AATA-TA-ATAT
* *
1970114 TATATTATAT
1 AATATAATAT
* *
1970124 TATATTATAT
1 AATATAATAT
1970134 AATA-AA-AT
1 AATATAATAT
1970142 AATAT-ATAT
1 AATATAATAT
1970151 AA
1 AA
1970153 AACATAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
8 7 0.12
9 21 0.35
10 21 0.35
11 3 0.05
12 8 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
AATATAATAT
Found at i:1970092 original size:5 final size:5
Alignment explanation
Indices: 1970074--1970152 Score: 60
Period size: 5 Copynumber: 16.4 Consensus size: 5
1970064 AAATATTTTA
* * *
1970074 AATAT AAT-T AATAT AATAT AAT-T AATAT TATATT ATATAT TATAT TATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA-T A-ATAT AATAT AATAT
* *
1970124 TATAT TATAT AATA- AA-AT AATAT -ATAT AA
1 AATAT AATAT AATAT AATAT AATAT AATAT AA
1970153 AACATAAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 14
0.78 0.05 0.17
Matches are distributed among these distances:
3 1 0.02
4 16 0.25
5 41 0.65
6 2 0.03
7 3 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (5 bp):
AATAT
Found at i:1970110 original size:17 final size:17
Alignment explanation
Indices: 1970076--1970127 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
1970066 ATATTTTAAA
1970076 TATAATTAATA-TA-A-
1 TATAATTAATATTATAT
1970090 TATAATTAATATTATAT
1 TATAATTAATATTATAT
1970107 TATATATT-ATATTATAT
1 TATA-ATTAATATTATAT
1970124 TATA
1 TATA
1970128 TTATATAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.32
15 2 0.06
16 1 0.03
17 17 0.50
18 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAATTAATATTATAT
Found at i:1970113 original size:12 final size:12
Alignment explanation
Indices: 1970084--1970134 Score: 63
Period size: 12 Copynumber: 4.4 Consensus size: 12
1970074 AATATAATTA
*
1970084 ATATAATATAATT
1 ATATATTAT-ATT
1970097 A-ATATTATATT
1 ATATATTATATT
1970108 ATATATTATA-T
1 ATATATTATATT
1970119 -TATATTATATT
1 ATATATTATATT
1970130 ATATA
1 ATATA
1970135 ATAAAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
10 9 0.26
11 6 0.18
12 18 0.53
13 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATATTATATT
Found at i:1976392 original size:15 final size:15
Alignment explanation
Indices: 1976372--1976407 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
1976362 GTTTGGATGA
1976372 GCGGTGAGGTACAGT
1 GCGGTGAGGTACAGT
1976387 GCGGTGAGGTACAGT
1 GCGGTGAGGTACAGT
1976402 GCGGTG
1 GCGGTG
1976408 CGTTTAGCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.14, G:0.50, T:0.19
Consensus pattern (15 bp):
GCGGTGAGGTACAGT
Found at i:1989353 original size:13 final size:14
Alignment explanation
Indices: 1989317--1989355 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1989307 TTATGTTAAA
1989317 TTAAAATAAAATTG
1 TTAAAATAAAATTG
1989331 TTAAATATAAAATT-
1 TTAAA-ATAAAATTG
*
1989345 TTAACATAAAA
1 TTAAAATAAAA
1989356 GTAGGACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 6 0.26
14 9 0.39
15 8 0.35
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
TTAAAATAAAATTG
Found at i:1990095 original size:31 final size:30
Alignment explanation
Indices: 1990060--1990122 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
1990050 TACAAAATGA
1990060 TCATTGAACTATTC-AAAAGTTTTCATTTAAG
1 TCATTGAACTATTCGAAAA-TTTT-ATTTAAG
**
1990091 TCATTGAGTTATTCTGAAAATTTTATTTAAG
1 TCATTGAACTATTC-GAAAATTTTATTTAAG
1990122 T
1 T
1990123 TACCGGGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 20 0.71
32 4 0.14
33 4 0.14
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (30 bp):
TCATTGAACTATTCGAAAATTTTATTTAAG
Found at i:1990689 original size:11 final size:11
Alignment explanation
Indices: 1990673--1990705 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1990663 CTTTTAAATA
1990673 ATTTAATAATT
1 ATTTAATAATT
1990684 ATTTAATAATT
1 ATTTAATAATT
*
1990695 TTTTAA-AATT
1 ATTTAATAATT
1990705 A
1 A
1990706 AACGATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 4 0.20
11 16 0.80
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTAATAATT
Found at i:1996763 original size:20 final size:21
Alignment explanation
Indices: 1996738--1996776 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1996728 TATATTTGAG
1996738 ATGTTA-CGTTTTAGTTACTT
1 ATGTTATCGTTTTAGTTACTT
*
1996758 ATGTTATCGTTTTCGTTAC
1 ATGTTATCGTTTTAGTTAC
1996777 AAAATGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.18, C:0.13, G:0.15, T:0.54
Consensus pattern (21 bp):
ATGTTATCGTTTTAGTTACTT
Found at i:1998542 original size:2 final size:2
Alignment explanation
Indices: 1998535--1998564 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1998525 TTTACTAGGA
1998535 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
1998565 GTTTAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2010339 original size:21 final size:22
Alignment explanation
Indices: 2010304--2010346 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
2010294 AACTTCTTTT
* *
2010304 TTTATTTCTAATATTATATTAA
1 TTTATTTCAAATATTAAATTAA
2010326 TTTA-TTCAAATATTAAATTAA
1 TTTATTTCAAATATTAAATTAA
2010347 AATATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTATTTCAAATATTAAATTAA
Found at i:2018623 original size:22 final size:20
Alignment explanation
Indices: 2018575--2018614 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2018565 ATTGATGTCC
2018575 TTTCATTGATTCTTCCTAAA
1 TTTCATTGATTCTTCCTAAA
*
2018595 TTGCATTGATT-TATCCTAAA
1 TTTCATTGATTCT-TCCTAAA
2018615 AATTTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (20 bp):
TTTCATTGATTCTTCCTAAA
Found at i:2026462 original size:34 final size:34
Alignment explanation
Indices: 2026424--2026490 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
2026414 CCACCAAAAT
2026424 GATAATATTTTGATTTAATCTTTTAAAAAATCAA
1 GATAATATTTTGATTTAATCTTTTAAAAAATCAA
2026458 GATAATATTTTGATTTAATCTTTTAAAAAATCA
1 GATAATATTTTGATTTAATCTTTTAAAAAATCA
2026491 TAAAGATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (34 bp):
GATAATATTTTGATTTAATCTTTTAAAAAATCAA
Found at i:2029559 original size:135 final size:135
Alignment explanation
Indices: 2029398--2029692 Score: 509
Period size: 135 Copynumber: 2.2 Consensus size: 135
2029388 TACAGCCCCT
* * * * *
2029398 AAGCAAATATGGCGACTGGTTTCAGCTTCTAGTAATGCAACTAATAGCGAGCTGAAAAAGGATGA
1 AAGCAAAAATGGAGACTGGTTTCAGCTTCTAGTAATACAACTAAGAGCGAGCTGAAAAAGGATAA
*
2029463 ACCTTTGGAATCATCTAGTAGTGATAGTTCTCAGAATTCTTGTCAAGCAAATGGGGATTCAAGAA
66 ACCTTTGGAATCATCTAGTAGTGATAGTTCTCAGAATTCTTGTCAAGCAAACGGGGATTCAAGAA
2029528 CTGTA
131 CTGTA
*
2029533 AAGCAAAAATGGAGACTGGTTTCAGCTTCTAGTAATACGACTAAGAGCGAGCTGAAAAAGGATAA
1 AAGCAAAAATGGAGACTGGTTTCAGCTTCTAGTAATACAACTAAGAGCGAGCTGAAAAAGGATAA
*
2029598 ACCTTTGGAATCATCTAGTAGTGATGGTTCTCAGAATTCTTGTCAAGCAAACGGGGATTCAAGAA
66 ACCTTTGGAATCATCTAGTAGTGATAGTTCTCAGAATTCTTGTCAAGCAAACGGGGATTCAAGAA
2029663 CTGTA
131 CTGTA
*
2029668 AAGCAAAAATGGAGACCGGTTTCAG
1 AAGCAAAAATGGAGACTGGTTTCAG
2029693 GAGGCATGGT
Statistics
Matches: 151, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 151 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (135 bp):
AAGCAAAAATGGAGACTGGTTTCAGCTTCTAGTAATACAACTAAGAGCGAGCTGAAAAAGGATAA
ACCTTTGGAATCATCTAGTAGTGATAGTTCTCAGAATTCTTGTCAAGCAAACGGGGATTCAAGAA
CTGTA
Found at i:2031839 original size:29 final size:29
Alignment explanation
Indices: 2031788--2031843 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2031778 CTTTGGACCT
* *
2031788 GATCAAATTAGTCCTTCTACTATTAAATG
1 GATCAAATTAGTCCCTATACTATTAAATG
* *
2031817 GATCAATTTAGTCCCTATTCTATTAAA
1 GATCAAATTAGTCCCTATACTATTAAA
2031844 AAGAATCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.18, G:0.09, T:0.39
Consensus pattern (29 bp):
GATCAAATTAGTCCCTATACTATTAAATG
Found at i:2042710 original size:31 final size:29
Alignment explanation
Indices: 2042675--2042746 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2042665 CGCTCCGTGT
* * *
2042675 CTAAAATATTACAATTTGATAACATAAGTGA
1 CTAAAATATAAC-ATTTCA-AACATAAATGA
*
2042706 CTAAAACATAACATTTCAAACATAAATGA
1 CTAAAATATAACATTTCAAACATAAATGA
*
2042735 CTAAAATGTAAC
1 CTAAAATATAAC
2042747 CCGAGACAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 20 0.57
30 5 0.14
31 10 0.29
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.28
Consensus pattern (29 bp):
CTAAAATATAACATTTCAAACATAAATGA
Found at i:2048390 original size:16 final size:16
Alignment explanation
Indices: 2048366--2048406 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2048356 TAGTAAAAAT
2048366 ATAATTTTATTATTTTA
1 ATAATTTTA-TATTTTA
*
2048383 AT-ATTTTATATTTTT
1 ATAATTTTATATTTTA
2048398 ATAATTTTA
1 ATAATTTTA
2048407 AAGATTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
16 12 0.55
17 2 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATAATTTTATATTTTA
Found at i:2048953 original size:25 final size:26
Alignment explanation
Indices: 2048925--2048978 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
2048915 TTTCTACTAT
* *
2048925 ATAAAATAATA-TTGGAATTAAAAAA
1 ATAAAATAATACATGAAATTAAAAAA
*
2048950 AT-AAATCATACATGAAATTAAAAAA
1 ATAAAATAATACATGAAATTAAAAAA
2048975 ATAA
1 ATAA
2048979 TTCTTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
24 7 0.29
25 16 0.67
26 1 0.04
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.26
Consensus pattern (26 bp):
ATAAAATAATACATGAAATTAAAAAA
Found at i:2050726 original size:25 final size:24
Alignment explanation
Indices: 2050690--2050742 Score: 70
Period size: 25 Copynumber: 2.2 Consensus size: 24
2050680 CACAAACGCA
2050690 GCTCTTTATGAGCGTCCTAATATAG
1 GCTCTTTATGAGCGTCCTAATAT-G
* * *
2050715 GCTCTTTGTGAGCTTCCTGATATG
1 GCTCTTTATGAGCGTCCTAATATG
2050739 GCTC
1 GCTC
2050743 GCTTGAACTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (24 bp):
GCTCTTTATGAGCGTCCTAATATG
Found at i:2078841 original size:2 final size:2
Alignment explanation
Indices: 2078834--2078858 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2078824 TTGCATACAA
2078834 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
2078859 ACGAAGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.