Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 9 of 105
Found at i:1627657 original size:24 final size:26
Alignment explanation
Indices: 1627630--1627688 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
1627620 TTTGTATATA
**
1627630 TTATTAATCTTCTCATTAAA-T-TTT
1 TTATTAAAATTCTCATTAAATTATTT
*
1627654 TTATTAAAATTTTCATTAAATTATTT
1 TTATTAAAATTCTCATTAAATTATTT
1627680 TTATTAAAA
1 TTATTAAAA
1627689 AAATTCTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 17 0.57
25 1 0.03
26 12 0.40
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATTAAAATTCTCATTAAATTATTT
Found at i:1627685 original size:14 final size:12
Alignment explanation
Indices: 1627644--1627688 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
1627634 TAATCTTCTC
*
1627644 ATTAAATTTTTT
1 ATTAAAATTTTT
*
1627656 ATTAAAATTTTC
1 ATTAAAATTTTT
1627668 ATTAAATTATTTTT
1 ATTAAA--ATTTTT
1627682 ATTAAAA
1 ATTAAAA
1627689 AAATTCTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
12 17 0.61
14 11 0.39
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTAAAATTTTT
Found at i:1628388 original size:12 final size:12
Alignment explanation
Indices: 1628371--1628407 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1628361 AACACCTTAC
1628371 ATATATATATTT
1 ATATATATATTT
1628383 ATATATATATTT
1 ATATATATATTT
*
1628395 AGTATATAGATTT
1 A-TATATATATTT
1628408 TTTATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 13 0.57
13 10 0.43
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (12 bp):
ATATATATATTT
Found at i:1629434 original size:20 final size:20
Alignment explanation
Indices: 1629388--1629437 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1629378 TATTTATTAT
* *
1629388 ATAAAAGTTGCTAATAAATA
1 ATAAAATTTACTAATAAATA
*
1629408 ATAAAATTTACTAATAAGTA
1 ATAAAATTTACTAATAAATA
1629428 ATAAAATTTA
1 ATAAAATTTA
1629438 TTTATGATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (20 bp):
ATAAAATTTACTAATAAATA
Found at i:1634281 original size:31 final size:31
Alignment explanation
Indices: 1634246--1634311 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
1634236 CATACCTAAT
*
1634246 ATTCTCTTGAT-AAAAGATGATCTATTAAAGA
1 ATTCT-TTGATAAAAAGATGATCGATTAAAGA
* *
1634277 ATTCTTTTATACAAAAGATGATCGATTAATGA
1 ATTCTTTGATA-AAAAGATGATCGATTAAAGA
1634309 ATT
1 ATT
1634312 TTAATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 5 0.17
32 21 0.70
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (31 bp):
ATTCTTTGATAAAAAGATGATCGATTAAAGA
Found at i:1641219 original size:33 final size:32
Alignment explanation
Indices: 1641152--1641219 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 32
1641142 TAAAAAAATT
*
1641152 ATTTTATATTTAAAATTATTTAAAAATATTAAA
1 ATTTTATAATTAAAATTATTTAAAAATA-TAAA
1641185 ATTTTA-AATTAAAATAATATTTAATAAATA-AAA
1 ATTTTATAATTAAAAT--TATTTAA-AAATATAAA
1641218 AT
1 AT
1641220 ATTTTTTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
32 8 0.26
33 11 0.35
34 7 0.23
35 5 0.16
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATTTTATAATTAAAATTATTTAAAAATATAAA
Found at i:1641220 original size:17 final size:17
Alignment explanation
Indices: 1641140--1641223 Score: 50
Period size: 17 Copynumber: 5.0 Consensus size: 17
1641130 AATTTTATAA
*
1641140 AATAAA-AAAATTATTT
1 AATAAATAAAAATATTT
* ** *
1641156 TATATTTAAAATTATTT
1 AATAAATAAAAATATTT
1641173 AA-AAATATTAAAAT-TTT
1 AATAAATA--AAAATATTT
* *
1641190 AAATTAA-AATAATATTT
1 -AATAAATAAAAATATTT
1641207 AATAAATAAAAATATTT
1 AATAAATAAAAATATTT
1641224 TTTAAATTAA
Statistics
Matches: 50, Mismatches: 11, Indels: 13
0.68 0.15 0.18
Matches are distributed among these distances:
16 15 0.30
17 26 0.52
18 7 0.14
19 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AATAAATAAAAATATTT
Found at i:1641691 original size:12 final size:12
Alignment explanation
Indices: 1641648--1641691 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
1641638 ATTATTATAC
*
1641648 AATAAATTAATT
1 AATAAATAAATT
*
1641660 AATAAATATATT
1 AATAAATAAATT
1641672 -ATATAATAAATT
1 AATA-AATAAATT
1641684 AATAAATA
1 AATAAATA
1641692 TTTTAATTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 3 0.11
12 21 0.78
13 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
AATAAATAAATT
Found at i:1641697 original size:12 final size:12
Alignment explanation
Indices: 1641648--1641698 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
1641638 ATTATTATAC
1641648 AATAAAT-TAATT
1 AATAAATAT-ATT
1641660 AATAAATATATT
1 AATAAATATATT
*
1641672 -ATATAATAAATT
1 AATA-AATATATT
*
1641684 AATAAATATTTT
1 AATAAATATATT
1641696 AAT
1 AAT
1641699 TATTCATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
11 3 0.09
12 26 0.79
13 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
AATAAATATATT
Found at i:1641777 original size:19 final size:19
Alignment explanation
Indices: 1641736--1641779 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
1641726 TTTAAAATTT
* * * *
1641736 TAATTTTTTAATTATTTAT
1 TAATTTTATAAATATTAAG
1641755 TAATTTTATAAATATTAAG
1 TAATTTTATAAATATTAAG
1641774 TAATTT
1 TAATTT
1641780 AACATGTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TAATTTTATAAATATTAAG
Found at i:1644277 original size:29 final size:29
Alignment explanation
Indices: 1644207--1644278 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
1644197 TTCATTTGAA
* *
1644207 ATAAAGATTTATATGGATACAAATCAAAGT
1 ATAAAGA-TTATTTGGATACAAATAAAAGT
*
1644237 ATAAATGATTATTTTGATAC-AATAAAAGT
1 ATAAA-GATTATTTGGATACAAATAAAAGT
1644266 ATAAAGACTTATT
1 ATAAAGA-TTATT
1644279 AAAAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 2 0.05
29 18 0.49
30 15 0.41
31 2 0.05
ACGTcount: A:0.49, C:0.06, G:0.11, T:0.35
Consensus pattern (29 bp):
ATAAAGATTATTTGGATACAAATAAAAGT
Found at i:1649332 original size:2 final size:2
Alignment explanation
Indices: 1649287--1649315 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1649277 TGTGTGTGTG
1649287 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 T
1649316 GTACACGTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1650428 original size:14 final size:14
Alignment explanation
Indices: 1650409--1650435 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1650399 TTTTTATATT
1650409 ATTTTAATTTAATA
1 ATTTTAATTTAATA
1650423 ATTTTAATTTAAT
1 ATTTTAATTTAAT
1650436 TATTAATCTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
ATTTTAATTTAATA
Found at i:1656972 original size:20 final size:21
Alignment explanation
Indices: 1656949--1656987 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1656939 AATTTATTTT
*
1656949 TTTATTT-ATAAAATTAAAAA
1 TTTATTTAAAAAAATTAAAAA
1656969 TTTATTTAAAAAAATTAAA
1 TTTATTTAAAAAAATTAAA
1656988 TTTTTATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
TTTATTTAAAAAAATTAAAAA
Found at i:1656993 original size:21 final size:20
Alignment explanation
Indices: 1656947--1656994 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1656937 TAAATTTATT
*
1656947 TTTTTATTTATAAAATTAAA
1 TTTTTATTTAAAAAATTAAA
**
1656967 AATTTATTTAAAAAAATTAAA
1 TTTTTATTT-AAAAAATTAAA
1656988 TTTTTAT
1 TTTTTAT
1656995 CACTTAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TTTTTATTTAAAAAATTAAA
Found at i:1657661 original size:6 final size:7
Alignment explanation
Indices: 1657646--1657676 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1657636 AATACTAAAA
1657646 TTTTATT
1 TTTTATT
1657653 TTTTATT
1 TTTTATT
1657660 TTTTA-T
1 TTTTATT
1657666 TTTTATT
1 TTTTATT
1657673 TTTT
1 TTTT
1657677 TCTCACCCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTATT
Found at i:1657677 original size:14 final size:14
Alignment explanation
Indices: 1657646--1657676 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1657636 AATACTAAAA
1657646 TTTTATTTTTTATT
1 TTTTATTTTTTATT
1657660 TTTTA-TTTTTATT
1 TTTTATTTTTTATT
1657673 TTTT
1 TTTT
1657677 TCTCACCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTATTTTTTATT
Found at i:1661069 original size:30 final size:30
Alignment explanation
Indices: 1660984--1661115 Score: 126
Period size: 30 Copynumber: 4.4 Consensus size: 30
1660974 ATAATTAATG
* * *
1660984 TTAAAAATATATTT-AAGTATAAATTAAAAGT
1 TTAAAAATTTATTTGAA-TGTAAATTAAAA-A
* * **
1661015 TTAAAAATTTACTTGGATACAAATTAAAAA
1 TTAAAAATTTATTTGAATGTAAATTAAAAA
*
1661045 TTAAAAGTTTATTTGAATGTAAATTAAAAA
1 TTAAAAATTTATTTGAATGTAAATTAAAAA
*
1661075 TTAAAAATTTATTTAAATGT-AA-TAAAAA
1 TTAAAAATTTATTTGAATGTAAATTAAAAA
*
1661103 TATAAAGATTTAT
1 T-TAAAAATTTAT
1661116 CTAAATAAAG
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.08
29 12 0.14
30 43 0.50
31 23 0.27
32 1 0.01
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (30 bp):
TTAAAAATTTATTTGAATGTAAATTAAAAA
Found at i:1663984 original size:13 final size:13
Alignment explanation
Indices: 1663966--1664004 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1663956 AATGATTAAA
1663966 TAAAAATTAAAAT
1 TAAAAATTAAAAT
*
1663979 TAAAAATCAAAAT
1 TAAAAATTAAAAT
*
1663992 CAATAAATTAAAA
1 TAA-AAATTAAAA
1664005 GATCTTGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAATTAAAAT
Found at i:1664214 original size:225 final size:228
Alignment explanation
Indices: 1663944--1664383 Score: 787
Period size: 225 Copynumber: 1.9 Consensus size: 228
1663934 ATTTGTAAAA
*
1663944 TTCTCTCTTTGAAATGATTAAATAAAAATTAAAATTAAAAATCAAAATCAATAAATTAAAAGATC
1 TTCTCTCTTTGAAATGATTAAATAAAAATAAAAATTAAAAATCAAAATCAATAAATTAAAAGATC
*
1664009 TTGTTACATAAAATAAATATACAAAATTTACAAAAATTTCAATAAATTTTGATATATATTTTTAA
66 TTGTTACATAAAATAAATATACAAAATTTAAAAAAATTTCAATAAATTTTGATATATATTTTTAA
*
1664074 ATAAATTTTTTAGT-AAAATATTGATAAA-TTTTTATCTTTAAATTAATATCGATCAAATTTAAA
131 ATAAATTTTTTAGTAAAAATATTAATAAATTTTTTATCTTTAAATTAATATCGATCAAATTTAAA
1664137 -TTTAAACAACATTTTTAAAGTTTTTTTCAAAT
196 TTTTAAACAACATTTTTAAAGTTTTTTTCAAAT
1664169 TTCTCTCTTTGAAATGATTAAATAAAAATAAAAATTAAAAATCAAAATCAATAAATTAAAAGATC
1 TTCTCTCTTTGAAATGATTAAATAAAAATAAAAATTAAAAATCAAAATCAATAAATTAAAAGATC
*
1664234 TTGTTACATAAAGTAAATATACAAAATTTAAAAAAATTTCAATAAATTTTGATATATATTTTTAA
66 TTGTTACATAAAATAAATATACAAAATTTAAAAAAATTTCAATAAATTTTGATATATATTTTTAA
* * *
1664299 ATAAATTTTTTAGTAAAAATATTAATAAATTTTTTTTCTTTAAGTTAGTATCGATCAAATTTAAA
131 ATAAATTTTTTAGTAAAAATATTAATAAATTTTTTATCTTTAAATTAATATCGATCAAATTTAAA
*
1664364 TTTTAAACAATATTTTTAAA
196 TTTTAAACAACATTTTTAAA
1664384 AATTCTTTTT
Statistics
Matches: 204, Mismatches: 8, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
225 141 0.69
226 13 0.06
227 32 0.16
228 18 0.09
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (228 bp):
TTCTCTCTTTGAAATGATTAAATAAAAATAAAAATTAAAAATCAAAATCAATAAATTAAAAGATC
TTGTTACATAAAATAAATATACAAAATTTAAAAAAATTTCAATAAATTTTGATATATATTTTTAA
ATAAATTTTTTAGTAAAAATATTAATAAATTTTTTATCTTTAAATTAATATCGATCAAATTTAAA
TTTTAAACAACATTTTTAAAGTTTTTTTCAAAT
Found at i:1668192 original size:15 final size:14
Alignment explanation
Indices: 1668163--1668196 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1668153 GATCTAAATC
*
1668163 TATTACTTTTTTGT
1 TATTTCTTTTTTGT
1668177 TATTTCTTTCTTTGT
1 TATTTCTTT-TTTGT
1668192 TATTT
1 TATTT
1668197 GTAATAGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.12, C:0.09, G:0.06, T:0.74
Consensus pattern (14 bp):
TATTTCTTTTTTGT
Found at i:1673786 original size:25 final size:27
Alignment explanation
Indices: 1673734--1673787 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1673724 AAAAAATTTT
*
1673734 TATAATTTTATATAAACAAGTATGATA
1 TATAATTTTATATAAACAAGTATAATA
1673761 TATAATTTT-TATACAA-AA-TATAATA
1 TATAATTTTATATA-AACAAGTATAATA
1673786 TA
1 TA
1673788 AATATACGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 8 0.32
26 6 0.24
27 11 0.44
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (27 bp):
TATAATTTTATATAAACAAGTATAATA
Found at i:1687883 original size:1 final size:1
Alignment explanation
Indices: 1687879--1687903 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1687869 ATAGTTTCTG
1687879 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1687904 CATTTGTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1694078 original size:50 final size:50
Alignment explanation
Indices: 1694003--1694104 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 50
1693993 AAGGCTATTG
1694003 TAAGTATCATGTTTACAGAATCAAGTAAACTACAGGAGTTTTATAAAGAT
1 TAAGTATCATGTTTACAGAATCAAGTAAACTACAGGAGTTTTATAAAGAT
* ** **
1694053 TAAGTTTCATGTTTATGGAATCAAGTAAACTATGGGAGTTTTATAAAGAT
1 TAAGTATCATGTTTACAGAATCAAGTAAACTACAGGAGTTTTATAAAGAT
1694103 TA
1 TA
1694105 TCAGGCTATG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.39, C:0.08, G:0.18, T:0.35
Consensus pattern (50 bp):
TAAGTATCATGTTTACAGAATCAAGTAAACTACAGGAGTTTTATAAAGAT
Found at i:1697859 original size:15 final size:15
Alignment explanation
Indices: 1697836--1697866 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1697826 AATTTGGTTA
*
1697836 ATTTTAAATTAAATT
1 ATTTAAAATTAAATT
1697851 ATTTAAAATTAAATT
1 ATTTAAAATTAAATT
1697866 A
1 A
1697867 AATAAATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTTAAAATTAAATT
Found at i:1698317 original size:17 final size:16
Alignment explanation
Indices: 1698287--1698330 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
1698277 ATAAATTAGA
*
1698287 AAATTTAAATTTATTC
1 AAATTTAAAATTATTC
1698303 AAATATTAAAATTATTC
1 AAAT-TTAAAATTATTC
1698320 AAA-TTAAAATT
1 AAATTTAAAATT
1698331 GAAATTCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.31
16 4 0.15
17 14 0.54
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTTAAAATTATTC
Found at i:1698576 original size:20 final size:20
Alignment explanation
Indices: 1698553--1698601 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1698543 TATATTTTTA
* *
1698553 AAAAATTTATATAAAACATT
1 AAAAATTCACATAAAACATT
1698573 AAAAATTCACATAAAACATT
1 AAAAATTCACATAAAACATT
1698593 AAAAATTCA
1 AAAAATTCA
1698602 AATCACTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATTCACATAAAACATT
Found at i:1698666 original size:2 final size:2
Alignment explanation
Indices: 1698654--1698695 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
1698644 CTTAAATCTA
* *
1698654 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT -T AC AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1698694 AT
1 AT
1698696 GGATATTTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1700220 original size:18 final size:16
Alignment explanation
Indices: 1700180--1700219 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1700170 TATTTTCTTT
*
1700180 AATTTTGTAATATAAG
1 AATTTTTTAATATAAG
1700196 AATTTTTTAATATAAG
1 AATTTTTTAATATAAG
1700212 AATTTTTT
1 AATTTTTT
1700220 TCATTAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (16 bp):
AATTTTTTAATATAAG
Found at i:1701461 original size:13 final size:13
Alignment explanation
Indices: 1701440--1701469 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1701430 TAAATTATAT
*
1701440 TATTTTTATATCA
1 TATTATTATATCA
1701453 TATTATTATATCA
1 TATTATTATATCA
1701466 TATT
1 TATT
1701470 TAAAATCGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTATTATATCA
Found at i:1701786 original size:29 final size:27
Alignment explanation
Indices: 1701742--1701797 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
1701732 GGAACAGTTC
1701742 TAAATTTTTAATTTT-AATGATAAAAAT
1 TAAATTTTTAATTTTAAAT-ATAAAAAT
1701769 TAAATTTTAATAATTTTAAATATAAAAAT
1 TAAATTTT--TAATTTTAAATATAAAAAT
1701798 AAAAACGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 8 0.31
29 15 0.58
30 3 0.12
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
TAAATTTTTAATTTTAAATATAAAAAT
Found at i:1704343 original size:3 final size:3
Alignment explanation
Indices: 1704335--1704376 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1704325 TCCTAAGTAA
*
1704335 AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1704377 CTTAATATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1704832 original size:14 final size:15
Alignment explanation
Indices: 1704813--1704850 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1704803 TATAGGTTAT
1704813 AATTTAAAA-ATAAA
1 AATTTAAAATATAAA
*
1704827 AATTTATAAATATTAA
1 AATTTA-AAATATAAA
1704843 AATTTAAA
1 AATTTAAA
1704851 TTTTAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 5 0.24
16 10 0.48
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AATTTAAAATATAAA
Found at i:1704844 original size:23 final size:23
Alignment explanation
Indices: 1704809--1704866 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
1704799 TATGTATAGG
1704809 TTAT-AAT-TTAAAAATAAAAAT
1 TTATAAATATTAAAAATAAAAAT
* * *
1704830 TTATAAATATTAAAATTTAAATT
1 TTATAAATATTAAAAATAAAAAT
1704853 TTA-AATATATTAAA
1 TTATAA-ATATTAAA
1704867 TGTTACTTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 4 0.13
22 5 0.16
23 22 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TTATAAATATTAAAAATAAAAAT
Found at i:1705032 original size:28 final size:28
Alignment explanation
Indices: 1704969--1705069 Score: 75
Period size: 28 Copynumber: 3.5 Consensus size: 28
1704959 ATAATTTTTA
*
1704969 TTAAAATT-TTAAATTGTATATATGTAT
1 TTAAAATTATTAAATTATATATATGTAT
* * *
1704996 TTTATATTATTATATTATA-ATATCGTAT
1 TTAAAATTATTAAATTATATATAT-GTAT
*
1705024 TTAAAATTATCAAATT-TA-ATTATTGTAAT
1 TTAAAATTATTAAATTATATA-TA-TGT-AT
1705053 TTAAAAATTATATAAAT
1 TT-AAAATTAT-TAAAT
1705070 CAATTTAAGT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
27 13 0.22
28 28 0.48
29 5 0.09
30 8 0.14
31 4 0.07
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (28 bp):
TTAAAATTATTAAATTATATATATGTAT
Found at i:1706226 original size:24 final size:24
Alignment explanation
Indices: 1706199--1706247 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1706189 ATATTTTTTA
1706199 ATATAAATATAAAATTAAATAAAT
1 ATATAAATATAAAATTAAATAAAT
* **
1706223 ATATACATATATTATTAAATAAAT
1 ATATAAATATAAAATTAAATAAAT
1706247 A
1 A
1706248 ATTAAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
ATATAAATATAAAATTAAATAAAT
Found at i:1707289 original size:20 final size:21
Alignment explanation
Indices: 1707242--1707290 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
1707232 AATGATATAA
*
1707242 TTTAAAATTTTGATAAAAAAT
1 TTTAAAATTTAGATAAAAAAT
* *
1707263 TAT-AAATTTAG-TAAAAATT
1 TTTAAAATTTAGATAAAAAAT
1707282 TTTAAAATT
1 TTTAAAATT
1707291 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 9 0.39
20 12 0.52
21 2 0.09
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
TTTAAAATTTAGATAAAAAAT
Found at i:1708043 original size:14 final size:14
Alignment explanation
Indices: 1708024--1708065 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
1708014 ATTATATTTG
1708024 ATAATTTAAAATAA
1 ATAATTTAAAATAA
*
1708038 ATAATTAAAAAATAA
1 ATAATT-TAAAATAA
1708053 AT-ATTTAAAATAA
1 ATAATTTAAAATAA
1708066 TTTCAACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 7 0.28
14 9 0.36
15 9 0.36
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAATTTAAAATAA
Found at i:1708051 original size:15 final size:15
Alignment explanation
Indices: 1708031--1708062 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1708021 TTGATAATTT
1708031 AAAATAAATAATTAA
1 AAAATAAATAATTAA
*
1708046 AAAATAAATATTTAA
1 AAAATAAATAATTAA
1708061 AA
1 AA
1708063 TAATTTCAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATAAATAATTAA
Found at i:1708506 original size:20 final size:20
Alignment explanation
Indices: 1708481--1708523 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1708471 TTTGAACAAT
1708481 TTTGGAGAGTTCAAAGCAAA
1 TTTGGAGAGTTCAAAGCAAA
*
1708501 TTTGGAGAGTTCAAATCAAA
1 TTTGGAGAGTTCAAAGCAAA
1708521 TTT
1 TTT
1708524 AGAAGTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (20 bp):
TTTGGAGAGTTCAAAGCAAA
Found at i:1709741 original size:29 final size:27
Alignment explanation
Indices: 1709668--1709742 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 27
1709658 TACTTTATAT
* *
1709668 TTATTTATATATAGTATTAATAAAAATA
1 TTATTTATATATAAT-TTAATAAAAAAA
*
1709696 TTATTTAATATCTTAATTTAATAAAAAAA
1 TTATTT-ATAT-ATAATTTAATAAAAAAA
1709725 TTACATTTATATATAATT
1 TT--ATTTATATATAATT
1709743 AAATTATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 6 0.15
29 22 0.56
30 7 0.18
31 4 0.10
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.48
Consensus pattern (27 bp):
TTATTTATATATAATTTAATAAAAAAA
Found at i:1715705 original size:29 final size:30
Alignment explanation
Indices: 1715647--1715716 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 30
1715637 CTTATAATTC
* *
1715647 AATTATTGAAAGTTAATTATGGCTTTTT-A
1 AATTATTGAAACTTAATTATGGATTTTTAA
1715676 AATTATTGAAACTTAATTAT-GATTTATTAA
1 AATTATTGAAACTTAATTATGGATTT-TTAA
*
1715706 AAATATTGAAA
1 AATTATTGAAA
1715717 TTTGCAATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.11
29 21 0.58
30 11 0.31
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (30 bp):
AATTATTGAAACTTAATTATGGATTTTTAA
Found at i:1716476 original size:21 final size:19
Alignment explanation
Indices: 1716437--1716479 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1716427 ATTTATGAAC
*
1716437 TTAATTAAATTTTATTATT
1 TTAATAAAATTTTATTATT
1716456 TTAATAAATATTTTAATTATT
1 TTAATAAA-ATTTT-ATTATT
1716477 TTA
1 TTA
1716480 TCCTTTAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATAAAATTTTATTATT
Found at i:1722543 original size:2 final size:2
Alignment explanation
Indices: 1722536--1722563 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1722526 TTGAGTACTG
1722536 TA 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 TA
1722564 ATTTCTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1725241 original size:56 final size:56
Alignment explanation
Indices: 1725144--1725300 Score: 226
Period size: 56 Copynumber: 2.8 Consensus size: 56
1725134 CTGCCCTATG
* *
1725144 CCTTTTGAGGATTTCATTTACTTTAAAGTCCAACCCTAACTAAAGGTTTGTTCCTA
1 CCTTTTGAGGATTTCATTTACTTTAAAATCCAACCCAAACTAAAGGTTTGTTCCTA
* * * * *
1725200 CCTTTAGAGGATTTCATTCACTTTAAAATCTAATCCC-AACTAAAGGTTTGTTCTTG
1 CCTTTTGAGGATTTCATTTACTTTAAAATCCAA-CCCAAACTAAAGGTTTGTTCCTA
*
1725256 CCTTTTGAGGATTTCATTTACTTTAAAATCGAACCCAAACTAAAG
1 CCTTTTGAGGATTTCATTTACTTTAAAATCCAACCCAAACTAAAG
1725301 CGTGATGCCT
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
55 3 0.03
56 84 0.93
57 3 0.03
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (56 bp):
CCTTTTGAGGATTTCATTTACTTTAAAATCCAACCCAAACTAAAGGTTTGTTCCTA
Found at i:1733334 original size:21 final size:20
Alignment explanation
Indices: 1733305--1733343 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1733295 AATATTACAC
*
1733305 TCAGATTTTATATTTTTTTTT
1 TCAGATTTT-TAGTTTTTTTT
*
1733326 TCAGTTTTTTAGTTTTTT
1 TCAGATTTTTAGTTTTTT
1733344 AATTCATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (20 bp):
TCAGATTTTTAGTTTTTTTT
Found at i:1734171 original size:21 final size:21
Alignment explanation
Indices: 1734132--1734172 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1734122 ACCTTTTACA
* *
1734132 ATTTTTTTATTTTAAATTTTT
1 ATTTTTTAATTATAAATTTTT
*
1734153 ATTTTTTAATTATATATTTT
1 ATTTTTTAATTATAAATTTT
1734173 GAAATAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (21 bp):
ATTTTTTAATTATAAATTTTT
Found at i:1734596 original size:26 final size:26
Alignment explanation
Indices: 1734567--1734617 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
1734557 TATATAAAAG
* * *
1734567 TATATATTTTATTATTAATTTTATTT
1 TATATATTATATTAATAAATTTATTT
1734593 TATATATTATATTAATAAATTTATT
1 TATATATTATATTAATAAATTTATT
1734618 ATTTGATATA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
TATATATTATATTAATAAATTTATTT
Found at i:1735400 original size:17 final size:19
Alignment explanation
Indices: 1735360--1735402 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
1735350 CTATCTAAAA
1735360 TTAATA-AAAAAATTAATTT
1 TTAATATAAAAAATTAA-TT
1735379 TTAATATAAAAAATT-A-T
1 TTAATATAAAAAATTAATT
1735396 TTAATAT
1 TTAATAT
1735403 TATTTTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 8 0.35
19 7 0.30
20 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTAATATAAAAAATTAATT
Found at i:1735426 original size:12 final size:12
Alignment explanation
Indices: 1735409--1735451 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1735399 ATATTATTTT
1735409 TTAAATATAAAA
1 TTAAATATAAAA
*
1735421 TTAAATA-AATA
1 TTAAATATAAAA
1735432 TATAAATATAAAA
1 T-TAAATATAAAA
1735445 TTAAATA
1 TTAAATA
1735452 AATTAGATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 4 0.15
12 19 0.70
13 4 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TTAAATATAAAA
Found at i:1735436 original size:18 final size:20
Alignment explanation
Indices: 1735409--1735451 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 20
1735399 ATATTATTTT
1735409 TTAAATATA-AAAT-T-AAA
1 TTAAATATATAAATATAAAA
1735426 -TAAATATATAAATATAAAA
1 TTAAATATATAAATATAAAA
1735445 TTAAATA
1 TTAAATA
1735452 AATTAGATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.36
17 4 0.18
18 1 0.05
19 3 0.14
20 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAAATATATAAATATAAAA
Found at i:1736852 original size:117 final size:113
Alignment explanation
Indices: 1736643--1736951 Score: 270
Period size: 117 Copynumber: 2.7 Consensus size: 113
1736633 AATTCTTTTT
* * * * * *
1736643 TTTTTTATATAAAATATTTAACAA-ATATTTTTTAAAATTATAAAAATATCTTTTTCTTAAAAAT
1 TTTTTTA-AAAAAATATGTAATAATATA-TTTTTAAAATTAT-AAAATATATATTT-TAAAAAAT
* * ** * * *
1736707 TTTATTTTTATTTGTG-G-GGCTCATTTATATC-A-TTTTTTTATTTTTTTAACCTT
62 TTTATTTTT-TATGCGCGAAAC-CAATTATATCAACTTTTTTTATCTTTTT-A--TC
* ** *
1736760 TTTCTTTAAAAAAATATTTAAT-ATATATTTTTAAAATTATTAAAAATATATATATTTTTAAGAT
1 TTT-TTTAAAAAAATATGTAATAATATATTTTTAAAATTA-T-AAAATATATAT-TTTAAAAAAT
1736824 TTTATTTTTTATGCGCGAAACCAATTATATCAAACTTTTTTTTATCTTTTTATC
62 TTTATTTTTTATGCGCGAAACCAATTATATC-AAC-TTTTTTTATCTTTTTATC
* *
1736878 TTTTTTAAATAAATATGTAATAATATATTTTTTAAATTATAAAATATATATTTTAAAAAATTTTA
1 TTTTTTAAAAAAATATGTAATAATATATTTTTAAAATTATAAAATATATATTTTAAAAAATTTTA
1736943 TTTTTTATG
66 TTTTTTATG
1736952 AGTAGAATCC
Statistics
Matches: 162, Mismatches: 19, Indels: 24
0.79 0.09 0.12
Matches are distributed among these distances:
115 20 0.12
116 28 0.17
117 71 0.44
118 27 0.17
119 1 0.01
120 1 0.01
121 14 0.09
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (113 bp):
TTTTTTAAAAAAATATGTAATAATATATTTTTAAAATTATAAAATATATATTTTAAAAAATTTTA
TTTTTTATGCGCGAAACCAATTATATCAACTTTTTTTATCTTTTTATC
Found at i:1737193 original size:8 final size:8
Alignment explanation
Indices: 1737180--1737236 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
1737170 ATTTGACTCA
1737180 TTTTTTTG
1 TTTTTTTG
1737188 TTTTTTTG
1 TTTTTTTG
*
1737196 TTTTTCTG
1 TTTTTTTG
*
1737204 TTTTTTCG
1 TTTTTTTG
1737212 ATTTTGTTT-
1 -TTTT-TTTG
*
1737221 TTGGTTTTG
1 TT-TTTTTG
1737230 TTTTTTT
1 TTTTTTT
1737237 ATGCTATTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
8 30 0.77
9 7 0.18
10 2 0.05
ACGTcount: A:0.02, C:0.04, G:0.14, T:0.81
Consensus pattern (8 bp):
TTTTTTTG
Found at i:1737753 original size:16 final size:18
Alignment explanation
Indices: 1737732--1737771 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
1737722 AAACTCCTTT
1737732 CTTTTTTT-TTTTT-TGC
1 CTTTTTTTGTTTTTATGC
1737748 CTTTTTTTGTTTTTATGC
1 CTTTTTTTGTTTTTATGC
*
1737766 ATTTTT
1 CTTTTT
1737772 ATTAAATCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 8 0.38
17 5 0.24
18 8 0.38
ACGTcount: A:0.05, C:0.10, G:0.07, T:0.78
Consensus pattern (18 bp):
CTTTTTTTGTTTTTATGC
Found at i:1737760 original size:18 final size:17
Alignment explanation
Indices: 1737733--1737771 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1737723 AACTCCTTTC
*
1737733 TTTTTTTTTTTT-TGCC
1 TTTTTTTTTTTTATGCA
1737749 TTTTTTTGTTTTTATGCA
1 TTTTTTT-TTTTTATGCA
1737767 TTTTT
1 TTTTT
1737772 ATTAAATCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 5 0.25
18 8 0.40
ACGTcount: A:0.05, C:0.08, G:0.08, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTTTTATGCA
Found at i:1738260 original size:18 final size:18
Alignment explanation
Indices: 1738240--1738273 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1738230 ATTTTTTACT
*
1738240 TTTTACAATTTT-TTTTG
1 TTTTAAAATTTTATTTTG
1738257 TTTTAAAATTTTATTTT
1 TTTTAAAATTTTATTTT
1738274 TAATTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTAAAATTTTATTTTG
Found at i:1739518 original size:25 final size:25
Alignment explanation
Indices: 1739490--1739551 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
1739480 AAACTGTCTA
1739490 TTTTTTAATAGACAGAAACTATTT-G
1 TTTTTTAATAGACA-AAACTATTTAG
* ** * *
1739515 TTTTTAAATAGTTAAAACTGTTTAT
1 TTTTTTAATAGACAAAACTATTTAG
1739540 TTTTTTAATAGA
1 TTTTTTAATAGA
1739552 TTTATTTGTC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
24 8 0.28
25 21 0.72
ACGTcount: A:0.35, C:0.05, G:0.10, T:0.50
Consensus pattern (25 bp):
TTTTTTAATAGACAAAACTATTTAG
Found at i:1739665 original size:26 final size:26
Alignment explanation
Indices: 1739631--1739686 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
1739621 AATTAGATAC
*
1739631 TTATCAACTTTAAATAAAATAAAATT
1 TTATAAACTTTAAATAAAATAAAATT
* *
1739657 TTATAAACTTTGAATAAAATAATATT
1 TTATAAACTTTAAATAAAATAAAATT
1739683 TTAT
1 TTAT
1739687 TTATTGCATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (26 bp):
TTATAAACTTTAAATAAAATAAAATT
Found at i:1744065 original size:35 final size:35
Alignment explanation
Indices: 1744026--1744096 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1744016 CCATTAATCA
1744026 TATGATAATTATTGAAATGACTAACAAGAAATTTC
1 TATGATAATTATTGAAATGACTAACAAGAAATTTC
1744061 TATGATAATTATTGAAATGACTAACAAGAAATTTC
1 TATGATAATTATTGAAATGACTAACAAGAAATTTC
1744096 T
1 T
1744097 TACTTGTTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.35
Consensus pattern (35 bp):
TATGATAATTATTGAAATGACTAACAAGAAATTTC
Found at i:1751340 original size:210 final size:210
Alignment explanation
Indices: 1750978--1751391 Score: 783
Period size: 210 Copynumber: 2.0 Consensus size: 210
1750968 CTGGTGGCTT
*
1750978 AGAGTTAGGGTCAGAAGGTTGAGATGCTAGTGGTGGTGGAGAGAAGCCGTGGCTGAGAGAAAAAT
1 AGAGTTAGGGTCAGAAGGTTGAGATGCTAGTGGTGGTGGAGAGAAGCCGTGACTGAGAGAAAAAT
*
1751043 GATCAGATGAAAGAGGAGAATCAACAGGAGAATGATCAGATGGTGGTGATTGAGCTTTTGGAATA
66 GATCAGATGAAAGAGGAGAATCAACAGGAGAATGATCAGATGGTGGTAATTGAGCTTTTGGAATA
1751108 GTCTTTGGTGGTGTTGACCTCTTGCTTAATGGAAATCGTGATACTGTGTGATTGTGCTTATTTTC
131 GTCTTTGGTGGTGTTGACCTCTTGCTTAATGGAAATCGTGATACTGTGTGATTGTGCTTATTTTC
1751173 TGCTTCTTCTTCAAG
196 TGCTTCTTCTTCAAG
*
1751188 AGAGTTAGGGTCAGAAGGTTGAGATGCTAGTGGTGGTGGAGAGAAGCCGTGACTGAGAGAAGAAT
1 AGAGTTAGGGTCAGAAGGTTGAGATGCTAGTGGTGGTGGAGAGAAGCCGTGACTGAGAGAAAAAT
1751253 GATCAGATGAAAGAGGAGAATCAACAGGAGAATGATCAGATGGTGGTAATTGAGCTTTTGGAATA
66 GATCAGATGAAAGAGGAGAATCAACAGGAGAATGATCAGATGGTGGTAATTGAGCTTTTGGAATA
* *
1751318 GTCTTTGGTGGTGTTGACCTCTTGCTTAATGGAAATCGTGATGCTGTGTGGTTGTGCTTATTTTC
131 GTCTTTGGTGGTGTTGACCTCTTGCTTAATGGAAATCGTGATACTGTGTGATTGTGCTTATTTTC
1751383 TGCTTCTTC
196 TGCTTCTTC
1751392 ATCATGTTTC
Statistics
Matches: 199, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
210 199 1.00
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.30
Consensus pattern (210 bp):
AGAGTTAGGGTCAGAAGGTTGAGATGCTAGTGGTGGTGGAGAGAAGCCGTGACTGAGAGAAAAAT
GATCAGATGAAAGAGGAGAATCAACAGGAGAATGATCAGATGGTGGTAATTGAGCTTTTGGAATA
GTCTTTGGTGGTGTTGACCTCTTGCTTAATGGAAATCGTGATACTGTGTGATTGTGCTTATTTTC
TGCTTCTTCTTCAAG
Found at i:1751425 original size:18 final size:18
Alignment explanation
Indices: 1751402--1751442 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1751392 ATCATGTTTC
1751402 TCTTGTT-CTTGTTGCTCT
1 TCTTGTTGC-TGTTGCTCT
*
1751420 TCTTGTTGCTGTTTCTCT
1 TCTTGTTGCTGTTGCTCT
1751438 TCTTG
1 TCTTG
1751443 ATGATTCTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.00, C:0.22, G:0.17, T:0.61
Consensus pattern (18 bp):
TCTTGTTGCTGTTGCTCT
Found at i:1751518 original size:24 final size:24
Alignment explanation
Indices: 1751456--1751523 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 24
1751446 ATTCTGTTGA
1751456 TCTTGCTGTTGTTGTTTATCTTCT
1 TCTTGCTGTTGTTGTTTATCTTCT
*
1751480 TCTTGATGATTTTGTTGTTTATCTTCT
1 TCTTGCTG---TTGTTGTTTATCTTCT
1751507 GT-TTGCTGTTGTTGTTT
1 -TCTTGCTGTTGTTGTTT
1751524 CTCATTCTCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
24 16 0.42
27 21 0.55
28 1 0.03
ACGTcount: A:0.06, C:0.12, G:0.19, T:0.63
Consensus pattern (24 bp):
TCTTGCTGTTGTTGTTTATCTTCT
Found at i:1753450 original size:36 final size:36
Alignment explanation
Indices: 1753401--1753474 Score: 103
Period size: 36 Copynumber: 2.1 Consensus size: 36
1753391 AATGCAGCAA
1753401 CAGTTTGCAGACTTTCTGCACCACTAACTTCTCCAT
1 CAGTTTGCAGACTTTCTGCACCACTAACTTCTCCAT
* * * * *
1753437 CAGTTTGCGGACTTTGTGCACCATTATCTTCTTCAT
1 CAGTTTGCAGACTTTCTGCACCACTAACTTCTCCAT
1753473 CA
1 CA
1753475 CCCAATAGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (36 bp):
CAGTTTGCAGACTTTCTGCACCACTAACTTCTCCAT
Found at i:1757659 original size:18 final size:17
Alignment explanation
Indices: 1757638--1757672 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1757628 AATTTATAAA
1757638 TTTAATCAAATTTTTATT
1 TTTAAT-AAATTTTTATT
*
1757656 TTTAATATATTTTTATT
1 TTTAATAAATTTTTATT
1757673 AATAAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTAATAAATTTTTATT
Found at i:1757682 original size:17 final size:17
Alignment explanation
Indices: 1757647--1757685 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1757637 ATTTAATCAA
** *
1757647 ATTTTTATTTTTAATAT
1 ATTTTTATTAATAAAAT
1757664 ATTTTTATTAATAAAAT
1 ATTTTTATTAATAAAAT
1757681 ATTTT
1 ATTTT
1757686 AAATTTAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTATTAATAAAAT
Found at i:1757879 original size:25 final size:25
Alignment explanation
Indices: 1757832--1757881 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1757822 AAAAGAAATT
* *
1757832 ATTTAAATTTAAATTAAATTTTAAA
1 ATTTAAATTTAAATCAAAATTTAAA
1757857 ATTTAAATTTTAAA-CAAAATTTAAA
1 ATTTAAA-TTTAAATCAAAATTTAAA
1757882 CTCAAATATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
ATTTAAATTTAAATCAAAATTTAAA
Found at i:1760517 original size:2 final size:2
Alignment explanation
Indices: 1760512--1760547 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1760502 ATATATATAT
*
1760512 AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG -G AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1760548 TTACTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1760630 original size:2 final size:2
Alignment explanation
Indices: 1760623--1760655 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1760613 TCATCTCTTC
1760623 AT AT 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 AT AT A
1760656 AAATGAGTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1763187 original size:5 final size:5
Alignment explanation
Indices: 1763171--1763202 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
1763161 ACTTGCAAAC
1763171 AAAGG AAA-G AAAGG AAAGG AAAGG AAAGG AAA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAA
1763203 AAGCTTCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:1772073 original size:30 final size:30
Alignment explanation
Indices: 1772038--1772103 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
1772028 AATAAACCAT
*
1772038 TTTTTAAACTTTAATTTATATCAAAATAAA
1 TTTTTAAACTTTAATTTATACCAAAATAAA
* * *
1772068 TTTTT-ATCTTTAATTTGTACCTAAATAAA
1 TTTTTAAACTTTAATTTATACCAAAATAAA
1772097 TTTTTAA
1 TTTTTAA
1772104 CATAAAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 25 0.81
30 6 0.19
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (30 bp):
TTTTTAAACTTTAATTTATACCAAAATAAA
Found at i:1772419 original size:7 final size:7
Alignment explanation
Indices: 1772407--1772448 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
1772397 GTCAGAAATT
1772407 GAAAAAA
1 GAAAAAA
1772414 GAAAAAA
1 GAAAAAA
1772421 GAAAAAA
1 GAAAAAA
1772428 -AAAAAA
1 GAAAAAA
*
1772434 AACAAGAAA
1 GA-AA-AAA
1772443 GAAAAA
1 GAAAAA
1772449 TTTATTGGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
6 6 0.19
7 17 0.55
8 4 0.13
9 4 0.13
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:1772431 original size:18 final size:19
Alignment explanation
Indices: 1772407--1772448 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
1772397 GTCAGAAATT
*
1772407 GAAAAAAGAAAA-AAGAAA
1 GAAAAAAAAAAACAAGAAA
1772425 -AAAAAAAAAAACAAGAAA
1 GAAAAAAAAAAACAAGAAA
1772443 GAAAAA
1 GAAAAA
1772449 TTTATTGGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 10 0.48
18 6 0.29
19 5 0.24
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (19 bp):
GAAAAAAAAAAACAAGAAA
Found at i:1774392 original size:2 final size:2
Alignment explanation
Indices: 1774385--1774418 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1774375 TCTGATTGGC
*
1774385 TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1774419 GGCTAATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1777866 original size:3 final size:3
Alignment explanation
Indices: 1777837--1777895 Score: 73
Period size: 3 Copynumber: 18.7 Consensus size: 3
1777827 TTTATTTTGT
* *
1777837 TTA TTAA TTA TTA GTA GTTA TTAA TTA TTA TTG TTA TTA TTA TTA TTA
1 TTA TT-A TTA TTA TTA -TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
1777885 TTA TTA TTA TT
1 TTA TTA TTA TT
1777896 TTAATAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
3 41 0.84
4 8 0.16
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1778242 original size:23 final size:24
Alignment explanation
Indices: 1778210--1778254 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1778200 TAAAAATTAC
1778210 TTTTATTTA-TTTTTACAAATAAGA
1 TTTTATTTATTTTTTA-AAATAAGA
1778234 TTTTA-TTATTTTTTAAAATAA
1 TTTTATTTATTTTTTAAAATAA
1778255 TTTATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTATTTATTTTTTAAAATAAGA
Found at i:1780503 original size:16 final size:16
Alignment explanation
Indices: 1780478--1780510 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1780468 TGATAAATGA
1780478 ATGATAATGATGATTT
1 ATGATAATGATGATTT
*
1780494 ATGATGATGATGATTT
1 ATGATAATGATGATTT
1780510 A
1 A
1780511 CAATGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.21, T:0.42
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:1780516 original size:16 final size:16
Alignment explanation
Indices: 1780484--1780517 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1780474 ATGAATGATA
**
1780484 ATGATGATTTATGATG
1 ATGATGATTTACAATG
1780500 ATGATGATTTACAATG
1 ATGATGATTTACAATG
1780516 AT
1 AT
1780518 TTTTAATGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.41
Consensus pattern (16 bp):
ATGATGATTTACAATG
Found at i:1780598 original size:27 final size:28
Alignment explanation
Indices: 1780568--1780620 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1780558 TGAATGATAG
1780568 CATATTTTGTA-A-TGATTTATAAATTGA
1 CATATTTTG-ACATTGATTTATAAATTGA
*
1780595 CATATTTTGACATTGATTTATGAATT
1 CATATTTTGACATTGATTTATAAATT
1780621 TGTGAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 1 0.04
27 10 0.43
28 12 0.52
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (28 bp):
CATATTTTGACATTGATTTATAAATTGA
Found at i:1784035 original size:2 final size:2
Alignment explanation
Indices: 1784030--1784077 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1784020 AAAAGAGTTT
1784030 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1784072 GA GA GA
1 GA GA GA
1784078 ATTTTACATT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1786366 original size:24 final size:25
Alignment explanation
Indices: 1786330--1786376 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1786320 CTAATTATAC
*
1786330 AATGATGAAATTTTTAGAAATTTCA
1 AATGATGAAATTTCTAGAAATTTCA
*
1786355 AATGAT-AAATTTCTATAAATTT
1 AATGATGAAATTTCTAGAAATTT
1786377 TTTATATGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.43
Consensus pattern (25 bp):
AATGATGAAATTTCTAGAAATTTCA
Found at i:1789483 original size:8 final size:8
Alignment explanation
Indices: 1789470--1789550 Score: 58
Period size: 8 Copynumber: 9.9 Consensus size: 8
1789460 ATAATGGGTG
1789470 AAAAAATA
1 AAAAAATA
1789478 AAAAAATA
1 AAAAAATA
* *
1789486 AGAAAA-C
1 AAAAAATA
*
1789493 AAAAAATGG
1 AAAAAAT-A
*
1789502 AAAAAA-C
1 AAAAAATA
*
1789509 AAAAAACA
1 AAAAAATA
1789517 AAAAAATAA
1 AAAAAAT-A
*
1789526 GAAAAAAGA
1 -AAAAAATA
1789535 AAAAAATA
1 AAAAAATA
1789543 GAAAAAAT
1 -AAAAAAT
1789551 GTAAAAGAAG
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
7 11 0.19
8 26 0.45
9 15 0.26
10 6 0.10
ACGTcount: A:0.81, C:0.04, G:0.07, T:0.07
Consensus pattern (8 bp):
AAAAAATA
Found at i:1789496 original size:15 final size:15
Alignment explanation
Indices: 1789478--1789537 Score: 52
Period size: 15 Copynumber: 3.9 Consensus size: 15
1789468 TGAAAAAATA
1789478 AAAAAATAAGAAAAC
1 AAAAAATAAGAAAAC
1789493 AAAAAATGGAA-AAAAC
1 AAAAAAT--AAGAAAAC
* * *
1789509 AAAAAACAAAAAAAT
1 AAAAAATAAGAAAAC
1789524 AAGAAAA-AAGAAAA
1 AA-AAAATAAGAAAA
1789538 AAATAGAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 2 0.05
15 19 0.50
16 15 0.39
17 2 0.05
ACGTcount: A:0.82, C:0.05, G:0.08, T:0.05
Consensus pattern (15 bp):
AAAAAATAAGAAAAC
Found at i:1789556 original size:18 final size:18
Alignment explanation
Indices: 1789469--1789549 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
1789459 AATAATGGGT
*
1789469 GAAAAAATAAAAAAATAA
1 GAAAAAAGAAAAAAATAA
*
1789487 GAAAACAA-AAAATGGAAAAAA
1 GAAAA-AAGAAAA---AAATAA
* *
1789508 CAAAAAACAAAAAAATAA
1 GAAAAAAGAAAAAAATAA
1789526 GAAAAAAGAAAAAAAT-A
1 GAAAAAAGAAAAAAATAA
1789543 GAAAAAA
1 GAAAAAA
1789550 TGTAAAAGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
17 8 0.15
18 28 0.53
19 2 0.04
20 2 0.04
21 13 0.25
ACGTcount: A:0.81, C:0.04, G:0.09, T:0.06
Consensus pattern (18 bp):
GAAAAAAGAAAAAAATAA
Found at i:1790331 original size:79 final size:79
Alignment explanation
Indices: 1790165--1790353 Score: 220
Period size: 79 Copynumber: 2.4 Consensus size: 79
1790155 TAACTTGTGG
* ** * *
1790165 GTTATGATCAAATGATGGAAATAATGTGGATCAATAGATGAAATTTGTTCTAAAATTGCTAGTGG
1 GTTATGATCAAATGATGGAAATAATGTGGATCAATAAACAAAATTTATTCTAAAATAGCTAGTGG
* *
1790230 TGCGAAGGCTATGA
66 TGAGAAGACTATGA
* * *
1790244 GTTATGATCAAATGATGGAAATAATGTGGATCAATAAACAAAATTTATTTTGAAATAGCTAGTGT
1 GTTATGATCAAATGATGGAAATAATGTGGATCAATAAACAAAATTTATTCTAAAATAGCTAGTGG
1790309 TGAGAA-ACT-TGTAA
66 TGAGAAGACTATG--A
* * * *
1790323 GTTGTGATCAAGTAATGAAAATAATGTGGAT
1 GTTATGATCAAATGATGGAAATAATGTGGAT
1790354 TAGTTGACAG
Statistics
Matches: 94, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
77 2 0.02
78 2 0.02
79 90 0.96
ACGTcount: A:0.39, C:0.06, G:0.23, T:0.32
Consensus pattern (79 bp):
GTTATGATCAAATGATGGAAATAATGTGGATCAATAAACAAAATTTATTCTAAAATAGCTAGTGG
TGAGAAGACTATGA
Found at i:1791152 original size:43 final size:43
Alignment explanation
Indices: 1791007--1791759 Score: 478
Period size: 43 Copynumber: 17.3 Consensus size: 43
1790997 GATTATTAAG
* ** *
1791007 GAGCTTTATTTATTTTTCAAAGTCATT-AGCCTCTTTTTAGAA
1 GAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
** * * * *
1791049 GAGTTTTATTTAGTTTTCAAAAGTCGTTGAGTCTCTGCTTA-AA
1 GAGCCTTATTTATTTTTC-AAAGTTGTTGAGCCTCTGTTTAGAA
* * **
1791092 GAAGCTTTATTTATTTTTCAAAATTGTTGAGTTTCTGTTTAGAA
1 G-AGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
* * ** * *
1791136 GAGCCTTGTTTGTTTTTTTCAAAGTCATTGAGCCTTTATTTAGAA
1 GAGCCTT-ATT-TATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
* * ** * * *
1791181 GAACCTTATTTACTTTTCAAAGTTGTTGAGTTTTTGATTAAAA
1 GAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
* * * * *
1791224 GAGCTTTATTTATTTTTCAAAGTTGTTGAACATCTATTTAGAG
1 GAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
* * ** *
1791267 GAGCCTTGTTTGTTTTTTTCAAAGTCATTGAGCCTCTATTTA-AA
1 GAGCCTT-ATT-TATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
* * * * *
1791311 GGAGCCTTATTTATTTTTCAAAGTTGTTAAACCTTTGATTAGAG
1 -GAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
* * * * * *
1791355 GAGCTTTATTTGTTTTTCAAAAGTTATTAAGTCTCTGTTTAGAG
1 GAGCCTTATTTATTTTTC-AAAGTTGTTGAGCCTCTGTTTAGAA
* * * * *
1791399 GAACTTTATTTTTTTTTCAAAGTTGTTAAGCCTCTGTTTAGAG
1 GAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
** * * ** *
1791442 GAGTTTTATTTATTTTTTTTAAA-TCGTTGAGCCTCTACTTAGAG
1 GAGCCTTATTTA--TTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
* * * * * *
1791486 GAGCTTTAGTTACTTTTT-AAAGACT-TTGAGTCTCTATTTAGAG
1 GAGCCTTATTTA-TTTTTCAAAG-TTGTTGAGCCTCTGTTTAGAA
** * * *
1791529 GAGCCTTATTTATTTTTTGAAGTTATTGAGCCTCTGCTTAGAG
1 GAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
* * * * * *
1791572 GAGCTTTAGTTACTTTTCAAAAGTCGTTGAGTCTCTATTTAGAA
1 GAGCCTTATTTATTTTTC-AAAGTTGTTGAGCCTCTGTTTAGAA
* * * * * *
1791616 TAACTTTATTTATTTTTCAAAGTCGTTGAACCTCTATTTAG-A
1 GAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
* ** *
1791658 GAAGCTTTATTTAATTTTTCAAAAGTTGTTGAGTATCTATTTA-AA
1 G-AGCCTTATTT-ATTTTTC-AAAGTTGTTGAGCCTCTGTTTAGAA
* ** *
1791703 GGAGCCTTATTTATTTTTTAAAGTCATTGAGCCTCTGCTTAGAA
1 -GAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
1791747 GAGCCTTATTTAT
1 GAGCCTTATTTAT
1791760 GAGCCTTTGT
Statistics
Matches: 561, Mismatches: 126, Indels: 47
0.76 0.17 0.06
Matches are distributed among these distances:
42 26 0.05
43 288 0.51
44 147 0.26
45 99 0.18
46 1 0.00
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (43 bp):
GAGCCTTATTTATTTTTCAAAGTTGTTGAGCCTCTGTTTAGAA
Found at i:1791209 original size:131 final size:130
Alignment explanation
Indices: 1791019--1791759 Score: 567
Period size: 131 Copynumber: 5.7 Consensus size: 130
1791009 GCTTTATTTA
* * *
1791019 TTTTTCAAAGTCATT-AGCCTCTTTTTAGAAGAGTTTTATTTAGTTTTCAAAAGTCGTTGAGTCT
1 TTTTTCAAAGTCATTGAGCCTCTATTTAGAAGAGCTTTATTTACTTTTC-AAAGTCGTTGAGTCT
* * * *
1791083 CTGCTTAAAGAAGCTTTATTTATTTTTCAAAATTGTTGAGTTTCTGTTTAGAAGAGCCTTGTTTG
65 CTGATTAAAGAAGCTTTATTTATTTTTCAAAATTGTTGAGTCTCTATTTAGAGGAGCCTTGTTT-
1791148 TT
129 TT
* * * * * *
1791150 TTTTTCAAAGTCATTGAGCCTTTATTTAGAAGAACCTTATTTACTTTTCAAAGTTGTTGAGTTTT
1 TTTTTCAAAGTCATTGAGCCTCTATTTAGAAGAGCTTTATTTACTTTTCAAAGTCGTTGAGTCTC
* *
1791215 TGATTAAA-AGAGCTTTATTTATTTTTCAAAGTTGTTGA-ACATCTATTTAGAGGAGCCTTGTTT
66 TGATTAAAGA-AGCTTTATTTATTTTTCAAAATTGTTGAGTC-TCTATTTAGAGGAGCCTTGTTT
1791278 GTT
129 -TT
* * * * **
1791281 TTTTTCAAAGTCATTGAGCCTCTATTTA-AAGGAGCCTTATTTATTTTTCAAAGTTGTTAAACCT
1 TTTTTCAAAGTCATTGAGCCTCTATTTAGAA-GAGCTTTATTTACTTTTCAAAGTCGTTGAGTCT
* * * * * * * *
1791345 TTGATTAGAGGAGCTTTATTTGTTTTTCAAAAGTTATTAAGTCTCTGTTTAGAGGA-ACTT-TAT
65 CTGATTAAAGAAGCTTTATTTATTTTTCAAAA-TTGTTGAGTCTCTATTTAGAGGAGCCTTGT-T
1791408 TTT
128 TTT
** * * * * * * *
1791411 TTTTTCAAAGTTGTTAAGCCTCTGTTTAGAGGAGTTTTATTTATTTTTTTTAAA-TCGTTGAGCC
1 TTTTTCAAAGTCATTGAGCCTCTATTTAGAAGAGCTTTATTTA--CTTTTCAAAGTCGTTGAGTC
* * * * *
1791475 TCT-ACTTAGAGGAGCTTTAGTTACTTTTT-AAAGACT-TTGAGTCTCTATTTAGAGGAGCCTTA
64 TCTGA-TTAAAGAAGCTTTATTTA-TTTTTCAAA-ATTGTTGAGTCTCTATTTAGAGGAGCCTTG
*
1791537 TTTAT
126 TTTTT
* * ** * *
1791542 TTTTT-GAAGTTATTGAGCCTCTGCTTAGAGGAGCTTTAGTTACTTTTCAAAAGTCGTTGAGTCT
1 TTTTTCAAAGTCATTGAGCCTCTATTTAGAAGAGCTTTATTTACTTTTC-AAAGTCGTTGAGTCT
* * * ** * * *
1791606 CT-ATTTAGAATAA-CTTTATTTATTTTTCAAAGTCGTTGAACCTCTATTTAGAGAAGCTTTATT
65 CTGA-TTA-AAGAAGCTTTATTTATTTTTCAAAATTGTTGAGTCTCTATTTAGAGGAGCCTTGTT
**
1791669 TAA
128 TTT
** ** * * * * *
1791672 TTTTTCAAAAGTTGTTGAGTATCTATTTA-AAGGAGCCTTATTTATTTTTTAAAGTCATTGAGCC
1 TTTTTC-AAAGTCATTGAGCCTCTATTTAGAA-GAGCTTTATTTACTTTTCAAAGTCGTTGAGTC
* *
1791736 TCTGCTTAGAAG-AGCCTTATTTAT
64 TCTGATTA-AAGAAGCTTTATTTAT
1791760 GAGCCTTTGT
Statistics
Matches: 496, Mismatches: 88, Indels: 52
0.78 0.14 0.08
Matches are distributed among these distances:
128 4 0.01
129 8 0.02
130 149 0.30
131 245 0.49
132 89 0.18
133 1 0.00
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (130 bp):
TTTTTCAAAGTCATTGAGCCTCTATTTAGAAGAGCTTTATTTACTTTTCAAAGTCGTTGAGTCTC
TGATTAAAGAAGCTTTATTTATTTTTCAAAATTGTTGAGTCTCTATTTAGAGGAGCCTTGTTTTT
Found at i:1791286 original size:88 final size:85
Alignment explanation
Indices: 1791005--1791759 Score: 346
Period size: 88 Copynumber: 8.7 Consensus size: 85
1790995 ATGATTATTA
* * * * ** * *
1791005 AGGAGCTTTATTTATTTTTCAAAGTCATT-AGCCTCTTTTTAGAA-GAGTTTTATTTAGTTTTCA
1 AGGAGCCTTATTTGTTTTTCAAAGTTATTGAGTCTCTGATTA-AAGGAGCTTTATTTATTTTTC-
* ** ** *
1791068 AAAGTCGTTGAGTCTCTGCTTAA
64 AAAGTTGTT-AACCTCTATTTAG
* * * * * * * *
1791091 AGAAGCTTTATTTATTTTTCAAAATTGTTGAGTTTCTGTTTAGAA-GAGCCTTGT-TTGTTTTTT
1 AGGAGCCTTATTTGTTTTTCAAAGTTATTGAGTCTCTGATTA-AAGGAG-CTT-TATT-TATTTT
** * *
1791154 TCAAAGTCATTGAGCCTTTATTTAG
62 TCAAAGTTGTT-AACCTCTATTTAG
* * ** * * * *
1791179 AAGAACCTTATTTACTTTTCAAAGTTGTTGAGTTTTTGATTAAAAGAGCTTTATTTATTTTTCAA
1 AGGAGCCTTATTTGTTTTTCAAAGTTATTGAGTCTCTGATTAAAGGAGCTTTATTTATTTTTCAA
*
1791244 AGTTGTTGAACATCTATTTAG
66 AGTTGTT-AACCTCTATTTAG
* * * *
1791265 AGGAGCCTTGTTTGTTTTTTTCAAAGTCATTGAGCCTCT-ATTTAAAGGAGCCTTATTTATTTTT
1 AGGAGCCTTATTTG--TTTTTCAAAGTTATTGAGTCTCTGA-TTAAAGGAGCTTTATTTATTTTT
*
1791329 CAAAGTTGTTAAACCTTTGA-TTAG
63 CAAAGTTGTT-AACCTCT-ATTTAG
* * * * * *
1791353 AGGAGCTTTATTTGTTTTTCAAAAGTTATTAAGTCTCTGTTTAGAGGAACTTTATTTTTTTTTCA
1 AGGAGCCTTATTTGTTTTTC-AAAGTTATTGAGTCTCTGATTAAAGGAGCTTTATTTATTTTTCA
*
1791418 AAGTTGTTAAGCCTCTGTTTAG
65 AAGTTGTTAA-CCTCTATTTAG
** * * ** * * *
1791440 AGGAGTTTTATTTATTTTTTTTAAA-TCGTTGAGCCTCT-ACTTAGAGGAGCTTTAGTTACTTTT
1 AGGAGCCTTA-TT-TGTTTTTCAAAGTTATTGAGTCTCTGA-TTAAAGGAGCTTTATTTA-TTTT
* **
1791503 T-AAAGACTT-TGAGTCTCTATTTAG
62 TCAAAG--TTGTTAACCTCTATTTAG
* ** * * * * *
1791527 AGGAGCCTTATTTATTTTTTGAAGTTATTGAGCCTCTGCTTAGAGGAGCTTTAGTTACTTTTCAA
1 AGGAGCCTTATTTGTTTTTCAAAGTTATTGAGTCTCTGATTAAAGGAGCTTTATTTATTTTTC-A
* **
1791592 AAGTCGTTGAGTCTCTATTTAG
65 AAGTTGTT-AACCTCTATTTAG
** * * * ** ** * *
1791614 AATAACTTTATTTATTTTTCAAAGTCGTTGAACCTCT-ATTTAGAGAAGCTTTATTTAATTTTTC
1 AGGAGCCTTATTTGTTTTTCAAAGTTATTGAGTCTCTGA-TTAAAGGAGCTTTATTT-ATTTTTC
*** *
1791678 AAAAGTTGTTGAGTATCTATTTAA
64 -AAAGTTGTT-AACCTCTATTTAG
* * * * * *
1791702 AGGAGCCTTATTTATTTTTTAAAGTCATTGAGCCTCTGCTTAGAA-GAGCCTTATTTAT
1 AGGAGCCTTATTTGTTTTTCAAAGTTATTGAGTCTCTGATTA-AAGGAGCTTTATTTAT
1791760 GAGCCTTTGT
Statistics
Matches: 530, Mismatches: 109, Indels: 59
0.76 0.16 0.08
Matches are distributed among these distances:
85 14 0.03
86 101 0.19
87 190 0.36
88 208 0.39
89 17 0.03
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (85 bp):
AGGAGCCTTATTTGTTTTTCAAAGTTATTGAGTCTCTGATTAAAGGAGCTTTATTTATTTTTCAA
AGTTGTTAACCTCTATTTAG
Found at i:1791426 original size:87 final size:86
Alignment explanation
Indices: 1791218--1791738 Score: 286
Period size: 87 Copynumber: 6.0 Consensus size: 86
1791208 GAGTTTTTGA
* * * * * *
1791218 TTAAAAGAGCTTTATTTATTTTTCAAAGTTGTTGAACATCT-ATTTAGAGGAGCCTTGTTTGTTT
1 TTAAAGGAACTTTATTTATTTTTCAAAGTTGTTAAACCTCTGA-TTAGAGGAGCTTTATTTG--T
*
1791282 TTTTCAAAGTCATTGAGCCTCTAT
63 TTTTCAAAGTCATTAAGCCTCTAT
* * *
1791306 TTAAAGGAGCCTTATTTATTTTTCAAAGTTGTTAAACCTTTGATTAGAGGAGCTTTATTTGTTTT
1 TTAAAGGAACTTTATTTATTTTTCAAAGTTGTTAAACCTCTGATTAGAGGAGCTTTATTTGTTTT
* * *
1791371 TCAAAAGTTATTAAGTCTCTGT
66 TC-AAAGTCATTAAGCCTCTAT
* * * * * *
1791393 TTAGAGGAACTTTATTTTTTTTTCAAAGTTGTTAAGCCTCTGTTTAGAGGAGTTTTATTTATTTT
1 TTAAAGGAACTTTATTTATTTTTCAAAGTTGTTAAACCTCTGATTAGAGGAGCTTTA-TT-TGTT
* * * *
1791458 TTTTAAA-TCGTTGAGCCTCTAC
64 TTTCAAAGTCATTAAGCCTCTAT
* * * * * ** * *
1791480 TTAGAGGAGCTTTAGTTACTTTTT-AAAGACT-TTGAGTCTCT-ATTTAGAGGAGCCTTATTTAT
1 TTAAAGGAACTTTATTTA-TTTTTCAAAG-TTGTTAAACCTCTGA-TTAGAGGAGCTTTATTTGT
** * * **
1791542 TTTTTGAAGTTATTGAGCCTCTGC
63 TTTTCAAAGTCATTAAGCCTCTAT
* * * * * * ** ** * *
1791566 TTAGAGGAGCTTTAGTTACTTTTCAAAAGTCGTTGAGTCTCT-ATTTAGAATAACTTTATTTATT
1 TTAAAGGAACTTTATTTATTTTTC-AAAGTTGTTAAACCTCTGA-TTAGAGGAGCTTTATTTGTT
*
1791630 TTTCAAAGTCGTTGAA-CCTCTAT
64 TTTCAAAGTCATT-AAGCCTCTAT
* * *** * * *
1791653 TTAGA-GAAGCTTTATTTAATTTTTCAAAAGTTGTTGAGTATCT-ATTTAAAGGAGCCTTATTTA
1 TTAAAGGAA-CTTTATTT-ATTTTTC-AAAGTTGTTAAACCTCTGA-TTAGAGGAGCTTTATTTG
* *
1791716 TTTTTTAAAGTCATTGAGCCTCT
62 TTTTTCAAAGTCATTAAGCCTCT
1791739 GCTTAGAAGA
Statistics
Matches: 350, Mismatches: 68, Indels: 30
0.78 0.15 0.07
Matches are distributed among these distances:
85 13 0.04
86 40 0.11
87 171 0.49
88 119 0.34
89 7 0.02
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.46
Consensus pattern (86 bp):
TTAAAGGAACTTTATTTATTTTTCAAAGTTGTTAAACCTCTGATTAGAGGAGCTTTATTTGTTTT
TCAAAGTCATTAAGCCTCTAT
Found at i:1791981 original size:14 final size:15
Alignment explanation
Indices: 1791962--1791992 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
1791952 TAATTTTGTT
1791962 AATAAAAA-TAAAAA
1 AATAAAAAGTAAAAA
1791976 AATAAAAAGTAAAAA
1 AATAAAAAGTAAAAA
1791991 AA
1 AA
1791993 ATGAAAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (15 bp):
AATAAAAAGTAAAAA
Found at i:1793948 original size:3 final size:3
Alignment explanation
Indices: 1793934--1793967 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
1793924 TTGCAAGTAG
*
1793934 TTA TTAA TTA TTA TTA TTA TTA TTA TTA CTA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
1793968 CTTTTAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:1796338 original size:2 final size:2
Alignment explanation
Indices: 1796331--1796356 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1796321 AAAAGAGTTT
1796331 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1796357 ATTTTACATT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1797703 original size:17 final size:16
Alignment explanation
Indices: 1797681--1797725 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
1797671 TTTATTTTGT
*
1797681 TTATTAATTGTTAGTAG
1 TTATTAATTATTA-TAG
*
1797698 TTATTAATTATTATTG
1 TTATTAATTATTATAG
1797714 TTATT-ATTATTA
1 TTATTAATTATTA
1797726 CTATTACTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 7 0.27
16 7 0.27
17 12 0.46
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (16 bp):
TTATTAATTATTATAG
Found at i:1812012 original size:6 final size:6
Alignment explanation
Indices: 1812001--1812026 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1811991 CTCTCATTGC
1812001 TTTGGT TTTGGT TTTGGT TTTGGT TT
1 TTTGGT TTTGGT TTTGGT TTTGGT TT
1812027 GATATTTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (6 bp):
TTTGGT
Found at i:1812628 original size:12 final size:13
Alignment explanation
Indices: 1812608--1812643 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
1812598 TTTAAATTTC
1812608 ATCATTTTTATAT
1 ATCATTTTTATAT
1812621 AT-ATTTTT-T-T
1 ATCATTTTTATAT
1812631 ATCATTTTTATAT
1 ATCATTTTTATAT
1812644 TTTATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
10 3 0.15
11 7 0.35
12 7 0.35
13 3 0.15
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.67
Consensus pattern (13 bp):
ATCATTTTTATAT
Found at i:1817700 original size:26 final size:26
Alignment explanation
Indices: 1817671--1817722 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1817661 ATTTCTGTGG
*
1817671 ATCAGCTAGAACCCAAAGTATGCATA
1 ATCAGCTAGAACCCAAAGCATGCATA
1817697 ATCAGCTAGAACCCAAAGCATGCATA
1 ATCAGCTAGAACCCAAAGCATGCATA
1817723 CAGTTCTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.25, G:0.15, T:0.17
Consensus pattern (26 bp):
ATCAGCTAGAACCCAAAGCATGCATA
Found at i:1821753 original size:101 final size:100
Alignment explanation
Indices: 1821618--1821904 Score: 450
Period size: 100 Copynumber: 2.9 Consensus size: 100
1821608 AAGAGGGAAA
*
1821618 AAAAAACCTTTCTTAAC-AAAAACCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTT
1 AAAAAA-CTTTATTAACAAAAAACCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTT
1821682 TGCAATCATAAAAAAGATATACACCTCAAAAAGAGC
65 TGCAATCATAAAAAAGATATACACCTCAAAAAGAGC
* * * *
1821718 AAAATAACTTTATTAACAAAAAACCCATATAAAATTTCATCAGAGGGAAATAACTAGCAATGTTT
1 AAAA-AACTTTATTAACAAAAAACCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTT
*
1821783 TGCAATCATAAAAAAGATATACACTTCAAAAAGAGC
65 TGCAATCATAAAAAAGATATACACCTCAAAAAGAGC
* ** * *
1821819 AAAAAACTTTATTAACAAAAACCCCATATCAAATTTCTTCTTTGGGAAATAATTAGCGATGTTTA
1 AAAAAACTTTATTAACAAAAAACCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTTT
1821884 GCAATCATAAAAAAGATATAC
66 GCAATCATAAAAAAGATATAC
1821905 TATCAAAAAG
Statistics
Matches: 170, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
100 86 0.51
101 84 0.49
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (100 bp):
AAAAAACTTTATTAACAAAAAACCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTTT
GCAATCATAAAAAAGATATACACCTCAAAAAGAGC
Found at i:1821866 original size:100 final size:99
Alignment explanation
Indices: 1821618--1821904 Score: 448
Period size: 101 Copynumber: 2.9 Consensus size: 99
1821608 AAGAGGGAAA
*
1821618 AAAAAACCTTTCTTAACAAAAACCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTTT
1 AAAAAA-CTTTATTAACAAAAACCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTTT
1821683 GCAATCATAAAAAAGATATACACCTCAAAAAGAGC
65 GCAATCATAAAAAAGATATACACCTCAAAAAGAGC
* * * *
1821718 AAAATAACTTTATTAACAAAAAACCCATATAAAATTTCATCAGAGGGAAATAACTAGCAATGTTT
1 AAAA-AACTTTATTAAC-AAAAACCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTT
*
1821783 TGCAATCATAAAAAAGATATACACTTCAAAAAGAGC
64 TGCAATCATAAAAAAGATATACACCTCAAAAAGAGC
** * *
1821819 AAAAAACTTTATTAACAAAAACCCCATATCAAATTTCTTCTTTGGGAAATAATTAGCGATGTTTA
1 AAAAAACTTTATTAACAAAAA-CCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTTT
1821884 GCAATCATAAAAAAGATATAC
65 GCAATCATAAAAAAGATATAC
1821905 TATCAAAAAG
Statistics
Matches: 170, Mismatches: 14, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
99 5 0.03
100 81 0.48
101 84 0.49
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (99 bp):
AAAAAACTTTATTAACAAAAACCCATATCAAATTTCTTCAGTGGGAAATAATTAGCAATGTTTTG
CAATCATAAAAAAGATATACACCTCAAAAAGAGC
Found at i:1823286 original size:6 final size:6
Alignment explanation
Indices: 1823275--1823304 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1823265 ATTATTCATG
*
1823275 CTCGAA CTCGAA CTCGAA CTCGGA CTCGAA
1 CTCGAA CTCGAA CTCGAA CTCGAA CTCGAA
1823305 ATATTTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (6 bp):
CTCGAA
Found at i:1823782 original size:87 final size:88
Alignment explanation
Indices: 1823653--1823828 Score: 336
Period size: 87 Copynumber: 2.0 Consensus size: 88
1823643 TCAATACATC
1823653 AAATACAAAACATAACTTTTTTTTAAAATTTTATACGAATTTTATTAAAATTTTAAATCGAATCA
1 AAATACAAAACATAACTTTTTTTTAAAATTTTATACGAATTTTATTAAAATTTTAAATCGAATCA
1823718 CTTTTTTTTTATATTATTTTCAT
66 CTTTTTTTTTATATTATTTTCAT
*
1823741 AAATACAAAACATAAC-TTTTTTTAAAATTTTATACGAATTTTATTAAAATTTTAAATTGAATCA
1 AAATACAAAACATAACTTTTTTTTAAAATTTTATACGAATTTTATTAAAATTTTAAATCGAATCA
1823805 CTTTTTTTTTATATTATTTTCAT
66 CTTTTTTTTTATATTATTTTCAT
1823828 A
1 A
1823829 TTATATCATT
Statistics
Matches: 87, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
87 71 0.82
88 16 0.18
ACGTcount: A:0.39, C:0.09, G:0.02, T:0.50
Consensus pattern (88 bp):
AAATACAAAACATAACTTTTTTTTAAAATTTTATACGAATTTTATTAAAATTTTAAATCGAATCA
CTTTTTTTTTATATTATTTTCAT
Found at i:1840588 original size:17 final size:16
Alignment explanation
Indices: 1840568--1840616 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
1840558 AAAATATTTT
1840568 TAAAATAAAAAAAATCA
1 TAAAATAAAAAAAAT-A
*
1840585 TAAATTCAAAAAAAATA
1 TAAAAT-AAAAAAAATA
*
1840602 GAAAATTAAAAAAAA
1 TAAAA-TAAAAAAAA
1840617 ATTATTAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (16 bp):
TAAAATAAAAAAAATA
Found at i:1842928 original size:19 final size:21
Alignment explanation
Indices: 1842904--1842942 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
1842894 TTAATGTTAA
1842904 AAAATAAAAA-A-ATAATTTT
1 AAAATAAAAATATATAATTTT
1842923 AAAATAAAAATATATAATTT
1 AAAATAAAAATATATAATTT
1842943 AAGGACATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
20 1 0.06
21 7 0.39
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATAAAAATATATAATTTT
Found at i:1851969 original size:3 final size:3
Alignment explanation
Indices: 1851961--1852023 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
1851951 TAATTTAAGG
1851961 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1852009 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
1852024 AATCTTTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1853689 original size:104 final size:105
Alignment explanation
Indices: 1853518--1853731 Score: 349
Period size: 104 Copynumber: 2.0 Consensus size: 105
1853508 TAAGGATCCT
* * *
1853518 CTAAACAAAAGGTATGCAATTTTTTAAAAAATAAATCAAGAAATAGGCTTCTTTAAATAAAGGCT
1 CTAAACAAAAGGTATGCAATTTTTTAAAAAATAAACCAAGAAATAGGCTTCTCTAAACAAAGGCT
*
1853583 AAATAACTTTAAATGATAAATGAGCTCATTTAAACAAAGG
66 AAATAACTTTAAATGAGAAATGAGCTCATTTAAACAAAGG
* *
1853623 CTAAACAAAAGGTATGCAATTTTTTTAAAAA-AAACCAAGAAATGGGCTTCTCTAAACAAAGGCT
1 CTAAACAAAAGGTATGCAATTTTTTAAAAAATAAACCAAGAAATAGGCTTCTCTAAACAAAGGCT
* *
1853687 AAATAACTTTAAATGAGAAATGAGCTCCTTTAAACAGAGG
66 AAATAACTTTAAATGAGAAATGAGCTCATTTAAACAAAGG
1853727 CTAAA
1 CTAAA
1853732 TAACTTTAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
104 71 0.70
105 30 0.30
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.27
Consensus pattern (105 bp):
CTAAACAAAAGGTATGCAATTTTTTAAAAAATAAACCAAGAAATAGGCTTCTCTAAACAAAGGCT
AAATAACTTTAAATGAGAAATGAGCTCATTTAAACAAAGG
Found at i:1853768 original size:43 final size:42
Alignment explanation
Indices: 1853673--1854092 Score: 345
Period size: 43 Copynumber: 9.9 Consensus size: 42
1853663 AATGGGCTTC
*
1853673 TCTAAACAAAGGCTAAATAACTTT-AAAT-GAGAAATGAGCTCCT
1 TCTAAACAGAGGCTAAATAACTTTAAAATAG-GAAATG-GCT-CT
*
1853716 T-TAAACAGAGGCTAAATAACTTTAAAATAGGAAATAGGCTAT
1 TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAAT-GGCTCT
* * *
1853758 TCTATACAGAGGCTAAATGACTTTAAAATAAGAAATGGACTTCT
1 TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAATGG-C-TCT
* * * * * *
1853802 T-TAAACAGATGTTAAATGACTTT-AAGTAGAAAATTGAGCTTT
1 TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAA-TG-GCTCT
* * * *
1853844 TCTATACAGAGGCTAAACAACTCTAAAATAGGAAATGGGCTCC
1 TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAAT-GGCTCT
* *
1853887 TCTAAACATAGGCTAAACAACTTT-AAATAGGAAATGAGCT-T
1 TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAATG-GCTCT
** * * *
1853928 CTCTATCCAAAGGCTAAACAACTTTAAAATAGGAAATAGGCTCC
1 -TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAAT-GGCTCT
* * * *
1853972 TCTAAACAGAGGCTAAATAATTTTAAAATAAGAAATAGACTCC
1 TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAAT-GGCTCT
* * * *
1854015 TCTAAACAAAGACTAAATAA-TTTTAAATAGAAAATGAGCT-T
1 TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAATG-GCTCT
* * *
1854056 CTCTAAATAGAGGCTAAACAACTTTAAAATAGAAAAT
1 -TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAAT
1854093 AGGACTGAAC
Statistics
Matches: 308, Mismatches: 50, Indels: 38
0.78 0.13 0.10
Matches are distributed among these distances:
41 2 0.01
42 100 0.32
43 190 0.62
44 16 0.05
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.27
Consensus pattern (42 bp):
TCTAAACAGAGGCTAAATAACTTTAAAATAGGAAATGGCTCT
Found at i:1853956 original size:85 final size:86
Alignment explanation
Indices: 1853661--1854092 Score: 439
Period size: 85 Copynumber: 5.1 Consensus size: 86
1853651 AAAAAACCAA
* * * *
1853661 GAAATGGGCTTCTCTAAACAAAGGCTAAATAACTTT-AAAT-GAGAAATGAGCTCCTTTAAACAG
1 GAAATGAGCTTCTCTATACAAAGGCTAAATAACTTTAAAATAG-GAAATGGGCTCCTCTAAACAG
1853724 AGGCTAAATAACTTTAAAATAG
65 AGGCTAAATAACTTTAAAATAG
* * * * * *
1853746 GAAAT-AGGCTAT-TCTATACAGAGGCTAAATGACTTTAAAATAAGAAATGGACTTCTTTAAACA
1 GAAATGA-GCT-TCTCTATACAAAGGCTAAATAACTTTAAAATAGGAAATGGGCTCCTCTAAACA
* * * *
1853809 GATGTTAAATGACTTT-AAGTAG
64 GAGGCTAAATAACTTTAAAATAG
* * * * * *
1853831 AAAATTGAGCTTTTCTATACAGAGGCTAAACAACTCTAAAATAGGAAATGGGCTCCTCTAAACAT
1 GAAA-TGAGCTTCTCTATACAAAGGCTAAATAACTTTAAAATAGGAAATGGGCTCCTCTAAACAG
*
1853896 AGGCTAAACAACTTT-AAATAG
65 AGGCTAAATAACTTTAAAATAG
* * *
1853917 GAAATGAGCTTCTCTATCCAAAGGCTAAACAACTTTAAAATAGGAAATAGGCTCCTCTAAACAGA
1 GAAATGAGCTTCTCTATACAAAGGCTAAATAACTTTAAAATAGGAAATGGGCTCCTCTAAACAGA
* *
1853982 GGCTAAATAATTTTAAAATAA
66 GGCTAAATAACTTTAAAATAG
* * * * * * * *
1854003 GAAAT-AGACTCCTCTAAACAAAGACTAAATAA-TTTTAAATAGAAAATGAGCTTCTCTAAATAG
1 GAAATGAG-CTTCTCTATACAAAGGCTAAATAACTTTAAAATAGGAAATGGGCTCCTCTAAACAG
*
1854066 AGGCTAAACAACTTTAAAATAG
65 AGGCTAAATAACTTTAAAATAG
*
1854088 AAAAT
1 GAAAT
1854093 AGGACTGAAC
Statistics
Matches: 287, Mismatches: 51, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
85 155 0.54
86 131 0.46
87 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (86 bp):
GAAATGAGCTTCTCTATACAAAGGCTAAATAACTTTAAAATAGGAAATGGGCTCCTCTAAACAGA
GGCTAAATAACTTTAAAATAG
Found at i:1854015 original size:128 final size:128
Alignment explanation
Indices: 1853661--1854094 Score: 471
Period size: 128 Copynumber: 3.4 Consensus size: 128
1853651 AAAAAACCAA
* * *
1853661 GAAATGGGCTTCTCTAAACAAAGGCTAAATAACTTTAAAT-GAGAAAT-GAGCTCCTTTAAACAG
1 GAAATGAGCTTCTCTAAACAAAGGCTAAACAACTTTAAATAGA-AAATAGAGCTCCTCTAAACAG
** * * * *
1853724 AGGCTAAATAACTTTAAAATAGGAAATAGGCTATTCTATACAGAGGCTAAATGACTTTAAAATAA
65 AGGCTAAATAACTTTAAAATAGGAAATAGGCTCCTCTAAACAAAGGCTAAATAACTTT-AAATAG
* * * * ** * * ** *
1853789 GAAATG-GACTTCTTTAAACAGATGTTAAATGACTTTAAGTAGAAAATTGAGCTTTTCTATACAG
1 GAAATGAG-CTTCTCTAAACAAAGGCTAAACAACTTTAAATAGAAAATAGAGCTCCTCTAAACAG
* * * * *
1853853 AGGCTAAACAACTCTAAAATAGGAAATGGGCTCCTCTAAACATAGGCTAAACAACTTTAAATAG
65 AGGCTAAATAACTTTAAAATAGGAAATAGGCTCCTCTAAACAAAGGCTAAATAACTTTAAATAG
** *
1853917 GAAATGAGCTTCTCTATCCAAAGGCTAAACAACTTTAAAATAGGAAATAG-GCTCCTCTAAACAG
1 GAAATGAGCTTCTCTAAACAAAGGCTAAACAACTTT-AAATAGAAAATAGAGCTCCTCTAAACAG
* * * * *
1853981 AGGCTAAATAATTTTAAAATAAGAAATAGACTCCTCTAAACAAAGACTAAATAATTTTAAATAG
65 AGGCTAAATAACTTTAAAATAGGAAATAGGCTCCTCTAAACAAAGGCTAAATAACTTTAAATAG
* * *
1854045 AAAATGAGCTTCTCTAAATAGAGGCTAAACAACTTTAAAATAGAAAATAG
1 GAAATGAGCTTCTCTAAACAAAGGCTAAACAACTTT-AAATAGAAAATAG
1854095 GACTGAACCT
Statistics
Matches: 251, Mismatches: 50, Indels: 10
0.81 0.16 0.03
Matches are distributed among these distances:
127 1 0.00
128 176 0.70
129 74 0.29
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (128 bp):
GAAATGAGCTTCTCTAAACAAAGGCTAAACAACTTTAAATAGAAAATAGAGCTCCTCTAAACAGA
GGCTAAATAACTTTAAAATAGGAAATAGGCTCCTCTAAACAAAGGCTAAATAACTTTAAATAG
Found at i:1854557 original size:65 final size:64
Alignment explanation
Indices: 1854367--1854573 Score: 225
Period size: 65 Copynumber: 3.2 Consensus size: 64
1854357 CCATAAGTAA
* * * * * ** *
1854367 AAAAAATAAATGATCTGGACTGAACAAAAATCAAAGATAAGTAACCGGGATTGAATCATAGGTTG
1 AAAAAATAAATAATCTAGATTGAACAAAGATCAAA-ATGAGTAACCGGGATTGAATCGCAGGTCG
* * ***
1854432 AAAAAATAAATACTCTAGATTGAACCAAGATTCAAAATGAGTAACTAAGATTGAATCGCAGGTCG
1 AAAAAATAAATAATCTAGATTGAACAAAGA-TCAAAATGAGTAACCGGGATTGAATCGCAGGTCG
* * * *
1854497 AAAAAATAAATAATCTAGATTGAACTAAGATCAAATATGAGTGACCGGGACTGAACCGCAGGTCG
1 AAAAAATAAATAATCTAGATTGAACAAAGATCAAA-ATGAGTAACCGGGATTGAATCGCAGGTCG
1854562 AAAAAATGAAAT
1 AAAAAAT-AAAT
1854574 TCAAAATTTC
Statistics
Matches: 118, Mismatches: 21, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
64 5 0.04
65 104 0.88
66 9 0.08
ACGTcount: A:0.47, C:0.13, G:0.19, T:0.21
Consensus pattern (64 bp):
AAAAAATAAATAATCTAGATTGAACAAAGATCAAAATGAGTAACCGGGATTGAATCGCAGGTCG
Found at i:1854593 original size:20 final size:21
Alignment explanation
Indices: 1854568--1854622 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1854558 GTCGAAAAAA
*
1854568 TGAAATTCAAAATT-TCAACT
1 TGAAATTCAAAATTCACAACT
*
1854588 TGAAATTCAAATATTCACAATT
1 TGAAATTCAAA-ATTCACAACT
1854610 TGGAAATTCAAAA
1 T-GAAATTCAAAA
1854623 ATTTGCAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 11 0.37
21 3 0.10
22 6 0.20
23 10 0.33
ACGTcount: A:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (21 bp):
TGAAATTCAAAATTCACAACT
Found at i:1854739 original size:37 final size:37
Alignment explanation
Indices: 1854670--1854740 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
1854660 ATATTCTAAG
* * * *
1854670 TTTCATAAGAAATTCACAAAGGTTTATGAATTTTAAC
1 TTTCACAAAAAATTCACAAAGATTTATAAATTTTAAC
1854707 TTTCACAAAAAATTCACAAAGATTTCA-AAATTTT
1 TTTCACAAAAAATTCACAAAGATTT-ATAAATTTT
1854741 CAAAAAGTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 28 0.97
38 1 0.03
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.37
Consensus pattern (37 bp):
TTTCACAAAAAATTCACAAAGATTTATAAATTTTAAC
Found at i:1855114 original size:80 final size:80
Alignment explanation
Indices: 1854975--1855127 Score: 209
Period size: 80 Copynumber: 1.9 Consensus size: 80
1854965 TTCTTATTTG
* * * *
1854975 AAAATTTAAGAGATTCACACCCAAAAGTTAAATATTCTTATTTGAAAAATTTAAGGATTCACATC
1 AAAATTTAAGAGATTCACACCCAAAAGTTAAAGATTCTTAGTTGAAAAACTTAAAGATTCACATC
1855040 CAAAATTTATATTAA
66 CAAAATTTATATTAA
* ** *
1855055 AAAATTTTAGAGATTCACA-TTATAAAGTTAAAGATTTTTAGTTGAAAAACTTAAAGATTCACAT
1 AAAATTTAAGAGATTCACACCCA-AAAGTTAAAGATTCTTAGTTGAAAAACTTAAAGATTCACAT
*
1855119 CGAAAATTT
65 CCAAAATTT
1855128 CAAAATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
79 1 0.02
80 62 0.98
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.35
Consensus pattern (80 bp):
AAAATTTAAGAGATTCACACCCAAAAGTTAAAGATTCTTAGTTGAAAAACTTAAAGATTCACATC
CAAAATTTATATTAA
Found at i:1856176 original size:13 final size:13
Alignment explanation
Indices: 1856160--1856184 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1856150 TTACTTATTT
1856160 TTTATTTTTTACC
1 TTTATTTTTTACC
1856173 TTTATTTTTTAC
1 TTTATTTTTTAC
1856185 ATTTTTTCAT
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:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTATTTTTTACC
Found at i:1856177 original size:20 final size:18
Alignment explanation
Indices: 1856141--1856183 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
1856131 TCAATTTAAG
1856141 TTTTT-TTTTTTACTTAT
1 TTTTTATTTTTTACTTAT
1856158 TTTTTATTTTTTACCTTTAT
1 TTTTTATTTTTTA-C-TTAT
1856178 TTTTTA
1 TTTTTA
1856184 CATTTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 7 0.30
19 1 0.04
20 10 0.43
ACGTcount: A:0.14, C:0.07, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTATTTTTTACTTAT
Found at i:1856182 original size:22 final size:22
Alignment explanation
Indices: 1856157--1856210 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1856147 TTTTTACTTA
1856157 TTTTTTATTTTTT-ACCTTTATT
1 TTTTTTATTTTTTCACCTTT-TT
** *
1856179 TTTTACATTTTTTCATCTTTTT
1 TTTTTTATTTTTTCACCTTTTT
*
1856201 CTTTTTATTT
1 TTTTTTATTT
1856211 CTCCTTCATC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTTTTATTTTTTCACCTTTTT
Found at i:1856208 original size:31 final size:31
Alignment explanation
Indices: 1856141--1856210 Score: 76
Period size: 31 Copynumber: 2.3 Consensus size: 31
1856131 TCAATTTAAG
1856141 TTTTT-TTTTTTACTTATTTTTTATTTTTTAC
1 TTTTTATTTTTTAC-TATTTTTTATTTTTTAC
*
1856172 -CTTTATTTTTTAC-ATTTTTTCATCTTTTT-C
1 TTTTTATTTTTTACTATTTTTT-AT-TTTTTAC
1856202 TTTTTATTT
1 TTTTTATTT
1856211 CTCCTTCATC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
29 7 0.21
30 6 0.18
31 20 0.61
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (31 bp):
TTTTTATTTTTTACTATTTTTTATTTTTTAC
Found at i:1856518 original size:19 final size:19
Alignment explanation
Indices: 1856469--1856522 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
1856459 TACCTCATCA
*
1856469 ATTTCTTTTTCTTTTTCCTT
1 ATTTTTTTTTCTTTTT-CTT
* *
1856489 ATTATTCTTTCTTTCTT-TT
1 ATTTTTTTTTCTTT-TTCTT
1856508 ATTTTTTTTTCTTTT
1 ATTTTTTTTTCTTTT
1856523 CATCATTTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 1 0.04
19 14 0.50
20 11 0.39
21 2 0.07
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (19 bp):
ATTTTTTTTTCTTTTTCTT
Found at i:1860459 original size:3 final size:3
Alignment explanation
Indices: 1860451--1860484 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1860441 TAATGAGTAA
1860451 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1860485 TCTAAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1861742 original size:18 final size:18
Alignment explanation
Indices: 1861715--1861777 Score: 76
Period size: 18 Copynumber: 3.5 Consensus size: 18
1861705 GACTTTTTTC
1861715 AAACAAAACAAATGAAATT
1 AAACAAAACAAAT-AAATT
1861734 AAA-AAAACAAATAAA-T
1 AAACAAAACAAATAAATT
*
1861750 AAACAAAACGAATTAAATT
1 AAACAAAAC-AAATAAATT
*
1861769 AAACTAAAC
1 AAACAAAAC
1861778 TAAACTAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
16 4 0.10
17 8 0.21
18 15 0.38
19 12 0.31
ACGTcount: A:0.70, C:0.11, G:0.03, T:0.16
Consensus pattern (18 bp):
AAACAAAACAAATAAATT
Found at i:1864278 original size:18 final size:18
Alignment explanation
Indices: 1864257--1864295 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
1864247 TGTGTTTGGT
*
1864257 ATATAAGAATATGATAAG
1 ATATAAGAAAATGATAAG
* *
1864275 ATATAATAAAATGATATG
1 ATATAAGAAAATGATAAG
1864293 ATA
1 ATA
1864296 AGTATGATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.13, T:0.31
Consensus pattern (18 bp):
ATATAAGAAAATGATAAG
Found at i:1867827 original size:6 final size:6
Alignment explanation
Indices: 1867807--1867844 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1867797 TAGTAAAAAT
1867807 TTTAAA TTT-AA -TTAAA TTTAAA TTTTAAA TTTAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTT
1867845 GACTCAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
4 2 0.07
5 4 0.14
6 17 0.59
7 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:1868053 original size:19 final size:21
Alignment explanation
Indices: 1868011--1868055 Score: 58
Period size: 19 Copynumber: 2.2 Consensus size: 21
1868001 TAATTTTTTA
*
1868011 ATTAAAATAATAAAAATATAT
1 ATTAAAATAATAAAAACATAT
*
1868032 ATTAAAAT-AT-AAAACATCT
1 ATTAAAATAATAAAAACATAT
1868051 ATTAA
1 ATTAA
1868056 GTTCATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 12 0.55
20 2 0.09
21 8 0.36
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAAAATAATAAAAACATAT
Done.