Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 7 of 147
Found at i:1341394 original size:29 final size:29
Alignment explanation
Indices: 1341331--1341407 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 29
1341321 AAGATTCGAA
* * *
1341331 TTTTAAGGGTTTGGATTTAAGTTTTGAGGG
1 TTTT-AGGGTTTGGATTTAAGTATGGAAGG
*
1341361 TTTTAGGGTTTGGTTTTAAGGTATGGAAGG
1 TTTTAGGGTTTGGATTTAA-GTATGGAAGG
*
1341391 -TTTAGGGTTTTGATTTA
1 TTTTAGGGTTTGGATTTA
1341408 GAGTTTAGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
29 29 0.73
30 11 0.28
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.48
Consensus pattern (29 bp):
TTTTAGGGTTTGGATTTAAGTATGGAAGG
Found at i:1341432 original size:14 final size:14
Alignment explanation
Indices: 1341391--1341433 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1341381 GTATGGAAGG
1341391 TTTAGGGTTTTGA-
1 TTTAGGGTTTTGAT
* *
1341404 TTTAGAGTTTAGAT
1 TTTAGGGTTTTGAT
*
1341418 TTTGGGGTTTTGAT
1 TTTAGGGTTTTGAT
1341432 TT
1 TT
1341434 AAGAGTTAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.16, C:0.00, G:0.28, T:0.56
Consensus pattern (14 bp):
TTTAGGGTTTTGAT
Found at i:1341495 original size:16 final size:16
Alignment explanation
Indices: 1341474--1341545 Score: 67
Period size: 15 Copynumber: 4.6 Consensus size: 16
1341464 GGGGAGGGGG
1341474 AGGGGTTTTGGATTTT
1 AGGGGTTTTGGATTTT
*
1341490 AGGGGTTTCGGATTTT
1 AGGGGTTTTGGATTTT
* *
1341506 -GAGATTTTGGATTTT
1 AGGGGTTTTGGATTTT
** *
1341521 AAAAGATTTTGGATTTT
1 -AGGGGTTTTGGATTTT
1341538 A-GGGTTTT
1 AGGGGTTTT
1341546 TAGAAACCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
15 17 0.36
16 16 0.34
17 14 0.30
ACGTcount: A:0.19, C:0.01, G:0.31, T:0.49
Consensus pattern (16 bp):
AGGGGTTTTGGATTTT
Found at i:1341953 original size:8 final size:8
Alignment explanation
Indices: 1341940--1341999 Score: 57
Period size: 8 Copynumber: 7.2 Consensus size: 8
1341930 TGCATCAAAT
1341940 AAAATAAA
1 AAAATAAA
**
1341948 AAAATATT
1 AAAATAAA
1341956 AAAATAACA
1 AAAATAA-A
*
1341965 AAAATAAT
1 AAAATAAA
*
1341973 AATATAAA
1 AAAATAAA
1341981 AAAATTAAA
1 AAAA-TAAA
*
1341990 AAATTAAA
1 AAAATAAA
1341998 AA
1 AA
1342000 TTTTTTTAAC
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
8 27 0.66
9 14 0.34
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAATAAA
Found at i:1341969 original size:17 final size:16
Alignment explanation
Indices: 1341937--1341999 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 16
1341927 TCATGCATCA
1341937 AATAAAATAAAAAAAT
1 AATAAAATAAAAAAAT
*
1341953 ATTAAAATAACAAAAAT
1 AATAAAATAA-AAAAAT
*
1341970 AATAATATAAAAAAATT
1 AATAAAATAAAAAAA-T
1341987 AA-AAAATTAAAAA
1 AATAAAA-TAAAAA
1342000 TTTTTTTAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
16 17 0.43
17 23 0.57
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AATAAAATAAAAAAAT
Found at i:1343054 original size:23 final size:24
Alignment explanation
Indices: 1343003--1343056 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1342993 ATTTTTTTAT
*
1343003 TTATTA-TTATTTTATATAATTAA
1 TTATTATTTATTTTATAAAATTAA
* *
1343026 TAATTATTTATTTTTTAAAATT-A
1 TTATTATTTATTTTATAAAATTAA
1343049 TTATTATT
1 TTATTATT
1343057 ATTAAAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (24 bp):
TTATTATTTATTTTATAAAATTAA
Found at i:1343061 original size:18 final size:18
Alignment explanation
Indices: 1343008--1343076 Score: 72
Period size: 18 Copynumber: 3.8 Consensus size: 18
1342998 TTTATTTATT
1343008 ATTATT-TTATATAATTAATA
1 ATTATTATTAT-T-ATTAA-A
1343028 ATTATTTATT-TT-TTAAA
1 ATTA-TTATTATTATTAAA
1343045 ATTATTATTATTATTAAA
1 ATTATTATTATTATTAAA
*
1343063 ATTATTAATATTAT
1 ATTATTATTATTAT
1343077 ACTGAAATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
16 5 0.11
17 7 0.16
18 22 0.50
20 5 0.11
21 3 0.07
22 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTATTATTATTATTAAA
Found at i:1343396 original size:7 final size:7
Alignment explanation
Indices: 1343379--1343410 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1343369 ATAATATTTG
1343379 AATATAAA
1 AATA-AAA
1343387 AATAAAA
1 AATAAAA
1343394 AATAAAA
1 AATAAAA
1343401 AATAAAA
1 AATAAAA
1343408 AAT
1 AAT
1343411 TCAAGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 20 0.83
8 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (7 bp):
AATAAAA
Found at i:1346376 original size:52 final size:52
Alignment explanation
Indices: 1346299--1346442 Score: 182
Period size: 52 Copynumber: 2.8 Consensus size: 52
1346289 ACTTGCCCAT
* * * *
1346299 TAAGAATCTCTTTCCTCTTAAAATTCTTCTCTTGTAAGTCAAACTTTCCTAA
1 TAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTAA
* * * *
1346351 TAAGAATCCCTTTTCTTTTAGAATTCTTCTCTTGCAAGTTAAACTTACCTAT
1 TAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTAA
* *
1346403 TAAGAAT-TCTCTTTCTCTTAGAATTCTTCTTTTACAAGTC
1 TAAGAATCTCT-TTTCTCTTAGAATTCTTCTCTTGCAAGTC
1346443 TTCTGGTCCA
Statistics
Matches: 78, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
51 2 0.03
52 76 0.97
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (52 bp):
TAAGAATCTCTTTTCTCTTAGAATTCTTCTCTTGCAAGTCAAACTTACCTAA
Found at i:1346483 original size:11 final size:11
Alignment explanation
Indices: 1346467--1346508 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
1346457 TCAATATCTG
1346467 ACAAATCTCAA
1 ACAAATCTCAA
*
1346478 ACAAATCTCTA
1 ACAAATCTCAA
*
1346489 ACAAATCGCAA
1 ACAAATCTCAA
1346500 ACAAATCTC
1 ACAAATCTC
1346509 TTATAAGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.50, C:0.29, G:0.02, T:0.19
Consensus pattern (11 bp):
ACAAATCTCAA
Found at i:1346492 original size:22 final size:22
Alignment explanation
Indices: 1346467--1346509 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
1346457 TCAATATCTG
*
1346467 ACAAATCTCAAACAAATCTCTA
1 ACAAATCGCAAACAAATCTCTA
1346489 ACAAATCGCAAACAAATCTCT
1 ACAAATCGCAAACAAATCTCT
1346510 TATAAGATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.49, C:0.28, G:0.02, T:0.21
Consensus pattern (22 bp):
ACAAATCGCAAACAAATCTCTA
Found at i:1346767 original size:23 final size:25
Alignment explanation
Indices: 1346737--1346792 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
1346727 TCTTCCCATG
1346737 TCTCAAACC-AT-GCACTTCTCACA
1 TCTCAAACCTATAGCACTTCTCACA
* * *
1346760 TCTTAAACCTTTAGCTCTTCTCACA
1 TCTCAAACCTATAGCACTTCTCACA
1346785 TCTCAAAC
1 TCTCAAAC
1346793 TTTCAGCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 8 0.30
24 1 0.04
25 18 0.67
ACGTcount: A:0.29, C:0.36, G:0.04, T:0.32
Consensus pattern (25 bp):
TCTCAAACCTATAGCACTTCTCACA
Found at i:1346780 original size:25 final size:25
Alignment explanation
Indices: 1346751--1346876 Score: 121
Period size: 25 Copynumber: 5.1 Consensus size: 25
1346741 AAACCATGCA
* *
1346751 CTTCTCACATCTTAAACCTTTAGCT
1 CTTCTCACATCTCAAACCTTCAGCT
*
1346776 CTTCTCACATCTCAAACTTTCAGCT
1 CTTCTCACATCTCAAACCTTCAGCT
* * *
1346801 CTT-GCACGTCTCGAACCTTCAGCT
1 CTTCTCACATCTCAAACCTTCAGCT
* * *
1346825 CTT-TCCACATCTTAAATCTTCAACT
1 CTTCT-CACATCTCAAACCTTCAGCT
* * *
1346850 CTTCTCACGTTTCGAACCTTCAGCT
1 CTTCTCACATCTCAAACCTTCAGCT
1346875 CT
1 CT
1346877 AATACCACTT
Statistics
Matches: 80, Mismatches: 19, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
24 20 0.25
25 59 0.74
26 1 0.01
ACGTcount: A:0.21, C:0.35, G:0.07, T:0.37
Consensus pattern (25 bp):
CTTCTCACATCTCAAACCTTCAGCT
Found at i:1346827 original size:49 final size:50
Alignment explanation
Indices: 1346765--1346876 Score: 140
Period size: 49 Copynumber: 2.3 Consensus size: 50
1346755 TCACATCTTA
* *
1346765 AACCTTTAGCTC-TTCTCACATCTCAAA-CTTTCAGCTCTT-GCACGTCTCG
1 AACCTTCAGCTCTTTC-CACATCTCAAATC-TTCAACTCTTCGCACGTCTCG
* * *
1346814 AACCTTCAGCTCTTTCCACATCTTAAATCTTCAACTCTTCTCACGTTTCG
1 AACCTTCAGCTCTTTCCACATCTCAAATCTTCAACTCTTCGCACGTCTCG
1346864 AACCTTCAGCTCT
1 AACCTTCAGCTCT
1346877 AATACCACTT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
49 30 0.55
50 25 0.45
ACGTcount: A:0.21, C:0.35, G:0.08, T:0.36
Consensus pattern (50 bp):
AACCTTCAGCTCTTTCCACATCTCAAATCTTCAACTCTTCGCACGTCTCG
Found at i:1347496 original size:52 final size:52
Alignment explanation
Indices: 1347407--1347552 Score: 204
Period size: 52 Copynumber: 2.8 Consensus size: 52
1347397 ATAACTATAT
* * * * **
1347407 AAACTTGCCCATTAAGAATCCCTCTCCTCTTATAATTCTTCTCTTGTAAGTC
1 AAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTACAAGTC
* *
1347459 AAACTTACCTATTAAGAATCCATTTCCTTTTAGAATTCTTCTCTTACAAGTC
1 AAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTACAAGTC
1347511 AAACTTACCTATTAAGAATCCCCTTT-CTCTTAGAATTCTTCT
1 AAACTTACCTATTAAGAAT-CCCTTTCCTCTTAGAATTCTTCT
1347553 TGTCCATCAA
Statistics
Matches: 83, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 78 0.94
53 5 0.06
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (52 bp):
AAACTTACCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCTTACAAGTC
Found at i:1347770 original size:18 final size:19
Alignment explanation
Indices: 1347729--1347770 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1347719 AATTGAGTTT
*
1347729 AATAAAAAAATTAATAATA
1 AATAAAAAAATTAATAAAA
*
1347748 TATAAAAAAATT-ATAAAA
1 AATAAAAAAATTAATAAAA
1347766 AATAA
1 AATAA
1347771 TTATAATTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAAAAAAATTAATAAAA
Found at i:1347851 original size:14 final size:14
Alignment explanation
Indices: 1347807--1347864 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
1347797 ATTTAGCGAT
1347807 AAAA-ATTT-TATC
1 AAAATATTTATATC
* * *
1347819 AACATTTTTAT-TA
1 AAAATATTTATATC
1347832 AAAATATTTATATC
1 AAAATATTTATATC
*
1347846 AAAATATATATATC
1 AAAATATTTATATC
1347860 AAAAT
1 AAAAT
1347865 TCATTAAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
12 3 0.08
13 13 0.36
14 20 0.56
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAATATTTATATC
Found at i:1349419 original size:13 final size:13
Alignment explanation
Indices: 1349401--1349425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1349391 TCTTGCTTAA
1349401 GTACTTAGTACAT
1 GTACTTAGTACAT
1349414 GTACTTAGTACA
1 GTACTTAGTACA
1349426 ACAAAATAAA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTACTTAGTACAT
Found at i:1349585 original size:15 final size:15
Alignment explanation
Indices: 1349565--1349596 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1349555 TTTGAAATAA
1349565 TAAGTTTGTAATGTT
1 TAAGTTTGTAATGTT
1349580 TAAGTTTGTAATGTT
1 TAAGTTTGTAATGTT
1349595 TA
1 TA
1349597 GCCTACTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (15 bp):
TAAGTTTGTAATGTT
Found at i:1351243 original size:20 final size:20
Alignment explanation
Indices: 1351212--1351259 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
1351202 AGTTCTTCAG
1351212 AAAATTAAAAAAAAAAACTCAA
1 AAAATT-AAAAAAAAAA-TCAA
*
1351234 AAAATTAAAAAAAAAATGAA
1 AAAATTAAAAAAAAAATCAA
1351254 AAAATT
1 AAAATT
1351260 TCTATATCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 9 0.36
21 10 0.40
22 6 0.24
ACGTcount: A:0.77, C:0.04, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAATTAAAAAAAAAATCAA
Found at i:1351671 original size:3 final size:3
Alignment explanation
Indices: 1351663--1351728 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
1351653 ACAGAAAAGG
1351663 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1351711 AAT AAT AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT
1351729 GATGATGATG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1351733 original size:3 final size:3
Alignment explanation
Indices: 1351727--1351752 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1351717 AATAATAGTA
1351727 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
1351753 AATAGTAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:1351868 original size:26 final size:27
Alignment explanation
Indices: 1351839--1351897 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
1351829 AGGCCCAGAT
* *
1351839 CAAAATAAGATC-AATTGAGCTTGGAC
1 CAAAATAAGACCAAATTGAGCTCGGAC
* *
1351865 CAAAATAAGCCCAAATTGAGCTCGGAT
1 CAAAATAAGACCAAATTGAGCTCGGAC
1351892 CAAAAT
1 CAAAAT
1351898 GAACCCAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.44, C:0.19, G:0.17, T:0.20
Consensus pattern (27 bp):
CAAAATAAGACCAAATTGAGCTCGGAC
Found at i:1351886 original size:27 final size:27
Alignment explanation
Indices: 1351851--1351905 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
1351841 AAATAAGATC
*
1351851 AATTGAGCTTGGACCAAAAT-AAGCCCA
1 AATTGAGCTCGGACCAAAATGAA-CCCA
*
1351878 AATTGAGCTCGGATCAAAATGAACCCA
1 AATTGAGCTCGGACCAAAATGAACCCA
1351905 A
1 A
1351906 TTGGAACTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (27 bp):
AATTGAGCTCGGACCAAAATGAACCCA
Found at i:1352254 original size:119 final size:120
Alignment explanation
Indices: 1352124--1352501 Score: 385
Period size: 119 Copynumber: 3.2 Consensus size: 120
1352114 AAACCATGAA
* * * * * *
1352124 TCATAAGAAATGATCTAGATTGAGCCAATATTAGGTGACTGAGACAAAACCATAAGTCAAAATAA
1 TCATAAGAAATGATTTGGACTGAGCCAAAATCAGGTGACTGAGACAAAACTATAAGTCAAAATAA
* * *
1352189 AAGCAACCAAGATCGAGTTGAGGTTG-AAATAAATGACTAG-GATGAAACCACAAG
66 AAGCGACCAAGATCGAGTCGAGGTGGCAAATAAATGA-TAGAGATGAAACCACAAG
* * * * *
1352243 TCATGAGAAATGATTTGGACTGAGCTAAGATCAGGTGACT-AGGATAAAATTATAAGTCAAAATA
1 TCATAAGAAATGATTTGGACTGAGCCAAAATCAGGTGACTGA-GACAAAACTATAAGTCAAAATA
* * * * * * *
1352307 AAA-CGACTAAGACCAAGTCGAGGTGGCAAATAAATGATTGAGATGGAATCGCAAG
65 AAAGCGACCAAGATCGAGTCGAGGTGGCAAATAAATGATAGAGATGAAACCACAAG
* * *
1352362 TCATAAGAAATGATTTGGACTAAGCCAAAATCAGGTGACTGGGACAAAACTACAAGTCAAAAT-A
1 TCATAAGAAATGATTTGGACTGAGCCAAAATCAGGTGACTGAGACAAAACTATAAGTCAAAATAA
* * * * *
1352426 AAGTGACCAAGATCGAGTCAAGGT--CAAAATTAAATGATCGAAACGAAACCACGAA-
66 AAGCGACCAAGATCGAGTCGAGGTGGC-AAA-TAAATGATAGAGATGAAACCAC-AAG
*
1352481 TCATAAGAAATGATCTGGACT
1 TCATAAGAAATGATTTGGACT
1352502 AACCGAGATT
Statistics
Matches: 211, Mismatches: 40, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
117 1 0.00
118 26 0.12
119 182 0.86
120 2 0.01
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.20
Consensus pattern (120 bp):
TCATAAGAAATGATTTGGACTGAGCCAAAATCAGGTGACTGAGACAAAACTATAAGTCAAAATAA
AAGCGACCAAGATCGAGTCGAGGTGGCAAATAAATGATAGAGATGAAACCACAAG
Found at i:1353406 original size:11 final size:11
Alignment explanation
Indices: 1353387--1353420 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1353377 TAACTTGAAC
*
1353387 TTCTCTTTTTT
1 TTCTTTTTTTT
1353398 TTC-TTTTTTT
1 TTCTTTTTTTT
1353408 TTCTTTTTTTT
1 TTCTTTTTTTT
1353419 TT
1 TT
1353421 GAATCAAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:1353407 original size:10 final size:10
Alignment explanation
Indices: 1353387--1353419 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
1353377 TAACTTGAAC
1353387 TTCTCTTTTTT
1 TTCT-TTTTTT
1353398 TTCTTTTTTT
1 TTCTTTTTTT
1353408 TTCTTTTTTT
1 TTCTTTTTTT
1353418 TT
1 TT
1353420 TGAATCAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (10 bp):
TTCTTTTTTT
Found at i:1360284 original size:12 final size:12
Alignment explanation
Indices: 1360267--1360317 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
1360257 TTTCAATTTG
1360267 TTTTATTTTATT
1 TTTTATTTTATT
1360279 TTTTATTCTGTATT
1 TTTTATT-T-TATT
*
1360293 TTGTATTTTATT
1 TTTTATTTTATT
*
1360305 TATTA-TTTATT
1 TTTTATTTTATT
1360316 TT
1 TT
1360318 ACTATTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
11 7 0.21
12 14 0.42
13 2 0.06
14 10 0.30
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:1361205 original size:7 final size:7
Alignment explanation
Indices: 1361169--1361214 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
1361159 TTTTTTTCAT
1361169 TTATTTA
1 TTATTTA
1361176 TTTATTTA
1 -TTATTTA
*
1361184 TTA-GTA
1 TTATTTA
*
1361190 TT-GTTA
1 TTATTTA
1361196 TTATTTA
1 TTATTTA
1361203 TTATTTA
1 TTATTTA
1361210 TTATT
1 TTATT
1361215 ATTTGTTTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
6 8 0.24
7 18 0.55
8 7 0.21
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (7 bp):
TTATTTA
Found at i:1361231 original size:26 final size:25
Alignment explanation
Indices: 1361177--1361231 Score: 58
Period size: 26 Copynumber: 2.1 Consensus size: 25
1361167 ATTTATTTAT
*
1361177 TTATTTATTAGTATTGTTATTATTTA
1 TTATTTATTAGTATTGTTATTA-TGA
*
1361203 TTATTTATTATTATTTGTTTATTA-GA
1 TTATTTATTAGTA-TTG-TTATTATGA
1361229 TTA
1 TTA
1361232 GAATTATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
26 16 0.64
27 3 0.12
28 6 0.24
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.65
Consensus pattern (25 bp):
TTATTTATTAGTATTGTTATTATGA
Found at i:1361259 original size:5 final size:5
Alignment explanation
Indices: 1361249--1361314 Score: 53
Period size: 5 Copynumber: 12.4 Consensus size: 5
1361239 TCAGTATTTC
* *
1361249 TTATT TTATT TTATT CTATTT TTATCC TTATTT TTATTT TTATTT TTATT
1 TTATT TTATT TTATT TTA-TT TTAT-T TTA-TT TTA-TT TTA-TT TTATT
*
1361299 TTATT TT-TA TTATT TT
1 TTATT TTATT TTATT TT
1361315 CTTTAAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
4 3 0.06
5 25 0.49
6 22 0.43
7 1 0.02
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:1361282 original size:12 final size:11
Alignment explanation
Indices: 1361243--1361309 Score: 82
Period size: 11 Copynumber: 5.9 Consensus size: 11
1361233 AATTATTCAG
1361243 TATTTCTTATTT
1 TATTT-TTATTT
*
1361255 TA-TTTTATTC
1 TATTTTTATTT
*
1361265 TATTTTTATCCT
1 TATTTTTAT-TT
1361277 TATTTTTATTTT
1 TATTTTTA-TTT
1361289 TATTTTTATTT
1 TATTTTTATTT
1361300 TATTTTTATT
1 TATTTTTATT
1361310 ATTTTCTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
10 7 0.15
11 21 0.44
12 19 0.40
13 1 0.02
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (11 bp):
TATTTTTATTT
Found at i:1361285 original size:6 final size:6
Alignment explanation
Indices: 1361243--1361309 Score: 70
Period size: 6 Copynumber: 11.7 Consensus size: 6
1361233 AATTATTCAG
* **
1361243 TATTTCT TA-TTT TA-TTT TA-TTC TATTTT TATCCT TATTTT TATTTT
1 TATTT-T TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
1361289 TATTTT TA-TTT TATTTT TATT
1 TATTTT TATTTT TATTTT TATT
1361310 ATTTTCTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
5 17 0.33
6 33 0.63
7 2 0.04
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (6 bp):
TATTTT
Found at i:1361288 original size:18 final size:17
Alignment explanation
Indices: 1361259--1361308 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1361249 TTATTTTATT
*
1361259 TTATTCTATTTTTATCC
1 TTATTTTATTTTTATCC
**
1361276 TTATTTTTATTTTTATTT
1 TTA-TTTTATTTTTATCC
1361294 TTATTTTATTTTTAT
1 TTATTTTATTTTTAT
1361309 TATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 15 0.52
18 14 0.48
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTTATTTTTATCC
Found at i:1361401 original size:58 final size:57
Alignment explanation
Indices: 1361331--1361727 Score: 437
Period size: 58 Copynumber: 6.8 Consensus size: 57
1361321 ATAAAATTCA
1361331 AAAAATATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTCT
1 AAAAA-ATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG-TTTCT
* * * *
1361390 AAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAA-TTTTCTTTAAAAATAAGTTTTTCA
1 AAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTC-TTGAAAATAAG--TTTCT
* *
1361449 AAAAAATATTTTT-GGAAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
1 AAAAAATATTTTTAAG-AAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG-TTTCT
** *
1361507 AAAAAATATTTTTGGGAAAAAGTTGAAAATATCAATTTTTCTTGAAAATAAGTTTTTTCT
1 AAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG---TTTCT
* * *
1361567 AAAAAATATTTTCGAAG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTCAT
1 AAAAAATATTTT-TAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTC-T
** * * *
1361625 AAAAGGTTTTTTCTTGAAG-AAAAGTTGAAAGTATCAATTTTT-TTCGAAATTAAAGTTACT
1 AAAA-AATATTT-TT-AAGAAAAAGTTGAAAGTATCAATTTTTCTT-GAAAAT-AAGTTTCT
*
1361685 AAAAAATATTTTGAAGAAAAA-TTGAAAGTATCAATTTTTCTTG
1 AAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTG
1361728 TACAAAAGCA
Statistics
Matches: 290, Mismatches: 32, Indels: 34
0.81 0.09 0.10
Matches are distributed among these distances:
57 31 0.11
58 102 0.35
59 62 0.21
60 88 0.30
61 7 0.02
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (57 bp):
AAAAAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTCT
Found at i:1361469 original size:117 final size:115
Alignment explanation
Indices: 1361327--1361727 Score: 490
Period size: 117 Copynumber: 3.4 Consensus size: 115
1361317 TTAAATAAAA
* *
1361327 TTCAAAAAATATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTCTAA
1 TTCAAAAAA-ATATTTTGAAG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAA
*
1361392 AAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTCTTTAAAAATAAGTTT
64 AAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTT-TTTGAAAATAAGTTT
1361445 TTCAAAAAAATATTTTTGGAA-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAA
1 TTCAAAAAAATA-TTTT-GAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAA
*
1361509 AAAATATTTTTGGGAAAAAGTTGAAAA-TATCAATTTTTCTTGAAAATAAGTTTT
64 AAAATATTTTTGAGAAAAAGTT-AAAAGTATCAATTTTT-TTGAAAATAAG-TTT
* *
1361563 TTCTAAAAAATATTTTCGAAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAG-TTTCATAA
1 TTCAAAAAAATATTTT-GAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTC-TAA
** * * *
1361627 AAGGTTTTTTCTTGA-AGAAAAGTTGAAAGTATCAATTTTTTTCGAAATTAAAG--T
64 AA-AATATTT-TTGAGA-AAAAGTTAAAAGTATCAATTTTTTT-GAAAAT-AAGTTT
* * * *
1361681 TACTAAAAAATATTTTGAAGAAAAATTGAAAGTATCAATTTTTCTTG
1 TTCAAAAAAATATTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTG
1361728 TACAAAAGCA
Statistics
Matches: 253, Mismatches: 17, Indels: 27
0.85 0.06 0.09
Matches are distributed among these distances:
116 1 0.00
117 125 0.49
118 86 0.34
119 12 0.05
120 26 0.10
121 3 0.01
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (115 bp):
TTCAAAAAAATATTTTGAAGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCTAAAA
AATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTTTGAAAATAAGTTT
Found at i:1361592 original size:60 final size:57
Alignment explanation
Indices: 1361330--1361727 Score: 448
Period size: 60 Copynumber: 6.8 Consensus size: 57
1361320 AATAAAATTC
*
1361330 AAAAAATATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGCTTTCT
1 AAAAAATAT-TTTTGAAG-AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG-TTTCT
* * *
1361390 AAAAAATATTTTTG-AGAAAAAGTTAAAAGTATCAA-TTTTCTTTAAAAATAAGTTTTTCA
1 AAAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTTC-TTGAAAATAAG--TTTCT
*
1361449 AAAAAATATTTTTGGAA-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAGCTTTCT
1 AAAAAATATTTTT-GAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG-TTTCT
* *
1361507 AAAAAATATTTTTG-GGAAAAAGTTGAAAATATCAATTTTTCTTGAAAATAAGTTTTTTCT
1 AAAAAATATTTTTGAAG-AAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAG---TTTCT
* * *
1361567 AAAAAATATTTTCGAAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAGTTTCAT
1 AAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTC-T
** * * *
1361625 AAAAGGTTTTTTCTTGAAGAAAAGTTGAAAGTATCAATTTTT-TTCGAAATTAAAGTTACT
1 AAAA-AATATTT-TTGAAGAAAAGTTGAAAGTATCAATTTTTCTT-GAAAAT-AAGTTTCT
*
1361685 AAAAAATA-TTTTGAAGAAAAATTGAAAGTATCAATTTTTCTTG
1 AAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTG
1361728 TACAAAAGCA
Statistics
Matches: 291, Mismatches: 31, Indels: 35
0.82 0.09 0.10
Matches are distributed among these distances:
57 39 0.13
58 89 0.31
59 55 0.19
60 100 0.34
61 8 0.03
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.38
Consensus pattern (57 bp):
AAAAAATATTTTTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAGTTTCT
Found at i:1364840 original size:15 final size:15
Alignment explanation
Indices: 1364820--1364850 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1364810 TTTGCATACA
*
1364820 TGCATTCTCATTCAT
1 TGCATTCTCACTCAT
1364835 TGCATTCTCACTCAT
1 TGCATTCTCACTCAT
1364850 T
1 T
1364851 ACACTTAACA
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:0.19, C:0.29, G:0.06, T:0.45
Consensus pattern (15 bp):
TGCATTCTCACTCAT
Found at i:1368820 original size:25 final size:26
Alignment explanation
Indices: 1368783--1368841 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
1368773 GAGCCTCATA
1368783 AGGAGAT-AGTTGACTTAGTGAATCT
1 AGGAGATGAGTTGACTTAGTGAATCT
*
1368808 AGGAGATGA-TTGATTTAGTGAATCT
1 AGGAGATGAGTTGACTTAGTGAATCT
1368833 -GAGAGATGA
1 AG-GAGATGA
1368842 AAAGAATAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 1 0.03
25 29 0.94
26 1 0.03
ACGTcount: A:0.34, C:0.05, G:0.31, T:0.31
Consensus pattern (26 bp):
AGGAGATGAGTTGACTTAGTGAATCT
Found at i:1373258 original size:40 final size:41
Alignment explanation
Indices: 1373109--1373389 Score: 220
Period size: 41 Copynumber: 6.8 Consensus size: 41
1373099 GTCAATGAGC
* * * *
1373109 AATTTATTTTTCAAAGTTGTGATGCTTCTAATTAGAGGAGC
1 AATTTATTCTTCAAAGTTGTGATGCCTCTGATTAGAGGAGT
* *
1373150 AATCTATTCTTCAAAGTTGTGATGCCTCTGATTAGATGAGT
1 AATTTATTCTTCAAAGTTGTGATGCCTCTGATTAGAGGAGT
*
1373191 AATTTATTCTTCAAAGTTGTGATGCCTCT-ATTTAGAGGGGT
1 AATTTATTCTTCAAAGTTGTGATGCCTCTGA-TTAGAGGAGT
1373232 AATTTA-T-TTCAAAAGTTGTTGA-GCCTCTGATTAGAGGAGCTT
1 AATTTATTCTTC-AAAGTTG-TGATGCCTCTGATTAGAGGAG--T
** * * * * *
1373274 TGTTTATTTTTCAAAGTCGTAGA-GCCTCTGATTAAAAGAAT
1 AATTTATTCTTCAAAGTTGT-GATGCCTCTGATTAGAGGAGT
* * * *
1373315 AATTTACTT-TTCAAAAGTCGTTGA-GCCTCTAATTAGAAGAGC
1 AATTTA-TTCTTC-AAAGTTG-TGATGCCTCTGATTAGAGGAGT
* * *
1373357 CATTTATT-TTCAAAGTCGTTGA-GCCTATGATTA
1 AATTTATTCTTCAAAGTTG-TGATGCCTCTGATTA
1373390 AATGAGCTTT
Statistics
Matches: 203, Mismatches: 25, Indels: 25
0.80 0.10 0.10
Matches are distributed among these distances:
39 3 0.01
40 43 0.21
41 94 0.46
42 36 0.18
43 24 0.12
44 3 0.01
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (41 bp):
AATTTATTCTTCAAAGTTGTGATGCCTCTGATTAGAGGAGT
Found at i:1373341 original size:42 final size:40
Alignment explanation
Indices: 1373154--1373440 Score: 168
Period size: 41 Copynumber: 6.8 Consensus size: 40
1373144 AGGAGCAATC
* * * *
1373154 TATTCTTCAAAGTTG-TGATGCCTCTGATTAGATGAGTAATT
1 TATT-TTCAAAGTCGTTGA-GCCTCTGATTAAAAGAATAATT
* * * **
1373195 TATTCTTCAAAGTTG-TGATGCCTCT-ATTTAGAGGGGTAATT
1 TATT-TTCAAAGTCGTTGA-GCCTCTGA-TTAAAAGAATAATT
* * ** **
1373236 TA-TTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTGTT
1 TATTTTC-AAAGTCGTTGAGCCTCTGATTA-A-AAGAATAATT
*
1373278 TATTTTTCAAAGTCGTAGAGCCTCTGATTAAAAGAATAATT
1 TA-TTTTCAAAGTCGTTGAGCCTCTGATTAAAAGAATAATT
* * ***
1373319 TACTTTTCAAAAGTCGTTGAGCCTCTAATTAGAAGAGCCATT
1 TA-TTTTC-AAAGTCGTTGAGCCTCTGATTAAAAGAATAATT
* * *
1373361 TATTTTCAAAGTCGTTGAGCCTATGATTAAATGAGCTTTATCTATT
1 TATTTTCAAAGTCGTTGAGCCTCTGATTAAA--AG---AAT-AATT
*
1373407 TATTTTCAAAGTCGTTGAGCCTCTGATTAGAAGA
1 TATTTTCAAAGTCGTTGAGCCTCTGATTAAAAGA
1373441 GCTTTGTTTA
Statistics
Matches: 198, Mismatches: 33, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
39 3 0.02
40 39 0.20
41 60 0.30
42 38 0.19
43 20 0.10
44 6 0.03
46 32 0.16
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (40 bp):
TATTTTCAAAGTCGTTGAGCCTCTGATTAAAAGAATAATT
Found at i:1373380 original size:125 final size:125
Alignment explanation
Indices: 1373154--1373440 Score: 314
Period size: 125 Copynumber: 2.3 Consensus size: 125
1373144 AGGAGCAATC
* * * * *
1373154 TATTCTTCAAAGTTGTGATGCCTCTGATTAGATGAGTAATTTATTCTTCAAAGTTGTGATGCCTC
1 TATTTTTCAAAGTCGTGA-GCCTCTGATTAGAAGAATAATTTATTCTTCAAAGTCGTGATGCCTC
* * * * * * * *
1373219 TATTTAGAGGGGTAATTTATTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTGT-T-
65 TAATTAGAAGAGCAATTTATTTCAAAAGTCGTTGAGCCTATGATTAAAGGAGCTTTATCTA
*
1373278 TATTTTTCAAAGTCGTAGAGCCTCTGATTAAAAGAATAATTTACTT-TTCAAAAGTCGTTGA-GC
1 TATTTTTCAAAGTCGT-GAGCCTCTGATTAGAAGAATAATTTA-TTCTTC-AAAGTCG-TGATGC
* *
1373341 CTCTAATTAGAAGAGCCATTTATTTTC-AAAGTCGTTGAGCCTATGATTAAATGAGCTTTATCTA
62 CTCTAATTAGAAGAGCAATTTA-TTTCAAAAGTCGTTGAGCCTATGATTAAAGGAGCTTTATCTA
*
1373405 TTTATTTTCAAAGTCGTTGAGCCTCTGATTAGAAGA
1 TAT-TTTTCAAAGTCG-TGAGCCTCTGATTAGAAGA
1373441 GCTTTGTTTA
Statistics
Matches: 136, Mismatches: 18, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
124 38 0.28
125 58 0.43
126 8 0.06
127 2 0.01
128 29 0.21
129 1 0.01
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.39
Consensus pattern (125 bp):
TATTTTTCAAAGTCGTGAGCCTCTGATTAGAAGAATAATTTATTCTTCAAAGTCGTGATGCCTCT
AATTAGAAGAGCAATTTATTTCAAAAGTCGTTGAGCCTATGATTAAAGGAGCTTTATCTA
Found at i:1373424 original size:46 final size:46
Alignment explanation
Indices: 1373233--1373482 Score: 176
Period size: 46 Copynumber: 5.7 Consensus size: 46
1373223 TAGAGGGGTA
* * * *
1373233 ATTTA-TTTCAAAAGTTGTTGAGCCTCTGATTAGAGGAGCTTTGT-T
1 ATTTATTTTC-AAAGTCGTTGAGCCTATGATTAGAAGAGCTTTATCT
* * * * *
1373278 -TAT-TTTTCAAAGTCGTAGAGCCTCTGATTA-AA-AG---AAT-A
1 ATTTATTTTCAAAGTCGTTGAGCCTATGATTAGAAGAGCTTTATCT
* *
1373316 ATTTACTTTTCAAAAGTCGTTGAGCCTCTAATTAGAAGAGC-----C-
1 ATTTA-TTTTC-AAAGTCGTTGAGCCTATGATTAGAAGAGCTTTATCT
1373358 ATTTATTTTCAAAGTCGTTGAGCCTATGATTA-AATGAGCTTTATCT
1 ATTTATTTTCAAAGTCGTTGAGCCTATGATTAGAA-GAGCTTTATCT
* * *
1373404 ATTTATTTTCAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTGTTT
1 ATTTATTTTCAAAGTCGTTGAGCCTATGATTAGAAGAGCTTTATCT
* * * *
1373450 ATAT-TTTTCAAAGTTGTTGAGCCTCTGCTTAGA
1 ATTTATTTTCAAAGTCGTTGAGCCTATGATTAGA
1373483 GGAATTTTGA
Statistics
Matches: 170, Mismatches: 18, Indels: 34
0.77 0.08 0.15
Matches are distributed among these distances:
38 1 0.01
39 4 0.02
40 24 0.14
41 12 0.07
42 26 0.15
43 22 0.13
44 8 0.05
45 28 0.16
46 43 0.25
47 2 0.01
ACGTcount: A:0.28, C:0.14, G:0.18, T:0.40
Consensus pattern (46 bp):
ATTTATTTTCAAAGTCGTTGAGCCTATGATTAGAAGAGCTTTATCT
Found at i:1373799 original size:20 final size:20
Alignment explanation
Indices: 1373771--1373827 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
1373761 CCTTATCTGT
*
1373771 TTATATATCTATTATTATTA
1 TTATTTATCTATTATTATTA
* *
1373791 TTATTTATCTATTAATATTT
1 TTATTTATCTATTATTATTA
1373811 TTATTTATCTAATTATT
1 TTATTTATCT-ATTATT
1373828 TTCTTTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 27 0.84
21 5 0.16
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTTATCTATTATTATTA
Found at i:1375412 original size:58 final size:57
Alignment explanation
Indices: 1375290--1375806 Score: 568
Period size: 58 Copynumber: 8.9 Consensus size: 57
1375280 TGTTTTTAAG
* * * * *
1375290 GAAAATTGGTACTTCCAACTTTTT-TC-AAAATATTTTTCTA-AAACTTTAATTTT-GA
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAA-ATT-ATTTTCAA
*
1375345 GAAAAATTGATACTTTCAACTTTTTCTCAAAAACATTTTTTTAGAAAATTATTTTCAAA
1 G-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAATTATTTTC-AA
* **
1375404 GAAAATTGATACTTTCAACTTTTCCTTGAAAATA-TTTTTTAGAAAACTTATTTTCAA
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAA-TTATTTTCAA
* *
1375461 GAAAAATTGATACTTTCAACTTTTTCTCAAATAT-TATTTTTTAGAAAAACTTATTTTTAA
1 G-AAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTTTAG-AAAA-TTATTTTCAA
1375521 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTTAGAAAATTTATTTTCAA
1 -GAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAA-TTATTTTCAA
*
1375579 GAAAAATTGATACTTTCAACTTTTTCTCGAAAATATTTTTTTAGAAAACTTATTTTCAA
1 G-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAA-TTATTTTCAA
* * * *
1375638 GGAAATTGATACTTTTAACTTTTTCCCAAAAATATATTTTTTA-AAAATTTTATTCTTAAA
1 GAAAATTGATACTTTCAACTTTTTCTCAAAAATAT-TTTTTTAGAAAA--TTATT-TTCAA
* **
1375698 GAAAATTGATACTTTCAACTTTTTCTCAAAAAAAAAATTTTTTT--AATTTTATTTTCAA
1 GAAAATTGATACTTTCAACTTTTTCTC---AAAAATATTTTTTTAGAAAATTATTTTCAA
* * *
1375756 GAAAAATTGATACTTTTAATTTTTTCTCAAAAATATTTCTTTTTGAAAATT
1 G-AAAATTGATACTTTCAACTTTTTCTCAAAAATATTT-TTTTAGAAAATT
1375807 TTTATTTTTT
Statistics
Matches: 399, Mismatches: 38, Indels: 46
0.83 0.08 0.10
Matches are distributed among these distances:
55 1 0.00
56 30 0.08
57 27 0.07
58 163 0.41
59 89 0.22
60 73 0.18
61 3 0.01
62 6 0.02
63 7 0.02
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (57 bp):
GAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTAGAAAATTATTTTCAA
Found at i:1375558 original size:118 final size:117
Alignment explanation
Indices: 1375282--1375793 Score: 609
Period size: 118 Copynumber: 4.4 Consensus size: 117
1375272 AAATATTTTG
* * *
1375282 TTTTTAAGGAAAATTGGTACTTCCAACTTTTT-TC-AAAATATTTTTCT-AAAACTTTAATTTT-
1 TTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTT-TAAAAAC-TT-ATTTTC
* *
1375343 GAGAAAAATTGATACTTTCAACTTTTTCTC-AAAAACATTTTTTTAGAAAA-TTA
63 AAGAAAAATTGATACTTTCAACTTTTTCTCAAAAAATATTTTTTTAGAAAACTTA
* * **
1375396 TTTTCAAAGAAAATTGATACTTTCAACTTTTCCTTGAAAATATTTTTTAGAAAACTTATTTTCAA
1 TTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTA-AAAACTTATTTTCAA
* *
1375461 GAAAAATTGATACTTTCAACTTTTTCTCAAATATTA-TTTTTTAGAAAAACTTA
65 GAAAAATTGATACTTTCAACTTTTTCTCAAAAAATATTTTTTTAG-AAAACTTA
* *
1375514 TTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAATTTATTTTCAA
1 TTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTA-AAAACTTATTTTCAA
*
1375579 GAAAAATTGATACTTTCAACTTTTTCTC-GAAAATATTTTTTTAGAAAACTTA
65 GAAAAATTGATACTTTCAACTTTTTCTCAAAAAATATTTTTTTAGAAAACTTA
* * *
1375631 TTTTCAAGG-AAATTGATACTTTTAACTTTTTCCCAAAAATATATTTTTTAAAAATTTTATTCTT
1 TTTTCAAGGAAAATTGATACTTTCAACTTTTTCTC-AAAA-ATATTTTTTAAAAA-CTTATT-TT
* * **
1375695 AAAG-AAAATTGATACTTTCAACTTTTTCTCAAAAAAAAAATTTTTTT---AATTTTA
62 CAAGAAAAATTGATACTTTCAACTTTTTCTC--AAAAAATATTTTTTTAGAAAACTTA
* * *
1375749 TTTTCAAGAAAAATTGATACTTTTAATTTTTTCTCAAAAATATTT
1 TTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTT
1375794 CTTTTTGAAA
Statistics
Matches: 351, Mismatches: 30, Indels: 31
0.85 0.07 0.08
Matches are distributed among these distances:
114 27 0.08
115 7 0.02
116 73 0.21
117 47 0.13
118 157 0.45
119 28 0.08
121 12 0.03
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.46
Consensus pattern (117 bp):
TTTTCAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAACTTATTTTCAAG
AAAAATTGATACTTTCAACTTTTTCTCAAAAAATATTTTTTTAGAAAACTTA
Found at i:1375587 original size:176 final size:174
Alignment explanation
Indices: 1375290--1375804 Score: 643
Period size: 176 Copynumber: 2.9 Consensus size: 174
1375280 TGTTTTTAAG
* * * * *
1375290 GAAAATTGGTACTTCCAACTTTTT-TCAAAA-TATTTTTCT--AAAACTTTAATTTTGAGAAAAA
1 GAAAATTGATACTTTCAACTTTTTCTCAAAATTATTTTT-TAAAAAAC-TTATTTTTAAGGAAAA
*
1375351 TTGATACTTTCAACTTTTTCTCAAAAACATTTTTTTAGAAAA-TTATTTTCAA-AGAAAATTGAT
64 TTGATACTTTCAACTTTTTCTCAAAAA-AATTTTTTAGAAAATTTATTTTCAAGA-AAAATTGAT
*
1375414 ACTTTCAACTTTTCCTTGAAAATA-TTTTTTAGAAAACTTATTTTCAA
127 ACTTTCAACTTTTCCTCGAAAATATTTTTTTAGAAAACTTATTTTCAA
1375461 GAAAAATTGATACTTTCAACTTTTTCTCAAATATTATTTTTTAGAAAAACTTATTTTTAAGGAAA
1 G-AAAATTGATACTTTCAACTTTTTCTCAAA-ATTATTTTTTA-AAAAACTTATTTTTAAGGAAA
*
1375526 ATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAGAAAATTTATTTTCAAGAAAAATTGATA
63 ATTGATACTTTCAACTTTTTCTCAAAAAAATTTTTTAGAAAATTTATTTTCAAGAAAAATTGATA
*
1375591 CTTTCAACTTTTTCTCGAAAATATTTTTTTAGAAAACTTATTTTCAA
128 CTTTCAACTTTTCCTCGAAAATATTTTTTTAGAAAACTTATTTTCAA
* * * ** * *
1375638 GGAAATTGATACTTTTAACTTTTTCCCAAAAATATATTTTTTAAAAATTTTATTCTTAAAGAAAA
1 GAAAATTGATACTTTCAACTTTTTCTC-AAAAT-TATTTTTTAAAAAACTTATTTTTAAGGAAAA
* *
1375703 TTGATACTTTCAACTTTTTCTCAAAAAAAAAATTTTTT--TAATTTTATTTTCAAGAAAAATTGA
64 TTGATACTTTCAACTTTTTCTC---AAAAAAATTTTTTAGAAAATTTATTTTCAAGAAAAATTGA
* * * * *
1375766 TACTTTTAATTTTTTCTCAAAAATATTTCTTTTTGAAAA
126 TACTTTCAACTTTTCCTCGAAAATATTT-TTTTAGAAAA
1375805 TTTTTATTTT
Statistics
Matches: 305, Mismatches: 23, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
171 1 0.00
172 21 0.07
173 5 0.02
174 2 0.01
175 19 0.06
176 146 0.48
177 90 0.30
178 9 0.03
179 12 0.04
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (174 bp):
GAAAATTGATACTTTCAACTTTTTCTCAAAATTATTTTTTAAAAAACTTATTTTTAAGGAAAATT
GATACTTTCAACTTTTTCTCAAAAAAATTTTTTAGAAAATTTATTTTCAAGAAAAATTGATACTT
TCAACTTTTCCTCGAAAATATTTTTTTAGAAAACTTATTTTCAA
Found at i:1375610 original size:28 final size:28
Alignment explanation
Indices: 1375523--1375611 Score: 67
Period size: 31 Copynumber: 3.1 Consensus size: 28
1375513 ATTTTTAAGG
1375523 AAAATTGATACTTTCAACTTTTTCTC-A
1 AAAATTGATACTTTCAACTTTTTCTCGA
** * * *
1375550 AAAA-T-ATTTTTTAGAAAATTTATTTTCAAGA
1 AAAATTGATACTTT--CAACTTT-TTCTC--GA
1375581 AAAATTGATACTTTCAACTTTTTCTCGA
1 AAAATTGATACTTTCAACTTTTTCTCGA
1375609 AAA
1 AAA
1375612 TATTTTTTTA
Statistics
Matches: 44, Mismatches: 10, Indels: 15
0.64 0.14 0.22
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 9 0.20
28 9 0.20
30 4 0.09
31 10 0.23
32 1 0.02
33 5 0.11
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (28 bp):
AAAATTGATACTTTCAACTTTTTCTCGA
Found at i:1375773 original size:31 final size:31
Alignment explanation
Indices: 1375683--1375778 Score: 83
Period size: 31 Copynumber: 3.2 Consensus size: 31
1375673 ATTTTTTAAA
* *
1375683 AATTTTATTCTTAAAG-AAAATTGATACTTTC
1 AATTTTATT-TTCAAGAAAAATTGATACTTTT
* * ** **
1375714 AACTTT-TTCTCAA-AAAAA-AAATTTTTTT
1 AATTTTATTTTCAAGAAAAATTGATACTTTT
1375742 AATTTTATTTTCAAGAAAAATTGATACTTTT
1 AATTTTATTTTCAAGAAAAATTGATACTTTT
1375773 AATTTT
1 AATTTT
1375779 TTCTCAAAAA
Statistics
Matches: 47, Mismatches: 14, Indels: 8
0.68 0.20 0.12
Matches are distributed among these distances:
28 10 0.21
29 13 0.28
30 7 0.15
31 17 0.36
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (31 bp):
AATTTTATTTTCAAGAAAAATTGATACTTTT
Found at i:1375797 original size:26 final size:27
Alignment explanation
Indices: 1375728--1375798 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 27
1375718 TTTTCTCAAA
*
1375728 AAAAAAATTT-TTTTAATTTTATTTTC
1 AAAAAAATTTCTTTTAATTTTATTCTC
1375754 AAGAAAAATTGATACTTTTAATTTT-TTCTC
1 AA-AAAAATT--T-CTTTTAATTTTATTCTC
*
1375784 AAAAATATTTCTTTT
1 AAAAAAATTTCTTTT
1375799 TGAAAATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
26 7 0.18
27 8 0.21
29 7 0.18
30 6 0.16
31 10 0.26
ACGTcount: A:0.38, C:0.07, G:0.03, T:0.52
Consensus pattern (27 bp):
AAAAAAATTTCTTTTAATTTTATTCTC
Found at i:1375895 original size:16 final size:16
Alignment explanation
Indices: 1375876--1375913 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
1375866 TAAATAACAC
1375876 ATAAAAAAACAAATAA
1 ATAAAAAAACAAATAA
* *
1375892 ATAAACAAACAAATGA
1 ATAAAAAAACAAATAA
1375908 ATAAAA
1 ATAAAA
1375914 TACCAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.13
Consensus pattern (16 bp):
ATAAAAAAACAAATAA
Found at i:1377598 original size:21 final size:21
Alignment explanation
Indices: 1377574--1377618 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
1377564 AACCAATGAT
1377574 AAATAAAAAAAC-AAATAAATC
1 AAATAAAAAAACAAAAT-AATC
*
1377595 AAATAAAAAAATAAAATAATC
1 AAATAAAAAAACAAAATAATC
1377616 AAA
1 AAA
1377619 GATCAGCCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.78, C:0.07, G:0.00, T:0.16
Consensus pattern (21 bp):
AAATAAAAAAACAAAATAATC
Found at i:1377608 original size:17 final size:16
Alignment explanation
Indices: 1377572--1377609 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
1377562 TAAACCAATG
1377572 ATAAATAAAAAAACAA
1 ATAAATAAAAAAACAA
1377588 ATAAATCAAATAAAA-AA
1 ATAAAT-AAA-AAAACAA
1377605 ATAAA
1 ATAAA
1377610 ATAATCAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 10 0.50
18 4 0.20
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (16 bp):
ATAAATAAAAAAACAA
Found at i:1378028 original size:17 final size:19
Alignment explanation
Indices: 1378006--1378046 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1377996 TCCAAGAAAG
1378006 TTTTTTT-TTTCAAA-ATA
1 TTTTTTTGTTTCAAATATA
*
1378023 TTTTTTTGTTTGAAATATA
1 TTTTTTTGTTTCAAATATA
1378042 TTTTT
1 TTTTT
1378047 CAAAAAGAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 6 0.29
19 8 0.38
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.68
Consensus pattern (19 bp):
TTTTTTTGTTTCAAATATA
Found at i:1378581 original size:31 final size:31
Alignment explanation
Indices: 1378546--1378611 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1378536 CAGAAAATTT
*
1378546 AAAATTCTTCAAAAAACCCAAAAA-ATTCTAA
1 AAAATT-TTCAAAAAACCCAAAAATATTCAAA
* *
1378577 AAAATTTTTAAAAAATCCAAAAATATTCAAA
1 AAAATTTTCAAAAAACCCAAAAATATTCAAA
1378608 AAAA
1 AAAA
1378612 ATTCCTAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 15 0.48
31 16 0.52
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (31 bp):
AAAATTTTCAAAAAACCCAAAAATATTCAAA
Found at i:1379130 original size:15 final size:15
Alignment explanation
Indices: 1379110--1379139 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1379100 TAATGAACCC
1379110 GATCGAAATAGGCCT
1 GATCGAAATAGGCCT
*
1379125 GATCGAAATGGGCCT
1 GATCGAAATAGGCCT
1379140 AGTTCGACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.20, G:0.30, T:0.20
Consensus pattern (15 bp):
GATCGAAATAGGCCT
Found at i:1379777 original size:12 final size:12
Alignment explanation
Indices: 1379762--1379808 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1379752 TTTATAAATG
1379762 AATTTGAAATTT
1 AATTTGAAATTT
*
1379774 AATTTAAATAATTT
1 AATTT-GA-AATTT
*
1379788 AATCTGAAATTT
1 AATTTGAAATTT
1379800 AATTT-AAAT
1 AATTTGAAAT
1379809 AATTTAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
11 4 0.14
12 14 0.48
13 2 0.07
14 9 0.31
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (12 bp):
AATTTGAAATTT
Found at i:1379788 original size:14 final size:14
Alignment explanation
Indices: 1379769--1379815 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
1379759 ATGAATTTGA
1379769 AATTTAATTTAAAT
1 AATTTAATTTAAAT
* *
1379783 AATTTAATCT-GA-
1 AATTTAATTTAAAT
1379795 AATTTAATTTAAAT
1 AATTTAATTTAAAT
1379809 AATTTAA
1 AATTTAA
1379816 ATAATTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
12 9 0.33
13 2 0.07
14 16 0.59
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (14 bp):
AATTTAATTTAAAT
Found at i:1379795 original size:26 final size:26
Alignment explanation
Indices: 1379766--1379815 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
1379756 TAAATGAATT
1379766 TGAAATTTAATTTAAATAATTTAATC
1 TGAAATTTAATTTAAATAATTTAATC
1379792 TGAAATTTAATTTAAATAATTTAA
1 TGAAATTTAATTTAAATAATTTAA
1379816 ATAATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (26 bp):
TGAAATTTAATTTAAATAATTTAATC
Found at i:1384662 original size:20 final size:20
Alignment explanation
Indices: 1384622--1384668 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
1384612 ATATATTTAC
*
1384622 AATATTAAAATTTAAATTTT
1 AATATTAAAATTTAAAGTTT
*
1384642 ATTATTAAAA-TTAAGAGTTT
1 AATATTAAAATTTAA-AGTTT
1384662 AATATTA
1 AATATTA
1384669 TATTAATAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (20 bp):
AATATTAAAATTTAAAGTTT
Found at i:1384795 original size:21 final size:21
Alignment explanation
Indices: 1384771--1384811 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1384761 AGTAATAGAT
1384771 GTGAGATTGATTATTATAATG
1 GTGAGATTGATTATTATAATG
*
1384792 GTGAGATTGATTATTGTAAT
1 GTGAGATTGATTATTATAAT
1384812 AATAATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (21 bp):
GTGAGATTGATTATTATAATG
Found at i:1384813 original size:24 final size:22
Alignment explanation
Indices: 1384762--1384814 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 22
1384752 ATTAAAAATA
1384762 GTAATAGATGTGAGATTGATTAT
1 GTAATA-ATGTGAGATTGATTAT
1384785 -T-ATAATGGTGAGATTGATTATT
1 GTAATAAT-GTGAGATTGATTA-T
1384807 GTAATAAT
1 GTAATAAT
1384815 AATAATTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
20 2 0.08
21 16 0.62
22 2 0.08
23 1 0.04
24 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.23, T:0.42
Consensus pattern (22 bp):
GTAATAATGTGAGATTGATTAT
Found at i:1395191 original size:10 final size:10
Alignment explanation
Indices: 1395168--1395197 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1395158 TATTTTATCA
1395168 ATTAAAAT-T
1 ATTAAAATAT
1395177 ATTAAAATAT
1 ATTAAAATAT
1395187 ATTAAAATAT
1 ATTAAAATAT
1395197 A
1 A
1395198 AAAACCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:1408006 original size:15 final size:16
Alignment explanation
Indices: 1407978--1408007 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1407968 TTTAAAAAAC
1407978 GTATATGATATAATTT
1 GTATATGATATAATTT
1407994 GTATATG-TATAATT
1 GTATATGATATAATT
1408008 ATATTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (16 bp):
GTATATGATATAATTT
Found at i:1408763 original size:27 final size:22
Alignment explanation
Indices: 1408706--1408761 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
1408696 TAAACAAAGT
1408706 TAATTTTATATTTAACATAACA
1 TAATTTTATATTTAACATAACA
1408728 TAATTTTATATTTAACATAACA
1 TAATTTTATATTTAACATAACA
1408750 TAATTTTATATT
1 TAATTTTATATT
1408762 ATTTTTTGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TAATTTTATATTTAACATAACA
Found at i:1409581 original size:29 final size:30
Alignment explanation
Indices: 1409538--1409609 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
1409528 TATATAAAAA
* * **
1409538 AATCATTTTGATCCTTATTCTTTTATTTT-
1 AATCAATTTAATCCTTATAATTTTATTTTG
*
1409567 TATCAATTTAATCCTTATAATTTTATTTTG
1 AATCAATTTAATCCTTATAATTTTATTTTG
*
1409597 AATCAAATTAATC
1 AATCAATTTAATC
1409610 TAAACAATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 24 0.69
30 11 0.31
ACGTcount: A:0.31, C:0.12, G:0.03, T:0.54
Consensus pattern (30 bp):
AATCAATTTAATCCTTATAATTTTATTTTG
Found at i:1414137 original size:12 final size:12
Alignment explanation
Indices: 1414120--1414157 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1414110 ATTATAAAAT
1414120 TTTAAATTTTAA
1 TTTAAATTTTAA
*
1414132 TTTAAATTTGAA
1 TTTAAATTTTAA
*
1414144 -TTAAATTTTTA
1 TTTAAATTTTAA
1414155 TTT
1 TTT
1414158 GATTTAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
TTTAAATTTTAA
Found at i:1414177 original size:28 final size:28
Alignment explanation
Indices: 1414131--1414210 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 28
1414121 TTAAATTTTA
1414131 ATTTAAATTTGAATT-AAATTTTTATTTG
1 ATTTAAA-TTGAATTAAAATTTTTATTTG
1414159 ATTTAAATTGAATTAAAATAAATTTTTTATTTG
1 ATTTAAATTGAATT---A-AAA-TTTTTATTTG
*
1414192 ATTTAAACTGAATTAAAAT
1 ATTTAAATTGAATTAAAAT
1414211 AAAATTTTTG
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
27 7 0.16
28 8 0.18
29 3 0.07
30 1 0.02
32 3 0.07
33 23 0.51
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (28 bp):
ATTTAAATTGAATTAAAATTTTTATTTG
Found at i:1414186 original size:33 final size:32
Alignment explanation
Indices: 1414145--1414219 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 32
1414135 AAATTTGAAT
*
1414145 TAAATTTTTATTTGATTTAAATTGAATTAAAA
1 TAAATTTTTATTTGATTTAAACTGAATTAAAA
1414177 TAAATTTTTTATTTGATTTAAACTGAATTAAAA
1 TAAA-TTTTTATTTGATTTAAACTGAATTAAAA
1414210 TAAAATTTTT
1 T-AAATTTTT
1414220 GATTCAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
32 4 0.10
33 33 0.82
34 3 0.08
ACGTcount: A:0.43, C:0.01, G:0.05, T:0.51
Consensus pattern (32 bp):
TAAATTTTTATTTGATTTAAACTGAATTAAAA
Found at i:1417860 original size:21 final size:22
Alignment explanation
Indices: 1417818--1417869 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1417808 ATCGAAATTA
1417818 ATAAAATATTATTTTTAAAAAT
1 ATAAAATATTATTTTTAAAAAT
*
1417840 ATAAAATATTATTTTT-TAAAT
1 ATAAAATATTATTTTTAAAAAT
1417861 AT-AAATATT
1 ATAAAATATT
1417870 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 6 0.21
22 16 0.55
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATATTATTTTTAAAAAT
Found at i:1417878 original size:30 final size:30
Alignment explanation
Indices: 1417842--1417902 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1417832 TTAAAAATAT
* * * *
1417842 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATAATTA
*
1417872 AAAATATCATTATATAAATATATATAATTA
1 AAAATATCATTATATAAATATAAATAATTA
1417902 A
1 A
1417903 TTAATTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATAATTA
Found at i:1422357 original size:2 final size:2
Alignment explanation
Indices: 1422350--1422374 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1422340 GACTCTTGTC
1422350 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
1422375 CTTTGCTCAA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1422856 original size:16 final size:17
Alignment explanation
Indices: 1422832--1422865 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1422822 CGTGACTCTA
*
1422832 TATCTCTTTTT-TTTTT
1 TATCCCTTTTTCTTTTT
1422848 TATCCCTTTTTCTTTTT
1 TATCCCTTTTTCTTTTT
1422865 T
1 T
1422866 GAAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.06, C:0.18, G:0.00, T:0.76
Consensus pattern (17 bp):
TATCCCTTTTTCTTTTT
Found at i:1433906 original size:3 final size:3
Alignment explanation
Indices: 1433900--1433935 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1433890 TGTTGTTTAG
1433900 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
1433936 AATTATATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1434418 original size:3 final size:3
Alignment explanation
Indices: 1434410--1434441 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1434400 ACCCTTTTAA
1434410 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1434442 CGTGAAATTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1446428 original size:23 final size:24
Alignment explanation
Indices: 1446375--1446447 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
1446365 TTATATAAAA
1446375 ATTAAATATATAATTTTTATTGTT
1 ATTAAATATATAATTTTTATTGTT
** * *
1446399 ACAAAATATGTATTTTTTATT-TT
1 ATTAAATATATAATTTTTATTGTT
* **
1446422 ATTAAATTTATATATAATTATTGTT
1 ATTAAATATATA-ATTTTTATTGTT
1446447 A
1 A
1446448 AAATTTTAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
23 10 0.28
24 23 0.64
25 3 0.08
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTAAATATATAATTTTTATTGTT
Found at i:1449327 original size:28 final size:29
Alignment explanation
Indices: 1449286--1449345 Score: 104
Period size: 28 Copynumber: 2.1 Consensus size: 29
1449276 ATGGGCAAAC
*
1449286 ATTTTCAGGAAACACTTTATTATCCTTTG
1 ATTTTCAGGAAACACTTTATCATCCTTTG
1449315 ATTTT-AGGAAACACTTTATCATCCTTTG
1 ATTTTCAGGAAACACTTTATCATCCTTTG
1449343 ATT
1 ATT
1449346 AGGTAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (29 bp):
ATTTTCAGGAAACACTTTATCATCCTTTG
Found at i:1450121 original size:32 final size:33
Alignment explanation
Indices: 1450085--1450172 Score: 101
Period size: 32 Copynumber: 2.7 Consensus size: 33
1450075 TGTCCTTCAC
*
1450085 TTGAGGTTCACGATTTTGCTTC-AGTTCTCTAT
1 TTGAGGTTCACGATTTTGCTACTAGTTCTCTAT
* * * *
1450117 TTGAGGTTCATGCTTTTGC-ACTGGTTCTTTAT
1 TTGAGGTTCACGATTTTGCTACTAGTTCTCTAT
1450149 TTGAGGTTCAC-ACTTTTGCTACTA
1 TTGAGGTTCACGA-TTTTGCTACTA
1450173 AGATTTTTTT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
31 1 0.02
32 41 0.91
33 3 0.07
ACGTcount: A:0.16, C:0.18, G:0.19, T:0.47
Consensus pattern (33 bp):
TTGAGGTTCACGATTTTGCTACTAGTTCTCTAT
Found at i:1458733 original size:44 final size:44
Alignment explanation
Indices: 1458685--1458773 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
1458675 CAAGTGAAGA
*
1458685 AGATTATTTTTAATTTATGAGATTTAAA-TTACATGTTTAATTAT
1 AGATTATTTTTAATTTATGA-AATTAAATTTACATGTTTAATTAT
*
1458729 AGATTATTTTTAATTTATGAAATTAAATTTATATGTTTAATTAT
1 AGATTATTTTTAATTTATGAAATTAAATTTACATGTTTAATTAT
1458773 A
1 A
1458774 TATTTAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 6 0.14
44 36 0.86
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.53
Consensus pattern (44 bp):
AGATTATTTTTAATTTATGAAATTAAATTTACATGTTTAATTAT
Found at i:1458929 original size:27 final size:26
Alignment explanation
Indices: 1458889--1458943 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
1458879 AAATAAAATG
1458889 ATATTATTTAATTTAATTTTATTAATA
1 ATATTATTTAATTTAATTTTATT-ATA
* *
1458916 ATATTATTTTATTTTATTTTATTATA
1 ATATTATTTAATTTAATTTTATTATA
1458942 AT
1 AT
1458944 TTTACATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (26 bp):
ATATTATTTAATTTAATTTTATTATA
Found at i:1459815 original size:2 final size:2
Alignment explanation
Indices: 1459808--1459840 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1459798 ATTTGTAATC
1459808 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1459841 TACATACGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1460232 original size:22 final size:22
Alignment explanation
Indices: 1460192--1460234 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1460182 TTTTTTTTGT
*
1460192 TTAATTAATGAATCTTAAAATA
1 TTAATTAATAAATCTTAAAATA
1460214 TTAATTAATAAAT-TCTAAAAT
1 TTAATTAATAAATCT-TAAAAT
1460235 CTTATTCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
TTAATTAATAAATCTTAAAATA
Found at i:1462724 original size:2 final size:2
Alignment explanation
Indices: 1462719--1462753 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1462709 ACACACTCAC
1462719 AG AG AG AG AG 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 AG AG AG AG AG A
1462754 CCTGCAACTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1470183 original size:21 final size:20
Alignment explanation
Indices: 1470143--1470187 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1470133 TTTTGATCTA
1470143 AAAAACAAATAATCAAAATT
1 AAAAACAAATAATCAAAATT
*
1470163 CAAAAACAATTAAT-AACAATT
1 -AAAAACAAATAATCAA-AATT
1470184 AAAA
1 AAAA
1470188 TTAAATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.69, C:0.11, G:0.00, T:0.20
Consensus pattern (20 bp):
AAAAACAAATAATCAAAATT
Found at i:1471116 original size:20 final size:22
Alignment explanation
Indices: 1471072--1471116 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1471062 ATTTTTATAC
**
1471072 TATCTAATTAAATTTATCGTAT
1 TATCTAATTAAATTTATAATAT
1471094 TATC-AATTAAATTTA-AATAT
1 TATCTAATTAAATTTATAATAT
1471114 TAT
1 TAT
1471117 TTTTAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 11 0.52
22 4 0.19
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (22 bp):
TATCTAATTAAATTTATAATAT
Found at i:1471173 original size:23 final size:23
Alignment explanation
Indices: 1471156--1471206 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
1471146 TTTATTAAAT
*
1471156 TTTTTTAATTATAATTATAATAA
1 TTTTTTAATAATAATTATAATAA
*
1471179 TTTTTTAATAATAACTA-AAGTAA
1 TTTTTTAATAATAATTATAA-TAA
1471202 TTTTT
1 TTTTT
1471207 ATTAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTTTTTAATAATAATTATAATAA
Found at i:1471582 original size:21 final size:19
Alignment explanation
Indices: 1471556--1471602 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
1471546 GTTTTATAAA
1471556 ATATTAATAATTTATATATTT
1 ATATTAAT-ATTTATATA-TT
*
1471577 ATATT-ATATTTTTATATT
1 ATATTAATATTTATATATT
*
1471595 AAATTAAT
1 ATATTAAT
1471603 TTATTATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.26
19 10 0.43
20 2 0.09
21 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATTAATATTTATATATT
Found at i:1471840 original size:64 final size:64
Alignment explanation
Indices: 1471771--1471898 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
1471761 TAATTCGATT
1471771 CAAATCAAAATTTTTATTTCATTTGAATTAAATTTAAATATTAAATGTATATATTATATTCGGA
1 CAAATCAAAATTTTTATTTCATTTGAATTAAATTTAAATATTAAATGTATATATTATATTCGGA
1471835 CAAATCAAAATTTTTATTTCATTTGAATTAAATTTAAATATTAAATGTATATATTATATTCGGA
1 CAAATCAAAATTTTTATTTCATTTGAATTAAATTTAAATATTAAATGTATATATTATATTCGGA
1471899 TTAAATTTCA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (64 bp):
CAAATCAAAATTTTTATTTCATTTGAATTAAATTTAAATATTAAATGTATATATTATATTCGGA
Found at i:1472039 original size:13 final size:13
Alignment explanation
Indices: 1472016--1472055 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1472006 ATATACTTAA
*
1472016 ATATATTAAAATT
1 ATATATAAAAATT
* *
1472029 TTATATAAAAATA
1 ATATATAAAAATT
1472042 ATATATAAAAATT
1 ATATATAAAAATT
1472055 A
1 A
1472056 AAAAAATTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATAAAAATT
Found at i:1473550 original size:15 final size:16
Alignment explanation
Indices: 1473524--1473561 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1473514 CTTTCTTTGC
*
1473524 AATAATATTTATA-CA
1 AATAAAATTTATATCA
*
1473539 ACTAAAATTTATATCA
1 AATAAAATTTATATCA
1473555 AATAAAA
1 AATAAAA
1473562 ATAAAGTACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (16 bp):
AATAAAATTTATATCA
Found at i:1476064 original size:11 final size:11
Alignment explanation
Indices: 1476050--1476078 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1476040 CCTCTGTCCT
1476050 CTCTCTTTTTC
1 CTCTCTTTTTC
1476061 CTCTCTTTTTC
1 CTCTCTTTTTC
1476072 CTCTCTT
1 CTCTCTT
1476079 CCCTACTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (11 bp):
CTCTCTTTTTC
Found at i:1476064 original size:13 final size:13
Alignment explanation
Indices: 1476046--1476077 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
1476036 GGTTCCTCTG
1476046 TCCTCTCTCTTTT
1 TCCTCTCTCTTTT
1476059 T-C-CTCTCTTTT
1 TCCTCTCTCTTTT
1476070 TCCTCTCT
1 TCCTCTCT
1476078 TCCCTACTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 4
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.59
12 2 0.12
13 5 0.29
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (13 bp):
TCCTCTCTCTTTT
Found at i:1482886 original size:52 final size:51
Alignment explanation
Indices: 1482819--1482919 Score: 143
Period size: 52 Copynumber: 2.0 Consensus size: 51
1482809 TCATACAAAG
* *
1482819 TAAGTTCTATCTGTAACCATAGCATATATAA-AAATA-AAAGTGCAATCAAAAA
1 TAAGATCTATCTGTAAACATAGCATATA-AATAAA-ACAAA-TGCAATCAAAAA
1482871 TAAGATCTATCTGTAAACATAGCATATAAATAAAACAAATGCAATCAAA
1 TAAGATCTATCTGTAAACATAGCATATAAATAAAACAAATGCAATCAAA
1482920 TATTATTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
51 13 0.29
52 32 0.71
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (51 bp):
TAAGATCTATCTGTAAACATAGCATATAAATAAAACAAATGCAATCAAAAA
Found at i:1483831 original size:15 final size:16
Alignment explanation
Indices: 1483795--1483831 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1483785 AACGCTGCTT
1483795 ATAGCAAAGGAAACTAC
1 ATAG-AAAGGAAACTAC
1483812 A-AGAAAGGAAACTA-
1 ATAGAAAGGAAACTAC
1483826 ATAGAA
1 ATAGAA
1483832 GAGAATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 15 0.79
16 2 0.11
17 1 0.05
ACGTcount: A:0.59, C:0.11, G:0.19, T:0.11
Consensus pattern (16 bp):
ATAGAAAGGAAACTAC
Found at i:1490178 original size:21 final size:22
Alignment explanation
Indices: 1490154--1490194 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1490144 TTGTTTTAAA
*
1490154 TTTAATA-AAATATATAATTTT
1 TTTAATATAAATATAAAATTTT
1490175 TTTAATATAAATATAAAATT
1 TTTAATATAAATATAAAATT
1490195 AATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAATATAAATATAAAATTTT
Found at i:1494707 original size:21 final size:22
Alignment explanation
Indices: 1494681--1494726 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
1494671 CTAAAAAAAT
1494681 TTGAAAAATTTATATTTA-ATA
1 TTGAAAAATTTATATTTATATA
* *
1494702 TTG-AAATTTTATTTTTATATA
1 TTGAAAAATTTATATTTATATA
1494723 TTGA
1 TTGA
1494727 TATTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (22 bp):
TTGAAAAATTTATATTTATATA
Found at i:1495489 original size:25 final size:26
Alignment explanation
Indices: 1495461--1495515 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
1495451 TTTTATATCG
*
1495461 ATATAAATTATA-ATATATAAT-TTTT
1 ATATAAAATATATAT-TATAATATTTT
*
1495486 ATATAAAATATATATTTTAATATTTT
1 ATATAAAATATATATTATAATATTTT
1495512 ATAT
1 ATAT
1495516 TATATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATATAAAATATATATTATAATATTTT
Found at i:1496880 original size:21 final size:20
Alignment explanation
Indices: 1496842--1496886 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
1496832 TTTTATATAT
*
1496842 TATTTTAATATATTTAAATA
1 TATTTTAATATATATAAATA
* *
1496862 TATTTTGATATGATATAAATT
1 TATTTTAATAT-ATATAAATA
1496883 TATT
1 TATT
1496887 ATTTTTTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTAATATATATAAATA
Found at i:1498243 original size:24 final size:24
Alignment explanation
Indices: 1498215--1498263 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1498205 GCACACATGT
* *
1498215 ATGCACAAATGTGCATGCGCAAAC
1 ATGCACAAATGCGCATGCACAAAC
*
1498239 ATGCACACATGCGCATGCACAAAC
1 ATGCACAAATGCGCATGCACAAAC
1498263 A
1 A
1498264 CACATATATC
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:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (24 bp):
ATGCACAAATGCGCATGCACAAAC
Found at i:1502616 original size:27 final size:28
Alignment explanation
Indices: 1502580--1502665 Score: 74
Period size: 27 Copynumber: 3.0 Consensus size: 28
1502570 ATCAAGTATC
1502580 ATATTA-ATTAATATATTTAT-AATTTA-
1 ATATTATATTAA-ATATTTATAAATTTAT
*
1502606 AGTA-TATATTAAA-ATTTTTTAAATTTAT
1 A-TATTATATTAAATA-TTTATAAATTTAT
1502634 ATATTATATTAAATATTTTATTATAATTTAT
1 ATATTATATTAAATA-TTTA-TA-AATTTAT
1502665 A
1 A
1502666 AATAATTCGT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
25 1 0.02
26 8 0.16
27 15 0.31
28 10 0.20
29 5 0.10
30 2 0.04
31 8 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
ATATTATATTAAATATTTATAAATTTAT
Found at i:1502626 original size:28 final size:30
Alignment explanation
Indices: 1502580--1502665 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 30
1502570 ATCAAGTATC
*
1502580 ATATTA-ATT-AATA-TATTTATAATTTA-
1 ATATTATATTAAATATTTTTTATAATTTAT
1502606 AGTA-TATATTAAA-ATTTTTTA-AATTTAT
1 A-TATTATATTAAATATTTTTTATAATTTAT
1502634 ATATTATATTAAATATTTTATTATAATTTAT
1 ATATTATATTAAATATTTT-TTATAATTTAT
1502665 A
1 A
1502666 AATAATTCGT
Statistics
Matches: 50, Mismatches: 1, Indels: 13
0.78 0.02 0.20
Matches are distributed among these distances:
26 3 0.06
27 14 0.28
28 17 0.34
29 5 0.10
30 3 0.06
31 8 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (30 bp):
ATATTATATTAAATATTTTTTATAATTTAT
Found at i:1504010 original size:13 final size:13
Alignment explanation
Indices: 1503992--1504050 Score: 61
Period size: 13 Copynumber: 4.6 Consensus size: 13
1503982 AATAATTTTA
*
1503992 AATATGATACAAT
1 AATATGATAAAAT
*
1504005 AATATGATATAAT
1 AATATGATAAAAT
1504018 AATGAT-ATATAAAT
1 AAT-ATGATA-AAAT
1504032 AATA--ATAAAAT
1 AATATGATAAAAT
1504043 AATATGAT
1 AATATGAT
1504051 TTAAAATTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
11 8 0.20
12 3 0.08
13 21 0.52
14 8 0.20
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.34
Consensus pattern (13 bp):
AATATGATAAAAT
Found at i:1510476 original size:4 final size:4
Alignment explanation
Indices: 1510469--1510493 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1510459 ATATATATAT
1510469 ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC A
1510494 CACACACACA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:1512865 original size:3 final size:3
Alignment explanation
Indices: 1512857--1512915 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
1512847 CATATAACCC
1512857 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1512905 ATA ATA ATA AT
1 ATA ATA ATA AT
1512916 CCTCTAAGAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1518137 original size:2 final size:2
Alignment explanation
Indices: 1518130--1518168 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1518120 TTTAGTTTTA
1518130 AT AT AT 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 AT AT AT A
1518169 AAACAAGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1521306 original size:12 final size:12
Alignment explanation
Indices: 1521285--1521356 Score: 51
Period size: 12 Copynumber: 6.0 Consensus size: 12
1521275 ATGCCTTTTG
*
1521285 ATAATTTAAAAT
1 ATAATATAAAAT
*
1521297 ATAATATAAAAA
1 ATAATATAAAAT
*
1521309 ATAATTTAAAAAT
1 ATAATAT-AAAAT
*
1521322 GATACATTTAAAAT
1 -ATA-ATATAAAAT
*
1521336 TTAATA-AAAAT
1 ATAATATAAAAT
1521347 A-AATA-AAAAT
1 ATAATATAAAAT
1521357 TTTATAATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
10 9 0.18
11 5 0.10
12 18 0.36
13 6 0.12
14 8 0.16
15 4 0.08
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (12 bp):
ATAATATAAAAT
Found at i:1522025 original size:52 final size:48
Alignment explanation
Indices: 1521915--1522046 Score: 167
Period size: 52 Copynumber: 2.7 Consensus size: 48
1521905 TTCACCTCCT
* *
1521915 CCACCTTATGAGTACAAGTCACCTCCACCACCGTCTCCTTCTCCACCA
1 CCACCTTATGAGTACAAGTCACCTCCACCACCCTCGCCTTCTCCACCA
*
1521963 CCACCTTATGAGCACTAAGTCACCTCCAGCCAACCCCTCGCCTTCTCCACCA
1 CCACCTTATGAGTAC-AAGTCACCTCCA-CC-A-CCCTCGCCTTCTCCACCA
* *
1522015 CCA-CTCTATGAGTACAAGTCCCCACCACCACC
1 CCACCT-TATGAGTACAAGTCACCTCCACCACC
1522047 ACCCAAAACC
Statistics
Matches: 73, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
48 16 0.22
49 13 0.18
50 4 0.05
51 13 0.18
52 27 0.37
ACGTcount: A:0.24, C:0.47, G:0.09, T:0.20
Consensus pattern (48 bp):
CCACCTTATGAGTACAAGTCACCTCCACCACCCTCGCCTTCTCCACCA
Found at i:1522173 original size:50 final size:47
Alignment explanation
Indices: 1522072--1522272 Score: 163
Period size: 50 Copynumber: 4.0 Consensus size: 47
1522062 AGAGAGCCCT
*
1522072 CATACTACTATAAGATCTCCACCAC-CCTTCCATCTCCATCACCACCTCCTC
1 CATA-TACTACAAG-TCTCCACCACTCCTTCCA---CCATCACCACCTCCTC
* * *
1522123 CATACTATTACAAGTCTCCACCACGTCCTTCCACCATCCACCCCCACCTC
1 CATA-TACTACAAGTCTCCACCAC-TCCTTCCACCAT-CACCACCTCCTC
* *
1522173 CATGATACTACAAGTCTCCAAGCCACCTCCATCC-CCATCTCCACCTCCTC
1 CAT-ATACTACAAGTCTCC-A-CCA-CTCCTTCCACCATCACCACCTCCTC
* * * *
1522223 CGTATACTACAAGTCTCCACCACCTTCCAATCCTCCATCCCCACCTCCTC
1 CATATACTACAAGTCTCCACCA-C-TCC-TTCCACCATCACCACCTCCTC
1522273 TCCAGTACTA
Statistics
Matches: 129, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
47 5 0.04
48 4 0.03
49 23 0.18
50 62 0.48
51 18 0.14
52 16 0.12
53 1 0.01
ACGTcount: A:0.24, C:0.49, G:0.04, T:0.23
Consensus pattern (47 bp):
CATATACTACAAGTCTCCACCACTCCTTCCACCATCACCACCTCCTC
Found at i:1522427 original size:48 final size:48
Alignment explanation
Indices: 1522337--1522526 Score: 213
Period size: 48 Copynumber: 3.9 Consensus size: 48
1522327 CCCCCATTCT
* * * *
1522337 CCATCACCACCTCCTCCTTACTGACTATAAATCCCCCACCACCTCCTTCA
1 CCATCACCACCTCATCCATACT-ACTACAAAT-CCCCACCACCTCCATCA
* * * *
1522387 CCATCGCCACCACATCCATACTACTACAAGTCCCCACCACCTCCATCT
1 CCATCACCACCTCATCCATACTACTACAAATCCCCACCACCTCCATCA
* *
1522435 CCATCACCACCTCATCCATACTATTACAAATCTCCACCACCTCCATCA
1 CCATCACCACCTCATCCATACTACTACAAATCCCCACCACCTCCATCA
* * * *
1522483 CCCTCACCACCGCCA-CCTTATTACTAC-AATCCCCACCACCTCCA
1 CCATCACCACC-TCATCCATACTACTACAAATCCCCACCACCTCCA
1522527 GTAAAGTCTC
Statistics
Matches: 119, Mismatches: 20, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
47 16 0.13
48 76 0.64
49 9 0.08
50 18 0.15
ACGTcount: A:0.27, C:0.50, G:0.02, T:0.21
Consensus pattern (48 bp):
CCATCACCACCTCATCCATACTACTACAAATCCCCACCACCTCCATCA
Found at i:1522431 original size:27 final size:26
Alignment explanation
Indices: 1522393--1522480 Score: 69
Period size: 27 Copynumber: 3.5 Consensus size: 26
1522383 TTCACCATCG
*
1522393 CCACCACATCCATACTACTACAAGTCC
1 CCACCACATCCATACTACTACAA-TCA
*
1522420 CCACCACCTCCAT-CT-C--C-ATCA
1 CCACCACATCCATACTACTACAATCA
* * *
1522441 CCACCTCATCCATACTATTACAAATCT
1 CCACCACATCCATACTACTAC-AATCA
*
1522468 CCACCACCTCCAT
1 CCACCACATCCAT
1522481 CACCCTCACC
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
21 13 0.28
22 3 0.06
23 1 0.02
25 2 0.04
26 2 0.04
27 26 0.55
ACGTcount: A:0.30, C:0.48, G:0.01, T:0.22
Consensus pattern (26 bp):
CCACCACATCCATACTACTACAATCA
Found at i:1522648 original size:48 final size:48
Alignment explanation
Indices: 1522372--1522669 Score: 155
Period size: 48 Copynumber: 6.2 Consensus size: 48
1522362 TATAAATCCC
* * * * * *
1522372 CCACCACCTCCTTCACCATCGCCACCA-CATCCATACTACTACAAGTCC
1 CCACCACCACCTCCACCATCACCTCCACCA-CCATACTATTACAAGTCT
* * * * *
1522420 CCACCACCTCCAT-CTCCATCACCACC-TCATCCATACTATTACAAATCT
1 CCACCACCACC-TCCACCATCACCTCCACCA-CCATACTATTACAAGTCT
* * * * * * *
1522468 CCACCACCTCCAT-CACCCTCACCACCGCCACCTTATTACTACAA---T
1 CCACCACCACC-TCCACCATCACCTCCACCACCATACTATTACAAGTCT
** * * *
1522513 CC-CCACCACCTCCAGTAAAGTCTCCTCCACCACCATATTATTATAAGTCT
1 CCACCACCACCTCCA--CCA-TCACCTCCACCACCATACTATTACAAGTCT
* * * * *
1522563 CCCCCACCACCTTCACCATCTCCTCCACGACCTTACTATTACAAGTCT
1 CCACCACCACCTCCACCATCACCTCCACCACCATACTATTACAAGTCT
* * * * * *
1522611 CCACCACCTCCTCCA-CATCACATTTCACCACCATACTACTACAAATCG
1 CCACCACCACCTCCACCATCAC-CTCCACCACCATACTATTACAAGTCT
1522659 CCACCACCACC
1 CCACCACCACC
1522670 ACCTAAATCT
Statistics
Matches: 198, Mismatches: 40, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
43 1 0.01
44 9 0.05
45 3 0.02
47 25 0.13
48 142 0.72
49 4 0.02
50 3 0.02
51 11 0.06
ACGTcount: A:0.28, C:0.48, G:0.03, T:0.22
Consensus pattern (48 bp):
CCACCACCACCTCCACCATCACCTCCACCACCATACTATTACAAGTCT
Found at i:1530819 original size:52 final size:51
Alignment explanation
Indices: 1530757--1530860 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 51
1530747 TCATACAAAG
1530757 TAAGATCTATCTGTAACCATAGCATATATAA-AAATAAAAATGCAATCAAATA
1 TAAGATCTATCTGTAACCATAGCATATA-AATAAA-AAAAATGCAATCAAATA
*
1530809 TAAGATCTATCTGTAACCATAGCATATAAATAAAACAAATGCAATCAAATA
1 TAAGATCTATCTGTAACCATAGCATATAAATAAAAAAAATGCAATCAAATA
1530860 T
1 T
1530861 TATTAAAGAA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
51 19 0.38
52 31 0.62
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.27
Consensus pattern (51 bp):
TAAGATCTATCTGTAACCATAGCATATAAATAAAAAAAATGCAATCAAATA
Found at i:1531767 original size:15 final size:16
Alignment explanation
Indices: 1531731--1531767 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1531721 TACGCTGCTT
1531731 ATAGCAAAGGAAACTAC
1 ATAG-AAAGGAAACTAC
1531748 A-AGAAAGGAAACTA-
1 ATAGAAAGGAAACTAC
1531762 ATAGAA
1 ATAGAA
1531768 GAGAATAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.05
15 15 0.79
16 2 0.11
17 1 0.05
ACGTcount: A:0.59, C:0.11, G:0.19, T:0.11
Consensus pattern (16 bp):
ATAGAAAGGAAACTAC
Found at i:1531883 original size:13 final size:13
Alignment explanation
Indices: 1531865--1531889 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1531855 TTCTTTTGAT
1531865 TTTTTTTTTATTC
1 TTTTTTTTTATTC
1531878 TTTTTTTTTATT
1 TTTTTTTTTATT
1531890 ATGGCCAGTA
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:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTTTTATTC
Found at i:1537469 original size:24 final size:24
Alignment explanation
Indices: 1537440--1537487 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1537430 TTTCTTTAAA
1537440 AATTGCTGAATCATTTCAAAAGAT
1 AATTGCTGAATCATTTCAAAAGAT
1537464 AATTGCTGAATCATTTCAAAAGAT
1 AATTGCTGAATCATTTCAAAAGAT
1537488 CAAAGGAGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
AATTGCTGAATCATTTCAAAAGAT
Found at i:1541827 original size:17 final size:14
Alignment explanation
Indices: 1541789--1541823 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1541779 CAGTTCTCAT
1541789 CAAACCAACAACTG
1 CAAACCAACAACTG
1541803 CAAACCAACAACTG
1 CAAACCAACAACTG
1541817 CAAACCA
1 CAAACCA
1541824 CCAAATCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.37, G:0.06, T:0.06
Consensus pattern (14 bp):
CAAACCAACAACTG
Found at i:1543391 original size:18 final size:18
Alignment explanation
Indices: 1543370--1543405 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1543360 CGATACAAAT
* *
1543370 TATAATATATAATTTTTA
1 TATAAAATATAAATTTTA
1543388 TATAAAATATAAATTTTA
1 TATAAAATATAAATTTTA
1543406 ATATTTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TATAAAATATAAATTTTA
Found at i:1544803 original size:21 final size:20
Alignment explanation
Indices: 1544765--1544811 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
1544755 TTTTATATAT
*
1544765 TATTTTAATATATTTAAATA
1 TATTTTAATATATATAAATA
* *
1544785 TATTTTGATATGATATAAATT
1 TATTTTAATAT-ATATAAATA
1544806 TATTTT
1 TATTTT
1544812 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
TATTTTAATATATATAAATA
Found at i:1546164 original size:24 final size:24
Alignment explanation
Indices: 1546136--1546184 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
1546126 GCACACATGT
* *
1546136 ATGCACAAATGTGCATGCGCAAAC
1 ATGCACAAATGCGCATGCACAAAC
*
1546160 ATGCACACATGCGCATGCACAAAC
1 ATGCACAAATGCGCATGCACAAAC
1546184 A
1 A
1546185 CACATATATC
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:0.39, C:0.29, G:0.18, T:0.14
Consensus pattern (24 bp):
ATGCACAAATGCGCATGCACAAAC
Found at i:1550980 original size:29 final size:29
Alignment explanation
Indices: 1550943--1551001 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1550933 AACTATAATG
* *
1550943 AAATATTTAATATGATATTTGAATTTTAA
1 AAATATTTAATATGATACTTGAATTATAA
* * *
1550972 AAATTTTTAATTTTATACTTGAATTATAA
1 AAATATTTAATATGATACTTGAATTATAA
1551001 A
1 A
1551002 TTTATTAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (29 bp):
AAATATTTAATATGATACTTGAATTATAA
Done.