Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008985.1 Hibiscus syriacus cultivar Beakdansim tig00112349_pilon, 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: 1528252
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 7 of 9
Found at i:1091431 original size:23 final size:22
Alignment explanation
Indices: 1091383--1091434 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 22
1091373 ACTTATCTCC
*
1091383 CTTTCTTCTTCTTCTTCCTTTA
1 CTTTCTTCTTCTCCTTCCTTTA
*
1091405 CTTTCTCTCTTCTCCCTTTCTTT-
1 CTTTCT-TCTTCT-CCTTCCTTTA
1091428 CTTTCTT
1 CTTTCTT
1091435 TCTCCTGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 12 0.46
24 7 0.27
ACGTcount: A:0.02, C:0.35, G:0.00, T:0.63
Consensus pattern (22 bp):
CTTTCTTCTTCTCCTTCCTTTA
Found at i:1091437 original size:20 final size:19
Alignment explanation
Indices: 1091378--1091439 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 19
1091368 TTGGAACTTA
1091378 TCTCCCTTTC-TTC-TTCT
1 TCTCCCTTTCTTTCTTTCT
* *
1091395 TCTTCCTTTACTTTCTCTCT
1 TCTCCCTTT-CTTTCTTTCT
1091415 TCTCCCTTTCTTTCTTTCTT
1 TCTCCCTTTCTTTCTTTC-T
1091435 TCTCC
1 TCTCC
1091440 TGCTCCATGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 8 0.22
18 1 0.03
19 11 0.30
20 17 0.46
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.60
Consensus pattern (19 bp):
TCTCCCTTTCTTTCTTTCT
Found at i:1091582 original size:20 final size:20
Alignment explanation
Indices: 1091557--1091594 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1091547 ATGTAGGGCT
1091557 GTGAATCATGTTGCAATACC
1 GTGAATCATGTTGCAATACC
*
1091577 GTGAATCATGTTGTAATA
1 GTGAATCATGTTGCAATA
1091595 ATGCAGCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.13, G:0.21, T:0.34
Consensus pattern (20 bp):
GTGAATCATGTTGCAATACC
Found at i:1091726 original size:28 final size:28
Alignment explanation
Indices: 1091671--1091748 Score: 102
Period size: 28 Copynumber: 2.8 Consensus size: 28
1091661 CTTGGTCGTC
* *
1091671 GGGCGTGCATGGCAACCTACCATGTCACG
1 GGGCGTGCATGGCGACCTA-CAAGTCACG
* *
1091700 GGGCGTGCATAGCGACCTACAAGTCACT
1 GGGCGTGCATGGCGACCTACAAGTCACG
*
1091728 GGGCGTGCATGGCGAACTACA
1 GGGCGTGCATGGCGACCTACA
1091749 GCGGGATTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 26 0.60
29 17 0.40
ACGTcount: A:0.23, C:0.28, G:0.32, T:0.17
Consensus pattern (28 bp):
GGGCGTGCATGGCGACCTACAAGTCACG
Found at i:1097379 original size:35 final size:35
Alignment explanation
Indices: 1097285--1097700 Score: 452
Period size: 35 Copynumber: 11.8 Consensus size: 35
1097275 TCAAATATAG
* * *
1097285 TTTTGGAAAATATATAATATATAGTTTTTGGAAACTTAT
1 TTTT-GAAAACATATAATATATAGTTTTT--AAA-ATAA
* *
1097324 TTTTAAAAACATATAGTATATAGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
*
1097359 TTTTGAAAACATATAATATATAGTTTTTTAAAAAAA
1 TTTTGAAAACATATAATATATAG-TTTTTAAAATAA
*
1097395 GGTTTTGAAAACATATAGTATATAGTTTTTAAAATAA
1 --TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* ***
1097432 TTTTGAAAACGTAT-A-ATATAGTTTTTAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
*
1097465 TTTTGAAAACATATAGTATATAGTTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAG-TTTTTAAAATAA
* *
1097501 TTTTAAAAACATATAGTATATAGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* ***
1097536 TTTTGAAAACGTAT-A-ATATAGTTTTTAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* *
1097569 TTTTGAAAACATATAGTATATAATTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* *
1097604 TTTTTAAAACGTATAATA-A-AGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
**
1097637 TTTTGAAAATGTATAATATATAG-TTTTAAAA-AA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* *
1097670 TGTTTTGAAAACGTATAATATATAATTTTTA
1 --TTTTGAAAACATATAATATATAGTTTTTA
1097701 CTTTTTGTAT
Statistics
Matches: 323, Mismatches: 41, Indels: 29
0.82 0.10 0.07
Matches are distributed among these distances:
33 87 0.27
34 10 0.03
35 118 0.37
36 50 0.15
37 11 0.03
38 43 0.13
39 4 0.01
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (35 bp):
TTTTGAAAACATATAATATATAGTTTTTAAAATAA
Found at i:1097552 original size:104 final size:105
Alignment explanation
Indices: 1097291--1097699 Score: 513
Period size: 104 Copynumber: 3.9 Consensus size: 105
1097281 ATAGTTTTGG
* * * * * *
1097291 AAAATATATAATATATAGTTTTTGGAAACTTATTTTTAAAAACATATAGTATATAGTTTTTAAAA
1 AAAACATATAGTATATAGTTTTT--AAA-ATAATTTTGAAAACGTATA-TATATAGTTTTTAAAA
*** * *
1097356 TAATTTTGAAAACATATAATATATAGTTTTTTAAAAAAAGGTTTTG
62 CGGTTTTGAAAACATATAATATATAGTTTTTTAAAATAA--TTTTA
1097402 AAAACATATAGTATATAGTTTTTAAAATAATTTTGAAAACGTATA-ATATAGTTTTTAAAACGGT
1 AAAACATATAGTATATAGTTTTTAAAATAATTTTGAAAACGTATATATATAGTTTTTAAAACGGT
*
1097466 TTTGAAAACATATAGTATATAGTTTTTTAAAATAATTTTA
66 TTTGAAAACATATAATATATAGTTTTTTAAAATAATTTTA
1097506 AAAACATATAGTATATAGTTTTTAAAATAATTTTGAAAACGTATA-ATATAGTTTTTAAAACGGT
1 AAAACATATAGTATATAGTTTTTAAAATAATTTTGAAAACGTATATATATAGTTTTTAAAACGGT
* * *
1097570 TTTGAAAACATATAGTATATA-ATTTTTAAAATAATTTTT
66 TTTGAAAACATATAATATATAGTTTTTTAAAATAATTTTA
* * * * **
1097609 AAAACGTATA--ATAAAGTTTTTAAAATAATTTTGAAAATGTATAATATATAGTTTTAAAAAATG
1 AAAACATATAGTATATAGTTTTTAAAATAATTTTGAAAACGTAT-ATATATAGTTTTTAAAACGG
* *
1097672 TTTTGAAAACGTATAATATATAATTTTT
65 TTTTGAAAACATATAATATATAGTTTTT
1097700 ACTTTTTGTA
Statistics
Matches: 272, Mismatches: 23, Indels: 13
0.88 0.07 0.04
Matches are distributed among these distances:
101 30 0.11
102 1 0.00
103 60 0.22
104 93 0.34
106 49 0.18
108 15 0.06
109 3 0.01
111 21 0.08
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.43
Consensus pattern (105 bp):
AAAACATATAGTATATAGTTTTTAAAATAATTTTGAAAACGTATATATATAGTTTTTAAAACGGT
TTTGAAAACATATAATATATAGTTTTTTAAAATAATTTTA
Found at i:1097589 original size:68 final size:69
Alignment explanation
Indices: 1097285--1097691 Score: 441
Period size: 68 Copynumber: 5.8 Consensus size: 69
1097275 TCAAATATAG
* * * *
1097285 TTTTGGAAAATATATAATATATAGTTTTTGGAAACTTATTTTTAAAAACATATAGTATATAGTTT
1 TTTT-GAAAACATATAATATATAGTTTTT--AAA-ATAATTTTGAAAACATATAG-ATATAGTTT
1097350 TTAAAATAA
61 TTAAAATAA
*
1097359 TTTTGAAAACATATAATATATAGTTTTTTAAAAAAAGGTTTTGAAAACATATAGTATATAGTTTT
1 TTTTGAAAACATATAATATATAG-TTTTTAAAATAA--TTTTGAAAACATATAG-ATATAGTTTT
1097424 TAAAATAA
62 TAAAATAA
* ***
1097432 TTTTGAAAACGTAT-A-ATATAGTTTTTAAAACGGTTTTGAAAACATATAGTATATAGTTTTTTA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAATTTTGAAAACATATAG-ATATAG-TTTTTA
1097495 AAATAA
64 AAATAA
* * *
1097501 TTTTAAAAACATATAGTATATAGTTTTTAAAATAATTTTGAAAACGTATA-ATATAGTTTTTAAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAATTTTGAAAACATATAGATATAGTTTTTAAA
***
1097565 ACGG
66 ATAA
* * * * *
1097569 TTTTGAAAACATATAGTATATAATTTTTAAAATAATTTTTAAAACGTATA-ATAAAGTTTTTAAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAATTTTGAAAACATATAGATATAGTTTTTAAA
1097633 ATAA
66 ATAA
** *
1097637 TTTTGAAAATGTATAATATATAG-TTTTAAAA-AATGTTTTGAAAACGTATA-ATATA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA--TTTTGAAAACATATAGATATA
1097692 TAATTTTTAC
Statistics
Matches: 293, Mismatches: 32, Indels: 22
0.84 0.09 0.06
Matches are distributed among these distances:
66 2 0.01
67 8 0.03
68 130 0.44
69 30 0.10
70 9 0.03
71 36 0.12
72 4 0.01
73 65 0.22
74 9 0.03
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (69 bp):
TTTTGAAAACATATAATATATAGTTTTTAAAATAATTTTGAAAACATATAGATATAGTTTTTAAA
ATAA
Found at i:1097605 original size:12 final size:12
Alignment explanation
Indices: 1097588--1097612 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1097578 CATATAGTAT
1097588 ATAATTTTTAAA
1 ATAATTTTTAAA
1097600 ATAATTTTTAAA
1 ATAATTTTTAAA
1097612 A
1 A
1097613 CGTATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATAATTTTTAAA
Found at i:1097729 original size:4 final size:4
Alignment explanation
Indices: 1097722--1097779 Score: 59
Period size: 4 Copynumber: 14.5 Consensus size: 4
1097712 CTATAGTTAG
*
1097722 TTAT TTAT ATTAT TTAT TT-T TTAT TTAT TTCAC TTAT TTATT TTAT TT-T
1 TTAT TTAT -TTAT TTAT TTAT TTAT TTAT TT-AT TTAT TTA-T TTAT TTAT
1097771 TT-T TTAT TT
1 TTAT TTAT TT
1097780 TCGTTTTTAG
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
3 9 0.19
4 27 0.57
5 11 0.23
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:1097736 original size:9 final size:8
Alignment explanation
Indices: 1097722--1097779 Score: 59
Period size: 9 Copynumber: 7.2 Consensus size: 8
1097712 CTATAGTTAG
1097722 TTATTTAT
1 TTATTTAT
1097730 ATTATTTAT
1 -TTATTTAT
1097739 TT-TTTAT
1 TTATTTAT
*
1097746 TTATTTCAC
1 TTATTT-AT
1097755 TTATTTATT
1 TTATTTA-T
1097764 TTATTT-T
1 TTATTTAT
1097771 TT-TTTAT
1 TTATTTAT
1097778 TT
1 TT
1097780 TCGTTTTTAG
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
6 3 0.07
7 13 0.30
8 6 0.14
9 21 0.49
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (8 bp):
TTATTTAT
Found at i:1100727 original size:21 final size:22
Alignment explanation
Indices: 1100702--1100765 Score: 96
Period size: 21 Copynumber: 3.0 Consensus size: 22
1100692 AACTTCAAAT
*
1100702 TGGGTTTGAGAGCTAATTCAGA
1 TGGGTCTGAGAGCTAATTCAGA
1100724 -GGGTCTGAGAGCTAA-TCAGA
1 TGGGTCTGAGAGCTAATTCAGA
*
1100744 TGGGTCTGAGAGCCAATTCAGA
1 TGGGTCTGAGAGCTAATTCAGA
1100766 ACAGATTCAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.13
21 28 0.74
22 5 0.13
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.25
Consensus pattern (22 bp):
TGGGTCTGAGAGCTAATTCAGA
Found at i:1101670 original size:16 final size:16
Alignment explanation
Indices: 1101646--1101684 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
1101636 TCTTCACAGT
*
1101646 GAAGGATATCATGCTC
1 GAAGTATATCATGCTC
1101662 GAAGTATATCATGCTC
1 GAAGTATATCATGCTC
1101678 GAAGTAT
1 GAAGTAT
1101685 CCAAGACCGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.28
Consensus pattern (16 bp):
GAAGTATATCATGCTC
Found at i:1102129 original size:36 final size:35
Alignment explanation
Indices: 1102027--1102463 Score: 395
Period size: 36 Copynumber: 12.6 Consensus size: 35
1102017 TCAAATATAG
* * *
1102027 TTTTGGAAAATATATAATATATAGTTTTTGGAAACTTAT
1 TTTT-GAAAACATATAATATATAGTTTTT--AAA-ATAA
* *
1102066 TTTTTAAAACATATAGTATATAGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* *
1102101 TTTTGAAAACTTATAATATATAGTTTTTTTTTAAAAAAA
1 TTTTGAAAACATATAATATATAG----TTTTTAAAATAA
* *
1102140 GGTTTTGAAAACATAT-A-GTATAGTTTTGAAAATAA
1 --TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* * ***
1102175 TTTTG-AAAC--GT-ATA-ATAGTTTTAAAAACGG
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
*
1102205 TTTTGAAAACATATAGTATATAGTTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAG-TTTTTAAAATAA
* *
1102241 TTTTAAAAACATATAGTATATAGTTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAG-TTTTTAAAATAA
* *
1102277 TTTTAAAAACATATAGTATATAGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
* **
1102312 TTTTGAAAACGTAT-A-ATATAGTTTTT-AAA-GG
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
*
1102343 TTTTGAAAACATATAGTATATAGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
1102378 TTTT--AAACATATAATA-A-AGTTTTTAAAATAA
1 TTTTGAAAACATATAATATATAGTTTTTAAAATAA
** *
1102409 TTTTGAAAATGTAT-A-ATATAGTTTTTAAAAATAG
1 TTTTGAAAACATATAATATATAGTTTTT-AAAATAA
*
1102443 TTTTGAAAACGTATAATATAT
1 TTTTGAAAACATATAATATAT
1102464 TTTTATATTT
Statistics
Matches: 334, Mismatches: 40, Indels: 51
0.79 0.09 0.12
Matches are distributed among these distances:
30 19 0.06
31 36 0.11
32 10 0.03
33 52 0.16
34 24 0.07
35 65 0.19
36 73 0.22
38 21 0.06
39 20 0.06
40 1 0.00
41 13 0.04
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (35 bp):
TTTTGAAAACATATAATATATAGTTTTTAAAATAA
Found at i:1102508 original size:11 final size:10
Alignment explanation
Indices: 1102492--1102547 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 10
1102482 ATATAGTTAG
1102492 TTTTATATTAT
1 TTTTAT-TTAT
1102503 TTTTATTTAT
1 TTTTATTTAT
1102513 TTCACTTATTTA-
1 TT---TTATTTAT
1102525 TTTTATTTAAT
1 TTTTATTT-AT
1102536 TTTT-TTTAT
1 TTTTATTTAT
1102545 TTT
1 TTT
1102548 CGTTTTTAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
9 11 0.28
10 10 0.25
11 10 0.25
12 2 0.05
13 7 0.17
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:1105018 original size:45 final size:44
Alignment explanation
Indices: 1104946--1105074 Score: 187
Period size: 39 Copynumber: 3.0 Consensus size: 44
1104936 AAGTATTTTC
1104946 AATATAATTACTCGGTATTGGTTGAGTATTTTTGAACATAGTTGG
1 AATATAATTACTC-GTATTGGTTGAGTATTTTTGAACATAGTTGG
*
1104991 AAATATAATTACTCGTATTGGTTGAGTA-TTTTCAAC-TA--T-G
1 -AATATAATTACTCGTATTGGTTGAGTATTTTTGAACATAGTTGG
*
1105031 TATATAATTACTCGTATTGGTTGAGTATTTTTGAACATAGTTGG
1 AATATAATTACTCGTATTGGTTGAGTATTTTTGAACATAGTTGG
1105075 TGGAAAAGTT
Statistics
Matches: 75, Mismatches: 3, Indels: 12
0.83 0.03 0.13
Matches are distributed among these distances:
39 26 0.35
40 8 0.11
41 3 0.04
43 3 0.04
44 8 0.11
45 14 0.19
46 13 0.17
ACGTcount: A:0.29, C:0.08, G:0.19, T:0.43
Consensus pattern (44 bp):
AATATAATTACTCGTATTGGTTGAGTATTTTTGAACATAGTTGG
Found at i:1106211 original size:24 final size:24
Alignment explanation
Indices: 1106184--1106241 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
1106174 TGTCCGTTTA
1106184 TTTATATTTATTT-TTGTTCGTTCG
1 TTTATATTTATTTATT-TTCGTTCG
* * *
1106208 TTTATAATCATTTATTTTTGTTCG
1 TTTATATTTATTTATTTTCGTTCG
1106232 TTTATATTTA
1 TTTATATTTA
1106242 ACATAATCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 26 0.93
25 2 0.07
ACGTcount: A:0.19, C:0.07, G:0.09, T:0.66
Consensus pattern (24 bp):
TTTATATTTATTTATTTTCGTTCG
Found at i:1107608 original size:73 final size:73
Alignment explanation
Indices: 1107469--1107615 Score: 197
Period size: 73 Copynumber: 2.0 Consensus size: 73
1107459 GTTTTTAATT
** *
1107469 AAATTTTATTTGAATTCAAATCACAAATTAACTTCACTACAGGGTTGGTACGAGTCTTGACGCGT
1 AAATTTTATTTGAATTCAAATCACAAATTAACTTCACTACAGGGTTGGTACGAGTCGAGACACGT
*
1107534 TCGCACTC
66 TCACACTC
* * * **
1107542 AAATTTTATTTGAATTCAAATCTA-TAATTAATTTCACTACAGTGTTGGTACTCGTCGAGACACG
1 AAATTTTATTTGAATTCAAATC-ACAAATTAACTTCACTACAGGGTTGGTACGAGTCGAGACACG
1107606 TTCACACTC
65 TTCACACTC
1107615 A
1 A
1107616 GCACAATGCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 63 0.98
74 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (73 bp):
AAATTTTATTTGAATTCAAATCACAAATTAACTTCACTACAGGGTTGGTACGAGTCGAGACACGT
TCACACTC
Found at i:1110392 original size:30 final size:30
Alignment explanation
Indices: 1110358--1110418 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1110348 TATTCACTCG
1110358 AGTCTGAGTAAAATAGAGACGACCATCGAT
1 AGTCTGAGTAAAATAGAGACGACCATCGAT
* * *
1110388 AGTCTGAGTAACATAGAGATGACCGTCGAT
1 AGTCTGAGTAAAATAGAGACGACCATCGAT
1110418 A
1 A
1110419 ATGACACTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (30 bp):
AGTCTGAGTAAAATAGAGACGACCATCGAT
Found at i:1111070 original size:2 final size:2
Alignment explanation
Indices: 1111063--1111099 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1111053 TCATTTACAA
1111063 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 A
1111100 CCACATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1116789 original size:9 final size:9
Alignment explanation
Indices: 1116775--1116799 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1116765 TATGTTGTTT
1116775 TTTTATTGC
1 TTTTATTGC
1116784 TTTTATTGC
1 TTTTATTGC
1116793 TTTTATT
1 TTTTATT
1116800 TTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.08, G:0.08, T:0.72
Consensus pattern (9 bp):
TTTTATTGC
Found at i:1119078 original size:67 final size:67
Alignment explanation
Indices: 1118970--1119099 Score: 179
Period size: 67 Copynumber: 1.9 Consensus size: 67
1118960 CATCTGCCTA
* * * * * *
1118970 CTGAGGTAACAAGTTAGACTCGAGATGATTCGACACTAAGCCAACAGTTAAAGATCACGAACCCC
1 CTGAGGTAAAAAGATAGACTCGAAACGATTCAACACAAAGCCAACAGTTAAAGATCACGAACCCC
1119035 TG
66 TG
* * *
1119037 CTGAGGTAAAAAGATGGACTCGAAACGATTCAACACAAAGCCAACAGTTGAAGATCGCGAACC
1 CTGAGGTAAAAAGATAGACTCGAAACGATTCAACACAAAGCCAACAGTTAAAGATCACGAACC
1119100 AGCTCGAAAG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (67 bp):
CTGAGGTAAAAAGATAGACTCGAAACGATTCAACACAAAGCCAACAGTTAAAGATCACGAACCCC
TG
Found at i:1121826 original size:36 final size:35
Alignment explanation
Indices: 1121786--1121898 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 35
1121776 TGATAAACTA
**
1121786 TGAGAACGTTTCCATGGAAACGAATTTTGTCTCTCT
1 TGAGAACGTTTCC-TTCAAACGAATTTTGTCTCTCT
** *
1121822 TGAGACATTTTTCCTTCAAACGAGTTTTGTCTCTCT
1 TGAGA-ACGTTTCCTTCAAACGAATTTTGTCTCTCT
* * *
1121858 TCAG-ACAGTTTCCTTTTAAACAAATTTTGTCTCTCT
1 TGAGAAC-GTTTCC-TTCAAACGAATTTTGTCTCTCT
1121894 TGAGA
1 TGAGA
1121899 CAATTTTTGT
Statistics
Matches: 61, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
34 1 0.02
35 5 0.08
36 49 0.80
37 6 0.10
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (35 bp):
TGAGAACGTTTCCTTCAAACGAATTTTGTCTCTCT
Found at i:1121900 original size:36 final size:36
Alignment explanation
Indices: 1121803--1121900 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 36
1121793 GTTTCCATGG
*
1121803 AAACGAATTTTGTCTCTCTTGAGACATTTTTCCTTC
1 AAACGAATTTTGTCTCTCTTGAGACATGTTTCCTTC
* * *
1121839 AAACGAGTTTTGTCTCTCTTCAGACA-GTTTCCTTTT
1 AAACGAATTTTGTCTCTCTTGAGACATGTTTCC-TTC
*
1121875 AAACAAATTTTGTCTCTCTTGAGACA
1 AAACGAATTTTGTCTCTCTTGAGACA
1121901 ATTTTTGTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 5 0.09
36 49 0.91
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.42
Consensus pattern (36 bp):
AAACGAATTTTGTCTCTCTTGAGACATGTTTCCTTC
Found at i:1121906 original size:21 final size:21
Alignment explanation
Indices: 1121873--1121925 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
1121863 CAGTTTCCTT
* *
1121873 TTAA-ACAAATTTTGTCTCTC
1 TTAAGACAATTTTTGTCTCCC
*
1121893 TTGAGACAATTTTTGTCTCCC
1 TTAAGACAATTTTTGTCTCCC
1121914 TTAAGACAATTT
1 TTAAGACAATTT
1121926 CTCTTGAAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.43
Consensus pattern (21 bp):
TTAAGACAATTTTTGTCTCCC
Found at i:1121982 original size:65 final size:64
Alignment explanation
Indices: 1121892--1122194 Score: 228
Period size: 65 Copynumber: 4.7 Consensus size: 64
1121882 TTTTGTCTCT
* * * * *
1121892 CTTGAGACAATTTTTGTCTCCCTTAAGACAATTTCTCTTGAAACATAAACTTTGAGAATGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACATAAACTTTGAG-ATGTTTCC
* * * * * *
1121957 CTTGAAACAAATTTTGCCTCTCTTAAGATC-GTTTTCCTTGAAAC--GAA-TTT----T-TCTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGA-CAATTTCCCTTGAAACATAAACTTTGAGATGTTTCC
** * **
1122013 CTTGAAATGAATTTTGTCTCTCTTGAGACAAATTCCCTTGAAACGAGTTTTATCTCTCTTGAGAT
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAAC-A----TA-AACT-TTGAGAT
1122078 AGTTTCC
59 -GTTTCC
* * * * * *
1122085 CTTGAAACATATTTTGTCTCCCTTGAGATATTTTCTCTTGAAACATAAACTTTGAGAACGTTTCC
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACATAAACTTTGAG-ATGTTTCC
* *
1122150 CTTGAAACTAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACA
1122195 AATTTTGTTT
Statistics
Matches: 182, Mismatches: 37, Indels: 38
0.71 0.14 0.15
Matches are distributed among these distances:
55 1 0.01
56 39 0.21
57 1 0.01
62 3 0.02
63 2 0.01
65 86 0.47
66 6 0.03
67 2 0.01
70 1 0.01
71 1 0.01
72 40 0.22
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.40
Consensus pattern (64 bp):
CTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCCCTTGAAACATAAACTTTGAGATGTTTCC
Found at i:1122017 original size:20 final size:21
Alignment explanation
Indices: 1121992--1122038 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
1121982 AGATCGTTTT
1121992 CCTTGAAACGAATTTT-TCTC
1 CCTTGAAACGAATTTTGTCTC
*
1122012 CCTTGAAATGAATTTTGTCTC
1 CCTTGAAACGAATTTTGTCTC
*
1122033 TCTTGA
1 CCTTGA
1122039 GACAAATTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (21 bp):
CCTTGAAACGAATTTTGTCTC
Found at i:1122069 original size:36 final size:36
Alignment explanation
Indices: 1122010--1122249 Score: 138
Period size: 36 Copynumber: 6.9 Consensus size: 36
1122000 CGAATTTTTC
* *
1122010 TCCCTTGAAATGAATTTTGTCTCTCTTGAGACAAAT
1 TCCCTTGAAACGAATTTTATCTCTCTTGAGACAAAT
* * **
1122046 TCCCTTGAAACGAGTTTTATCTCTCTTGAGATAGTT
1 TCCCTTGAAACGAATTTTATCTCTCTTGAGACAAAT
* * * **
1122082 TCCCTTGAAAC-ATATTTTGTCTCCCTTGAGATATTT
1 TCCCTTGAAACGA-ATTTTATCTCTCTTGAGACAAAT
* ** **
1122118 TCTCTTGAAAC--A---TA-AACT-TTGAGA-ACGTT
1 TCCCTTGAAACGAATTTTATCTCTCTTGAGACA-AAT
* * **
1122147 TCCCTTGAAACTAATTTTGTCTCTCTTGAGACAGTT
1 TCCCTTGAAACGAATTTTATCTCTCTTGAGACAAAT
* * * * **
1122183 TCCCTTGAAACAAATTTTGTTTCTCTTGAGATAGTT
1 TCCCTTGAAACGAATTTTATCTCTCTTGAGACAAAT
* * *
1122219 TCTCTTGAAACAAATTTTGTCTCTCTTGAGA
1 TCCCTTGAAACGAATTTTATCTCTCTTGAGA
1122250 TAGTTTCTCT
Statistics
Matches: 169, Mismatches: 25, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
28 1 0.01
29 18 0.11
30 1 0.01
31 2 0.01
34 2 0.01
35 3 0.02
36 141 0.83
37 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (36 bp):
TCCCTTGAAACGAATTTTATCTCTCTTGAGACAAAT
Found at i:1122178 original size:137 final size:138
Alignment explanation
Indices: 1122010--1122392 Score: 483
Period size: 137 Copynumber: 2.8 Consensus size: 138
1122000 CGAATTTTTC
** * *
1122010 TCCCTTGAAA-TGAATTTTGTCTCTCTTGAGACAAATTCCCTTGAAACGAGTTTTATCTCTCTTG
1 TCCCTTGAAACT-AATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTG
* * *
1122074 AGATAGTTTCCCTTGAAACATATTTTGTCTCCCTTGAGATATTTTCTCTTG-AA-ACATAAA-CT
65 AGATAGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGATAGTTTCTCTTGAAATACA-AAATCT
1122136 TTGAGAAC-GTT
129 TTGA-AACTG-T
* *
1122147 TCCCTTGAAACTAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTTTCTCTTGA
1 TCCCTTGAAACTAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGA
* *
1122212 GATAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAATACAAAATCTTT
66 GATAGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGATAGTTTCTCTTGAAATACAAAATCTTT
*
1122277 GAATCTGT
131 GAAACTGT
* ** *
1122285 TCCCTTGAAACAAATTTCATCTC-CATTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTA
1 TCCCTTGAAACTAATTTTGTCTCTC-TTGAGACAGTTTCCCTTGAAAC-AAGTTTTGTCTCTCT-
* * *
1122349 T-AGACAGTTTCCCTTGAAACAAATTTTATCTCACTTGGGATAGT
63 TGAGATAGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGATAGT
1122393 GAAGAAAAAG
Statistics
Matches: 216, Mismatches: 22, Indels: 14
0.86 0.09 0.06
Matches are distributed among these distances:
137 104 0.48
138 50 0.23
139 61 0.28
140 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (138 bp):
TCCCTTGAAACTAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAGTTTTGTCTCTCTTGA
GATAGTTTCCCTTGAAACAAATTTTGTCTCACTTGAGATAGTTTCTCTTGAAATACAAAATCTTT
GAAACTGT
Found at i:1122210 original size:21 final size:21
Alignment explanation
Indices: 1122180--1122247 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
1122170 TCTTGAGACA
*
1122180 GTTTCCCTTGAAACAAATTTT
1 GTTTCTCTTGAAACAAATTTT
* *
1122201 GTTTCTCTTG----AGA--TA
1 GTTTCTCTTGAAACAAATTTT
1122216 GTTTCTCTTGAAACAAATTTT
1 GTTTCTCTTGAAACAAATTTT
*
1122237 GTCTCTCTTGA
1 GTTTCTCTTGA
1122248 GATAGTTTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
15 11 0.31
17 2 0.06
19 2 0.06
21 20 0.57
ACGTcount: A:0.24, C:0.18, G:0.13, T:0.46
Consensus pattern (21 bp):
GTTTCTCTTGAAACAAATTTT
Found at i:1122211 original size:101 final size:101
Alignment explanation
Indices: 1122045--1122230 Score: 300
Period size: 101 Copynumber: 1.8 Consensus size: 101
1122035 TTGAGACAAA
* * *
1122045 TTCCCTTGAAACGAGTTTTATCTCTCTTGAGATAGTTTCCCTTGAAACATATTTTGTCTCCCTTG
1 TTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG
*
1122110 AGATATTTTCTCTTGAAACATAAACTTTGAGAACGT
66 AGATAGTTTCTCTTGAAACATAAACTTTGAGAACGT
* * * *
1122146 TTCCCTTGAAACTAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTTTCTCTTG
1 TTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG
1122211 AGATAGTTTCTCTTGAAACA
66 AGATAGTTTCTCTTGAAACA
1122231 AATTTTGTCT
Statistics
Matches: 77, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 77 1.00
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (101 bp):
TTCCCTTGAAACGAATTTTATCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTG
AGATAGTTTCTCTTGAAACATAAACTTTGAGAACGT
Found at i:1122250 original size:36 final size:36
Alignment explanation
Indices: 1122136--1122264 Score: 197
Period size: 36 Copynumber: 3.6 Consensus size: 36
1122126 AACATAAACT
*
1122136 TTGAGA-ACGTTTCCCTTGAAACTAATTTTGTCTCTC
1 TTGAGATA-GTTTCCCTTGAAACAAATTTTGTCTCTC
* *
1122172 TTGAGACAGTTTCCCTTGAAACAAATTTTGTTTCTC
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTC
*
1122208 TTGAGATAGTTTCTCTTGAAACAAATTTTGTCTCTC
1 TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTC
*
1122244 TTGAGATAGTTTCTCTTGAAA
1 TTGAGATAGTTTCCCTTGAAA
1122265 TACAAAATCT
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
36 86 0.99
37 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.15, T:0.43
Consensus pattern (36 bp):
TTGAGATAGTTTCCCTTGAAACAAATTTTGTCTCTC
Found at i:1122314 original size:102 final size:103
Alignment explanation
Indices: 1122182--1122367 Score: 279
Period size: 102 Copynumber: 1.8 Consensus size: 103
1122172 TTGAGACAGT
** * *
1122182 TTCCCTTGAAACAAATTTTGTTTCTCTTGAGATAGTTTCTCTTGAAACAAA-TTTTGTCTCTCT-
1 TTCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTA
* *
1122245 TGAGATAGTTTCTCTTGAAATACAAAATCTTTGAATCTG
66 T-AGACAGTTTCCCTTGAAATACAAAATCTTTGAATCTG
1122284 TTCCCTTGAAACAAATTTCATCTC-CATTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCT
1 TTCCCTTGAAACAAATTTCATCTCTC-TTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCT
1122348 ATAGACAGTTTCCCTTGAAA
65 ATAGACAGTTTCCCTTGAAA
1122368 CAAATTTTAT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
101 1 0.01
102 45 0.60
103 28 0.37
104 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.40
Consensus pattern (103 bp):
TTCCCTTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACAAAGTTTTGTCTCTCTA
TAGACAGTTTCCCTTGAAATACAAAATCTTTGAATCTG
Found at i:1122838 original size:131 final size:131
Alignment explanation
Indices: 1122604--1122999 Score: 557
Period size: 131 Copynumber: 3.0 Consensus size: 131
1122594 AAGAGATTGT
* * *
1122604 TCAACTGTTTT-CTCGATTATATCACAGAAGGAGGTAGATCAGCATCGACATCACGTTTGATTCC
1 TCAACT-TTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCA-CGACATCTCGTTCGATTCC
* * * * *
1122668 ATCATAGAA-GAGGTGGATCGATATTTTTATTTCGCTCAAATCCATCGTATAAGGATTTGGATCA
64 ATCACAGAAGGAGGTGGATCGACAATTTTATTTCGCTCAAATCCATCGCATAAGGAGTTGGATCA
1122732 ACA
129 ACA
* *
1122735 TCAACTTTTTGCTTGATTCTATCACAGAGGGAGGTAGATCAGCACGACATCTCGTTCGATTCCAT
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACGACATCTCGTTCGATTCCAT
* * *
1122800 CACAGAAGGAGGTAGATCGACAATTTTATTTCACTCAAATCTATCGCATAAGGAGTTGGATCAAC
66 CACAGAAGGAGGTGGATCGACAATTTTATTTCGCTCAAATCCATCGCATAAGGAGTTGGATCAAC
1122865 A
131 A
* *
1122866 TCAAATTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCA-CAACGACATCTCGTTCAATTCCA
1 TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGC-ACGACATCTCGTTCGATTCCA
* * * *
1122930 TCACATAAGGAGGTGGATAGAC-ATTTTCATTTCGCTCAAATCCATCGCATACGGAGTTGAATCA
65 TCACAGAAGGAGGTGGATCGACAATTTT-ATTTCGCTCAAATCCATCGCATAAGGAGTTGGATCA
1122994 ACA
129 ACA
1122997 TCA
1 TCA
1123000 TCAATATTGC
Statistics
Matches: 237, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
130 35 0.15
131 202 0.85
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.30
Consensus pattern (131 bp):
TCAACTTTTTGCTCGATTCTATCACAGAAGGAGGTAGATCAGCACGACATCTCGTTCGATTCCAT
CACAGAAGGAGGTGGATCGACAATTTTATTTCGCTCAAATCCATCGCATAAGGAGTTGGATCAAC
A
Found at i:1122906 original size:44 final size:43
Alignment explanation
Indices: 1122727--1122906 Score: 130
Period size: 44 Copynumber: 4.1 Consensus size: 43
1122717 TAAGGATTTG
* * *
1122727 GATCAACATCAACTTTTTGCTTGATTCTATCACAGAGGGAGGTA
1 GATCAACA-CAAATTTTTGCTCGATTCTATCACAGAAGGAGGTA
* * * * * *
1122771 GATCAGCACGACA-TCTCGTTCGATTCCATCACAGAAGGAGGTA
1 GATCAACAC-AAATTTTTGCTCGATTCTATCACAGAAGGAGGTA
* ** * * * * * * *
1122814 GATCGACA-ATTTTATTTCACTCAAATCTATCGCATAAGGAGTTG
1 GATCAACACAAATT-TTT-GCTCGATTCTATCACAGAAGGAGGTA
1122858 GATCAACATCAAATTTTTGCTCGATTCTATCACAGAAGGAGGTA
1 GATCAACA-CAAATTTTTGCTCGATTCTATCACAGAAGGAGGTA
1122902 GATCA
1 GATCA
1122907 CAACGACATC
Statistics
Matches: 96, Mismatches: 34, Indels: 12
0.68 0.24 0.08
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 32 0.33
44 56 0.58
45 3 0.03
46 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (43 bp):
GATCAACACAAATTTTTGCTCGATTCTATCACAGAAGGAGGTA
Found at i:1122940 original size:43 final size:44
Alignment explanation
Indices: 1122750--1122943 Score: 133
Period size: 44 Copynumber: 4.5 Consensus size: 44
1122740 TTTTTGCTTG
* * * *
1122750 ATTCTATCACAGAGGGAGGTAGATCAGC-ACGACATCTCGTTCG
1 ATTCTATCACAGAAGGAGGTAGATCAACAACGACATCTCGCTCA
* * **** * *
1122793 ATTCCATCACAGAAGGAGGTAGATCGACAATTTTATTTCACTCA
1 ATTCTATCACAGAAGGAGGTAGATCAACAACGACATCTCGCTCA
* * * * * * * * * *
1122837 AATCTATCGCATAAGGAGTTGGATCAACATC-AAATTTTTGCTCG
1 ATTCTATCACAGAAGGAGGTAGATCAACAACGACA-TCTCGCTCA
*
1122881 ATTCTATCACAGAAGGAGGTAGATC-ACAACGACATCTCGTTCA
1 ATTCTATCACAGAAGGAGGTAGATCAACAACGACATCTCGCTCA
* *
1122924 ATTCCATCACATAAGGAGGT
1 ATTCTATCACAGAAGGAGGT
1122944 GGATAGACAT
Statistics
Matches: 109, Mismatches: 39, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
43 52 0.48
44 57 0.52
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (44 bp):
ATTCTATCACAGAAGGAGGTAGATCAACAACGACATCTCGCTCA
Found at i:1124435 original size:23 final size:22
Alignment explanation
Indices: 1124409--1124473 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 22
1124399 TTTGTACTTA
1124409 TTTTATTTTTTATTTTATGTTTT
1 TTTTATTTTTTATTTT-TGTTTT
*
1124432 TTTTACTATTATTATTATTTGTTTT
1 TTTTA-T-TTTTTATT-TTTGTTTT
*
1124457 TTTAAATTATTTTATTT
1 TTT-TATT-TTTTATTT
1124474 AAGTTTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
23 5 0.15
24 3 0.09
25 23 0.68
26 3 0.09
ACGTcount: A:0.20, C:0.02, G:0.03, T:0.75
Consensus pattern (22 bp):
TTTTATTTTTTATTTTTGTTTT
Found at i:1124471 original size:25 final size:24
Alignment explanation
Indices: 1124416--1124473 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
1124406 TTATTTTATT
*
1124416 TTTTATTTTATGTTTTTTTTACTA
1 TTTTATTTTATGTTTTTTTAACTA
*
1124440 TTATTATTATT-TGTTTTTTTAAATTA
1 TT-TTATT-TTATGTTTTTTT-AACTA
1124466 TTTTATTT
1 TTTTATTT
1124474 AAGTTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
25 19 0.66
26 7 0.24
ACGTcount: A:0.21, C:0.02, G:0.03, T:0.74
Consensus pattern (24 bp):
TTTTATTTTATGTTTTTTTAACTA
Found at i:1124479 original size:24 final size:24
Alignment explanation
Indices: 1124429--1124473 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
1124419 TATTTTATGT
*
1124429 TTTTTTTACTATTATTATTATTTG
1 TTTTTTTACAATTATTATTATTTG
1124453 TTTTTTTA-AATTATT-TTATTT
1 TTTTTTTACAATTATTATTATTT
1124474 AAGTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTTTTACAATTATTATTATTTG
Found at i:1128025 original size:31 final size:29
Alignment explanation
Indices: 1127984--1128060 Score: 91
Period size: 29 Copynumber: 2.6 Consensus size: 29
1127974 TATACAAAAG
*
1127984 GTGCCCAACGTATGCATTTAGTTCCAGTTTA
1 GTGCCTAACGT-T-CATTTAGTTCCAGTTTA
* *
1128015 GTGCCTAACGTTTATTTCGTTCCAGTTTA
1 GTGCCTAACGTTCATTTAGTTCCAGTTTA
*
1128044 GTGTCTAACGTTTCATT
1 GTGCCTAACG-TTCATT
1128061 CCGTAACTCA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 24 0.60
30 6 0.15
31 10 0.25
ACGTcount: A:0.19, C:0.21, G:0.18, T:0.42
Consensus pattern (29 bp):
GTGCCTAACGTTCATTTAGTTCCAGTTTA
Found at i:1128038 original size:29 final size:29
Alignment explanation
Indices: 1127999--1128056 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1127989 CAACGTATGC
1127999 ATTTAGTTCCAGTTTAGTGCCTAACGTTT
1 ATTTAGTTCCAGTTTAGTGCCTAACGTTT
* *
1128028 ATTTCGTTCCAGTTTAGTGTCTAACGTTT
1 ATTTAGTTCCAGTTTAGTGCCTAACGTTT
1128057 CATTCCGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.19, C:0.17, G:0.17, T:0.47
Consensus pattern (29 bp):
ATTTAGTTCCAGTTTAGTGCCTAACGTTT
Found at i:1133241 original size:14 final size:14
Alignment explanation
Indices: 1133222--1133257 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1133212 AATTCCTTCC
*
1133222 CAAAATAATTTTAT
1 CAAAATAATTTGAT
1133236 CAAAATAATTTGAT
1 CAAAATAATTTGAT
*
1133250 CACAATAA
1 CAAAATAA
1133258 AAACTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.33
Consensus pattern (14 bp):
CAAAATAATTTGAT
Found at i:1137801 original size:16 final size:16
Alignment explanation
Indices: 1137752--1137801 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
1137742 TTTAAGGACT
*
1137752 AAATTG-AATACATATA
1 AAATTGAAATAAAT-TA
* *
1137768 AAAGTGAAAT-ATTTA
1 AAATTGAAATAAATTA
1137783 AAATTGAAATAAATTA
1 AAATTGAAATAAATTA
1137799 AAA
1 AAA
1137802 AACACAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
15 11 0.41
16 13 0.48
17 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (16 bp):
AAATTGAAATAAATTA
Found at i:1137923 original size:15 final size:13
Alignment explanation
Indices: 1137891--1138085 Score: 61
Period size: 13 Copynumber: 14.4 Consensus size: 13
1137881 AATTGAAAAA
1137891 ATATAATATATAT
1 ATATAATATATAT
1137904 ATATAATATA-AGT
1 ATATAATATATA-T
*
1137917 -T-T-ATATATAA
1 ATATAATATATAT
1137927 ACTATAAT-TATAT
1 A-TATAATATATAT
1137940 -TATAAACTATATAATT
1 ATAT-AA-TATAT-A-T
1137956 ATTATAAGCTATATAT
1 A-TATAA--TATATAT
* *
1137972 ATA-AATTATGTTT
1 ATATAA-TATATAT
1137985 ATATGAACTATATAT
1 ATAT-AA-TATATAT
*
1138000 GTA-AATTATATAT
1 ATATAA-TATATAT
*
1138013 GTATAA-ACTATA-
1 ATATAATA-TATAT
*
1138025 A-AAAATATATAGT
1 ATATAATATATA-T
* *
1138038 TTATAAACTATAATTT
1 ATAT-AA-TAT-ATAT
*
1138054 ATATTATATATAT
1 ATATAATATATAT
1138067 ATATATATATATAT
1 ATATA-ATATATAT
1138081 ATATA
1 ATATA
1138086 TTATTCAAAG
Statistics
Matches: 137, Mismatches: 19, Indels: 51
0.66 0.09 0.25
Matches are distributed among these distances:
10 5 0.04
11 12 0.09
12 7 0.05
13 48 0.35
14 26 0.19
15 15 0.11
16 10 0.07
17 5 0.04
18 9 0.07
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:1137945 original size:18 final size:19
Alignment explanation
Indices: 1137892--1137950 Score: 72
Period size: 18 Copynumber: 3.2 Consensus size: 19
1137882 ATTGAAAAAA
1137892 TATAA-TATATATATATAA-
1 TATAATTATATATATA-AAC
1137910 TATAAGTT-TATATATAAAC
1 TATAA-TTATATATATAAAC
1137929 TATAATTATAT-TATAAAC
1 TATAATTATATATATAAAC
1137947 TATA
1 TATA
1137951 TAATTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
18 20 0.54
19 16 0.43
20 1 0.03
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (19 bp):
TATAATTATATATATAAAC
Found at i:1137958 original size:18 final size:18
Alignment explanation
Indices: 1137917--1137970 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
1137907 TAATATAAGT
*
1137917 TTATATATAAACTATA-AT
1 TTAT-TATAAACTATATAA
1137935 TATATTATAAACTATATAA
1 T-TATTATAAACTATATAA
*
1137954 TTATTATAAGCTATATA
1 TTATTATAAACTATATA
1137971 TATAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 27 0.84
19 5 0.16
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (18 bp):
TTATTATAAACTATATAA
Found at i:1137979 original size:20 final size:18
Alignment explanation
Indices: 1137922--1137980 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
1137912 TAAGTTTATA
*
1137922 TATAAACTATA-ATTATAT
1 TATAAACTATATAATA-AT
*
1137940 TATAAACTATATAATTAT
1 TATAAACTATATAATAAT
*
1137958 TATAAGCTATATATATAAAT
1 TATAAACTATATA-AT-AAT
1137978 TAT
1 TAT
1137981 GTTTATATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
18 25 0.74
19 4 0.12
20 5 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
TATAAACTATATAATAAT
Found at i:1138021 original size:28 final size:27
Alignment explanation
Indices: 1137958--1138078 Score: 90
Period size: 28 Copynumber: 4.5 Consensus size: 27
1137948 ATATAATTAT
* * *
1137958 TATAAGCTATATATATAAATTATGTTTA
1 TATAAACTATATAT-TAAATTATATATA
* *
1137986 TATGAACTATATATGTAAATTATATATG
1 TATAAACTATATAT-TAAATTATATATA
* *
1138014 TATAAACTATA-A--AAAATATATAGTT
1 TATAAACTATATATTAAATTATATA-TA
*
1138039 TATAAACTATA-ATTTATATTATATATA
1 TATAAACTATATA-TTAAATTATATATA
*
1138066 TATATA-TATATAT
1 TATAAACTATATAT
1138079 ATATATATTA
Statistics
Matches: 75, Mismatches: 13, Indels: 12
0.75 0.13 0.12
Matches are distributed among these distances:
24 9 0.12
25 13 0.17
26 5 0.07
27 8 0.11
28 40 0.53
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (27 bp):
TATAAACTATATATTAAATTATATATA
Found at i:1138065 original size:2 final size:2
Alignment explanation
Indices: 1138053--1138086 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1138043 AACTATAATT
1138053 TA TA T- 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 TA T
1138087 TATTCAAAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1138222 original size:19 final size:19
Alignment explanation
Indices: 1138200--1138252 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
1138190 AAAATAAAGG
1138200 GAAATTGAGAATTTAGAGA
1 GAAATTGAGAATTTAGAGA
* * * * *
1138219 GAAATTAAAAAATTGGAGG
1 GAAATTGAGAATTTAGAGA
1138238 GAAATTGAGAATTTA
1 GAAATTGAGAATTTA
1138253 AATTTTATTT
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.49, C:0.00, G:0.25, T:0.26
Consensus pattern (19 bp):
GAAATTGAGAATTTAGAGA
Found at i:1138347 original size:15 final size:15
Alignment explanation
Indices: 1138327--1138355 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1138317 AACTATAATT
1138327 TATATTATATATATA
1 TATATTATATATATA
1138342 TATATTATATATAT
1 TATATTATATATAT
1138356 TATTCAAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:1138718 original size:2 final size:2
Alignment explanation
Indices: 1138713--1138760 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1138703 TCTCTCTCTC
1138713 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1138754 TA T- TA TA
1 TA TA TA TA
1138761 AACACTATGC
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.05
2 42 0.95
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1138774 original size:29 final size:29
Alignment explanation
Indices: 1138716--1138782 Score: 66
Period size: 29 Copynumber: 2.3 Consensus size: 29
1138706 CTCTCTCTAT
* * *
1138716 ATATATATATATATATATATATATATATA
1 ATATATATATATATATAAACATATACATA
*
1138745 ATATATATATAT-TATAAACACTATGCATA
1 ATATATATATATATATAAACA-TATACATA
1138774 A-ACTATATA
1 ATA-TATATA
1138783 AAGTAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 7 0.22
29 25 0.78
ACGTcount: A:0.51, C:0.06, G:0.01, T:0.42
Consensus pattern (29 bp):
ATATATATATATATATAAACATATACATA
Found at i:1138819 original size:6 final size:6
Alignment explanation
Indices: 1138808--1138880 Score: 56
Period size: 6 Copynumber: 11.3 Consensus size: 6
1138798 TATTTTATAA
* * * *
1138808 AACCCT AACCCT AAACCT AAACCCT AATCAT AAACCCT AACCTT AACCCTT
1 AACCCT AACCCT AACCCT -AACCCT AACCCT -AACCCT AACCCT AACCC-T
*
1138859 AACTCT AAACCCT AACCTCT AA
1 AACCCT -AACCCT AACC-CT AA
1138881 ACTATATATA
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
6 29 0.56
7 23 0.44
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (6 bp):
AACCCT
Found at i:1138833 original size:7 final size:7
Alignment explanation
Indices: 1138807--1138882 Score: 56
Period size: 7 Copynumber: 11.6 Consensus size: 7
1138797 ATATTTTATA
1138807 AAACCCT
1 AAACCCT
1138814 -AACCCT
1 AAACCCT
1138820 AAA-CCT
1 AAACCCT
1138826 AAACCCT
1 AAACCCT
* *
1138833 -AATCAT
1 AAACCCT
1138839 AAACCCT
1 AAACCCT
1138846 -AA-CCT
1 AAACCCT
*
1138851 TAACCCT
1 AAACCCT
* *
1138858 TAACTCT
1 AAACCCT
1138865 AAACCCT
1 AAACCCT
1138872 -AACCTCT
1 AAACC-CT
1138879 AAAC
1 AAAC
1138883 TATATATAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 13
0.73 0.09 0.17
Matches are distributed among these distances:
5 3 0.05
6 24 0.44
7 25 0.45
8 3 0.05
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:1138867 original size:26 final size:25
Alignment explanation
Indices: 1138814--1138876 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 25
1138804 ATAAAACCCT
1138814 AACCCTAAACCTAAACCCTAATCATA
1 AACCCT-AACCTAAACCCTAATCATA
*
1138840 AACCCTAACCTTAACCCTTAACTC-TA
1 AACCCTAACCTAAACCC-TAA-TCATA
1138866 AACCCTAACCT
1 AACCCTAACCT
1138877 CTAAACTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
25 10 0.29
26 22 0.65
27 2 0.06
ACGTcount: A:0.40, C:0.38, G:0.00, T:0.22
Consensus pattern (25 bp):
AACCCTAACCTAAACCCTAATCATA
Found at i:1138874 original size:13 final size:13
Alignment explanation
Indices: 1138814--1138882 Score: 72
Period size: 13 Copynumber: 5.2 Consensus size: 13
1138804 ATAAAACCCT
1138814 AACCCTAAAC-CTA
1 AACCCT-AACTCTA
1138827 AACCCTAA-TCATA
1 AACCCTAACTC-TA
*
1138840 AACCCTAAC-CTT
1 AACCCTAACTCTA
1138852 AACCCTTAACTCTA
1 AACCC-TAACTCTA
1138866 AACCCTAACCTCTA
1 AACCCTAA-CTCTA
1138880 AAC
1 AAC
1138883 TATATATAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.19
13 24 0.50
14 15 0.31
ACGTcount: A:0.41, C:0.38, G:0.00, T:0.22
Consensus pattern (13 bp):
AACCCTAACTCTA
Found at i:1138941 original size:20 final size:19
Alignment explanation
Indices: 1138905--1138945 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
1138895 ATAGTACATG
1138905 TATATAAACCATGTATAGTA
1 TATATAAACCATGTATA-TA
*
1138925 TATATAAACTA-G-ATATA
1 TATATAAACCATGTATATA
1138942 TATA
1 TATA
1138946 ACCTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 6 0.30
18 3 0.15
19 1 0.05
20 10 0.50
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (19 bp):
TATATAAACCATGTATATA
Found at i:1138962 original size:15 final size:14
Alignment explanation
Indices: 1138923--1138968 Score: 67
Period size: 15 Copynumber: 3.3 Consensus size: 14
1138913 CCATGTATAG
1138923 TATATATA-AACTA
1 TATATATATAACTA
*
1138936 GATATATATAACCTA
1 TATATATATAA-CTA
1138951 TATATATATAACTA
1 TATATATATAACTA
1138965 TATA
1 TATA
1138969 AAGTAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 7 0.24
14 9 0.31
15 13 0.45
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (14 bp):
TATATATATAACTA
Found at i:1139088 original size:20 final size:20
Alignment explanation
Indices: 1139050--1139088 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1139040 AACTCTAAAC
**
1139050 CCTAAACTCTAAATTATAAT
1 CCTAAACTCTAAACCATAAT
*
1139070 CCTAAACTTTAAACCATAA
1 CCTAAACTCTAAACCATAA
1139089 ATACTTAACC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (20 bp):
CCTAAACTCTAAACCATAAT
Found at i:1139495 original size:17 final size:15
Alignment explanation
Indices: 1139473--1139508 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
1139463 CCATGTATTG
1139473 TATATATA-AACTATA
1 TATATATATAACT-TA
1139488 TATATATATAACTTA
1 TATATATATAACTTA
1139503 TATATA
1 TATATA
1139509 AACTATATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (15 bp):
TATATATATAACTTA
Found at i:1139629 original size:13 final size:13
Alignment explanation
Indices: 1139611--1139639 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1139601 CCCTAAATCC
1139611 TAAACCATAACTT
1 TAAACCATAACTT
1139624 TAAACCATAACTT
1 TAAACCATAACTT
1139637 TAA
1 TAA
1139640 CTTAAACACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACCATAACTT
Found at i:1140044 original size:20 final size:21
Alignment explanation
Indices: 1139995--1140045 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
1139985 TAAATAATTT
*
1139995 TATATAATATGTATGTATAAAC
1 TATAT-ATATGTATGTAAAAAC
* *
1140017 CATGTATA-GTATGTAAAAAC
1 TATATATATGTATGTAAAAAC
1140037 TATATATAT
1 TATATATAT
1140046 ACCTATATAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 3 0.13
22 3 0.13
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (21 bp):
TATATATATGTATGTAAAAAC
Found at i:1140166 original size:20 final size:21
Alignment explanation
Indices: 1140136--1140175 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1140126 AGTATATAAA
*
1140136 TATAGAACCCTAAACTCTAAT
1 TATAGAACCCTAAACCCTAAT
1140157 TATA-AACCCTAAACCCTAA
1 TATAGAACCCTAAACCCTAA
1140176 CCTTAAATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.45, C:0.28, G:0.03, T:0.25
Consensus pattern (21 bp):
TATAGAACCCTAAACCCTAAT
Found at i:1140169 original size:7 final size:7
Alignment explanation
Indices: 1140159--1140209 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
1140149 ACTCTAATTA
1140159 TAAACCC
1 TAAACCC
1140166 TAAACCC
1 TAAACCC
*
1140173 T-AACCT
1 TAAACCC
* *
1140179 TAAATCA
1 TAAACCC
*
1140186 TAAACAC
1 TAAACCC
*
1140193 TAAACCA
1 TAAACCC
1140200 TAAACCC
1 TAAACCC
1140207 TAA
1 TAA
1140210 TATATGAACT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 5 0.15
7 29 0.85
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (7 bp):
TAAACCC
Found at i:1140171 original size:27 final size:27
Alignment explanation
Indices: 1140141--1140210 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
1140131 ATAAATATAG
* *
1140141 AACCCTAAACTCTAATTATAAACCCTA
1 AACCCTAAACTCTAATCATAAACACTA
*
1140168 AACCCTAACCT-TAAATCATAAACACTA
1 AACCCTAAACTCT-AATCATAAACACTA
* *
1140195 AACCATAAACCCTAAT
1 AACCCTAAACTCTAAT
1140211 ATATGAACTA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
26 1 0.03
27 33 0.94
28 1 0.03
ACGTcount: A:0.47, C:0.30, G:0.00, T:0.23
Consensus pattern (27 bp):
AACCCTAAACTCTAATCATAAACACTA
Found at i:1140182 original size:20 final size:20
Alignment explanation
Indices: 1140141--1140209 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
1140131 ATAAATATAG
* *
1140141 AACCCTAAACTCTAA-TTATA
1 AACCCTAAACACTAACCT-TA
*
1140161 AACCCTAAACCCTAACCTTA
1 AACCCTAAACACTAACCTTA
* * *
1140181 AATCATAAACACTAAACCATA
1 AACCCTAAACACT-AACCTTA
1140202 AACCCTAA
1 AACCCTAA
1140210 TATATGAACT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
20 26 0.67
21 13 0.33
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (20 bp):
AACCCTAAACACTAACCTTA
Found at i:1140201 original size:14 final size:14
Alignment explanation
Indices: 1140158--1140209 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
1140148 AACTCTAATT
1140158 ATAAACCCTAAACC
1 ATAAACCCTAAACC
* * *
1140172 CT-AACCTTAAATC
1 ATAAACCCTAAACC
*
1140185 ATAAACACTAAACC
1 ATAAACCCTAAACC
1140199 ATAAACCCTAA
1 ATAAACCCTAA
1140210 TATATGAACT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 10 0.34
14 19 0.66
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (14 bp):
ATAAACCCTAAACC
Found at i:1140589 original size:16 final size:16
Alignment explanation
Indices: 1140568--1140603 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
1140558 ATAAACCATG
1140568 TATAGTAAATATAAAC
1 TATAGTAAATATAAAC
1140584 TATAGTAAATATAAAC
1 TATAGTAAATATAAAC
1140600 TATA
1 TATA
1140604 TATATAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (16 bp):
TATAGTAAATATAAAC
Found at i:1140617 original size:2 final size:2
Alignment explanation
Indices: 1140612--1140637 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1140602 TATATATAAC
1140612 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
1140638 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1140688 original size:2 final size:2
Alignment explanation
Indices: 1140637--1140672 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1140627 TCTCTCTCTC
1140637 TA TA TA TA 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 TA TA TA TA
1140673 GTAAATTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1140768 original size:21 final size:21
Alignment explanation
Indices: 1140744--1140787 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
1140734 ATAAATTAGG
* *
1140744 AACCCTAAACCTTAAATCATA
1 AACCATAAACCTTAAACCATA
*
1140765 AACCATAAACTTTAAACCATA
1 AACCATAAACCTTAAACCATA
1140786 AA
1 AA
1140788 TACTAAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (21 bp):
AACCATAAACCTTAAACCATA
Found at i:1141038 original size:611 final size:586
Alignment explanation
Indices: 1140037--1141206 Score: 1703
Period size: 611 Copynumber: 2.0 Consensus size: 586
1140027 ATGTAAAAAC
* * *
1140037 TATATATATACCTATATATATACAAACTATATAAAGTAAATTACTTATATGGTTTATAGAAGCAC
1 TATATATATACATATATATATACAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
* *
1140102 TATGCATAAACTATAAAGTAATAAAGTATATAAATATAGAACCCTAAACTCTAATTATAAACCCT
66 TATGCATAAACTATAAAGTAATAAAGTATATAAATATAGAACCCTAAACTCTAATCATAAACCAT
* * * *
1140167 AAACCCTAACCTTAAATCATAAACACTAAACCATAAACCCTAATATATGAACTAGCACTAATACA
131 AAACCCTAACCATAAATCATAAACACCAAACCATAAAACCTAATAAATGAACTAGCACTAATACA
* *
1140232 TATATATTGTAATAAAAGAGTGGCTTATGTATTGGGCCTATGTAAATTAATGTAAATAGACTAGC
196 TATATATTGTAATAAAAGAGTGGCTTATGTATTGGGCATATGTAAACTAATGTAAATAGACTAGC
*
1140297 ACTATTGTAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAATAAATGGGC
261 ACTATTGCAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAATAAATGGGC
1140362 TATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATACATGT
326 TATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATACATGT
1140427 ACTACTATTTATGAACCATATAATATGCAA-TGACATACTAATTATTTAACACCTAATTAATCAT
391 ACTACTA-TTATGAACCATATAATATGCAAGTGACATACTAA-TATTTAACACCTAATTAATCAT
1140491 GTTTTATATAATTTATATTTAAATAAGTTTATTAATTTTATTAAATAATTTTATATAATATGTAT
454 GTTTTATATAA-TT-TATTTAAATAA--TT-TT-A--TTA--AAAT-A-TTTATATAATATGTAT
1140556 GTATAAACCATGTATAGTAAATATAAACTATAGTAAATATAAACTATATATATAACCTCTCTCTC
507 GTATAAACCATGTATAGTAAATATAAA-TATA-TAAATATAAA-TATATATATAACCTCTCTCTC
1140621 TCTCTCTCTCTCTCTCTA
569 TCTCTCTCTCTCTCTCTA
* * * *
1140639 TATATATATATATATATATATATATA-TATATATAGTAAATTACTTATATAGTTTATAGAAACAC
1 TATATATATACATATATATATACAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
1140703 TATGCATAAACTATATAAAGTAATAAAGTATATAAAT-TAGGAACCCTAAAC-CTTAAATCATAA
66 TATGCATAAAC--TATAAAGTAATAAAGTATATAAATATA-GAACCCTAAACTC-T-AATCATAA
** *
1140766 ACCATAAACTTTAAACCATAAAT-ACTAAATGCTAACCAAACCCTAAAACCTAATGTAAATGAAC
126 ACCATAAACCCT-AACCATAAATCA-TAAA--C--ACCAAACCATAAAACCTAA--TAAATGAAC
*
1140830 TAGCACTAATGCATATATATTTGTAAT-AAAGAGTGGGCTTATGTATT-GGCATATGTAAACTAA
183 TAGCACTAATACATATATA-TTGTAATAAAAGAGT-GGCTTATGTATTGGGCATATGTAAACTAA
1140893 TGTAAATAGACTAGCACTATTGCAAATGGACTTATTTTT-GGTTTTATTATTACTTATTCATAAC
246 TGTAAATAGACTAGCACTATTGCAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAAC
*
1140957 AACAAATAAAT-GGCTATTAATGTGAATTAACCTAACATGCAACT-AAATATTAATTATGCAAAT
311 AACAAATAAATGGGCTATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAAT
*
1141020 GAAATTAATATGACATGTACTACTATTATGAACCATATAATATGTAATGTGACATACTAATATTT
376 GAAATT-A-AT-ACATGTACTACTATTATGAACCATATAATATGCAA-GTGACATACTAATATTT
*
1141085 AACACCTAATTAATCATGTTTTATATAATTTATTTAAATAATTTTATTAATATATTTATATAATA
437 AACACCTAATTAATCATGTTTTATATAATTTATTTAAATAATTTTATTAAAATATTTATATAATA
* * * *
1141150 TGTATGTATAAACCATGTATAGTATATATATATATATATATATATATATATATATAA
502 TGTATGTATAAACCATGTATAGTAAATATAAATATATAAATATAAATATATATATAA
1141207 GTAAATTACT
Statistics
Matches: 521, Mismatches: 27, Indels: 46
0.88 0.05 0.08
Matches are distributed among these distances:
596 11 0.02
597 8 0.02
598 4 0.01
599 41 0.08
600 1 0.00
601 49 0.09
602 25 0.05
603 39 0.07
604 17 0.03
605 14 0.03
606 2 0.00
607 3 0.01
608 24 0.05
609 61 0.12
610 61 0.12
611 131 0.25
612 30 0.06
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (586 bp):
TATATATATACATATATATATACAAACTATATAAAGTAAATTACTTATATAGTTTATAGAAACAC
TATGCATAAACTATAAAGTAATAAAGTATATAAATATAGAACCCTAAACTCTAATCATAAACCAT
AAACCCTAACCATAAATCATAAACACCAAACCATAAAACCTAATAAATGAACTAGCACTAATACA
TATATATTGTAATAAAAGAGTGGCTTATGTATTGGGCATATGTAAACTAATGTAAATAGACTAGC
ACTATTGCAAATGGACTTATTTTTGGGTTTTATTATTACTTATTCATAACAACAAATAAATGGGC
TATTAATGTGAATTAACCTAACATGCAACTAAAATACTAATTATGCAAATGAAATTAATACATGT
ACTACTATTATGAACCATATAATATGCAAGTGACATACTAATATTTAACACCTAATTAATCATGT
TTTATATAATTTATTTAAATAATTTTATTAAAATATTTATATAATATGTATGTATAAACCATGTA
TAGTAAATATAAATATATAAATATAAATATATATATAACCTCTCTCTCTCTCTCTCTCTCTCTCT
A
Found at i:1141140 original size:22 final size:23
Alignment explanation
Indices: 1141103--1141148 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
1141093 ATTAATCATG
*
1141103 TTTTATATAATTTATTTAAATAA
1 TTTTATATAATATATTTAAATAA
*
1141126 TTTTAT-TAATATATTTATATAA
1 TTTTATATAATATATTTAAATAA
1141148 T
1 T
1141149 ATGTATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTTATATAATATATTTAAATAA
Found at i:1141222 original size:2 final size:2
Alignment explanation
Indices: 1141167--1141205 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
1141157 ATAAACCATG
1141167 TA TA GTA TA TA 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 TA TA TA TA TA
1141206 AGTAAATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1141293 original size:7 final size:7
Alignment explanation
Indices: 1141278--1141326 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
1141268 ATTTTTATAA
1141278 AAACCCT
1 AAACCCT
*
1141285 AAGCCCT
1 AAACCCT
1141292 AAACCCT
1 AAACCCT
1141299 AAA-CCT
1 AAACCCT
*
1141305 AAACACT
1 AAACCCT
*
1141312 AAACCAT
1 AAACCCT
1141319 -AACCCT
1 AAACCCT
1141325 AA
1 AA
1141327 TGTAAATAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
6 11 0.32
7 23 0.68
ACGTcount: A:0.47, C:0.37, G:0.02, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:1141307 original size:13 final size:13
Alignment explanation
Indices: 1141278--1141326 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
1141268 ATTTTTATAA
*
1141278 AAACCCTAAGCCCT
1 AAACCCTAA-ACCT
1141292 AAACCCTAAACCT
1 AAACCCTAAACCT
*
1141305 AAACACTAAACC-
1 AAACCCTAAACCT
1141317 ATAACCCTAA
1 A-AACCCTAA
1141327 TGTAAATAGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 1 0.03
13 21 0.68
14 9 0.29
ACGTcount: A:0.47, C:0.37, G:0.02, T:0.14
Consensus pattern (13 bp):
AAACCCTAAACCT
Found at i:1141515 original size:23 final size:23
Alignment explanation
Indices: 1141484--1141527 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1141474 TTATTTTTTC
1141484 TTTAGATAAATTAAACTATATAA
1 TTTAGATAAATTAAACTATATAA
*
1141507 TTTATATAAATTAAACTATAT
1 TTTAGATAAATTAAACTATAT
1141528 TAAATTTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (23 bp):
TTTAGATAAATTAAACTATATAA
Found at i:1142329 original size:31 final size:31
Alignment explanation
Indices: 1142294--1142353 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
1142284 TAATTTAACG
1142294 TTATACTTTTAGGTGTTTTGAACTATCACAA
1 TTATACTTTTAGGTGTTTTGAACTATCACAA
1142325 TTATACTTTTAGGTGTTTTGAACTATCAC
1 TTATACTTTTAGGTGTTTTGAACTATCAC
1142354 GACTATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (31 bp):
TTATACTTTTAGGTGTTTTGAACTATCACAA
Found at i:1144785 original size:45 final size:44
Alignment explanation
Indices: 1144708--1144806 Score: 128
Period size: 45 Copynumber: 2.2 Consensus size: 44
1144698 TTCCTTTTTT
* * *
1144708 TTTCTTTT-TTTTTTCTATAATTTCTTTCAGTTAGGGTTTCCCC
1 TTTCTTTTCTTTTTTATATAATTACTTTCAGTTAGGGTTTCCAC
* *
1144751 TTTCTTTTCTTCTTTTATATAATTACTTTTAGTTAGGGTTTCTAC
1 TTTCTTTTCTT-TTTTATATAATTACTTTCAGTTAGGGTTTCCAC
1144796 TTTCTTCTTCT
1 TTTCTT-TTCT
1144807 AGATCTCCGT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
43 8 0.17
44 2 0.04
45 34 0.71
46 4 0.08
ACGTcount: A:0.13, C:0.17, G:0.08, T:0.62
Consensus pattern (44 bp):
TTTCTTTTCTTTTTTATATAATTACTTTCAGTTAGGGTTTCCAC
Found at i:1149030 original size:19 final size:21
Alignment explanation
Indices: 1149006--1149046 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1148996 TCAACTTACT
1149006 AAAAT-GG-GTGTAGATTCTG
1 AAAATGGGTGTGTAGATTCTG
1149025 AAAATGGGTGTGTAGATTCTG
1 AAAATGGGTGTGTAGATTCTG
1149046 A
1 A
1149047 CTATGCAGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (21 bp):
AAAATGGGTGTGTAGATTCTG
Found at i:1150071 original size:43 final size:43
Alignment explanation
Indices: 1150023--1150104 Score: 139
Period size: 44 Copynumber: 1.9 Consensus size: 43
1150013 AAATTTCCCC
1150023 TTTC-TTTCTTCTTTTCCATAATTGCTTTCAGTTAGGGTTCATT
1 TTTCTTTTCTTCTTTTCCATAATTGC-TTCAGTTAGGGTTCATT
*
1150066 TTTCTTTTCTTCTTTTCTATAATTGCTTCAGTTAGGGTT
1 TTTCTTTTCTTCTTTTCCATAATTGCTTCAGTTAGGGTT
1150105 TTTACTTTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
43 17 0.46
44 20 0.54
ACGTcount: A:0.13, C:0.17, G:0.12, T:0.57
Consensus pattern (43 bp):
TTTCTTTTCTTCTTTTCCATAATTGCTTCAGTTAGGGTTCATT
Found at i:1150114 original size:44 final size:45
Alignment explanation
Indices: 1150022--1150117 Score: 137
Period size: 44 Copynumber: 2.2 Consensus size: 45
1150012 CAAATTTCCC
1150022 CTTTC-TTTCTTCTTTTCCATAATTGCTTTCAGTTAGGGTTCATT
1 CTTTCTTTTCTTCTTTTCCATAATTGCTTTCAGTTAGGGTTCATT
* *
1150066 -TTTCTTTTCTTCTTTTCTATAATTGC-TTCAGTTAGGGTT-TTT
1 CTTTCTTTTCTTCTTTTCCATAATTGCTTTCAGTTAGGGTTCATT
1150108 ACTTTCTTTT
1 -CTTTCTTTT
1150118 TCTAGATCTC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
42 2 0.04
43 17 0.36
44 28 0.60
ACGTcount: A:0.12, C:0.18, G:0.10, T:0.59
Consensus pattern (45 bp):
CTTTCTTTTCTTCTTTTCCATAATTGCTTTCAGTTAGGGTTCATT
Found at i:1155353 original size:11 final size:12
Alignment explanation
Indices: 1155324--1155358 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
1155314 TAACTAATTA
*
1155324 AATTGAATTTAT
1 AATTCAATTTAT
1155336 AATTCAATTTAT
1 AATTCAATTTAT
1155348 -ATTCAATTTAT
1 AATTCAATTTAT
1155359 GAAAAATCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.51
Consensus pattern (12 bp):
AATTCAATTTAT
Found at i:1179231 original size:20 final size:20
Alignment explanation
Indices: 1179162--1179231 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
1179152 TCAGTCAGAG
*
1179162 AGTATCGATAACAACA-TGT-
1 AGTATCGATAACAA-AGGGTC
* *
1179181 AGGTATCGATACCAAAGGGTT
1 A-GTATCGATAACAAAGGGTC
* * *
1179202 AGTGTTGATAATAAAGGGTC
1 AGTATCGATAACAAAGGGTC
1179222 AGTATCGATA
1 AGTATCGATA
1179232 TCTATGAACA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
19 2 0.05
20 36 0.92
21 1 0.03
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.27
Consensus pattern (20 bp):
AGTATCGATAACAAAGGGTC
Found at i:1181424 original size:24 final size:24
Alignment explanation
Indices: 1181393--1181438 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1181383 AACTCCGATG
*
1181393 TCTATGCCATATTGAATAACTCGA
1 TCTATGCCATATTGAACAACTCGA
1181417 TCTATGCCATATTGAACAACTC
1 TCTATGCCATATTGAACAACTC
1181439 AAATGCAGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.33
Consensus pattern (24 bp):
TCTATGCCATATTGAACAACTCGA
Found at i:1186278 original size:23 final size:23
Alignment explanation
Indices: 1186245--1186288 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1186235 ATTACATATA
*
1186245 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCAAAGGACCACGTAGAAT
*
1186268 TGTCCCAAAGGACCGCGTAGA
1 TGTCCCAAAGGACCACGTAGA
1186289 CCCTCGACTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
TGTCCCAAAGGACCACGTAGAAT
Found at i:1187691 original size:3 final size:3
Alignment explanation
Indices: 1187678--1187709 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
1187668 AGCACGTTGG
1187678 AGA AGA A-A AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1187710 GTTTTCCAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1188385 original size:28 final size:27
Alignment explanation
Indices: 1188350--1188403 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
1188340 AAATTTAAAA
* *
1188350 TATTAAATGTATATACA-ATTATTTTAT
1 TATTAAAT-TAAATAAATATTATTTTAT
1188377 TATTCAAATTAAATAAATATTATTTTA
1 TATT-AAATTAAATAAATATTATTTTA
1188404 ATTTGACACT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 10 0.43
28 13 0.57
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (27 bp):
TATTAAATTAAATAAATATTATTTTAT
Found at i:1188456 original size:22 final size:22
Alignment explanation
Indices: 1188387--1188457 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
1188377 TATTCAAATT
1188387 AAATAAATATTATTTTAATTTGA
1 AAATAAATATTATTTTAATTT-A
* * * * *
1188410 CACT-CATTTTATTATTAAATT-
1 AAATAAATATTATT-TTAATTTA
*
1188431 AAATAGATATTATTTTAATTTA
1 AAATAAATATTATTTTAATTTA
1188453 AAATA
1 AAATA
1188458 TTAAAAAGTA
Statistics
Matches: 35, Mismatches: 10, Indels: 7
0.67 0.19 0.13
Matches are distributed among these distances:
21 8 0.23
22 19 0.54
23 8 0.23
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (22 bp):
AAATAAATATTATTTTAATTTA
Found at i:1211726 original size:20 final size:20
Alignment explanation
Indices: 1211699--1211747 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1211689 TATCTTCAAT
1211699 ATCGATACCTTACCCAAGTC
1 ATCGATACCTTACCCAAGTC
* *
1211719 ATCTATACCTTACCCAAGTT
1 ATCGATACCTTACCCAAGTC
1211739 ATCGATACC
1 ATCGATACC
1211748 CTAGCTGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.33, G:0.08, T:0.29
Consensus pattern (20 bp):
ATCGATACCTTACCCAAGTC
Found at i:1224877 original size:144 final size:145
Alignment explanation
Indices: 1224617--1224904 Score: 533
Period size: 144 Copynumber: 2.0 Consensus size: 145
1224607 CTAGTTTTAA
* *
1224617 CTTATTTTTTAGAAATCATTGAGGAAAATGCTTCTCTCAAGTTTGGGGGTGGTAGGGTTCCCAAA
1 CTTATTTTTTAGAAAGCATTGAGGAAAATGCTTCTCTCAAGTTTGGGGGAGGTAGGGTTCCCAAA
*
1224682 TCATTGCATGATAGTATTAGTATAATGAATATGCCATGACATTAGTAAGTGTTAGAATTAGTAAG
66 TCATTGCATGATAGTATTAGTATAATGAATATGCCATGAAATTAGTAAGTGTTAGAATTAGTAAG
1224747 TGCCCAGGA-CAATG
131 TGCCCAGGAGCAATG
*
1224761 CTTATTTTTTAGAAAGCATTGAGGACAATGCTTCTCTCAAGTTTGGGGGAGGTAGGGTTCCCAAA
1 CTTATTTTTTAGAAAGCATTGAGGAAAATGCTTCTCTCAAGTTTGGGGGAGGTAGGGTTCCCAAA
1224826 TCATTGCATGATAGTATTAGTATAATGAATATGCCATGAAATTAGTAAGTGTTAGAATTAGTAAG
66 TCATTGCATGATAGTATTAGTATAATGAATATGCCATGAAATTAGTAAGTGTTAGAATTAGTAAG
1224891 TGCCCAGGAGCAAT
131 TGCCCAGGAGCAAT
1224905 CGAACCTTGT
Statistics
Matches: 139, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
144 135 0.97
145 4 0.03
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (145 bp):
CTTATTTTTTAGAAAGCATTGAGGAAAATGCTTCTCTCAAGTTTGGGGGAGGTAGGGTTCCCAAA
TCATTGCATGATAGTATTAGTATAATGAATATGCCATGAAATTAGTAAGTGTTAGAATTAGTAAG
TGCCCAGGAGCAATG
Found at i:1225399 original size:20 final size:20
Alignment explanation
Indices: 1225370--1225408 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1225360 AGAGCTCATA
*
1225370 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
1225390 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
1225409 GTGGTGAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:1229281 original size:20 final size:20
Alignment explanation
Indices: 1229255--1229304 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1229245 CCGATACCAC
1229255 AGTATCGATATTCAGCCTAG
1 AGTATCGATATTCAGCCTAG
*
1229275 TGTATCGATATTCAGCCTAG
1 AGTATCGATATTCAGCCTAG
1229295 AGTATCGATA
1 AGTATCGATA
1229305 CTACCTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (20 bp):
AGTATCGATATTCAGCCTAG
Found at i:1235836 original size:21 final size:21
Alignment explanation
Indices: 1235806--1235848 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1235796 TTTGGCAGTG
*
1235806 TAAAGAAAGGGATTGATCCTT
1 TAAAGAAAGGGATCGATCCTT
*
1235827 TAAAGGAAGGGATCGATCCTT
1 TAAAGAAAGGGATCGATCCTT
1235848 T
1 T
1235849 CCAACGAGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.28
Consensus pattern (21 bp):
TAAAGAAAGGGATCGATCCTT
Found at i:1235915 original size:20 final size:19
Alignment explanation
Indices: 1235885--1235938 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
1235875 CTGGAATCCT
* *
1235885 AGGGATCGATCCTTTTTCA
1 AGGGATAGATCCTTTTCCA
* * *
1235904 AGGGGATTGATCATTTTCCT
1 A-GGGATAGATCCTTTTCCA
1235924 AGGGATAGATCCTTT
1 AGGGATAGATCCTTT
1235939 GAGCCAAAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (19 bp):
AGGGATAGATCCTTTTCCA
Found at i:1237825 original size:12 final size:12
Alignment explanation
Indices: 1237804--1237858 Score: 69
Period size: 12 Copynumber: 4.7 Consensus size: 12
1237794 TAAGGCAACA
1237804 TTTT-TTCTTTC
1 TTTTCTTCTTTC
*
1237815 TTTTCTTCTTTA
1 TTTTCTTCTTTC
1237827 TTTTCTTCTTTC
1 TTTTCTTCTTTC
*
1237839 TTCTCTTC-TTC
1 TTTTCTTCTTTC
1237850 TTGTTCTTC
1 TT-TTCTTC
1237859 CTCATTTTCC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 9 0.24
12 29 0.76
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:1239323 original size:20 final size:19
Alignment explanation
Indices: 1239289--1239366 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 19
1239279 TACTAGAATC
1239289 CAAGGGATCGATCCTTTTT
1 CAAGGGATCGATCCTTTTT
*
1239308 CAAGGAGATCGGTCCTTTGGTT
1 CAAGG-GATCGATCCTTT--TT
*
1239330 AAAGGGATCGATCCTTTTT
1 CAAGGGATCGATCCTTTTT
*
1239349 CTAGGAGATCGATCCTTT
1 CAAGG-GATCGATCCTTT
1239367 GAGCCAAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
19 10 0.20
20 23 0.46
21 11 0.22
22 6 0.12
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.35
Consensus pattern (19 bp):
CAAGGGATCGATCCTTTTT
Found at i:1239347 original size:41 final size:41
Alignment explanation
Indices: 1239290--1239367 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1239280 ACTAGAATCC
*
1239290 AAGGGATCGATCCTTTTTCAAGGAGATCGGTCCTTTGGTTA
1 AAGGGATCGATCCTTTTTCAAGGAGATCGATCCTTTGGTTA
*
1239331 AAGGGATCGATCCTTTTTCTAGGAGATCGATCCTTTG
1 AAGGGATCGATCCTTTTTCAAGGAGATCGATCCTTTG
1239368 AGCCAAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.35
Consensus pattern (41 bp):
AAGGGATCGATCCTTTTTCAAGGAGATCGATCCTTTGGTTA
Found at i:1244225 original size:35 final size:35
Alignment explanation
Indices: 1244179--1244260 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 35
1244169 GAAGATAAAG
* *
1244179 AAAAGATTTAAAATAAAATACCTAAA-GATGATCCT
1 AAAACATTTAAAATAAAAT-CCTAAATGATAATCCT
*
1244214 AAAA-ATATTAAAATAAAATCCTAAATGATAATTCT
1 AAAACAT-TTAAAATAAAATCCTAAATGATAATCCT
1244249 AAAACATTTAAA
1 AAAACATTTAAA
1244261 TTCAAACTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
34 8 0.19
35 32 0.76
36 2 0.05
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (35 bp):
AAAACATTTAAAATAAAATCCTAAATGATAATCCT
Found at i:1244807 original size:26 final size:26
Alignment explanation
Indices: 1244778--1244831 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1244768 CAGTGATCCC
1244778 AACATAGGGGGTGTGTAATTGTAGGT
1 AACATAGGGGGTGTGTAATTGTAGGT
1244804 AACATAGGGGGTGTGTAATTGTAGGT
1 AACATAGGGGGTGTGTAATTGTAGGT
1244830 AA
1 AA
1244832 AGCTGATAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.30
Consensus pattern (26 bp):
AACATAGGGGGTGTGTAATTGTAGGT
Found at i:1245961 original size:24 final size:24
Alignment explanation
Indices: 1245928--1245973 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1245918 TTCCTAATTC
*
1245928 TGGTGGTGATTATATTGTGTTTTG
1 TGGTGATGATTATATTGTGTTTTG
1245952 TGGTGATGATTATATTGTGTTT
1 TGGTGATGATTATATTGTGTTT
1245974 GAGAGGGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.54
Consensus pattern (24 bp):
TGGTGATGATTATATTGTGTTTTG
Found at i:1250664 original size:21 final size:20
Alignment explanation
Indices: 1250638--1250676 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1250628 ACAAACTTGG
1250638 TCTATAGTGGCATGTTTTATC
1 TCTATAGTGGCAT-TTTTATC
1250659 TCTATAGTGGCATTTTTA
1 TCTATAGTGGCATTTTTA
1250677 AAGTGCCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.21, C:0.13, G:0.18, T:0.49
Consensus pattern (20 bp):
TCTATAGTGGCATTTTTATC
Found at i:1258602 original size:2 final size:2
Alignment explanation
Indices: 1258553--1258587 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1258543 AACTCACATT
1258553 TA 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 TA T
1258588 GTGTGTGTGT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1264399 original size:22 final size:21
Alignment explanation
Indices: 1264360--1264400 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1264350 AAAAGACAAA
**
1264360 AAGAAAAAAAAATCAGAATAG
1 AAGAAAAAAAAAGAAGAATAG
1264381 AAGAAAAGAAAAAGAAGAAT
1 AAGAAAA-AAAAAGAAGAAT
1264401 TTCAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.73, C:0.02, G:0.17, T:0.07
Consensus pattern (21 bp):
AAGAAAAAAAAAGAAGAATAG
Found at i:1270478 original size:12 final size:12
Alignment explanation
Indices: 1270461--1270492 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1270451 TTACAAGAGA
1270461 TATAACAGGAGT
1 TATAACAGGAGT
1270473 TATAACAGGAGT
1 TATAACAGGAGT
1270485 TATAACAG
1 TATAACAG
1270493 TAATTACTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.25
Consensus pattern (12 bp):
TATAACAGGAGT
Found at i:1276024 original size:64 final size:64
Alignment explanation
Indices: 1275950--1276090 Score: 282
Period size: 64 Copynumber: 2.2 Consensus size: 64
1275940 TACACTAGGG
1275950 TGTGCATCGGTGCTCTAATTTGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
1 TGTGCATCGGTGCTCTAATTTGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
1276014 TGTGCATCGGTGCTCTAATTTGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
1 TGTGCATCGGTGCTCTAATTTGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
1276078 TGTGCATCGGTGC
1 TGTGCATCGGTGC
1276091 ATAAAATCAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 77 1.00
ACGTcount: A:0.21, C:0.18, G:0.26, T:0.35
Consensus pattern (64 bp):
TGTGCATCGGTGCTCTAATTTGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
Found at i:1276105 original size:64 final size:63
Alignment explanation
Indices: 1275950--1276160 Score: 230
Period size: 64 Copynumber: 3.3 Consensus size: 63
1275940 TACACTAGGG
* **
1275950 TGTGCATCGGTGCTCTAATTTGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
1 TGTGCATCGGTGC-ATAAAATGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
* **
1276014 TGTGCATCGGTGCTCTAATTTGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
1 TGTGCATCGGTGC-ATAAAATGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
* * * *
1276078 TGTGCATCGGTGCATAAAAT-CAATTCGATGTTTTAATAA-AACTCGGAGTGCATCGATGCAT-G
1 TGTGCATCGGTGCATAAAATGC--TTCGATGTTTCAA-AATAGC-CAGAGTGCATTGATGCATGG
1276140 TCT
62 T-T
* *
1276143 GGTGCATTGGTGCATAAA
1 TGTGCATCGGTGCATAAA
1276161 TTGTATTCGA
Statistics
Matches: 133, Mismatches: 9, Indels: 9
0.88 0.06 0.06
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 93 0.70
65 35 0.26
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.34
Consensus pattern (63 bp):
TGTGCATCGGTGCATAAAATGCTTCGATGTTTCAAAATAGCCAGAGTGCATTGATGCATGGTT
Found at i:1278871 original size:23 final size:22
Alignment explanation
Indices: 1278831--1278909 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
1278821 CACGGCAAAG
1278831 TGCATCGATGCA-CATTCAAGGAA
1 TGCATCGATGCATC-TTCAAGG-A
* *
1278854 TGCATCGGTGCATCTTC-ATGA
1 TGCATCGATGCATCTTCAAGGA
* *
1278875 TGTATCGATGCATATTCAAAGGA
1 TGCATCGATGCATCTTC-AAGGA
1278898 TGCATCGATGCA
1 TGCATCGATGCA
1278910 CTAGTTAGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 28 0.61
24 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCTTCAAGGA
Found at i:1281799 original size:19 final size:19
Alignment explanation
Indices: 1281775--1281812 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1281765 TCATTATCAA
1281775 ATTTTAGTTTAGGCAACCC
1 ATTTTAGTTTAGGCAACCC
1281794 ATTTTAGTTTAGGCAACCC
1 ATTTTAGTTTAGGCAACCC
1281813 TCGAACTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (19 bp):
ATTTTAGTTTAGGCAACCC
Found at i:1284885 original size:65 final size:63
Alignment explanation
Indices: 1284731--1284886 Score: 163
Period size: 65 Copynumber: 2.4 Consensus size: 63
1284721 ACACTAGGGT
* * * *
1284731 GTGCATCGGTGCACTAATTTGCTTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTT
1 GTGCATCGGTGCA-TAAATTGATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTTG
* ** * *
1284795 GTGTATCGGTGCATAAAATCAATTCGATGTTTTAATAA-AACTTAGAGTGCATCGATGCAT-GTC
1 GTGCATCGGTGCAT-AAATTGATTCGATGTTTCAA-AATAAC-CAGAGTGCATCGATGCATGGT-
1284858 TG
62 TG
1284860 GTGCATCGGTGCATAAATTGTATTCGA
1 GTGCATCGGTGCATAAATTG-ATTCGA
1284887 AATGGGTGTA
Statistics
Matches: 75, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
63 1 0.01
64 35 0.47
65 39 0.52
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (63 bp):
GTGCATCGGTGCATAAATTGATTCGATGTTTCAAAATAACCAGAGTGCATCGATGCATGGTTG
Found at i:1294610 original size:23 final size:22
Alignment explanation
Indices: 1294579--1294651 Score: 69
Period size: 23 Copynumber: 3.3 Consensus size: 22
1294569 TAAGCTACCA
*
1294579 AAAGGCAGAGAAAAACGTGTCAC
1 AAAGACAGAG-AAAACGTGTCAC
* *
1294602 AAAGACAGAGATAAACGTTTCAT
1 AAAGACAGAGA-AAACGTGTCAC
* *
1294625 AAAGGCAGAG--AACATGTCAC
1 AAAGACAGAGAAAACGTGTCAC
1294645 AAAGACA
1 AAAGACA
1294652 TAATTATTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
20 13 0.32
22 1 0.02
23 27 0.66
ACGTcount: A:0.49, C:0.16, G:0.22, T:0.12
Consensus pattern (22 bp):
AAAGACAGAGAAAACGTGTCAC
Found at i:1296064 original size:28 final size:27
Alignment explanation
Indices: 1296046--1296101 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
1296036 ATAAATATTA
1296046 AATAAATCAAAGAGGAAAAAAAGAAAAT
1 AATAAATCAAA-AGGAAAAAAAGAAAAT
*
1296074 AATAAATCAAAAGG-AAAAAAGTAAAT
1 AATAAATCAAAAGGAAAAAAAGAAAAT
1296100 AA
1 AA
1296102 AGGAAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 13 0.48
27 3 0.11
28 11 0.41
ACGTcount: A:0.71, C:0.04, G:0.12, T:0.12
Consensus pattern (27 bp):
AATAAATCAAAAGGAAAAAAAGAAAAT
Found at i:1296090 original size:19 final size:18
Alignment explanation
Indices: 1296063--1296110 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
1296053 CAAAGAGGAA
*
1296063 AAAAAGAAAATAA-TAAAT
1 AAAAGGAAAA-AAGTAAAT
1296081 CAAAAGGAAAAAAGTAAAT
1 -AAAAGGAAAAAAGTAAAT
1296100 -AAAGGAAAAAA
1 AAAAGGAAAAAA
1296111 AGTTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 11 0.41
18 2 0.07
19 14 0.52
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.10
Consensus pattern (18 bp):
AAAAGGAAAAAAGTAAAT
Found at i:1296119 original size:28 final size:29
Alignment explanation
Indices: 1296082--1296149 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
1296072 ATAATAAATC
* *
1296082 AAAAGGAAAAAAGT-AAA-TAAAG-GAAA
1 AAAAGAAAAAAAATAAAATTAAAGAGAAA
**
1296108 AAAAGTTAAAAAATAAAATTAAAGAGAAA
1 AAAAGAAAAAAAATAAAATTAAAGAGAAA
1296137 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
1296150 ACAGAAAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 11 0.32
27 3 0.09
28 5 0.15
29 15 0.44
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.10
Consensus pattern (29 bp):
AAAAGAAAAAAAATAAAATTAAAGAGAAA
Found at i:1296145 original size:27 final size:25
Alignment explanation
Indices: 1296082--1296147 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 25
1296072 ATAATAAATC
*
1296082 AAAAGGAAAAAAGTAAATAAAGGAA
1 AAAAAGAAAAAAGTAAATAAAGGAA
1296107 AAAAAGTTAAAAAA-TAAAATTAAAGAGAA
1 AAAAAG--AAAAAAGT-AAA-TAAAG-GAA
1296136 AAAAAGAAAAAA
1 AAAAAGAAAAAA
1296148 AAACAGAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
25 5 0.14
26 1 0.03
27 15 0.43
28 5 0.14
29 9 0.26
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.11
Consensus pattern (25 bp):
AAAAAGAAAAAAGTAAATAAAGGAA
Found at i:1296183 original size:9 final size:8
Alignment explanation
Indices: 1296166--1296191 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1296156 AATACTATTT
1296166 AATAAAAA
1 AATAAAAA
1296174 AATAAAAA
1 AATAAAAA
1296182 AATAAAAA
1 AATAAAAA
1296190 AA
1 AA
1296192 GTTAAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:1297694 original size:38 final size:35
Alignment explanation
Indices: 1297648--1297931 Score: 302
Period size: 37 Copynumber: 7.7 Consensus size: 35
1297638 TCCAAAATCT
1297648 TTTTAAAAACTATATATTATACGTATTTTTAAAAATG
1 TTTTAAAAACTATATATTATA--TATTTTTAAAAATG
*
1297685 TTTTAAAAAACTATATAATATATATATTTTCAAAAATG
1 TTTT-AAAAACTATAT-AT-TATATATTTTTAAAAATG
*
1297723 TTTTAAAAAACTATATATTATATATATTTTCAAAATG
1 TTTT-AAAAACTATATATTATATAT-TTTTAAAAATG
* * *
1297760 TTTTTAAAAACTATATAATATATAAATGTTTTCAAAGTG
1 -TTTTAAAAACTATAT-AT-TATATAT-TTTTAAAAATG
*
1297799 TTTTCAAAACTATATATTATATAAATTTTTAAAAATG
1 TTTTAAAAACTATATATTATAT--ATTTTTAAAAATG
* * *
1297836 -TTTCAAAACTATATATTATATAAGTTTTCAAAATG
1 TTTTAAAAACTATATATTATAT-ATTTTTAAAAATG
1297871 ATTTTAAAAACTATATATTATATATTTTCT-AAAATG
1 -TTTTAAAAACTATATATTATATATTTT-TAAAAATG
*
1297907 TTTAAAAAAAACTATATATTATATA
1 TTT--TAAAAACTATATATTATATA
1297932 CATTTTCAAA
Statistics
Matches: 218, Mismatches: 15, Indels: 28
0.84 0.06 0.11
Matches are distributed among these distances:
35 15 0.07
36 42 0.19
37 77 0.35
38 62 0.28
39 18 0.08
40 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (35 bp):
TTTTAAAAACTATATATTATATATTTTTAAAAATG
Found at i:1297727 original size:75 final size:71
Alignment explanation
Indices: 1297614--1297942 Score: 369
Period size: 75 Copynumber: 4.4 Consensus size: 71
1297604 AATATTTAAA
* *
1297614 AAAACAAC-ATATAATATATAAATTTCCAAAATCTTTTTAAAAACTATATATTATACGTATTTTT
1 AAAA-AACTATATAATATAT-AATTTTCAAAAT-GTTTTAAAAACTATATATTATA--TATTTTT
1297678 AAAAATGTTTT
61 AAAAATGTTTT
*
1297689 AAAAAACTATATAATATATATATTTTCAAAAATGTTTTAAAAAACTATATATTATATATATTTTC
1 AAAAAACTATATAATATATA-ATTTTC-AAAATGTTTT-AAAAACTATATATTATATAT-TTTTA
1297754 AAAATGTTTT
62 AAAATGTTTT
* * *
1297764 TAAAAACTATATAATATATAAATGTTTTCAAAGTGTTTTCAAAACTATATATTATATAAATTTTT
1 AAAAAACTATATAATATAT-AA--TTTTCAAAATGTTTTAAAAACTATATATTATAT--ATTTTT
1297829 AAAAATG-TTT
61 AAAAATGTTTT
* *
1297839 -CAAAACTATATATTATATAAGTTTTCAAAATGATTTTAAAAACTATATATTATATATTTTCT-A
1 AAAAAACTATATAATATATAA-TTTTCAAAATG-TTTTAAAAACTATATATTATATATTTT-TAA
*
1297902 AAATGTTTAA
63 AAATGTTT-T
*
1297912 AAAAAACTATATATTATATACATTTTCAAAA
1 AAAAAACTATATAATATATA-ATTTTCAAAA
1297943 ACCGTTTGCA
Statistics
Matches: 225, Mismatches: 13, Indels: 33
0.83 0.05 0.12
Matches are distributed among these distances:
71 11 0.05
72 14 0.06
73 23 0.10
74 50 0.22
75 78 0.35
76 42 0.19
77 7 0.03
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (71 bp):
AAAAAACTATATAATATATAATTTTCAAAATGTTTTAAAAACTATATATTATATATTTTTAAAAA
TGTTTT
Found at i:1297956 original size:37 final size:35
Alignment explanation
Indices: 1297622--1297968 Score: 290
Period size: 37 Copynumber: 9.3 Consensus size: 35
1297612 AAAAAACAAC
* * * *
1297622 ATATAATATATAAATTTCCAAAATCTTTTTAAAAACT
1 ATATATTATAT-AATTTTCAAAA-ATGTTTAAAAACT
*
1297659 ATATATTATACGT-ATTTTTAAAAATGTTTTAAAAAACT
1 ATATATTATA--TAATTTTCAAAAATG-TTT-AAAAACT
*
1297697 ATATAATATATATATTTTCAAAAATGTTTTAAAAAACT
1 ATATATTATATA-ATTTTCAAAAATG-TTT-AAAAACT
1297735 ATATATTATATATATTTTC-AAAATGTTTTTAAAAACT
1 ATATATTATATA-ATTTTCAAAAATG--TTTAAAAACT
* * *
1297772 ATATAATATATAAATGTTTTC-AAAGTGTTTTCAAAACT
1 ATATATTATAT-AA--TTTTCAAAAATG-TTTAAAAACT
* *
1297810 ATATATTATATAAATTTTTAAAAATGTTTCAAAACT
1 ATATATTATAT-AATTTTCAAAAATGTTTAAAAACT
1297846 ATATATTATATAAGTTTTC-AAAATGATTTTAAAAACT
1 ATATATTATATAA-TTTTCAAAAATG--TTTAAAAACT
*
1297883 ATATATTATAT-ATTTTCTAAAATGTTTAAAAAAAACT
1 ATATATTATATAATTTTCAAAAATGTTT---AAAAACT
* **
1297920 ATATATTATATACATTTTCAAAAACCGTTTGCAAACT
1 ATATATTATATA-ATTTTCAAAAA-TGTTTAAAAACT
*
1297957 ATATAATATATA
1 ATATATTATATA
1297969 TGTATAAAAA
Statistics
Matches: 268, Mismatches: 21, Indels: 42
0.81 0.06 0.13
Matches are distributed among these distances:
34 3 0.01
35 13 0.05
36 38 0.14
37 103 0.38
38 86 0.32
39 21 0.08
40 4 0.01
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (35 bp):
ATATATTATATAATTTTCAAAAATGTTTAAAAACT
Found at i:1299347 original size:18 final size:19
Alignment explanation
Indices: 1299312--1299348 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1299302 CACGGAATGT
1299312 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
1299332 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
1299349 GGATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Done.