Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 116 of 199
Found at i:35382619 original size:18 final size:18
Alignment explanation
Indices: 35382596--35382631 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35382586 TTAATATGCA
35382596 TAGTCATGATTTGCAATC
1 TAGTCATGATTTGCAATC
*
35382614 TAGTCATGGTTTGCAATC
1 TAGTCATGATTTGCAATC
35382632 ATTTTCACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (18 bp):
TAGTCATGATTTGCAATC
Found at i:35386796 original size:14 final size:14
Alignment explanation
Indices: 35386774--35386809 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
35386764 CATAGGTATC
35386774 TAAAAAAATGGAAA
1 TAAAAAAATGGAAA
* *
35386788 TAAATAAATGTAAA
1 TAAAAAAATGGAAA
35386802 TAAAAAAA
1 TAAAAAAA
35386810 GTAAATACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.08, T:0.19
Consensus pattern (14 bp):
TAAAAAAATGGAAA
Found at i:35386815 original size:13 final size:13
Alignment explanation
Indices: 35386774--35386816 Score: 50
Period size: 14 Copynumber: 3.2 Consensus size: 13
35386764 CATAGGTATC
*
35386774 TAAAAAAATGGAAA
1 TAAAAAAA-GTAAA
*
35386788 TAAATAAATGTAAA
1 TAAA-AAAAGTAAA
35386802 TAAAAAAAGTAAA
1 TAAAAAAAGTAAA
35386815 TA
1 TA
35386817 CATATTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 10 0.40
14 12 0.48
15 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (13 bp):
TAAAAAAAGTAAA
Found at i:35386849 original size:2 final size:2
Alignment explanation
Indices: 35386837--35386873 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
35386827 AATTATGAAA
*
35386837 AT AT GT 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
35386874 GGAAAAATGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35386985 original size:23 final size:23
Alignment explanation
Indices: 35386957--35387001 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
35386947 ATATATTTGG
35386957 ACTATA-AAATATACATAAAACAA
1 ACTATACAAATAT-CATAAAACAA
*
35386980 ACTATACAAATATTATAAAACA
1 ACTATACAAATATCATAAAACA
35387002 GAAATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (23 bp):
ACTATACAAATATCATAAAACAA
Found at i:35387566 original size:17 final size:17
Alignment explanation
Indices: 35387544--35387588 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
35387534 ATACAGATAC
35387544 AATAATAATAACATAG-T
1 AATAATAATAA-ATAGAT
35387561 AATAATTAA-AAATAGAT
1 AATAA-TAATAAATAGAT
35387578 AATAATAATAA
1 AATAATAATAA
35387589 TAACATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.28
17 15 0.60
18 3 0.12
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (17 bp):
AATAATAATAAATAGAT
Found at i:35390557 original size:38 final size:38
Alignment explanation
Indices: 35390506--35390621 Score: 166
Period size: 38 Copynumber: 3.1 Consensus size: 38
35390496 TCAAGTGAAA
35390506 AAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATC
1 AAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATC
35390544 AAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATC
1 AAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATC
* * *
35390582 AAGTGACAAAGTGATAAG---TGGCTACACTTATCTGATC
1 AAGTGA-TAAGTGGT-AGTTTTAGCTACACTTATCTGATC
35390619 AAG
1 AAG
35390622 AAACAAAGTG
Statistics
Matches: 73, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
37 21 0.29
38 44 0.60
39 6 0.08
40 2 0.03
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.33
Consensus pattern (38 bp):
AAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATC
Found at i:35390765 original size:36 final size:37
Alignment explanation
Indices: 35390527--35390904 Score: 469
Period size: 37 Copynumber: 10.0 Consensus size: 37
35390517 GGTAGTTTTA
* * *
35390527 GCTACACTTATCTGATCAAGTGA-TAAGTGGT-AGTTTTA
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAG---TG
35390565 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
**
35390602 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
* **
35390639 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
* **
35390676 GTTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
35390713 GTTACACTTATCTGATCAAGTGACAAAGTGATAAGT-
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
* *
35390749 GCTAAACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAA---GT-G
35390790 CTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT-
1 -----GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
35390831 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGT-
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
*
35390867 GCTACACTTATCTGATCAAGTGGCAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
35390904 G
1 G
35390905 TAGCCTAGCT
Statistics
Matches: 311, Mismatches: 16, Indels: 27
0.88 0.05 0.08
Matches are distributed among these distances:
36 100 0.32
37 144 0.46
38 23 0.07
39 8 0.03
40 2 0.01
43 2 0.01
46 32 0.10
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.29
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
Found at i:35390859 original size:82 final size:82
Alignment explanation
Indices: 35390715--35390867 Score: 279
Period size: 82 Copynumber: 1.9 Consensus size: 82
35390705 GATAAGTGGT
35390715 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
35390780 TAAGTGGTAGCTTTAGC
66 TAAGTGGTAGCTTTAGC
* * *
35390797 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTACACTTATCTGATCAAGTGATAAAGTGA
1 TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
35390862 TAAGTG
66 TAAGTG
35390868 CTACACTTAT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 68 1.00
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (82 bp):
TACACTTATCTGATCAAGTGACAAAGTGATAAGTGCTAAACTTATCTGATCAAGAGACAAAGTGA
TAAGTGGTAGCTTTAGC
Found at i:35395107 original size:29 final size:29
Alignment explanation
Indices: 35395060--35395129 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 29
35395050 TACAATAATG
* *
35395060 TAAATGACTAAAACGTAACATT-TCAAACA
1 TAAATAACTAAAACATAAC-TTATCAAACA
*
35395089 TAAATAACTAAAATATAACTTGAATCAAACA
1 TAAATAACTAAAACATAACTT--ATCAAACA
*
35395120 AAAATAACTA
1 TAAATAACTA
35395130 TTTTAATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
28 2 0.06
29 16 0.47
31 16 0.47
ACGTcount: A:0.57, C:0.14, G:0.04, T:0.24
Consensus pattern (29 bp):
TAAATAACTAAAACATAACTTATCAAACA
Found at i:35395341 original size:18 final size:20
Alignment explanation
Indices: 35395320--35395358 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
35395310 AAATAAAAAC
*
35395320 ATAAAAA-AGAAA-TTCATA
1 ATAAAAACAAAAAGTTCATA
35395338 ATAAAAACAAAAAGTTCATA
1 ATAAAAACAAAAAGTTCATA
35395358 A
1 A
35395359 AAATGTGGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.67, C:0.08, G:0.05, T:0.21
Consensus pattern (20 bp):
ATAAAAACAAAAAGTTCATA
Found at i:35395559 original size:84 final size:85
Alignment explanation
Indices: 35395428--35395585 Score: 300
Period size: 84 Copynumber: 1.9 Consensus size: 85
35395418 AAACAAAACG
35395428 TAAAAAATAGAAACTAAAAATCAAACAAAAAAACCCATAAATCATTCAATAATTTTCACATTGAA
1 TAAAAAATAGAAACTAAAAATCAAACAAAAAAACCCATAAATCATTCAATAATTTTCACATTGAA
35395493 AAAAATGAAGTCGTTTTGTT
66 AAAAATGAAGTCGTTTTGTT
*
35395513 TAAAAAATAGAAACTAAAAAT-AAATAAAAAAACCCATAAATCATTCAATAATTTTCACATTGAA
1 TAAAAAATAGAAACTAAAAATCAAACAAAAAAACCCATAAATCATTCAATAATTTTCACATTGAA
35395577 AAAAATGAA
66 AAAAATGAA
35395586 TTCAACGAAT
Statistics
Matches: 72, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
84 51 0.71
85 21 0.29
ACGTcount: A:0.57, C:0.12, G:0.06, T:0.25
Consensus pattern (85 bp):
TAAAAAATAGAAACTAAAAATCAAACAAAAAAACCCATAAATCATTCAATAATTTTCACATTGAA
AAAAATGAAGTCGTTTTGTT
Found at i:35396760 original size:40 final size:39
Alignment explanation
Indices: 35396716--35396851 Score: 127
Period size: 40 Copynumber: 3.4 Consensus size: 39
35396706 AAGAAGATGA
*
35396716 ATAAAATTATAAAAATGTAAAAAGATATATATATATGTAT
1 ATAAAATTATAAAAAT-TAAAAAAATATATATATATGTAT
35396756 ATAAAAATTAT-AAAATATAAAAAAATATATA-AGTATGTAT
1 AT-AAAATTATAAAAAT-TAAAAAAATATATATA-TATGTAT
* * *
35396796 AT-ATATTCATGAAAATAAAAAAAATATGTATATAGATATGTAT
1 ATAAAATT-ATAAAAATTAAAAAAATA--TATAT--ATATGTAT
35396839 ATAAAA-TATAAAA
1 ATAAAATTATAAAA
35396852 TATATATATA
Statistics
Matches: 80, Mismatches: 6, Indels: 18
0.77 0.06 0.17
Matches are distributed among these distances:
38 4 0.05
39 12 0.15
40 34 0.43
41 12 0.15
42 5 0.06
43 10 0.12
44 3 0.04
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.33
Consensus pattern (39 bp):
ATAAAATTATAAAAATTAAAAAAATATATATATATGTAT
Found at i:35396997 original size:3 final size:3
Alignment explanation
Indices: 35396982--35397070 Score: 56
Period size: 3 Copynumber: 29.0 Consensus size: 3
35396972 TGAATGAGTA
* *
35396982 AAT AAT TAT AAT AAT AAT AAGT AAGT AAT AA- AAT AA- ATAC AAT AAT
1 AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT AAT AAT A-AT AAT AAT
** * * * *
35397028 AGC AAT AAT AAT ATTT AAA AAT AAT AAT AAT AGT AAA AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35397071 GATATTGTTA
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
2 3 0.05
3 53 0.80
4 10 0.15
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:35397082 original size:18 final size:19
Alignment explanation
Indices: 35397031--35397093 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 19
35397021 CAATAATAGC
*
35397031 AATAATAATATTTAAAAAT
1 AATAATAATAGTTAAAAAT
35397050 AATAATAATAG-TAAAAAT
1 AATAATAATAGTTAAAAAT
* * *
35397068 AATGAT-ATTGTTAAAATT
1 AATAATAATAGTTAAAAAT
35397086 AATTAATA
1 AA-TAATA
35397094 GCAAAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
17 3 0.08
18 20 0.56
19 13 0.36
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
AATAATAATAGTTAAAAAT
Found at i:35397836 original size:20 final size:22
Alignment explanation
Indices: 35397811--35397869 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 22
35397801 ATGCGAAAAC
35397811 AAAAAGAAAAGAAAAA-GAA-A
1 AAAAAGAAAAGAAAAAGGAACA
*
35397831 AAAAAGAAAACAAAAAGGAATCA
1 AAAAAGAAAAGAAAAAGGAA-CA
35397854 AACAAAG-AAAGAAAAA
1 AA-AAAGAAAAGAAAAA
35397870 AATAGAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 15 0.45
21 3 0.09
23 11 0.33
24 4 0.12
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAGAAAAGAAAAAGGAACA
Found at i:35397855 original size:11 final size:11
Alignment explanation
Indices: 35397805--35397847 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
35397795 TTTAGTATGC
35397805 GAAAACAAAAA
1 GAAAACAAAAA
*
35397816 GAAAAGAAAAA
1 GAAAACAAAAA
35397827 G-AAA-AAAAA
1 GAAAACAAAAA
35397836 GAAAACAAAAA
1 GAAAACAAAAA
35397847 G
1 G
35397848 GAATCAAACA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 6 0.21
10 6 0.21
11 17 0.59
ACGTcount: A:0.81, C:0.05, G:0.14, T:0.00
Consensus pattern (11 bp):
GAAAACAAAAA
Found at i:35398011 original size:6 final size:6
Alignment explanation
Indices: 35398002--35398031 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
35397992 GTTATTTTAG
35398002 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT
35398032 CTGTTTGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:35398017 original size:18 final size:18
Alignment explanation
Indices: 35397996--35398031 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35397986 TTACTTGTTA
35397996 TTTTAGTTTTCTTTTTCT
1 TTTTAGTTTTCTTTTTCT
**
35398014 TTTTCTTTTTCTTTTTCT
1 TTTTAGTTTTCTTTTTCT
35398032 CTGTTTGCTA
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:0.03, C:0.14, G:0.03, T:0.81
Consensus pattern (18 bp):
TTTTAGTTTTCTTTTTCT
Found at i:35403746 original size:20 final size:21
Alignment explanation
Indices: 35403701--35403746 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
35403691 AGAAAACTAT
35403701 TAAACTTATTAAAAATTAATAA
1 TAAA-TTATTAAAAATTAATAA
*
35403723 -AAATTATTTAAAATTAA-AA
1 TAAATTATTAAAAATTAATAA
35403742 TAAAT
1 TAAAT
35403747 ATTCAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 2 0.09
20 17 0.77
21 3 0.14
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
TAAATTATTAAAAATTAATAA
Found at i:35406255 original size:28 final size:28
Alignment explanation
Indices: 35406212--35406268 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
35406202 TCTTTCTCTG
* *
35406212 GTTAGCACTTACTGATCTGTTAGTATTT
1 GTTAGCACTTAATGATCTATTAGTATTT
35406240 GTTAGCACTTAATGATCTATTAGTATTT
1 GTTAGCACTTAATGATCTATTAGTATTT
35406268 G
1 G
35406269 ATGCTAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.25, C:0.12, G:0.18, T:0.46
Consensus pattern (28 bp):
GTTAGCACTTAATGATCTATTAGTATTT
Found at i:35417082 original size:17 final size:17
Alignment explanation
Indices: 35417060--35417096 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
35417050 CATGATCGAT
35417060 AAGTTCATTCCGAGTTG
1 AAGTTCATTCCGAGTTG
35417077 AAGTTCATTCCGAGTTG
1 AAGTTCATTCCGAGTTG
35417094 AAG
1 AAG
35417097 AACGGTAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.32
Consensus pattern (17 bp):
AAGTTCATTCCGAGTTG
Found at i:35423811 original size:26 final size:24
Alignment explanation
Indices: 35423782--35423843 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 24
35423772 AAGCCATGAT
35423782 CGGTAAGCTCAT-TCCGAGCTGAAAAA
1 CGGTAAGCTCATAT-CGAGCTG--AAA
*
35423808 CGGTAAGCTC-TATCGAGTTGAAA
1 CGGTAAGCTCATATCGAGCTGAAA
35423831 CGGTAAGCTCATA
1 CGGTAAGCTCATA
35423844 AGAGCGGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
23 13 0.39
24 2 0.06
25 7 0.21
26 11 0.33
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (24 bp):
CGGTAAGCTCATATCGAGCTGAAA
Found at i:35424936 original size:19 final size:18
Alignment explanation
Indices: 35424914--35424953 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
35424904 TGAATAAAAC
35424914 TTATCTA-TCTAAATAAGAT
1 TTATCTACT-TAAATAA-AT
35424933 TTATCTACTTAAATAAAT
1 TTATCTACTTAAATAAAT
35424951 TTA
1 TTA
35424954 AAAAATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 5 0.25
19 14 0.70
20 1 0.05
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (18 bp):
TTATCTACTTAAATAAAT
Found at i:35429258 original size:42 final size:42
Alignment explanation
Indices: 35429199--35429279 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
35429189 AAGAGTCCTA
35429199 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAGGG
1 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAGGG
* *
35429241 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAA
1 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAA
35429280 AATAAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.48, C:0.16, G:0.06, T:0.30
Consensus pattern (42 bp):
AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAGGG
Found at i:35429287 original size:42 final size:41
Alignment explanation
Indices: 35429199--35429292 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 41
35429189 AAGAGTCCTA
**
35429199 AAAATAATTCCCTTATTCTAATAAACTACTAAAACATAAGGG
1 AAAAT-ATTCCCTTATTCTAATAAACTACTAAAACATAAAAG
* *
35429241 AAAATAGTTCCCTTATTCTAATAAACTACTAAAAGATAAAAT
1 AAAATA-TTCCCTTATTCTAATAAACTACTAAAACATAAAAG
35429283 AAAATATTCC
1 AAAATATTCC
35429293 TAGAATATGA
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
41 5 0.11
42 42 0.89
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (41 bp):
AAAATATTCCCTTATTCTAATAAACTACTAAAACATAAAAG
Found at i:35429332 original size:19 final size:18
Alignment explanation
Indices: 35429310--35429349 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
35429300 TGAATAAAAC
35429310 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
35429329 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
35429347 TTA
1 TTA
35429350 AAACATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:35434290 original size:3 final size:3
Alignment explanation
Indices: 35434284--35434310 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
35434274 TATTATTATT
35434284 ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC
35434311 TCTGCGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:35434727 original size:20 final size:20
Alignment explanation
Indices: 35434702--35434741 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
35434692 ATATAAATTC
35434702 GTATGT-ATGAATGCTTGCAT
1 GTATGTAAT-AATGCTTGCAT
35434722 GTATGTACATAATGCTTGCA
1 GTATGTA-ATAATGCTTGCA
35434742 CGTACATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 10 0.56
22 2 0.11
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (20 bp):
GTATGTAATAATGCTTGCAT
Found at i:35445835 original size:22 final size:23
Alignment explanation
Indices: 35445797--35445860 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
35445787 GGTGGTGGTG
*
35445797 TGGTGGTG-CTAATGTGGTTGA-A
1 TGGTGGTGATTAA-GTGGTTGATA
*
35445819 TGGTGGTGATTAAGTGG-TCATA
1 TGGTGGTGATTAAGTGGTTGATA
**
35445841 TGGTGGTGATTTGGTGGTTG
1 TGGTGGTGATTAAGTGGTTG
35445861 TTGGCTGGTG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 2 0.06
22 28 0.82
23 4 0.12
ACGTcount: A:0.16, C:0.03, G:0.42, T:0.39
Consensus pattern (23 bp):
TGGTGGTGATTAAGTGGTTGATA
Found at i:35463325 original size:17 final size:16
Alignment explanation
Indices: 35463294--35463340 Score: 58
Period size: 17 Copynumber: 2.9 Consensus size: 16
35463284 AGGGAAATTG
*
35463294 AAACTAAGTAAAAACT
1 AAACTAAATAAAAACT
35463310 AAACTAAATGAAAAACT
1 AAACTAAAT-AAAAACT
* *
35463327 GAACTGAATAAAAA
1 AAACTAAATAAAAA
35463341 ATTGCCCATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.64, C:0.11, G:0.09, T:0.17
Consensus pattern (16 bp):
AAACTAAATAAAAACT
Found at i:35468290 original size:13 final size:13
Alignment explanation
Indices: 35468272--35468297 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35468262 GAGTTTACTG
35468272 AAATTATTATAAT
1 AAATTATTATAAT
35468285 AAATTATTATAAT
1 AAATTATTATAAT
35468298 TATGATTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AAATTATTATAAT
Found at i:35471620 original size:20 final size:20
Alignment explanation
Indices: 35471595--35471634 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
35471585 AATACTTAGT
35471595 TTTAATTTTTAGACTTTATA
1 TTTAATTTTTAGACTTTATA
35471615 TTTAATTTTTAGACTTTATA
1 TTTAATTTTTAGACTTTATA
35471635 AATAAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (20 bp):
TTTAATTTTTAGACTTTATA
Found at i:35482989 original size:27 final size:27
Alignment explanation
Indices: 35482946--35482997 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
35482936 ATAGTAAACA
*
35482946 CGGGGTAGTTCAATGGGACAGTAAATG
1 CGGGGTAGTTCAATGGGACAATAAATG
**
35482973 CGGGGTAGTTCGCTGGGACAATAAA
1 CGGGGTAGTTCAATGGGACAATAAA
35482998 AAACAAGTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.29, C:0.13, G:0.37, T:0.21
Consensus pattern (27 bp):
CGGGGTAGTTCAATGGGACAATAAATG
Found at i:35485394 original size:13 final size:14
Alignment explanation
Indices: 35485376--35485404 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
35485366 AAAATTGCTT
35485376 AAAAATCAAG-CAA
1 AAAAATCAAGTCAA
35485389 AAAAATCAAGTCAA
1 AAAAATCAAGTCAA
35485403 AA
1 AA
35485405 GCCACTAAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.69, C:0.14, G:0.07, T:0.10
Consensus pattern (14 bp):
AAAAATCAAGTCAA
Found at i:35497686 original size:18 final size:20
Alignment explanation
Indices: 35497651--35497688 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35497641 ACATATTTTT
*
35497651 TATATTATGTTATTTTTATA
1 TATATTATGTTATATTTATA
35497671 TATATTATG-TA-ATTTATA
1 TATATTATGTTATATTTATA
35497689 ACACATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 9 0.53
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (20 bp):
TATATTATGTTATATTTATA
Found at i:35500080 original size:105 final size:105
Alignment explanation
Indices: 35499902--35500846 Score: 1096
Period size: 105 Copynumber: 9.1 Consensus size: 105
35499892 ACCAGGCTAC
* * * * *
35499902 CACTTTTCGGTAGTCTGGACAATCTACGTAAGCT--TGTG--GTTCAATAGTTTGTCCGCTAATA
1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA
*
35499963 TTTCTTACAGCATCTGGGGTACTTTCTTTCATTGAAGGGA
66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
*** * * *
35500003 CACTTTTCGATAGTCTGGATGGTCTAGGTAAGCTAGAGTCCCGTTTAGTAGTTTGTCTGGTAATA
1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA
* *
35500068 TTCCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGG
66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
* * * * * * *
35500108 CCCTTCTCAATAGTTTGGACGATCTAGGTAAGCTAGAGTGCCTTTCAGTAGTTTGTCTGCTTATA
1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA
*
35500173 TTTCTTACAGCATTTTGGGTACTTTCTTTCATTGAAGGGA
66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
* * * * * *
35500213 CACTTTTCAATAGTTTGGACAACCTAGGTAAGCTAAAGTGCCTTTCAGTAGTTTGTCTGCTCATA
1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA
* *
35500278 TTTCTTACAGCATTTTGGGTACTTTCTTTAATTGAAGGGA
66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
* * * * *
35500318 CACTTATCAATAGTTTGGACGATCTAGGTAAGCTAAAGTGCCGTTCAGTAGTTTGTCTGCTAATA
1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA
**
35500383 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAATAGA
66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
* ** * * * *
35500423 CAGTTTTCGATAGTCCAGACAATCTAGGTAAGCTAGAGCGCGGTTCGGTAGTTTGTCTGCAAATA
1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA
* ** * ** *
35500488 TCTCGAACAGCATTTTGGGTACTTTCTTTTGTTGAAGAGA
66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
* ** * * * * *
35500528 CGCTTTTCGATAGTCCAGATAGTCTAGGTAAGCTATGA--G--GTTTAATAGTTTGTCCGCTAAT
1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTA-GAGTGCCGTTCAGTAGTTTGTCTGCTAAT
* * * * * *
35500589 ATTTCTTTCAGTATTTTGAGTACTTTCTTTCATTGAGGGGG
65 ATTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
* * * **
35500630 CACTTTTTGATAGTCTGGACAATCTAGGCAACCTAGAGTGTGGTTCAGTAGTTTGTCTGCTAATA
1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA
*
35500695 TTTCTTACAGCATTTGGGGTACTTTGTTTCATTGAAGGGA
66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
* * ** **
35500735 CAATTATCGATAGTCCAGACAATCTAGGTAAGCTAGAGTGTGGTTCAGTAGTTTGTCTGCTAATA
1 CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA
* * * *
35500800 TTTCTTACTGCATTAGGGGTACTTTCTATCGTTGAAGGGA
66 TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
35500840 CACTTTT
1 CACTTTT
35500847 ATTGACCTTG
Statistics
Matches: 720, Mismatches: 115, Indels: 14
0.85 0.14 0.02
Matches are distributed among these distances:
101 31 0.04
102 74 0.10
103 3 0.00
104 1 0.00
105 609 0.85
106 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (105 bp):
CACTTTTCGATAGTCTGGACAATCTAGGTAAGCTAGAGTGCCGTTCAGTAGTTTGTCTGCTAATA
TTTCTTACAGCATTTGGGGTACTTTCTTTCATTGAAGGGA
Found at i:35504334 original size:25 final size:23
Alignment explanation
Indices: 35504302--35504350 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 23
35504292 GTTTTTTCAT
35504302 TATTTTACTATCATTTCTCTATTA
1 TATTTTACTATCATTTCT-TATTA
**
35504326 TATTATTACTATTTTTTCTTATTA
1 TATT-TTACTATCATTTCTTATTA
35504350 T
1 T
35504351 TAAATACTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (23 bp):
TATTTTACTATCATTTCTTATTA
Found at i:35504351 original size:22 final size:22
Alignment explanation
Indices: 35504293--35504352 Score: 54
Period size: 25 Copynumber: 2.7 Consensus size: 22
35504283 TTTATCATTG
35504293 TTTTTTC--ATTATT-TTACTA
1 TTTTTTCTTATTATTATTACTA
**
35504312 TCATTTCTCTATTATATTATTACTA
1 TTTTTTCT-TA-T-TATTATTACTA
35504337 TTTTTTCTTATTATTA
1 TTTTTTCTTATTATTA
35504353 AATACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
19 5 0.16
22 6 0.19
23 2 0.06
24 6 0.19
25 12 0.39
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (22 bp):
TTTTTTCTTATTATTATTACTA
Found at i:35513617 original size:23 final size:23
Alignment explanation
Indices: 35513590--35513655 Score: 96
Period size: 23 Copynumber: 2.9 Consensus size: 23
35513580 TGTTATGATC
* * *
35513590 AGTGGTAGCTACGACTACATTAT
1 AGTGGTAGCTTCGGCTACATTAG
*
35513613 CGTGGTAGCTTCGGCTACATTAG
1 AGTGGTAGCTTCGGCTACATTAG
35513636 AGTGGTAGCTTCGGCTACAT
1 AGTGGTAGCTTCGGCTACAT
35513656 ATCAGTGTGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (23 bp):
AGTGGTAGCTTCGGCTACATTAG
Found at i:35513662 original size:23 final size:23
Alignment explanation
Indices: 35513587--35513662 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
35513577 CAGTGTTATG
* *
35513587 ATCAGTGGTAGCTACGACTACATT
1 ATCAGTGGTAGCTTCGGCTACA-T
35513611 ATC-GTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
35513633 -TAGAGTGGTAGCTTCGGCTACAT
1 AT-CAGTGGTAGCTTCGGCTACAT
35513656 ATCAGTG
1 ATCAGTG
35513663 TGGCACTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
21 1 0.02
22 1 0.02
23 39 0.87
24 4 0.09
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:35513912 original size:23 final size:25
Alignment explanation
Indices: 35513866--35513913 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
35513856 GAAATTGCTA
* *
35513866 AGAAATGTTTGATTAGTTATATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
35513891 AGAAATG-TTAATT-GTTAAATGAG
1 AGAAATGTTTAATTAGTTAAATGAG
35513914 TATTTATAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 9 0.43
24 5 0.24
25 7 0.33
ACGTcount: A:0.40, C:0.00, G:0.23, T:0.38
Consensus pattern (25 bp):
AGAAATGTTTAATTAGTTAAATGAG
Found at i:35520351 original size:42 final size:41
Alignment explanation
Indices: 35520282--35520404 Score: 122
Period size: 42 Copynumber: 3.0 Consensus size: 41
35520272 GAGTTTCAAA
* * * *
35520282 TTAACCC-TATTGGGTTTCTGTTTAGCTCTTTTGAGCTTCAG
1 TTAACCCTTA-TGGGTTTCCGTTCAGCTCTTATGAGCTTCAC
*
35520323 TATAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTCCC
1 T-TAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTCAC
* * * * *
35520365 TTCAATCCTTATGGGTTTCCATTTAGCACTTATGTGCTTC
1 TT-AACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTC
35520405 TGTGTAGCCT
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.03
42 65 0.94
43 2 0.03
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (41 bp):
TTAACCCTTATGGGTTTCCGTTCAGCTCTTATGAGCTTCAC
Found at i:35520356 original size:21 final size:21
Alignment explanation
Indices: 35520330--35520398 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
35520320 CAGTATAACC
*
35520330 CTTATGGGTTTCCGTTCAGCT
1 CTTATGGGTTTCCATTCAGCT
* * * *
35520351 CTTATGAGCTTCCCTTCA-AT
1 CTTATGGGTTTCCATTCAGCT
* *
35520371 CCTTATGGGTTTCCATTTAGCA
1 -CTTATGGGTTTCCATTCAGCT
35520393 CTTATG
1 CTTATG
35520399 TGCTTCTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
20 1 0.03
21 35 0.97
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (21 bp):
CTTATGGGTTTCCATTCAGCT
Found at i:35526582 original size:27 final size:27
Alignment explanation
Indices: 35526539--35526625 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 27
35526529 TGGCAACTAA
* *
35526539 GATAGTCAACCGAGACAGTAAACATGG
1 GATAGTCCACTGAGACAGTAAACATGG
* * *
35526566 GATAGTCCATTGGGACAGTAAACACGG
1 GATAGTCCACTGAGACAGTAAACATGG
* * *
35526593 AATATTCCACTGAGATAGTAAACATGG
1 GATAGTCCACTGAGACAGTAAACATGG
35526620 GATAGT
1 GATAGT
35526626 TTGCCGGGAC
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (27 bp):
GATAGTCCACTGAGACAGTAAACATGG
Found at i:35528977 original size:31 final size:31
Alignment explanation
Indices: 35528939--35528997 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
35528929 ACAGGGCCGT
* *
35528939 GTATCTAAACTGTGTCACAGACTGAAGCAAC
1 GTATCTAAACCGTGTCACAGACTAAAGCAAC
*
35528970 GTATCTAAACCGTGTCACCGACTAAAGC
1 GTATCTAAACCGTGTCACAGACTAAAGC
35528998 TGTGCAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (31 bp):
GTATCTAAACCGTGTCACAGACTAAAGCAAC
Found at i:35532026 original size:34 final size:34
Alignment explanation
Indices: 35531983--35532047 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
35531973 TTAATGTTGA
35531983 TCGAATAACGTAGCTTCCATAGTTTTCTTTTTGG
1 TCGAATAACGTAGCTTCCATAGTTTTCTTTTTGG
35532017 TCGAATAACGTAGCTTCCATAGTTTTCTTTT
1 TCGAATAACGTAGCTTCCATAGTTTTCTTTT
35532048 CTCCCATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (34 bp):
TCGAATAACGTAGCTTCCATAGTTTTCTTTTTGG
Found at i:35560274 original size:4 final size:4
Alignment explanation
Indices: 35560260--35560298 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
35560250 ATCTTTTCAT
*
35560260 GTTA ATTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTT
1 GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTTA GTT
35560299 GATAAGTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
GTTA
Found at i:35560450 original size:27 final size:26
Alignment explanation
Indices: 35560420--35560476 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
35560410 CATTATTTAC
35560420 TTTTGAGTTAATAAAATTCTC-TTTGAG
1 TTTT-AGTTAA-AAAATTCTCTTTTGAG
* * *
35560447 TTTTCGTTTAAAAATTTTCTTTTGAG
1 TTTTAGTTAAAAAATTCTCTTTTGAG
35560473 TTTT
1 TTTT
35560477 TTTTGAAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 8 0.31
26 14 0.54
27 4 0.15
ACGTcount: A:0.25, C:0.07, G:0.12, T:0.56
Consensus pattern (26 bp):
TTTTAGTTAAAAAATTCTCTTTTGAG
Found at i:35562042 original size:20 final size:20
Alignment explanation
Indices: 35562013--35562052 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
35562003 AGACTTTGAA
35562013 CCATTCCATTTACTTAATTT
1 CCATTCCATTTACTTAATTT
*
35562033 CCATTGCATTTACTTAATTT
1 CCATTCCATTTACTTAATTT
35562053 AGCTTAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.03, T:0.50
Consensus pattern (20 bp):
CCATTCCATTTACTTAATTT
Found at i:35563029 original size:137 final size:138
Alignment explanation
Indices: 35562770--35563038 Score: 308
Period size: 137 Copynumber: 2.0 Consensus size: 138
35562760 AAAATGGGCT
* * * * *
35562770 TGCTTACACAAGCTGAAGGTCAGAATGTAAGCTCCACGATGCTGCTCACTCAAGCAGATGAGTAT
1 TGCTCACACAAGCTGAAGGTCAAAATGTAAGCTACACGATGCTGCTCACACAAGCAGACGAGTAT
** * * * * * ** * *
35562835 CCGTAACTAATGTCAGACCTCAACCATCGGTAGGACATTTAGGACTAGCACCCGAAACATGGTAA
66 CCACAACTAATGCCAGAACTCAACCATCAGTAGAAAATACAAGACCAGCACCCGAAACATGGTAA
35562900 CCTGGGTC
131 CCTGGGTC
*** * *
35562908 TGCTCACACAAGCTGGCTGTCAAAATGT-AGCTACACGATGCTGCTTACACAAGCTGACGAGTAT
1 TGCTCACACAAGCTGAAGGTCAAAATGTAAGCTACACGATGCTGCTCACACAAGCAGACGAGTAT
**
35562972 CCACAAC-ATATGCCAGAACTCAACCATCAGTAGAAAATACAAGACCAGCACTTGAAACATGGTA
66 CCACAACTA-ATGCCAGAACTCAACCATCAGTAGAAAATACAAGACCAGCACCCGAAACATGGTA
35563036 ACC
130 ACC
35563039 CTAATGACAT
Statistics
Matches: 107, Mismatches: 23, Indels: 3
0.80 0.17 0.02
Matches are distributed among these distances:
136 1 0.01
137 83 0.78
138 23 0.21
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.20
Consensus pattern (138 bp):
TGCTCACACAAGCTGAAGGTCAAAATGTAAGCTACACGATGCTGCTCACACAAGCAGACGAGTAT
CCACAACTAATGCCAGAACTCAACCATCAGTAGAAAATACAAGACCAGCACCCGAAACATGGTAA
CCTGGGTC
Found at i:35569461 original size:41 final size:40
Alignment explanation
Indices: 35569416--35569512 Score: 95
Period size: 43 Copynumber: 2.3 Consensus size: 40
35569406 ATAATTGAAA
35569416 ATATGGAAAATTTTTAAAAAAGTTATCAAAAATTATAAAAT
1 ATAT-GAAAATTTTTAAAAAAGTTATCAAAAATTATAAAAT
* * * * *
35569457 ATATGATAATTCTTTTTACAAAATTTATTAAATATTATAAAAT
1 ATATGA-AA--ATTTTTAAAAAAGTTATCAAAAATTATAAAAT
35569500 ATCATAGAAAATT
1 AT-AT-GAAAATT
35569513 ATAAAAGCTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
40 2 0.04
41 6 0.13
42 2 0.04
43 29 0.64
44 4 0.09
45 2 0.04
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (40 bp):
ATATGAAAATTTTTAAAAAAGTTATCAAAAATTATAAAAT
Found at i:35569499 original size:10 final size:10
Alignment explanation
Indices: 35569476--35569565 Score: 52
Period size: 10 Copynumber: 9.4 Consensus size: 10
35569466 TTCTTTTTAC
35569476 AAAAT-TTAT
1 AAAATATTAT
*
35569485 TAAATATTAT
1 AAAATATTAT
*
35569495 AAAATATCAT
1 AAAATATTAT
35569505 AGAAA-ATTAT
1 A-AAATATTAT
*
35569515 AAAAGCTATGA-
1 AAAA--TATTAT
35569526 AAAATA-T-T
1 AAAATATTAT
35569534 AAAATATTATT
1 AAAATATTA-T
*
35569545 GAAA-ATTAT
1 AAAATATTAT
35569554 AAAA-ATT-T
1 AAAATATTAT
35569562 AAAA
1 AAAA
35569566 AGTACCACTC
Statistics
Matches: 64, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
8 11 0.17
9 17 0.27
10 22 0.34
11 11 0.17
12 3 0.05
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.34
Consensus pattern (10 bp):
AAAATATTAT
Found at i:35569515 original size:20 final size:18
Alignment explanation
Indices: 35569476--35569557 Score: 65
Period size: 20 Copynumber: 4.2 Consensus size: 18
35569466 TTCTTTTTAC
* *
35569476 AAAATTTATTAAATATTAT
1 AAAATATATGAAA-ATTAT
35569495 AAAATATCATAGAAAATTAT
1 AAAATAT-AT-GAAAATTAT
** *
35569515 AAAAGCTATGAAAAATATT
1 AAAATATATGAAAATTA-T
35569534 AAAATATTATTGAAAATTAT
1 AAAATA-TA-TGAAAATTAT
35569554 AAAA
1 AAAA
35569558 ATTTAAAAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
18 7 0.14
19 13 0.26
20 19 0.38
21 11 0.22
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (18 bp):
AAAATATATGAAAATTAT
Found at i:35569564 original size:8 final size:9
Alignment explanation
Indices: 35569485--35569566 Score: 51
Period size: 9 Copynumber: 8.7 Consensus size: 9
35569475 CAAAATTTAT
*
35569485 TAAATATTA
1 TAAAAATTA
*
35569494 TAAAATATCA
1 TAAAA-ATTA
35569504 TAGAAAATTA
1 TA-AAAATTA
**
35569514 TAAAAGCTA
1 TAAAAATTA
35569523 TGAAAAA-TA
1 T-AAAAATTA
35569532 TTAAAATATTA
1 -TAAAA-ATTA
*
35569543 TTGAAAATTA
1 -TAAAAATTA
35569553 TAAAAATT-
1 TAAAAATTA
35569561 TAAAAA
1 TAAAAA
35569567 GTACCACTCT
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
8 6 0.10
9 23 0.39
10 20 0.34
11 10 0.17
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (9 bp):
TAAAAATTA
Found at i:35569835 original size:9 final size:8
Alignment explanation
Indices: 35569818--35569919 Score: 59
Period size: 9 Copynumber: 12.1 Consensus size: 8
35569808 TGACTTTTTT
35569818 TTTTATAA
1 TTTTATAA
35569826 TTTCTATAA
1 TTT-TATAA
35569835 TTTTATCAA
1 TTTTAT-AA
35569844 TTTTCATAA
1 TTTT-ATAA
*
35569853 TTTTAATTAT
1 TTTT-A-TAA
*
35569863 TTTTATCA
1 TTTTATAA
35569871 TTTTAATAAA
1 TTTT-AT-AA
*
35569881 TTTTTTAAA
1 TTTTAT-AA
35569890 TTTT-T--
1 TTTTATAA
35569895 TTTTATAA
1 TTTTATAA
*
35569903 TTTTTATGA
1 -TTTTATAA
35569912 TTTT-TAA
1 TTTTATAA
35569919 T
1 T
35569920 AATTCTTAAT
Statistics
Matches: 76, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
5 4 0.05
6 1 0.01
7 3 0.04
8 16 0.21
9 39 0.51
10 13 0.17
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (8 bp):
TTTTATAA
Found at i:35569838 original size:18 final size:17
Alignment explanation
Indices: 35569817--35569934 Score: 59
Period size: 18 Copynumber: 6.8 Consensus size: 17
35569807 ATGACTTTTT
*
35569817 TTTTTATAATTTCTATAA
1 TTTTAATAATTT-TATAA
35569835 TTTT-ATCAATTTTCATAA
1 TTTTAAT-AATTTT-ATAA
* *
35569853 TTTTAATTATTTTTATCA
1 TTTTAA-TAATTTTATAA
*
35569871 TTTTAATAAATTTTTTAAA
1 TTTTAAT-AATTTTAT-AA
35569890 TTTT--T--TTTTATAA
1 TTTTAATAATTTTATAA
* *
35569903 TTTTTATGATTTTTAATAA
1 TTTTAAT-AATTTT-ATAA
35569922 TTCTTAAT-ATTTT
1 TT-TTAATAATTTT
35569935 TTGCTACACT
Statistics
Matches: 79, Mismatches: 8, Indels: 26
0.70 0.07 0.23
Matches are distributed among these distances:
13 6 0.08
14 5 0.06
15 1 0.01
17 5 0.06
18 40 0.51
19 17 0.22
20 5 0.06
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (17 bp):
TTTTAATAATTTTATAA
Found at i:35569864 original size:27 final size:26
Alignment explanation
Indices: 35569817--35569935 Score: 68
Period size: 27 Copynumber: 4.5 Consensus size: 26
35569807 ATGACTTTTT
*
35569817 TTTTTATAATTTCTATAA-TTTTATCAA
1 TTTTAATAATTT-TATAATTTTTATC-A
* *
35569844 TTTTCATAATTTTAATTATTTTTATCA
1 TTTTAATAATTTT-ATAATTTTTATCA
* *
35569871 TTTTAATAAATTTTTTAAATTTT-T--
1 TTTTAAT-AATTTTATAATTTTTATCA
* *
35569895 TTTT-ATAATTTTTATGATTTTTAATAA
1 TTTTAATAA-TTTTATAATTTTT-ATCA
*
35569922 TTCTTAATATTTTT
1 TT-TTAATAATTTT
35569936 TGCTACACTA
Statistics
Matches: 72, Mismatches: 10, Indels: 19
0.71 0.10 0.19
Matches are distributed among these distances:
22 2 0.03
23 12 0.17
24 4 0.06
25 1 0.01
26 2 0.03
27 29 0.40
28 19 0.26
29 3 0.04
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (26 bp):
TTTTAATAATTTTATAATTTTTATCA
Found at i:35569933 original size:19 final size:19
Alignment explanation
Indices: 35569893--35569935 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
35569883 TTTTAAATTT
* *
35569893 TTTTTTATAATTTTTATGA
1 TTTTTAATAATTTTAATGA
35569912 TTTTTAATAATTCTTAAT-A
1 TTTTTAATAATT-TTAATGA
35569931 TTTTT
1 TTTTT
35569936 TGCTACACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTAATAATTTTAATGA
Found at i:35570614 original size:34 final size:35
Alignment explanation
Indices: 35570566--35570650 Score: 104
Period size: 34 Copynumber: 2.5 Consensus size: 35
35570556 CCCATTTTTT
*
35570566 AATAAACATTAAAAATATATTTTAAAA-ATAATAAA
1 AATAAA-AATAAAAATATATTTTAAAAGATAATAAA
**
35570601 AATAAAAAT-AAAA-ATATTTTAAAAGTATTTTAAA
1 AATAAAAATAAAAATATATTTTAAAAG-ATAATAAA
35570635 AATAAAAATAAAAATA
1 AATAAAAATAAAAATA
35570651 AAAAAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 11 0.26
33 4 0.09
34 17 0.40
35 10 0.23
36 1 0.02
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (35 bp):
AATAAAAATAAAAATATATTTTAAAAGATAATAAA
Found at i:35570623 original size:11 final size:11
Alignment explanation
Indices: 35570609--35570638 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
35570599 AAAATAAAAA
35570609 TAAAAATATTT
1 TAAAAATATTT
*
35570620 TAAAAGTATTT
1 TAAAAATATTT
35570631 TAAAAATA
1 TAAAAATA
35570639 AAAATAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (11 bp):
TAAAAATATTT
Found at i:35571319 original size:6 final size:6
Alignment explanation
Indices: 35571308--35571348 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
35571298 ATTCTAAACG
* * *
35571308 TTAAAA TTAAAA TTAAAA TTAAAA TTAGAA TAAAAA GTAAA
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAA
35571349 GAAAAATTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (6 bp):
TTAAAA
Found at i:35578187 original size:18 final size:18
Alignment explanation
Indices: 35578164--35578198 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
35578154 TAGTCTTTTA
*
35578164 GATGCACTTGTTGAGTGT
1 GATGCACTGGTTGAGTGT
35578182 GATGCACTGGTTGAGTG
1 GATGCACTGGTTGAGTG
35578199 CTAATCACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.11, G:0.37, T:0.34
Consensus pattern (18 bp):
GATGCACTGGTTGAGTGT
Found at i:35586463 original size:14 final size:15
Alignment explanation
Indices: 35586444--35586473 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
35586434 CAACTTCACC
35586444 TCCCAGCTCG-CTAT
1 TCCCAGCTCGCCTAT
35586458 TCCCAGCTCGCCTAT
1 TCCCAGCTCGCCTAT
35586473 T
1 T
35586474 TGCGAGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.13, C:0.43, G:0.13, T:0.30
Consensus pattern (15 bp):
TCCCAGCTCGCCTAT
Found at i:35590421 original size:20 final size:20
Alignment explanation
Indices: 35590396--35590433 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35590386 ATGAATATTA
35590396 TGTGGTGTCAATAGTGGTTT
1 TGTGGTGTCAATAGTGGTTT
* *
35590416 TGTGGTGTGATTAGTGGT
1 TGTGGTGTCAATAGTGGT
35590434 CGGTAAGGAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.39, T:0.45
Consensus pattern (20 bp):
TGTGGTGTCAATAGTGGTTT
Found at i:35590764 original size:31 final size:31
Alignment explanation
Indices: 35590729--35590800 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
35590719 ATGCCTTTTA
* * *
35590729 TATTTCAAATCTATAATTTCCCTAGCTCACT
1 TATTTGAAATCAATAATTTCCCTACCTCACT
*
35590760 TATTTGAAAACAATAATTTCCCTACCTCACT
1 TATTTGAAATCAATAATTTCCCTACCTCACT
35590791 TATTTGAAAT
1 TATTTGAAAT
35590801 ATGAAAGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.33, C:0.22, G:0.04, T:0.40
Consensus pattern (31 bp):
TATTTGAAATCAATAATTTCCCTACCTCACT
Found at i:35599952 original size:8 final size:8
Alignment explanation
Indices: 35599941--35599965 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
35599931 ATTTTATTAT
35599941 ATATAATA
1 ATATAATA
35599949 ATATAATA
1 ATATAATA
35599957 ATATAATA
1 ATATAATA
35599965 A
1 A
35599966 CATACATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATAATA
Found at i:35606316 original size:22 final size:22
Alignment explanation
Indices: 35606286--35606328 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35606276 ACACCAAAAC
*
35606286 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
*
35606308 AGGCCTTTAGCTGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
35606329 AGTGTCGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.21, G:0.26, T:0.44
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:35606684 original size:43 final size:43
Alignment explanation
Indices: 35606423--35606709 Score: 174
Period size: 43 Copynumber: 6.7 Consensus size: 43
35606413 TTTTAGAAAT
** * *
35606423 AAACGCCGCTAAAGACCAAGACCTTTAGTGGCG-C-TTTCACCAC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTCA--AC
* ** * * **
35606466 AACCGCCGCTAAAGGTCATGGTCTTTAGCGGCG-CTTACCAAAC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTC-AAC
*** * * * *
35606509 AAACGCCGCTAAAGAAAATGACCTTTAGCGACG-CTACTCCAAC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCT-TTTCAAC
* * * * *
35606552 AATCACCGCTAAATACCCTGATCTTTAACGGCG-CTTCTCCAGA-
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTT-TTCA-AC
* *
35606595 AAATGCCGCTACAGACCCTGATCTTTAGCGGCGCCTTTTCAAC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTCAAC
* * * **
35606638 AAACGCTGCTAAAGTCCCTGATCTTTAGCGGCG-TTTTTCTCTC
1 AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTC-AAC
* *
35606681 AAACGCCGCTGAAGACCATGATCTTTAGC
1 AAACGCCGCTAAAGACCCTGATCTTTAGC
35606710 AGCACTTTTC
Statistics
Matches: 190, Mismatches: 46, Indels: 16
0.75 0.18 0.06
Matches are distributed among these distances:
42 6 0.03
43 175 0.92
44 8 0.04
45 1 0.01
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCCTGATCTTTAGCGGCGCCTTTTCAAC
Found at i:35607086 original size:21 final size:21
Alignment explanation
Indices: 35607053--35607097 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35607043 TTTTACGCTG
* *
35607053 CTCTGCTTCCCTCGCTGTAGC
1 CTCTACTTCCCTCGCTGCAGC
*
35607074 CTCTACTTTCCTCGCTGCAGC
1 CTCTACTTCCCTCGCTGCAGC
35607095 CTC
1 CTC
35607098 AGCTTCTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.44, G:0.16, T:0.33
Consensus pattern (21 bp):
CTCTACTTCCCTCGCTGCAGC
Found at i:35607108 original size:21 final size:22
Alignment explanation
Indices: 35607053--35607108 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
35607043 TTTTACGCTG
* *
35607053 CTCT-GCTTCCCTCGCTGTAGC
1 CTCTAGCTTCTCTCGCTGCAGC
35607074 CTCTA-CTT-TCCTCGCTGCAGC
1 CTCTAGCTTCT-CTCGCTGCAGC
35607095 CTC-AGCTTCTCTCG
1 CTCTAGCTTCTCTCG
35607109 ATGCCCCATC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
20 1 0.03
21 27 0.93
22 1 0.03
ACGTcount: A:0.07, C:0.43, G:0.16, T:0.34
Consensus pattern (22 bp):
CTCTAGCTTCTCTCGCTGCAGC
Found at i:35607191 original size:65 final size:66
Alignment explanation
Indices: 35607094--35607246 Score: 186
Period size: 66 Copynumber: 2.3 Consensus size: 66
35607084 CTCGCTGCAG
*** **
35607094 CCTCAGCTTCTCTCGATGCCCCATCTGTTTTAAGCTGCT-GCT-GAGTTCTTCATA-CTTTCGTT
1 CCTCAGCTTCTCTCGATGTTGCATCTACTTTAAGCTG-TAGCTGGAGTTCTTCATATCTTT-GTT
35607156 GAA
64 GAA
* * * *
35607159 TCTCAGCTTCTCTCGCTGTTGCATCTACTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGA
1 CCTCAGCTTCTCTCGATGTTGCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
35607224 A
66 A
35607225 CCTCAGCTTCTCTCGATGTTGC
1 CCTCAGCTTCTCTCGATGTTGC
35607247 CTCCGCTTTA
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
64 1 0.01
65 32 0.43
66 37 0.50
67 4 0.05
ACGTcount: A:0.15, C:0.27, G:0.17, T:0.41
Consensus pattern (66 bp):
CCTCAGCTTCTCTCGATGTTGCATCTACTTTAAGCTGTAGCTGGAGTTCTTCATATCTTTGTTGA
A
Found at i:35607233 original size:66 final size:66
Alignment explanation
Indices: 35607136--35607260 Score: 180
Period size: 66 Copynumber: 1.9 Consensus size: 66
35607126 AGCTGCTGCT
* * *
35607136 GAGTTCTTCATACTTTCGTTGAATCTCAGCTTCTCTCGCTGTTGCATCTACTTTAAGTTGTAGCT
1 GAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGTTGCATCCACTTTAAGTTGTAGCT
35607201 G
66 G
* * *
35607202 GAGTTCTTCATATCTTT-TTTGAACCTCAGCTTCTCTCGATGTTGCCTCCGCTTTAAGTT
1 GAGTTCTTCATA-CTTTCGTTGAACCTCAGCTTCTCTCGATGTTGCATCCACTTTAAGTT
35607261 TTGTAATTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
66 48 0.92
67 4 0.08
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.43
Consensus pattern (66 bp):
GAGTTCTTCATACTTTCGTTGAACCTCAGCTTCTCTCGATGTTGCATCCACTTTAAGTTGTAGCT
G
Found at i:35607491 original size:30 final size:30
Alignment explanation
Indices: 35607455--35607514 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
35607445 TGATAATCCG
35607455 GTTATCAATGTCGTCAATATGAACAGAACT
1 GTTATCAATGTCGTCAATATGAACAGAACT
35607485 GTTATCAATGTCGTCAATATGAACAGAACT
1 GTTATCAATGTCGTCAATATGAACAGAACT
35607515 ATCACTGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (30 bp):
GTTATCAATGTCGTCAATATGAACAGAACT
Found at i:35610167 original size:9 final size:9
Alignment explanation
Indices: 35610150--35610275 Score: 106
Period size: 9 Copynumber: 14.9 Consensus size: 9
35610140 TAAGTATAAT
*
35610150 TAAGCTATG
1 TAAGTTATG
35610159 TAAGTTATG
1 TAAGTTATG
*
35610168 TAAGTTATA
1 TAAGTTATG
*
35610177 TAAGTTGTG
1 TAAGTTATG
*
35610186 T-A-TAATG
1 TAAGTTATG
35610193 TAAGTTATG
1 TAAGTTATG
*
35610202 AAAGTTATG
1 TAAGTTATG
35610211 T-A-TTATG
1 TAAGTTATG
*
35610218 TAAGTTATT
1 TAAGTTATG
*
35610227 TAAGTTGTG
1 TAAGTTATG
35610236 T-A-TTATG
1 TAAGTTATG
*
35610243 TAAGTCATG
1 TAAGTTATG
* *
35610252 TAGGCTATG
1 TAAGTTATG
35610261 T-A-TTATG
1 TAAGTTATG
35610268 TAAGTTAT
1 TAAGTTAT
35610276 AATAAGTAAG
Statistics
Matches: 90, Mismatches: 19, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
7 20 0.22
8 7 0.08
9 63 0.70
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (9 bp):
TAAGTTATG
Found at i:35610197 original size:25 final size:25
Alignment explanation
Indices: 35610163--35610282 Score: 143
Period size: 25 Copynumber: 4.8 Consensus size: 25
35610153 GCTATGTAAG
*
35610163 TTATGTAAGTTATATAAGTTGTGTA
1 TTATGTAAGTTATATAAGTTATGTA
*
35610188 TAATGTAAGTTATGA-AAGTTATGTA
1 TTATGTAAGTTAT-ATAAGTTATGTA
* *
35610213 TTATGTAAGTTATTTAAGTTGTGTA
1 TTATGTAAGTTATATAAGTTATGTA
* * * *
35610238 TTATGTAAGTCATGTAGGCTATGTA
1 TTATGTAAGTTATATAAGTTATGTA
35610263 TTATGTAAGTTATAATAAGT
1 TTATGTAAGTTAT-ATAAGT
35610283 AAGTTATGAA
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
25 74 0.95
26 4 0.05
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.45
Consensus pattern (25 bp):
TTATGTAAGTTATATAAGTTATGTA
Found at i:35610218 original size:50 final size:50
Alignment explanation
Indices: 35610151--35610282 Score: 183
Period size: 50 Copynumber: 2.6 Consensus size: 50
35610141 AAGTATAATT
*
35610151 AAGCTATGTAAGTTATGTAAGTTATATAAGTTGTGTATAATGTAAGTTATGA
1 AAGCTATGT-A-TTATGTAAGTTATATAAGTTGTGTATAATGTAAGTCATGA
* * * *
35610203 AAGTTATGTATTATGTAAGTTATTTAAGTTGTGTATTATGTAAGTCATGT
1 AAGCTATGTATTATGTAAGTTATATAAGTTGTGTATAATGTAAGTCATGA
*
35610253 AGGCTATGTATTATGTAAGTTATAATAAGT
1 AAGCTATGTATTATGTAAGTTAT-ATAAGT
35610283 AAGTTATGAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
50 57 0.80
51 6 0.08
52 8 0.11
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.43
Consensus pattern (50 bp):
AAGCTATGTATTATGTAAGTTATATAAGTTGTGTATAATGTAAGTCATGA
Found at i:35610306 original size:34 final size:34
Alignment explanation
Indices: 35610267--35610343 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 34
35610257 TATGTATTAT
*
35610267 GTAAGTTATA-ATAAGTAAGTTATGAAAGTTATATA
1 GTAAGTTATATAT-A-TAAGTTACGAAAGTTATATA
*
35610302 -TAAGTT-TATATATAAGTTACGTAAGTTATATA
1 GTAAGTTATATATATAAGTTACGAAAGTTATATA
35610334 TGTAAGTTAT
1 -GTAAGTTAT
35610344 GTGTTGTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
32 18 0.50
33 3 0.08
34 14 0.39
35 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.16, T:0.42
Consensus pattern (34 bp):
GTAAGTTATATATATAAGTTACGAAAGTTATATA
Found at i:35610312 original size:12 final size:12
Alignment explanation
Indices: 35610295--35610319 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35610285 GTTATGAAAG
35610295 TTATATATAAGT
1 TTATATATAAGT
35610307 TTATATATAAGT
1 TTATATATAAGT
35610319 T
1 T
35610320 ACGTAAGTTA
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:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TTATATATAAGT
Found at i:35610339 original size:22 final size:21
Alignment explanation
Indices: 35610302--35610342 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
35610292 AAGTTATATA
35610302 TAAGTTTATATATAAGTTACG
1 TAAGTTTATATATAAGTTACG
*
35610323 TAAGTTATATATGTAAGTTA
1 TAAGTT-TATATATAAGTTA
35610343 TGTGTTGTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.39, C:0.02, G:0.15, T:0.44
Consensus pattern (21 bp):
TAAGTTTATATATAAGTTACG
Found at i:35610567 original size:9 final size:9
Alignment explanation
Indices: 35610497--35610649 Score: 65
Period size: 9 Copynumber: 17.2 Consensus size: 9
35610487 NNNNNNNGTA
35610497 TTATGTAAG
1 TTATGTAAG
*
35610506 TTATTTAAG
1 TTATGTAAG
*
35610515 TTATTTAAG
1 TTATGTAAG
*
35610524 TTGTGT-A-
1 TTATGTAAG
35610531 TTATGTAAG
1 TTATGTAAG
* *
35610540 TCATGTAGG
1 TTATGTAAG
*
35610549 CTATGT--G
1 TTATGTAAG
35610556 TTATGTAAG
1 TTATGTAAG
35610565 TTAT-T-A-
1 TTATGTAAG
*
35610571 -TAAGTAAG
1 TTATGTAAG
*
35610579 TTATGAAAG
1 TTATGTAAG
*
35610588 TTATATATAAG
1 -T-TATGTAAG
*
35610599 TTTATATATAAG
1 --T-TATGTAAG
35610611 TTATGTAAG
1 TTATGTAAG
35610620 TTATTGTGTAAG
1 TTA---TGTAAG
35610632 TTATGT--G
1 TTATGTAAG
*
35610639 TTGTGTAAG
1 TTATGTAAG
35610648 TT
1 TT
35610650 TATATATAAA
Statistics
Matches: 112, Mismatches: 16, Indels: 32
0.70 0.10 0.20
Matches are distributed among these distances:
5 2 0.02
6 1 0.01
7 19 0.17
8 3 0.03
9 59 0.53
10 2 0.02
11 6 0.05
12 20 0.18
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:35610588 original size:23 final size:24
Alignment explanation
Indices: 35610555--35610599 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
35610545 TAGGCTATGT
*
35610555 GTTATGTAAGTTAT-TATAAGTAA
1 GTTATGAAAGTTATATATAAGTAA
35610578 GTTATGAAAGTTATATATAAGT
1 GTTATGAAAGTTATATATAAGT
35610600 TTATATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (24 bp):
GTTATGAAAGTTATATATAAGTAA
Found at i:35610604 original size:32 final size:32
Alignment explanation
Indices: 35610568--35610761 Score: 126
Period size: 32 Copynumber: 6.2 Consensus size: 32
35610558 ATGTAAGTTA
*
35610568 TTATAAGTAAGTTATGAAAGTTATATATAAGT
1 TTATAAGTAAGTTATGTAAGTTATATATAAGT
* *
35610600 TTATATA-TAAGTTATGTAAGTTATTGTGTAAG-
1 TTATA-AGTAAGTTATGTAAGTTA-TATATAAGT
* *
35610632 TTAT--GT--GTTGTGTAAGTTTATATATAAATT
1 TTATAAGTAAGTTATGTAAG-TTATATAT-AAGT
*
35610662 TTATTTAAGTTA-TGTATGTAAGTTATATATAAGT
1 TTA--TAAGTAAGT-TATGTAAGTTATATATAAGT
*
35610696 TTATATA-TAAGTTATGTAAGTTATCATGTAAG-
1 TTATA-AGTAAGTTATGTAAGTTAT-ATATAAGT
* *
35610728 TTAT--GT--GTTGTGTAAGTTTATATATAAAT
1 TTATAAGTAAGTTATGTAAG-TTATATATAAGT
35610757 TTATA
1 TTATA
35610762 TATGTTATGT
Statistics
Matches: 128, Mismatches: 14, Indels: 42
0.70 0.08 0.23
Matches are distributed among these distances:
28 26 0.20
29 13 0.10
30 5 0.04
32 45 0.35
33 15 0.12
34 8 0.06
35 9 0.07
36 7 0.05
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.48
Consensus pattern (32 bp):
TTATAAGTAAGTTATGTAAGTTATATATAAGT
Found at i:35610619 original size:21 final size:21
Alignment explanation
Indices: 35610595--35610733 Score: 66
Period size: 21 Copynumber: 6.0 Consensus size: 21
35610585 AAGTTATATA
35610595 TAAGTTTATATATAAGTTATG
1 TAAGTTTATATATAAGTTATG
* *
35610616 TAAG-TTATTGTGTAAGTTATGTGTTG
1 TAAGTTTA-TATATAAGTTA-----TG
* *
35610642 TGTAAGTTTATATATAAATTTTATT
1 --TAAGTTTATATAT-AA-GTTATG
* * *
35610667 TAAGTTATGTATGTAAGTTATATA
1 TAAGTT-TATATATAAG-T-TATG
35610691 TAAGTTTATATATAAGTTATG
1 TAAGTTTATATATAAGTTATG
*
35610712 TAAG-TTATCATGTAAGTTATG
1 TAAGTTTAT-ATATAAGTTATG
35610733 T
1 T
35610734 GTTGTGTAAG
Statistics
Matches: 89, Mismatches: 14, Indels: 30
0.67 0.11 0.23
Matches are distributed among these distances:
20 7 0.08
21 32 0.36
22 1 0.01
23 17 0.19
24 14 0.16
25 1 0.01
26 2 0.02
28 7 0.08
29 5 0.06
30 3 0.03
ACGTcount: A:0.34, C:0.01, G:0.17, T:0.49
Consensus pattern (21 bp):
TAAGTTTATATATAAGTTATG
Found at i:35610653 original size:49 final size:49
Alignment explanation
Indices: 35610595--35610783 Score: 208
Period size: 49 Copynumber: 3.9 Consensus size: 49
35610585 AAGTTATATA
*
35610595 TAAGTTTATATATAAGTTATGTAAGTTATTGTGTAAGTTATGTGTTGTG
1 TAAGTTTATATATAAGTTATGTAAGTTATTATGTAAGTTATGTGTTGTG
* * * *
35610644 TAAGTTTATATATAAATTTTATTTAAGTTATGTATGTAAGTTA-----TATA
1 TAAGTTTATATAT-AA-GTTATGTAAGTTAT-TATGTAAGTTATGTGTTGTG
*
35610691 TAAGTTTATATATAAGTTATGTAAGTTATCATGTAAGTTATGTGTTGTG
1 TAAGTTTATATATAAGTTATGTAAGTTATTATGTAAGTTATGTGTTGTG
* * * *
35610740 TAAGTTTATATATAAATTTATATATGTTATGTATGTAAATTATG
1 TAAGTTTATATAT-AAGTTATGTAAGTTAT-TATGTAAGTTATG
35610784 ATATGATTGA
Statistics
Matches: 115, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
44 10 0.09
45 12 0.10
46 2 0.02
47 15 0.13
49 28 0.24
50 15 0.13
51 23 0.20
52 10 0.09
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (49 bp):
TAAGTTTATATATAAGTTATGTAAGTTATTATGTAAGTTATGTGTTGTG
Found at i:35610671 original size:96 final size:97
Alignment explanation
Indices: 35610565--35610787 Score: 330
Period size: 96 Copynumber: 2.3 Consensus size: 97
35610555 GTTATGTAAG
**
35610565 TTATTATAAGTAA-GTTATGAAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATTGTGT
1 TTATTATAAGTAATG-TATGAAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATCATGT
35610629 AAGTTATGTGTTGTGTAAGTTTATATATAAATT
65 AAGTTATGTGTTGTGTAAGTTTATATATAAATT
* *
35610662 TTATT-TAAGTTATGTATGTAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATCATGTA
1 TTATTATAAGTAATGTATGAAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATCATGTA
35610726 AGTTATGTGTTGTGTAAGTTTATATATAAA-T
66 AGTTATGTGTTGTGTAAGTTTATATATAAATT
* *
35610757 TTA-TATATGTTATGTATGTAAA-TTATGATAT
1 TTATTATAAGTAATGTATG-AAAGTTAT-ATAT
35610788 GATTGATAAA
Statistics
Matches: 116, Mismatches: 6, Indels: 9
0.89 0.05 0.07
Matches are distributed among these distances:
94 1 0.01
95 20 0.17
96 89 0.77
97 6 0.05
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (97 bp):
TTATTATAAGTAATGTATGAAAGTTATATATAAGTTTATATATAAGTTATGTAAGTTATCATGTA
AGTTATGTGTTGTGTAAGTTTATATATAAATT
Found at i:35610707 original size:36 final size:36
Alignment explanation
Indices: 35610642--35610713 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
35610632 TTATGTGTTG
*
35610642 TGTAAGTTTATATATAAATTTTATTTAAGTTATGTA
1 TGTAAGTTTATATATAAATTTTATATAAGTTATGTA
*
35610678 TGTAAG-TTATATATAAGTTTATATATAAGTTATGTA
1 TGTAAGTTTATATATAAATTT-TATATAAGTTATGTA
35610714 AGTTATCATG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 13 0.39
36 20 0.61
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (36 bp):
TGTAAGTTTATATATAAATTTTATATAAGTTATGTA
Found at i:35610724 original size:12 final size:11
Alignment explanation
Indices: 35610557--35610731 Score: 77
Period size: 12 Copynumber: 16.1 Consensus size: 11
35610547 GGCTATGTGT
35610557 TATGTAAGTTA
1 TATGTAAGTTA
35610568 TTATAAGTAAG-T-
1 -TAT--GTAAGTTA
*
35610580 TATGAAAGTTA
1 TATGTAAGTTA
*
35610591 TATATAAGTTTA
1 TATGTAAG-TTA
*
35610603 TATATAAG-T-
1 TATGTAAGTTA
35610612 TATGTAAGTTA
1 TATGTAAGTTA
*
35610623 TTGTGTAAG-T-
1 -TATGTAAGTTA
35610633 TATGT--G-T-
1 TATGTAAGTTA
*
35610640 TGTGTAAGTTTA
1 TATGTAAG-TTA
* * *
35610652 TATATAAATTT
1 TATGTAAGTTA
*
35610663 TATTTAAGTTA
1 TATGTAAGTTA
35610674 TGTATGTAAGTTA
1 --TATGTAAGTTA
*
35610687 TATATAAGTTTA
1 TATGTAAG-TTA
*
35610699 TATATAAG-T-
1 TATGTAAGTTA
35610708 TATGTAAGTTA
1 TATGTAAGTTA
35610719 TCATGTAAGTTA
1 T-ATGTAAGTTA
35610731 T
1 T
35610732 GTGTTGTGTA
Statistics
Matches: 127, Mismatches: 17, Indels: 38
0.70 0.09 0.21
Matches are distributed among these distances:
7 6 0.05
9 23 0.18
10 5 0.04
11 29 0.23
12 48 0.38
13 11 0.09
14 5 0.04
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.47
Consensus pattern (11 bp):
TATGTAAGTTA
Found at i:35610832 original size:19 final size:19
Alignment explanation
Indices: 35610793--35610837 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
35610783 GATATGATTG
*
35610793 ATAAATTTTTCAAATATAT
1 ATAAAATTTTCAAATATAT
35610812 ATAAAATTTT-AATATATAT
1 ATAAAATTTTCAA-ATATAT
35610831 ATTAAAA
1 A-TAAAA
35610838 ATGTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 16 0.70
20 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAAAATTTTCAAATATAT
Found at i:35610832 original size:21 final size:22
Alignment explanation
Indices: 35610804--35610856 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
35610794 TAAATTTTTC
* *
35610804 AAATATATATAAAATTTTA-AT
1 AAATATATATAAAAATGTATAT
*
35610825 ATATATAT-TAAAAATGTATAT
1 AAATATATATAAAAATGTATAT
35610846 AAATATATATA
1 AAATATATATA
35610857 TCAAAGATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 8 0.31
21 16 0.62
22 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
AAATATATATAAAAATGTATAT
Found at i:35613345 original size:4 final size:4
Alignment explanation
Indices: 35613336--35613365 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
35613326 AATTTCACGT
*
35613336 TTTA TTTA TTTA TTTA TATA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
35613366 GTATGTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:35613443 original size:21 final size:21
Alignment explanation
Indices: 35613377--35613443 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
35613367 TATGTTTCAT
35613377 TAAAA-TTTTAAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
35613399 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
35613419 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
35613440 TAAA
1 TAAA
35613444 TTTTAGTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.41
21 7 0.19
22 6 0.16
23 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.43
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:35613476 original size:11 final size:11
Alignment explanation
Indices: 35613462--35613494 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
35613452 TTTTATTTCC
35613462 TTTTTATATTT
1 TTTTTATATTT
35613473 TTTTTATA-TT
1 TTTTTATATTT
*
35613483 TTCTTATATTT
1 TTTTTATATTT
35613494 T
1 T
35613495 GGTCCTGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATATTT
Found at i:35614144 original size:7 final size:7
Alignment explanation
Indices: 35614132--35614206 Score: 53
Period size: 7 Copynumber: 10.1 Consensus size: 7
35614122 CTTGATACCT
35614132 TAAACCC
1 TAAACCC
35614139 TAAACCC
1 TAAACCC
*
35614146 TTAACCCC
1 -TAAACCC
*
35614154 TAACCCC
1 TAAACCC
35614161 TAAATCCCC
1 TAAA--CCC
35614170 TAAACCCC
1 TAAA-CCC
*
35614178 TAAATTCC
1 TAAA-CCC
35614186 T-AACCC
1 TAAACCC
*
35614192 TTAACCC
1 TAAACCC
*
35614199 TTAACCC
1 TAAACCC
35614206 T
1 T
35614207 TTAACCTCAA
Statistics
Matches: 59, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
6 3 0.05
7 32 0.54
8 17 0.29
9 7 0.12
ACGTcount: A:0.33, C:0.44, G:0.00, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:35614149 original size:15 final size:14
Alignment explanation
Indices: 35614129--35614212 Score: 62
Period size: 15 Copynumber: 5.6 Consensus size: 14
35614119 ACCCTTGATA
35614129 CCTTAAACCCTAAAC
1 CCTTAAACCCT-AAC
*
35614144 CCTTAACCCCTAAC
1 CCTTAAACCCTAAC
*
35614158 CCCTAAATCCCCTAAAC
1 CCTTAAA--CCCT-AAC
* *
35614175 CCCTAAATTCCTAAC
1 CCTTAAA-CCCTAAC
35614190 CCTT-AACCCTTAAC
1 CCTTAAACCC-TAAC
*
35614204 CCTTTAACC
1 CCTTAAACC
35614213 TCAATCCCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
13 2 0.04
14 18 0.32
15 20 0.35
16 7 0.12
17 10 0.18
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (14 bp):
CCTTAAACCCTAAC
Found at i:35614179 original size:8 final size:8
Alignment explanation
Indices: 35614132--35614181 Score: 61
Period size: 7 Copynumber: 6.5 Consensus size: 8
35614122 CTTGATACCT
35614132 TAAA-CCC
1 TAAACCCC
35614139 TAAA-CCC
1 TAAACCCC
*
35614146 TTAACCCC
1 TAAACCCC
35614154 T-AACCCC
1 TAAACCCC
35614161 TAAATCCCC
1 TAAA-CCCC
35614170 TAAACCCC
1 TAAACCCC
35614178 TAAA
1 TAAA
35614182 TTCCTAACCC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
7 17 0.44
8 14 0.36
9 8 0.21
ACGTcount: A:0.38, C:0.44, G:0.00, T:0.18
Consensus pattern (8 bp):
TAAACCCC
Found at i:35614869 original size:41 final size:41
Alignment explanation
Indices: 35614809--35615163 Score: 398
Period size: 41 Copynumber: 8.7 Consensus size: 41
35614799 AAATGTTTTT
* *
35614809 GCGGCGCTTTT-TCAAAAACGCCGCTAAAGATCTGAGTACTA
1 GCGGCGCTTTTCT-AAAAACGCCGCTAAAGATCTGAGCATTA
* * *
35614850 GCGGCGCTTTTCTATAAACGCCGCTAAAGATTTGAGTA-T-
1 GCGGCGCTTTTCTAAAAACGCCGCTAAAGATCTGAGCATTA
* * ** *
35614889 GCGGTGATTTTGGAAAAACGCCGATAAAGATCTGAGCATTA
1 GCGGCGCTTTTCTAAAAACGCCGCTAAAGATCTGAGCATTA
* *
35614930 GCAGCGC--TTCTACAGAAACGCCGCTAAATATCTGAGCATTA
1 GCGGCGCTTTTCTA-A-AAACGCCGCTAAAGATCTGAGCATTA
* * *
35614971 CCGGCGCTTTTCCAAAAACGCCGCTAAAGACCTGAGCATTA
1 GCGGCGCTTTTCTAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
35615012 GCGGCGCTTATCAAAAAACGCCGCCAAAGATCTGAGCATTA
1 GCGGCGCTTTTCTAAAAACGCCGCTAAAGATCTGAGCATTA
* * *
35615053 GCGGCGCTTATCAAAAAACGCCGCCAAAGATCTGAGCATTA
1 GCGGCGCTTTTCTAAAAACGCCGCTAAAGATCTGAGCATTA
* *
35615094 GCGGCGCTTTTAC-AAAAACGCCGCTAAAGATCTGGGAATTA
1 GCGGCGCTTTT-CTAAAAACGCCGCTAAAGATCTGAGCATTA
* *
35615135 GCGGCGCTTTTTTTTAAAACGCCGCTAAA
1 GCGGCGC-TTTTCTAAAAACGCCGCTAAA
35615164 TCCCCGAAAG
Statistics
Matches: 271, Mismatches: 33, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
39 33 0.12
40 3 0.01
41 210 0.77
42 21 0.08
43 4 0.01
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.23
Consensus pattern (41 bp):
GCGGCGCTTTTCTAAAAACGCCGCTAAAGATCTGAGCATTA
Found at i:35619676 original size:2 final size:2
Alignment explanation
Indices: 35619669--35619700 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
35619659 TTTGTACTAT
35619669 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35619701 CCATATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35633136 original size:28 final size:28
Alignment explanation
Indices: 35633060--35633137 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
35633050 TATAATATGT
*
35633060 ATAAATTAAAAGGTTAAAATAAGTTTGA
1 ATAAATTAAAATGTTAAAATAAGTTTGA
* *
35633088 ATAAATTAACAATATTGAAATAAG-TTGAA
1 ATAAATTAA-AATGTTAAAATAAGTTTG-A
35633117 ATAAATTAAAATGTTAAAATA
1 ATAAATTAAAATGTTAAAATA
35633138 TTGGAAAGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 22 0.51
29 21 0.49
ACGTcount: A:0.56, C:0.01, G:0.10, T:0.32
Consensus pattern (28 bp):
ATAAATTAAAATGTTAAAATAAGTTTGA
Found at i:35634160 original size:20 final size:19
Alignment explanation
Indices: 35634126--35634181 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
35634116 TTTTTCATAT
*
35634126 AGAAAATAGAAAGAAACAA
1 AGAAAACAGAAAGAAACAA
**
35634145 AGAAAACAGTAAAGAAACGC
1 AGAAAACAG-AAAGAAACAA
*
35634165 AGAGAAAGAGAAAGAAA
1 AGA-AAACAGAAAGAAA
35634182 AAGAGAAAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 8 0.26
20 18 0.58
21 5 0.16
ACGTcount: A:0.68, C:0.07, G:0.21, T:0.04
Consensus pattern (19 bp):
AGAAAACAGAAAGAAACAA
Found at i:35635332 original size:175 final size:175
Alignment explanation
Indices: 35635041--35635792 Score: 1308
Period size: 175 Copynumber: 4.3 Consensus size: 175
35635031 CTATTCCACC
*
35635041 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGAGAGATAAGACCTGATGCGATCT
1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT
*
35635106 ACTCTACTGTAACTTCAGAGAGATAAGATTC-TTTATTTTAATCCGTTCCACTATAATCTTAAGG
66 ACTCTACTGTAACTTCAGAGAGATAAGA-TCATTTATTTTAATCCGTTCCACTATAATCTCAAGG
* * *
35635170 AAATAGGATTACTGGCTTCAATTTGCTCTGTTGTAATCTCAGGGAG
130 AAATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
* *
35635216 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGAGAGATAAGACCTGATACGATCT
1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT
* * * *
35635281 ACTCTACTGTAACTTCAGAGACATAAGATCCTTTATTTTAATCTGTTCCACTATAATCTCAGGGA
66 ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGTTCCACTATAATCTCAAGGA
*
35635346 AATATGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
131 AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
*
35635391 ATAAGATCTGTAATTCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT
1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT
* *
35635456 ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATTCGTTCCACTGTAATCTCAAGGA
66 ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGTTCCACTATAATCTCAAGGA
*
35635521 AATAGGATTACTGTCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
131 AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
*
35635566 ATAAGATCTGTGATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT
1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT
* *
35635631 ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGTTCCACTGTAATCTCAGGGA
66 ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGTTCCACTATAATCTCAAGGA
35635696 AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
131 AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
*
35635741 ATAAGATCTGTAATTCTTCGGTCTATTCCACTATAATCTCAGGGAGATAAGA
1 ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGA
35635793 TCTGTAATTC
Statistics
Matches: 549, Mismatches: 27, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
174 2 0.00
175 547 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (175 bp):
ATAAGATCTGTAATTCTTCGGTCTATTCCACTGTAATCTCAGGGAGATAAGACCTGATGCGATCT
ACTCTACTGTAACTTCAGAGAGATAAGATCATTTATTTTAATCCGTTCCACTATAATCTCAAGGA
AATAGGATTACTGGCTTCAATCTGCTCCGCTGTAATCTCAGGGAG
Found at i:35635427 original size:46 final size:46
Alignment explanation
Indices: 35635201--35635884 Score: 468
Period size: 46 Copynumber: 15.5 Consensus size: 46
35635191 TTTGCTCTGT
*
35635201 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
* * * * * *
35635247 TGTAATCTCAGAGAGATAAGACCTG--ATAC--GA-TCTACTCTAC
1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
* * * * *
35635288 TGTAA-CTTCAGAGACATAAGATCCT-TTATT-TT-AATCTGTTCCAC
1 TGTAATC-TCAGGGAGATAAGAT-CTGTAATTCTTCAGTCTATTCCAC
* * * * * * ** *
35635332 TATAATCTCAGGGAAATATGA--T-TACTGGCTTCAATCTGCTCCGC
1 TGTAATCTCAGGGAGATAAGATCTGTAAT-TCTTCAGTCTATTCCAC
35635376 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
* * * * *
35635422 TGTAATCTCAGGGAGATAAGACCTG--ATGC--GA-TCTACTCTAC
1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
* * * * *
35635463 TGTAA-CTTCAGAGAGATAAGATCAT-TTATT-TTAATTC-GTTCCAC
1 TGTAATC-TCAGGGAGATAAGATC-TGTAATTCTTCAGTCTATTCCAC
* * * * * ** *
35635507 TGTAATCTCAAGGAAATAGGA--T-TACTGTCTTCAATCTGCTCCGC
1 TGTAATCTCAGGGAGATAAGATCTGTAAT-TCTTCAGTCTATTCCAC
* *
35635551 TGTAATCTCAGGGAGATAAGATCTGTGATTCTTCGGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
* * * * *
35635597 TGTAATCTCAGGGAGATAAGACCTG--ATGC--GA-TCTACTCTAC
1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
* * * **
35635638 TGTAA-CTTCAGAGAGATAAGATCAT-TTATT-TT-AATCCGTTCCAC
1 TGTAATC-TCAGGGAGATAAGATC-TGTAATTCTTCAGTCTATTCCAC
* * * * * ** *
35635682 TGTAATCTCAGGGAAATAGGA--T-TACTGGCTTCAATCTGCTCCGC
1 TGTAATCTCAGGGAGATAAGATCTGTAAT-TCTTCAGTCTATTCCAC
*
35635726 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
* *
35635772 TATAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
*
35635818 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCGGTCTATTCCAC
1 TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
35635864 TGTAATCTCAGGGAGATAAGA
1 TGTAATCTCAGGGAGATAAGA
35635885 CCTGATGCGA
Statistics
Matches: 500, Mismatches: 96, Indels: 84
0.74 0.14 0.12
Matches are distributed among these distances:
40 3 0.01
41 89 0.18
42 6 0.01
43 17 0.03
44 152 0.30
45 5 0.01
46 220 0.44
47 8 0.02
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (46 bp):
TGTAATCTCAGGGAGATAAGATCTGTAATTCTTCAGTCTATTCCAC
Found at i:35635820 original size:23 final size:23
Alignment explanation
Indices: 35635794--35635869 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
35635784 GAGATAAGAT
35635794 CTGTAATTCTTCGGTCTATTCCA
1 CTGTAATTCTTCGGTCTATTCCA
*** ***
35635817 CTGTAA-TC-TCAGGGAGATAAGA
1 CTGTAATTCTTC-GGTCTATTCCA
35635839 TCTGTAATTCTTCGGTCTATTCCA
1 -CTGTAATTCTTCGGTCTATTCCA
35635863 CTGTAAT
1 CTGTAAT
35635870 CTCAGGGAGA
Statistics
Matches: 37, Mismatches: 12, Indels: 8
0.65 0.21 0.14
Matches are distributed among these distances:
21 2 0.05
22 7 0.19
23 19 0.51
24 7 0.19
25 2 0.05
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (23 bp):
CTGTAATTCTTCGGTCTATTCCA
Found at i:35646475 original size:25 final size:25
Alignment explanation
Indices: 35646428--35646475 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
35646418 TTTGTATTAA
* **
35646428 AAAAACAAAAATTTTAGTTGTCGAC
1 AAAAACAAAAAATTTAGGAGTCGAC
*
35646453 AAAAACAAAAAATTTGGGAGTCG
1 AAAAACAAAAAATTTAGGAGTCG
35646476 CCACTGATCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (25 bp):
AAAAACAAAAAATTTAGGAGTCGAC
Found at i:35647533 original size:28 final size:28
Alignment explanation
Indices: 35647456--35647533 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
35647446 TATAATATGT
*
35647456 ATAAATTAAAAGGTTAAAATAAGTTTGA
1 ATAAATTAAAATGTTAAAATAAGTTTGA
* *
35647484 ATAAATTAACAATATTGAAATAAG-TTGA
1 ATAAATTAA-AATGTTAAAATAAGTTTGA
35647512 GATAAATTAAAATGTTAAAATA
1 -ATAAATTAAAATGTTAAAATA
35647534 TTGGAAAGAG
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
28 23 0.53
29 20 0.47
ACGTcount: A:0.55, C:0.01, G:0.12, T:0.32
Consensus pattern (28 bp):
ATAAATTAAAATGTTAAAATAAGTTTGA
Found at i:35647831 original size:23 final size:24
Alignment explanation
Indices: 35647796--35647840 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
35647786 TGGAAATTTA
*
35647796 AATAATGATACATAATAAATTTTG
1 AATAATGAAACATAATAAATTTTG
**
35647820 AATAAT-AAACATGGTAAATTT
1 AATAATGAAACATAATAAATTT
35647841 ATATAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.36
Consensus pattern (24 bp):
AATAATGAAACATAATAAATTTTG
Found at i:35648553 original size:20 final size:19
Alignment explanation
Indices: 35648519--35648586 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 19
35648509 TTTTTCGTAT
*
35648519 AGAAAATAGAAAGAAACAA
1 AGAAAACAGAAAGAAACAA
**
35648538 AGAAAACAGTAAAGAAACGC
1 AGAAAACAG-AAAGAAACAA
*
35648558 AGAGAAAGAGAAAG-AA-AA
1 AGA-AAACAGAAAGAAACAA
*
35648576 AGAAAAGAGAA
1 AGAAAACAGAA
35648587 CCACCTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
17 8 0.20
18 3 0.07
19 10 0.24
20 15 0.37
21 5 0.12
ACGTcount: A:0.69, C:0.06, G:0.22, T:0.03
Consensus pattern (19 bp):
AGAAAACAGAAAGAAACAA
Found at i:35649127 original size:26 final size:26
Alignment explanation
Indices: 35649090--35649143 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
35649080 ACTGATGGAC
35649090 TTTTAATAATTTTGTTT-TTT-TTTAT
1 TTTTAATAATTTT-TTTGTTTATTTAT
*
35649115 TTTTTATATATTTTTTTGTTTATTTAT
1 TTTTAATA-ATTTTTTTGTTTATTTAT
35649142 TT
1 TT
35649144 GATTTGGGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 10 0.40
26 8 0.32
27 7 0.28
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.78
Consensus pattern (26 bp):
TTTTAATAATTTTTTTGTTTATTTAT
Found at i:35649128 original size:16 final size:17
Alignment explanation
Indices: 35649109--35649149 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
35649099 TTTTGTTTTT
35649109 TTTTATTT-TTTATATA
1 TTTTATTTGTTTATATA
*
35649125 TTTT-TTTGTTTATTTA
1 TTTTATTTGTTTATATA
*
35649141 TTTGATTTG
1 TTTTATTTG
35649150 GGCTGAGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (17 bp):
TTTTATTTGTTTATATA
Found at i:35658618 original size:20 final size:21
Alignment explanation
Indices: 35658593--35658632 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
35658583 TCTAACTAGT
35658593 TTTGAACATTTTTA-TATATA
1 TTTGAACATTTTTACTATATA
**
35658613 TTTGAATTTTTTTACTATAT
1 TTTGAACATTTTTACTATAT
35658633 TTTTATTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTGAACATTTTTACTATATA
Found at i:35664366 original size:17 final size:17
Alignment explanation
Indices: 35664346--35664383 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
35664336 GGTTGTCTAT
*
35664346 TTTTCTTTATTTATTTA
1 TTTTCATTATTTATTTA
35664363 TTTTCATTATTTATTTA
1 TTTTCATTATTTATTTA
35664380 TTTT
1 TTTT
35664384 TATTTCCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCATTATTTATTTA
Found at i:35665472 original size:18 final size:18
Alignment explanation
Indices: 35665444--35665485 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
35665434 CAAATATACA
*
35665444 AATACTAAATAAAATTAAT
1 AATA-TAAATAAAAATAAT
*
35665463 TATATAAATAAAAATAAT
1 AATATAAATAAAAATAAT
35665481 AATAT
1 AATAT
35665486 GTGGGAGATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AATATAAATAAAAATAAT
Found at i:35671517 original size:23 final size:24
Alignment explanation
Indices: 35671490--35671537 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
35671480 CATTATCAAG
* *
35671490 TCATTCCAAACTTGC-CATAAGAT
1 TCATTCAAAACATGCACATAAGAT
35671513 TCATTCAAAACATGCATCATAAGAT
1 TCATTCAAAACATGCA-CATAAGAT
35671538 AACCAAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.62
25 8 0.38
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (24 bp):
TCATTCAAAACATGCACATAAGAT
Found at i:35672205 original size:42 final size:42
Alignment explanation
Indices: 35672146--35672243 Score: 169
Period size: 42 Copynumber: 2.3 Consensus size: 42
35672136 TTTACCTCAT
*
35672146 TGCTCACACGAGCTATGGGTCAAAATGTAAGCTATACGATAC
1 TGCTCACACGAGCTATGGGTCAAAATGTAAGCTACACGATAC
* *
35672188 TGCTCTCACGAGCTATGGGTCAAAATGTAAGCTACATGATAC
1 TGCTCACACGAGCTATGGGTCAAAATGTAAGCTACACGATAC
35672230 TGCTCACACGAGCT
1 TGCTCACACGAGCT
35672244 GTGGAGTATC
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.24
Consensus pattern (42 bp):
TGCTCACACGAGCTATGGGTCAAAATGTAAGCTACACGATAC
Found at i:35679979 original size:22 final size:22
Alignment explanation
Indices: 35679930--35679982 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
35679920 TATAAGTCCA
**
35679930 AAAAAT-AAAATAAAAACAGCT
1 AAAAATAAAAATAAAAACAAAT
* *
35679951 AACAATAAAAATAAAAATAAAT
1 AAAAATAAAAATAAAAACAAAT
35679973 AAAAATAAAA
1 AAAAATAAAA
35679983 CTAATACTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 5 0.19
22 21 0.81
ACGTcount: A:0.77, C:0.06, G:0.02, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAATAAAAACAAAT
Found at i:35680553 original size:14 final size:14
Alignment explanation
Indices: 35680534--35680560 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35680524 GACTGTTATT
35680534 TTTTAATTTTTTAA
1 TTTTAATTTTTTAA
35680548 TTTTAATTTTTTA
1 TTTTAATTTTTTA
35680561 TTAATACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTAATTTTTTAA
Found at i:35683690 original size:19 final size:19
Alignment explanation
Indices: 35683666--35683757 Score: 148
Period size: 19 Copynumber: 4.8 Consensus size: 19
35683656 AGTCTTCAAG
35683666 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
35683685 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
35683704 GATATGCGACCTTAGATAT
1 GATATGCAATCTTAGATAT
*
35683723 GATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATAT
35683742 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
35683758 AGATATGATT
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 65 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:35683709 original size:38 final size:38
Alignment explanation
Indices: 35683666--35683780 Score: 167
Period size: 38 Copynumber: 2.9 Consensus size: 38
35683656 AGTCTTCAAG
35683666 GATATGCAATCTTAGATATGATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGTAATCTTAGATAT
* *
35683704 GATATGCGACCTTAGATATGATATGTAATCTTAGATAT
1 GATATGCAATCTTAGATATGATATGTAATCTTAGATAT
*
35683742 GATATGCAATCTTAGAAGATATGATTTTGTAATCTTAGA
1 GATATGCAATCTT---AGATATGA-TATGTAATCTTAGA
35683781 GATTTAATTT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
38 47 0.69
41 8 0.12
42 13 0.19
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATATGTAATCTTAGATAT
Found at i:35684014 original size:23 final size:23
Alignment explanation
Indices: 35683970--35684014 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
35683960 TCTTATTTTG
* *
35683970 TTGATTTGTGTATCATTTATTTA
1 TTGATTTGTATATCATTGATTTA
**
35683993 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATCATTGATTT
35684015 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATCATTGATTTA
Found at i:35689432 original size:14 final size:15
Alignment explanation
Indices: 35689406--35689438 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
35689396 TCCCAAGCTG
35689406 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
35689421 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
35689435 GGAA
1 GGAA
35689439 AAACGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Done.