Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 44 of 126
Found at i:13099698 original size:11 final size:11
Alignment explanation
Indices: 13099682--13099733 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
13099672 AACGATCAAA
13099682 GTCAACGGCCG
1 GTCAACGGCCG
13099693 GTCAACGGCCG
1 GTCAACGGCCG
* * *
13099704 ATCAATGGTCG
1 GTCAACGGCCG
*
13099715 GTCAACGGCTG
1 GTCAACGGCCG
13099726 GTCAACGG
1 GTCAACGG
13099734 TTTGACTTGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.15
Consensus pattern (11 bp):
GTCAACGGCCG
Found at i:13099874 original size:24 final size:25
Alignment explanation
Indices: 13099840--13099887 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
13099830 TAAAAAAAAG
*
13099840 GTTAATGGGTTTTAA-AGGGTTTGT
1 GTTAATGGGTTTTAATAGGATTTGT
*
13099864 GTTAATTGGTTTTAATAGGATTTG
1 GTTAATGGGTTTTAATAGGATTTG
13099888 GGATTAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.23, C:0.00, G:0.29, T:0.48
Consensus pattern (25 bp):
GTTAATGGGTTTTAATAGGATTTGT
Found at i:13102779 original size:29 final size:31
Alignment explanation
Indices: 13102736--13102800 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
13102726 GCAAATGCTT
13102736 TTAAAATTA-TCTTTTAAAAT-ATAAAATTA
1 TTAAAATTATTCTTTTAAAATAATAAAATTA
*
13102765 TTAAAATTATTTTTTTAAAATAATAAAATTA
1 TTAAAATTATTCTTTTAAAATAATAAAATTA
13102796 TTAAA
1 TTAAA
13102801 TAATTTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
29 9 0.27
30 10 0.30
31 14 0.42
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (31 bp):
TTAAAATTATTCTTTTAAAATAATAAAATTA
Found at i:13102807 original size:30 final size:30
Alignment explanation
Indices: 13102747--13102807 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
13102737 TAAAATTATC
*
13102747 TTTTAAAATATAAAATTATTAAAATTATTT
1 TTTTAAAATATAAAATTATTAAAATAATTT
13102777 TTTTAAAATAATAAAATTATT-AAATAATTT
1 TTTTAAAAT-ATAAAATTATTAAAATAATTT
13102807 T
1 T
13102808 CAACAAGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTTAAAATATAAAATTATTAAAATAATTT
Found at i:13103044 original size:28 final size:28
Alignment explanation
Indices: 13103004--13103059 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
13102994 GTATAGGTGA
13103004 AGGTTTTGGAATTCGTCCCCATCTTCTT
1 AGGTTTTGGAATTCGTCCCCATCTTCTT
13103032 AGGTTTTGGAATTCGTCCCCATCTTCTT
1 AGGTTTTGGAATTCGTCCCCATCTTCTT
13103060 CCCCAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.43
Consensus pattern (28 bp):
AGGTTTTGGAATTCGTCCCCATCTTCTT
Found at i:13103996 original size:21 final size:22
Alignment explanation
Indices: 13103967--13104016 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
13103957 TTCAAAATTT
*
13103967 TTTTTAAAAATAATTTT-AT-A
1 TTTTAAAAAATAATTTTAATAA
13103987 TTTTAAAAAATAATTTTAATAA
1 TTTTAAAAAATAATTTTAATAA
13104009 TTTTAAAA
1 TTTTAAAA
13104017 TCATTTGCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 16 0.59
21 2 0.07
22 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTTTAAAAAATAATTTTAATAA
Found at i:13107069 original size:30 final size:29
Alignment explanation
Indices: 13107033--13107104 Score: 117
Period size: 29 Copynumber: 2.4 Consensus size: 29
13107023 ATTAAAATTA
13107033 TTTAATAATTTTATTACTTAAAAAAATAAT
1 TTTAATAATTTTA-TACTTAAAAAAATAAT
* *
13107063 TTTAATAATTTTATATTTTAAAAAATAAT
1 TTTAATAATTTTATACTTAAAAAAATAAT
13107092 TTTAATAATTTTA
1 TTTAATAATTTTA
13107105 AAATCATTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTAATAATTTTATACTTAAAAAAATAAT
Found at i:13107091 original size:20 final size:22
Alignment explanation
Indices: 13107066--13107107 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
13107056 AAATAATTTT
13107066 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
13107086 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
13107108 TCATTTATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Found at i:13107108 original size:20 final size:20
Alignment explanation
Indices: 13107057--13107113 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
13107047 TACTTAAAAA
13107057 AATAATTTT--AATAATTTT
1 AATAATTTTAAAATAATTTT
13107075 -AT-ATTTTAAAAAATAATTTT
1 AATAATTTT--AAAATAATTTT
*
13107095 AATAATTTTAAAATCATTT
1 AATAATTTTAAAATAATTT
13107114 ATTGACGTGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 5 0.16
17 2 0.06
20 18 0.56
21 2 0.06
22 5 0.16
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
AATAATTTTAAAATAATTTT
Found at i:13107992 original size:12 final size:12
Alignment explanation
Indices: 13107954--13107992 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
13107944 GGGATACAGA
*
13107954 TATTAAATTTTT
1 TATTAATTTTTT
* *
13107966 TAATAATTTTCT
1 TATTAATTTTTT
13107978 TATTAATTTTTT
1 TATTAATTTTTT
13107990 TAT
1 TAT
13107993 ACAAAAGGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTAATTTTTT
Found at i:13111321 original size:31 final size:31
Alignment explanation
Indices: 13111286--13111361 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
13111276 ATTTTTTAAA
* *
13111286 AATGTGTACAATTGAATCAAAATCAAAGTTT
1 AATGTGCACAATTGAATCAAAACCAAAGTTT
* * *
13111317 AATGTGCACATTTGAATTACAACCAAAGTTT
1 AATGTGCACAATTGAATCAAAACCAAAGTTT
* * *
13111348 CATGTACATAATTG
1 AATGTGCACAATTG
13111362 CACCAAATCA
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (31 bp):
AATGTGCACAATTGAATCAAAACCAAAGTTT
Found at i:13114802 original size:17 final size:17
Alignment explanation
Indices: 13114769--13114837 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 17
13114759 TGTCACTATG
13114769 TATTTTAAA-ATTAAAAAA
1 TATTTTAAATA-T-AAAAA
*
13114787 TATATTAAATATAAAATA
1 TATTTTAAATATAAAA-A
*
13114805 TAATTTTTAATA-AAAAA
1 T-ATTTTAAATATAAAAA
*
13114822 TATTTTAAAGATAAAA
1 TATTTTAAATATAAAA
13114838 TGTGAATTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
16 8 0.19
17 10 0.24
18 15 0.36
19 9 0.21
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (17 bp):
TATTTTAAATATAAAAA
Found at i:13114965 original size:13 final size:13
Alignment explanation
Indices: 13114947--13114971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13114937 TTTTAATTTA
13114947 ATATATAAATAAT
1 ATATATAAATAAT
13114960 ATATATAAATAA
1 ATATATAAATAA
13114972 AAATATTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATATATAAATAAT
Found at i:13119575 original size:21 final size:21
Alignment explanation
Indices: 13119549--13119591 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
13119539 ATGTATTCAT
13119549 TCCTTATATAGAAATGTTTAG
1 TCCTTATATAGAAATGTTTAG
13119570 TCCTTATATAGAAATGTTTAG
1 TCCTTATATAGAAATGTTTAG
13119591 T
1 T
13119592 GACTTGTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (21 bp):
TCCTTATATAGAAATGTTTAG
Found at i:13119947 original size:31 final size:31
Alignment explanation
Indices: 13119911--13119978 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
13119901 CCCTAAAATG
*
13119911 AAAAATTTTCATTTAGGCCGTTTAAAAA-TAT
1 AAAAATTTTCATTTAAGCC-TTTAAAAATTAT
* * *
13119942 TAAAATTTTGATTTAATCCTTTAAAAATTAT
1 AAAAATTTTCATTTAAGCCTTTAAAAATTAT
13119973 AAAAAT
1 AAAAAT
13119979 GTAGGTTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (31 bp):
AAAAATTTTCATTTAAGCCTTTAAAAATTAT
Found at i:13122757 original size:21 final size:21
Alignment explanation
Indices: 13122732--13122780 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
13122722 CCAAACATGG
*
13122732 CCGTGTGGTTA-TCCCACATGC
1 CCGTGTGGTTACT-CCACACGC
*
13122753 TCGTGTGGTTACTCCACACGC
1 CCGTGTGGTTACTCCACACGC
13122774 CCGTGTG
1 CCGTGTG
13122781 CTCATCCGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.12, C:0.33, G:0.27, T:0.29
Consensus pattern (21 bp):
CCGTGTGGTTACTCCACACGC
Found at i:13122818 original size:42 final size:42
Alignment explanation
Indices: 13122767--13122875 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
13122757 GTGGTTACTC
*
13122767 CACACGCCCGTGTGCTCAT-CCGTGTAACTCATTAACTT-GGCT
1 CACATGCCCGTGT-CT-ATCCCGTGTAACTCATTAACTTGGGCT
* *
13122809 CACATGCCCGTGTCTTTGCCCGTGTAACTCATTGACTTGGGCT
1 CACATGCCCGTGTCTAT-CCCGTGTAACTCATTAACTTGGGCT
** *
13122852 -ACATGCTTGTGTCTTAGCCCGTGT
1 CACATGCCCGTGTC-TATCCCGTGT
13122876 GTTAGCTCAT
Statistics
Matches: 56, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
40 1 0.02
41 2 0.04
42 48 0.86
43 5 0.09
ACGTcount: A:0.16, C:0.30, G:0.22, T:0.32
Consensus pattern (42 bp):
CACATGCCCGTGTCTATCCCGTGTAACTCATTAACTTGGGCT
Found at i:13124537 original size:14 final size:15
Alignment explanation
Indices: 13124518--13124546 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13124508 ATCCTTTTCA
13124518 AAAGTTAAT-CCCTT
1 AAAGTTAATACCCTT
13124532 AAAGTTAATACCCTT
1 AAAGTTAATACCCTT
13124547 TTCAACCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (15 bp):
AAAGTTAATACCCTT
Found at i:13124615 original size:31 final size:31
Alignment explanation
Indices: 13124574--13124657 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 31
13124564 ATATCTTTTA
*
13124574 GGATACAACCTTTCCAATAGATATCCATTTC
1 GGATATAACCTTTCCAATAGATATCCATTTC
* *
13124605 GGATATAACCTTTTCAATATATATATATCCATTTC
1 GGATATAACC-TTTC--CA-ATAGATATCCATTTC
*
13124640 GGATATAACCTTTTCAAT
1 GGATATAACCTTTCCAAT
13124658 TTTCGATATT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
31 11 0.25
32 5 0.11
34 4 0.09
35 24 0.55
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.38
Consensus pattern (31 bp):
GGATATAACCTTTCCAATAGATATCCATTTC
Found at i:13129836 original size:21 final size:21
Alignment explanation
Indices: 13129793--13129836 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
13129783 ATAAATACGA
* *
13129793 TATTTTTAATTTTTGTTCATT
1 TATTTTTAATCTTTATTCATT
* *
13129814 TATTTTTTATCTTTATTCGTT
1 TATTTTTAATCTTTATTCATT
13129835 TA
1 TA
13129837 ATTTGTTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (21 bp):
TATTTTTAATCTTTATTCATT
Found at i:13141411 original size:15 final size:15
Alignment explanation
Indices: 13141391--13141423 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
13141381 ACTGCTCCTA
*
13141391 CTTTTTCTTCTTCTT
1 CTTTTTCTACTTCTT
13141406 CTTTTTCTACTTCTT
1 CTTTTTCTACTTCTT
13141421 CTT
1 CTT
13141424 CTGAATATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.03, C:0.27, G:0.00, T:0.70
Consensus pattern (15 bp):
CTTTTTCTACTTCTT
Found at i:13146034 original size:23 final size:25
Alignment explanation
Indices: 13146008--13146053 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13145998 CCAATTAAGG
13146008 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
13146031 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
13146054 TGGATTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:13154149 original size:23 final size:23
Alignment explanation
Indices: 13154119--13154167 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
13154109 ACTAATCTCG
*
13154119 TTTAAAATATAATTAT-ATATTAT
1 TTTAAAATAGAATTATAATA-TAT
13154142 TTTAAAATAGAATTATAATATAT
1 TTTAAAATAGAATTATAATATAT
13154165 TTT
1 TTT
13154168 GACCTACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.88
24 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
TTTAAAATAGAATTATAATATAT
Found at i:13157171 original size:3 final size:3
Alignment explanation
Indices: 13157163--13157197 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
13157153 CCTTCCTCTT
13157163 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
13157198 CCATCACTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13162254 original size:21 final size:21
Alignment explanation
Indices: 13162228--13162278 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
13162218 GGGAAGTTTA
13162228 TACCGATACAAG-TATGACTAC
1 TACCGATAC-AGTTATGACTAC
* *
13162249 TACCGATACAGTTATTACTTC
1 TACCGATACAGTTATGACTAC
13162270 TACCGATAC
1 TACCGATAC
13162279 TACAAACTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.29
Consensus pattern (21 bp):
TACCGATACAGTTATGACTAC
Found at i:13170020 original size:17 final size:17
Alignment explanation
Indices: 13169998--13170036 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
13169988 AGGTGGAGAA
**
13169998 CTTGTTCGTTGAGAATT
1 CTTGTTCGCAGAGAATT
13170015 CTTGTTCGCAGAGAATT
1 CTTGTTCGCAGAGAATT
13170032 CTTGT
1 CTTGT
13170037 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (17 bp):
CTTGTTCGCAGAGAATT
Found at i:13174769 original size:23 final size:24
Alignment explanation
Indices: 13174717--13174769 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
13174707 TTAATGGTCG
*
13174717 AAATT-AAATTGTAATTTTTACAA
1 AAATTAAAAATGTAATTTTTACAA
*
13174740 TAA-TAAAAATGTAATTTTTA-AA
1 AAATTAAAAATGTAATTTTTACAA
13174762 AAATTAAA
1 AAATTAAA
13174770 TCAAAATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATTAAAAATGTAATTTTTACAA
Found at i:13178551 original size:21 final size:22
Alignment explanation
Indices: 13178514--13178556 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
13178504 ACTTTCATCA
*
13178514 TTAAGCTTTAATTAACC-ATTT
1 TTAACCTTTAATTAACCTATTT
13178535 TTAACCTTT-ATTAAACCTATTT
1 TTAACCTTTAATT-AACCTATTT
13178557 ATAATCAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 12 0.63
22 4 0.21
ACGTcount: A:0.33, C:0.16, G:0.02, T:0.49
Consensus pattern (22 bp):
TTAACCTTTAATTAACCTATTT
Found at i:13178933 original size:25 final size:25
Alignment explanation
Indices: 13178904--13179109 Score: 258
Period size: 25 Copynumber: 8.4 Consensus size: 25
13178894 TTACACATTA
*
13178904 ATCACATTAACACATATAAGCATTT
1 ATCACATTAACACATATAAGCATAT
* *
13178929 ATCACATTAACACCTATAAGCATGT
1 ATCACATTAACACATATAAGCATAT
*
13178954 ATCACATTAACACATATAAGCGTAT
1 ATCACATTAACACATATAAGCATAT
* * *
13178979 ATCACGTTAACACCTATAAGCATGT
1 ATCACATTAACACATATAAGCATAT
* *
13179004 ATCACGTTAACACATATAAGCGTAT
1 ATCACATTAACACATATAAGCATAT
* *
13179029 ATCACGTTAACAC--ATAAGCGTAT
1 ATCACATTAACACATATAAGCATAT
* *
13179052 ATCACGTTAACAC--ATAAGCGTAT
1 ATCACATTAACACATATAAGCATAT
*
13179075 ATCACATTAACACATATACGCATAT
1 ATCACATTAACACATATAAGCATAT
13179100 ATCACATTAA
1 ATCACATTAA
13179110 TCAATAGTCA
Statistics
Matches: 164, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
23 45 0.27
25 119 0.73
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (25 bp):
ATCACATTAACACATATAAGCATAT
Found at i:13178963 original size:50 final size:50
Alignment explanation
Indices: 13178904--13179109 Score: 285
Period size: 50 Copynumber: 4.2 Consensus size: 50
13178894 TTACACATTA
* * *
13178904 ATCACATTAACACATATAAGCATTTATCACATTAACACCTATAAGCATGT
1 ATCACATTAACACATATAAGCGTATATCACATTAACACCTATAAGCATAT
* *
13178954 ATCACATTAACACATATAAGCGTATATCACGTTAACACCTATAAGCATGT
1 ATCACATTAACACATATAAGCGTATATCACATTAACACCTATAAGCATAT
* * *
13179004 ATCACGTTAACACATATAAGCGTATATCACGTTAACA-C-ATAAGCGTAT
1 ATCACATTAACACATATAAGCGTATATCACATTAACACCTATAAGCATAT
* * *
13179052 ATCACGTTAACAC--ATAAGCGTATATCACATTAACACATATACGCATAT
1 ATCACATTAACACATATAAGCGTATATCACATTAACACCTATAAGCATAT
13179100 ATCACATTAA
1 ATCACATTAA
13179110 TCAATAGTCA
Statistics
Matches: 143, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
46 21 0.15
48 38 0.27
49 1 0.01
50 83 0.58
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (50 bp):
ATCACATTAACACATATAAGCGTATATCACATTAACACCTATAAGCATAT
Found at i:13179163 original size:25 final size:25
Alignment explanation
Indices: 13179117--13179174 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
13179107 TAATCAATAG
* *
13179117 TCACATTAACATATACAAGCATATA
1 TCACATTAACACATACAAGCATAAA
***
13179142 TCACATTAACACATATGGGCATAAA
1 TCACATTAACACATACAAGCATAAA
13179167 TCACATTA
1 TCACATTA
13179175 CTCTATAGTC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.28
Consensus pattern (25 bp):
TCACATTAACACATACAAGCATAAA
Found at i:13181560 original size:5 final size:5
Alignment explanation
Indices: 13181552--13181596 Score: 65
Period size: 5 Copynumber: 8.8 Consensus size: 5
13181542 TTTAGTTTTA
13181552 TATTT TATTT TATTT TATTT GT-TTT TACTTT TATTT TATTT TATT
1 TATTT TATTT TATTT TATTT -TATTT TA-TTT TATTT TATTT TATT
13181597 ATGCATTGTA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
4 1 0.03
5 30 0.81
6 6 0.16
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:13181583 original size:26 final size:26
Alignment explanation
Indices: 13181536--13181614 Score: 88
Period size: 26 Copynumber: 2.9 Consensus size: 26
13181526 AACCAAAGTG
*
13181536 ATTTCATTTAGTTTTATA-TTTTATTTT
1 ATTTTATTT-GTTTT-TACTTTTATTTT
13181563 ATTTTATTTGTTTTTACTTTTATTTT
1 ATTTTATTTGTTTTTACTTTTATTTT
* *
13181589 ATTTTATTATGCATTGTACTTTTATT
1 ATTTTATT-TG-TTTTTACTTTTATT
13181615 GTTTCGTCAG
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.04
26 22 0.48
27 10 0.22
28 12 0.26
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.70
Consensus pattern (26 bp):
ATTTTATTTGTTTTTACTTTTATTTT
Found at i:13181584 original size:21 final size:20
Alignment explanation
Indices: 13181554--13181592 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
13181544 TAGTTTTATA
13181554 TTTTATTTTATTTTATTTGT
1 TTTTATTTTATTTTATTTGT
13181574 TTTTACTTTTATTTTATTT
1 TTTTA-TTTTATTTTATTT
13181593 TATTATGCAT
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:0.15, C:0.03, G:0.03, T:0.79
Consensus pattern (20 bp):
TTTTATTTTATTTTATTTGT
Found at i:13186103 original size:31 final size:31
Alignment explanation
Indices: 13186068--13186128 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
13186058 TCAAAAATCT
13186068 AAAAGTATAAGAAATAAAATTGATCAAATTG
1 AAAAGTATAAGAAATAAAATTGATCAAATTG
* * * * *
13186099 AAAAGTGTATGGACTAAAATTGATTAAATT
1 AAAAGTATAAGAAATAAAATTGATCAAATT
13186129 AAAGTGCAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.52, C:0.03, G:0.15, T:0.30
Consensus pattern (31 bp):
AAAAGTATAAGAAATAAAATTGATCAAATTG
Found at i:13193399 original size:146 final size:146
Alignment explanation
Indices: 13193135--13193427 Score: 586
Period size: 146 Copynumber: 2.0 Consensus size: 146
13193125 ACTCTTCGCA
13193135 GAATTCTTCAAACTTCTCTGAGGTGTACTCTGCCTTATTGTCTGATCTTACCATTTTGAGCTTGC
1 GAATTCTTCAAACTTCTCTGAGGTGTACTCTGCCTTATTGTCTGATCTTACCATTTTGAGCTTGC
13193200 AGTCACTTTGATTCTCAACCATGACTTTAAATTTGAAGAAGATTTCAACCACCTACTTTCATATA
66 AGTCACTTTGATTCTCAACCATGACTTTAAATTTGAAGAAGATTTCAACCACCTACTTTCATATA
13193265 GTGAACTTGTTTCCAT
131 GTGAACTTGTTTCCAT
13193281 GAATTCTTCAAACTTCTCTGAGGTGTACTCTGCCTTATTGTCTGATCTTACCATTTTGAGCTTGC
1 GAATTCTTCAAACTTCTCTGAGGTGTACTCTGCCTTATTGTCTGATCTTACCATTTTGAGCTTGC
13193346 AGTCACTTTGATTCTCAACCATGACTTTAAATTTGAAGAAGATTTCAACCACCTACTTTCATATA
66 AGTCACTTTGATTCTCAACCATGACTTTAAATTTGAAGAAGATTTCAACCACCTACTTTCATATA
13193411 GTGAACTTGTTTCCAT
131 GTGAACTTGTTTCCAT
13193427 G
1 G
13193428 GGTCCGCAAA
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 147 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (146 bp):
GAATTCTTCAAACTTCTCTGAGGTGTACTCTGCCTTATTGTCTGATCTTACCATTTTGAGCTTGC
AGTCACTTTGATTCTCAACCATGACTTTAAATTTGAAGAAGATTTCAACCACCTACTTTCATATA
GTGAACTTGTTTCCAT
Found at i:13196776 original size:2 final size:2
Alignment explanation
Indices: 13196771--13196798 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13196761 TATATATATA
13196771 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
13196799 AGGAGAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:13200138 original size:18 final size:17
Alignment explanation
Indices: 13200115--13200173 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
13200105 TGGATTGTTT
13200115 TTATGTTTAAATCGATTA
1 TTATGTTTAAATC-ATTA
* * *
13200133 TTATGTTGAAAT-ACTG
1 TTATGTTTAAATCATTA
13200149 TT-TGTTTTAAATCAATTA
1 TTATG-TTTAAATC-ATTA
13200167 TTATGTT
1 TTATGTT
13200174 GGAATATTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 8
0.69 0.13 0.18
Matches are distributed among these distances:
15 2 0.06
16 10 0.32
18 17 0.55
19 2 0.06
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.53
Consensus pattern (17 bp):
TTATGTTTAAATCATTA
Found at i:13200236 original size:34 final size:33
Alignment explanation
Indices: 13200120--13200233 Score: 147
Period size: 34 Copynumber: 3.4 Consensus size: 33
13200110 TGTTTTTATG
* * *
13200120 TTTAAATCGATTATTATGTTGAAATACTGTTTGT
1 TTTAAATCGATTATTATGTTG-AATATTGCTTCT
*
13200154 TTTAAATCAATTATTATGTTGGAATATTGCTTCT
1 TTTAAATCGATTATTATGTT-GAATATTGCTTCT
*
13200188 TTTAAATCGATTGTTATGGTTGAATATTGCTTCT
1 TTTAAATCGATTATTAT-GTTGAATATTGCTTCT
*
13200222 TTTGAATCGATT
1 TTTAAATCGATT
13200234 GTTTATATGT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
34 67 0.94
35 4 0.06
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (33 bp):
TTTAAATCGATTATTATGTTGAATATTGCTTCT
Found at i:13200276 original size:55 final size:55
Alignment explanation
Indices: 13200209--13200313 Score: 156
Period size: 55 Copynumber: 1.9 Consensus size: 55
13200199 TGTTATGGTT
* ** *
13200209 GAATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATGGACTGTTACATTG
1 GAATATTACTTCTTTTGAATAAATTGCTTATATGTTTAAATGGACTGTTACATTG
* *
13200264 GAATATTACTTCTTTTGAATAAATTGCTTATATGTTTAAATTGATTGTTA
1 GAATATTACTTCTTTTGAATAAATTGCTTATATGTTTAAATGGACTGTTA
13200314 AGTTGCAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 44 1.00
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.49
Consensus pattern (55 bp):
GAATATTACTTCTTTTGAATAAATTGCTTATATGTTTAAATGGACTGTTACATTG
Found at i:13201394 original size:3 final size:3
Alignment explanation
Indices: 13201386--13201410 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
13201376 TTTCGAAAAC
13201386 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
13201411 CTCTACTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:13205951 original size:17 final size:17
Alignment explanation
Indices: 13205899--13205958 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
13205889 TTCTTATCCT
13205899 TGGCAGACAATATCGCC
1 TGGCAGACAATATCGCC
** * *
13205916 TGGTGGACAGTA-CAACC
1 TGGCAGACAATATC-GCC
13205933 TGGCAGACAATATCGCC
1 TGGCAGACAATATCGCC
*
13205950 TGACAGACA
1 TGGCAGACA
13205959 TGATTCGCAA
Statistics
Matches: 32, Mismatches: 9, Indels: 4
0.71 0.20 0.09
Matches are distributed among these distances:
16 1 0.03
17 30 0.94
18 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.17
Consensus pattern (17 bp):
TGGCAGACAATATCGCC
Found at i:13210553 original size:34 final size:34
Alignment explanation
Indices: 13210508--13210602 Score: 86
Period size: 34 Copynumber: 2.8 Consensus size: 34
13210498 CATTGTTAAT
* * * *
13210508 ATCGTCAGTTTATCTAACTAGTGTTGGGC-ACAC
1 ATCGTCGGTTTATCTAACTAGCGCTGGGCGAAAC
*
13210541 ATTCGTCGGTTTAGCTTAA-TAGCGCTGGGCGTAAAC
1 A-TCGTCGGTTTATC-TAACTAGCGCTGGGCG-AAAC
* *
13210577 ATCGTTGGTTTATCTAACTAGAGCTG
1 ATCGTCGGTTTATCTAACTAGCGCTG
13210603 AGCTCACAGG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
33 1 0.02
34 23 0.47
35 21 0.43
36 4 0.08
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (34 bp):
ATCGTCGGTTTATCTAACTAGCGCTGGGCGAAAC
Found at i:13212491 original size:20 final size:21
Alignment explanation
Indices: 13212455--13212504 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
13212445 ATTGACATGG
*
13212455 TTTATATTAAGTGTAAATA-GA
1 TTTA-ATTAAGTGTAAAAATGA
13212476 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
13212497 -TTAATTAA
1 TTTAATTAA
13212505 AGCTTAATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:13219715 original size:20 final size:21
Alignment explanation
Indices: 13219679--13219728 Score: 52
Period size: 20 Copynumber: 2.4 Consensus size: 21
13219669 ATTGGCATGG
*
13219679 TTTATATTAAGTGTAAATA-GA
1 TTTA-ATTAAGTGTAAAAATGA
13219700 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
13219721 -TTAATTAA
1 TTTAATTAA
13219729 AGCTTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:13226490 original size:177 final size:177
Alignment explanation
Indices: 13226194--13226553 Score: 684
Period size: 177 Copynumber: 2.0 Consensus size: 177
13226184 CAACATTACT
13226194 TTGTTTGGTTGTTCGTTTTTGTGTTCTTTGCTAGTATATCAGACAATGTTGTTTCAATTGGTATT
1 TTGTTTGGTTGTTCGTTTTTGTGTTCTTTGCTAGTATATCAGACAATGTTGTTTCAATTGGTATT
* * *
13226259 ACATTTTAGTCATTTGCTTATATTCAACCATTGCTTTAATTTGTTGAAATAAGTGGCAGATGACA
66 ACATTTTAGTCATATGCTTATATTAAACCATCGCTTTAATTTGTTGAAATAAGTGGCAGATGACA
13226324 ATAACTAACAATCAAGCTTCAGTTGCTTGGCTGCTACAATTTTCAAC
131 ATAACTAACAATCAAGCTTCAGTTGCTTGGCTGCTACAATTTTCAAC
13226371 TTGTTTGGTTGTTCGTTTTTGTGTTCTTTGCTAGTATATCAGACAATGTTGTTTCAATTGGTATT
1 TTGTTTGGTTGTTCGTTTTTGTGTTCTTTGCTAGTATATCAGACAATGTTGTTTCAATTGGTATT
13226436 ACATTTTAGTCATATGCTTATATTAAACCATCGCTTTAATTTGTTGAAATAAGTGGCAGATGACA
66 ACATTTTAGTCATATGCTTATATTAAACCATCGCTTTAATTTGTTGAAATAAGTGGCAGATGACA
*
13226501 ATAACTAACGATCAAGCTTCAGTTGCTTGGCTGCTACAATTTTCAAC
131 ATAACTAACAATCAAGCTTCAGTTGCTTGGCTGCTACAATTTTCAAC
13226548 TTGTTT
1 TTGTTT
13226554 ATTTAATGTT
Statistics
Matches: 179, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
177 179 1.00
ACGTcount: A:0.25, C:0.14, G:0.17, T:0.43
Consensus pattern (177 bp):
TTGTTTGGTTGTTCGTTTTTGTGTTCTTTGCTAGTATATCAGACAATGTTGTTTCAATTGGTATT
ACATTTTAGTCATATGCTTATATTAAACCATCGCTTTAATTTGTTGAAATAAGTGGCAGATGACA
ATAACTAACAATCAAGCTTCAGTTGCTTGGCTGCTACAATTTTCAAC
Found at i:13234243 original size:15 final size:15
Alignment explanation
Indices: 13234205--13234245 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
13234195 AGAGAGAATA
*
13234205 GAGAAGAAAGAGACT
1 GAGAAGAACGAGACT
13234220 GAGAAGAACGAGACT
1 GAGAAGAACGAGACT
13234235 GAGAAGAACGA
1 GAGAAGAACGA
13234246 TATTGATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.51, C:0.10, G:0.34, T:0.05
Consensus pattern (15 bp):
GAGAAGAACGAGACT
Found at i:13238614 original size:42 final size:42
Alignment explanation
Indices: 13238567--13238650 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
13238557 TATATTGTTT
*
13238567 TGTAACATCCGCGTTATTGAACCGGAGTTGGAACAGTAATAG
1 TGTAACATCCGCGTGATTGAACCGGAGTTGGAACAGTAATAG
* * * * *
13238609 TGTAACATCTGCGTGCTTGAATCGGATTTGGAACAGTGATAG
1 TGTAACATCCGCGTGATTGAACCGGAGTTGGAACAGTAATAG
13238651 AGTACAATTG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (42 bp):
TGTAACATCCGCGTGATTGAACCGGAGTTGGAACAGTAATAG
Found at i:13240548 original size:6 final size:6
Alignment explanation
Indices: 13240541--13240575 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
13240531 TGATCAAAAG
*
13240541 TGAAAG TGAAAC TGAAAC TGAAAC TGAAAC TGAAA
1 TGAAAC TGAAAC TGAAAC TGAAAC TGAAAC TGAAA
13240576 GTGATATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.51, C:0.11, G:0.20, T:0.17
Consensus pattern (6 bp):
TGAAAC
Found at i:13241567 original size:15 final size:15
Alignment explanation
Indices: 13241547--13241579 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
13241537 CATTCCATAT
13241547 ATTTATTT-TTTTATC
1 ATTTATTTATTTT-TC
13241562 ATTTATTTATTTTTC
1 ATTTATTTATTTTTC
13241577 ATT
1 ATT
13241580 CTCTTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (15 bp):
ATTTATTTATTTTTC
Found at i:13243620 original size:21 final size:21
Alignment explanation
Indices: 13243596--13243653 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
13243586 TAAAAGTAAG
*
13243596 ACTTGTTTCGGTAGAA-TAGTC
1 ACTTGTATCGGTAGAACT-GTC
* *
13243617 ACTTGTATCGCTAAAACTGTC
1 ACTTGTATCGGTAGAACTGTC
13243638 ACTTGTATCGGTAGAA
1 ACTTGTATCGGTAGAA
13243654 GGCTGCACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 30 0.97
22 1 0.03
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACTGTC
Found at i:13247383 original size:27 final size:26
Alignment explanation
Indices: 13247353--13247405 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
13247343 ATTAAAACCC
13247353 AAATTATTAATGAAAT-ATTTTATATTT
1 AAATTATTAA--AAATAATTTTATATTT
*
13247380 AAATTATTAAATATAATTTTATATTT
1 AAATTATTAAAAATAATTTTATATTT
13247406 TATTATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 11 0.46
27 10 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
AAATTATTAAAAATAATTTTATATTT
Found at i:13263509 original size:14 final size:14
Alignment explanation
Indices: 13263490--13263524 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
13263480 GTGTGCAAAT
13263490 CTGACATAATTGCA
1 CTGACATAATTGCA
13263504 CTGACATAATTGCA
1 CTGACATAATTGCA
13263518 CTGACAT
1 CTGACAT
13263525 CTTTACTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (14 bp):
CTGACATAATTGCA
Found at i:13267076 original size:59 final size:60
Alignment explanation
Indices: 13266978--13267094 Score: 200
Period size: 59 Copynumber: 2.0 Consensus size: 60
13266968 ACTATAAAAG
* *
13266978 GAGGCATCTCCCTCCTCATTGTAAATCACTTCATTGAGTAATTGAATTTTTTAGAGTAAA
1 GAGGCATCTCCCTCCTCATTGTAAATCACTTCATTGAGTAATTGAATTCTTGAGAGTAAA
*
13267038 GAGGTATCTCCC-CCTCATTGTAAATCACTTCATTGAGTAATTGAATTCTTGAGAGTA
1 GAGGCATCTCCCTCCTCATTGTAAATCACTTCATTGAGTAATTGAATTCTTGAGAGTA
13267095 TTCACTCAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
59 43 0.80
60 11 0.20
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (60 bp):
GAGGCATCTCCCTCCTCATTGTAAATCACTTCATTGAGTAATTGAATTCTTGAGAGTAAA
Found at i:13268536 original size:46 final size:46
Alignment explanation
Indices: 13268469--13268567 Score: 198
Period size: 46 Copynumber: 2.2 Consensus size: 46
13268459 GTTTCTAAAA
13268469 ATCCTTATCTTCATTCTCTTAACTTTACATATGCTGAAGGACTAAG
1 ATCCTTATCTTCATTCTCTTAACTTTACATATGCTGAAGGACTAAG
13268515 ATCCTTATCTTCATTCTCTTAACTTTACATATGCTGAAGGACTAAG
1 ATCCTTATCTTCATTCTCTTAACTTTACATATGCTGAAGGACTAAG
13268561 ATCCTTA
1 ATCCTTA
13268568 CCAGCTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.28, C:0.22, G:0.10, T:0.39
Consensus pattern (46 bp):
ATCCTTATCTTCATTCTCTTAACTTTACATATGCTGAAGGACTAAG
Found at i:13269510 original size:21 final size:21
Alignment explanation
Indices: 13269481--13269557 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
13269471 AATAGTGCAA
*
13269481 ACTTTTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
*
13269502 AGTTCTACCGATACAAGTGAC
1 ACTTCTACCGATACAAGTGAC
* * * ***
13269523 TCTTCTACCAAAACAAGTTTT
1 ACTTCTACCGATACAAGTGAC
13269544 ACTTCTACCGATAC
1 ACTTCTACCGATAC
13269558 TAAAAACTTC
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTGAC
Found at i:13276694 original size:29 final size:29
Alignment explanation
Indices: 13276660--13276716 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
13276650 TTCTAAAAAA
13276660 TATTTTATAA-AAAAACATATTT-TTTTTAC
1 TATTTTA-AATAAAAA-ATATTTATTTTTAC
*
13276689 TATTTTAAATATAAAATATTTATTTTTA
1 TATTTTAAATAAAAAATATTTATTTTTA
13276717 TAATATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (29 bp):
TATTTTAAATAAAAAATATTTATTTTTAC
Found at i:13282384 original size:21 final size:21
Alignment explanation
Indices: 13282351--13282390 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
13282341 ATGAACTTTA
*
13282351 ATTTTTTAAAATTTTGTATCT
1 ATTTTTTAAAATTTGGTATCT
**
13282372 ATTTTTTTTAATTTGGTAT
1 ATTTTTTAAAATTTGGTAT
13282391 TTGAATGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (21 bp):
ATTTTTTAAAATTTGGTATCT
Found at i:13282393 original size:27 final size:27
Alignment explanation
Indices: 13282363--13282414 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
13282353 TTTTTAAAAT
* *
13282363 TTTGTATCTATTTTTTTTAATTTGGTA
1 TTTGAATCAATTTTTTTTAATTTGGTA
*
13282390 TTTGAATGAATTTTTTTTAATTTGG
1 TTTGAATCAATTTTTTTTAATTTGG
13282415 ATTAATTTTT
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:0.21, C:0.02, G:0.13, T:0.63
Consensus pattern (27 bp):
TTTGAATCAATTTTTTTTAATTTGGTA
Found at i:13286055 original size:24 final size:24
Alignment explanation
Indices: 13286016--13286061 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
13286006 CTTTGTTTCT
*
13286016 TCCTTCTCATTTTCATTTTCTTCC
1 TCCTTCTCATTTTCATCTTCTTCC
13286040 TCCTTCTC-TTTCTCATCTTCTT
1 TCCTTCTCATTT-TCATCTTCTT
13286062 GATTGACTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.07, C:0.35, G:0.00, T:0.59
Consensus pattern (24 bp):
TCCTTCTCATTTTCATCTTCTTCC
Found at i:13290174 original size:104 final size:104
Alignment explanation
Indices: 13289994--13290202 Score: 337
Period size: 104 Copynumber: 2.0 Consensus size: 104
13289984 CTGGAACGTT
* *
13289994 GCTAGCGCATTACATAAGCCAAACGGCATCGGTCGAAAAGCAAAAGTACTAAAAGGGCATGTAAA
1 GCTAGCGCATTACACAAGCCAAACGGCATCCGTCGAAAAGCAAAAGTACTAAAAGGGCATGTAAA
13290059 TGTGGTTTTTGCTTAATCTTCCGGTGCAAAAGCTATTTG
66 TGTGGTTTTTGCTTAATCTTCCGGTGCAAAAGCTATTTG
* * *
13290098 GCTAGTGCATTACACAATCCAAATGGCATCCGTCGAAAAGCAAAAGTACTAAAAGGGCATGTAAA
1 GCTAGCGCATTACACAAGCCAAACGGCATCCGTCGAAAAGCAAAAGTACTAAAAGGGCATGTAAA
* * * *
13290163 TGTGGTTTTTGCTTGATCTTCTGGTGCAATAGTTATTTG
66 TGTGGTTTTTGCTTAATCTTCCGGTGCAAAAGCTATTTG
13290202 G
1 G
13290203 TTGTATTCAG
Statistics
Matches: 96, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
104 96 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (104 bp):
GCTAGCGCATTACACAAGCCAAACGGCATCCGTCGAAAAGCAAAAGTACTAAAAGGGCATGTAAA
TGTGGTTTTTGCTTAATCTTCCGGTGCAAAAGCTATTTG
Found at i:13298394 original size:72 final size:71
Alignment explanation
Indices: 13298272--13298443 Score: 231
Period size: 72 Copynumber: 2.4 Consensus size: 71
13298262 GTTATGAAAG
* * *
13298272 TAAATATG-GGAGTTTGTTATTCATGCCATGAGACCGTAAATATGTCGATATGTTATTCATGCCA
1 TAAATATGTGG-GTATGTTATTCATGCCATGAGACAGTAAATATATCGATATGTTA-TCATGCCA
* *
13298336 TGTGATAG
64 TGTGACAA
* * * *
13298344 TAAATGTGTGGGTATGTTATTCATGTCGTGAGACAGTAAATATATGGATATGTTATCATGCCATG
1 TAAATATGTGGGTATGTTATTCATGCCATGAGACAGTAAATATATCGATATGTTATCATGCCATG
13298409 TGACAA
66 TGACAA
13298415 TAAATATGTGGGTATG-TATTCATGCCATG
1 TAAATATGTGGGTATGTTATTCATGCCATG
13298444 TGATAGTGAT
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
70 11 0.13
71 29 0.33
72 45 0.52
73 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (71 bp):
TAAATATGTGGGTATGTTATTCATGCCATGAGACAGTAAATATATCGATATGTTATCATGCCATG
TGACAA
Found at i:13298419 original size:35 final size:36
Alignment explanation
Indices: 13298270--13298446 Score: 207
Period size: 36 Copynumber: 5.0 Consensus size: 36
13298260 CTGTTATGAA
* *
13298270 AGTAAATATG-GGAGTTTGTTATTCATGCCATGAGAC
1 AGTAAATATGTGGA-TATGTTATTCATGCCATGTGAC
* * *
13298306 CGTAAATATGTCGATATGTTATTCATGCCATGTGAT
1 AGTAAATATGTGGATATGTTATTCATGCCATGTGAC
* * * * *
13298342 AGTAAATGTGTGGGTATGTTATTCATGTCGTGAGAC
1 AGTAAATATGTGGATATGTTATTCATGCCATGTGAC
*
13298378 AGTAAATATATGGATATGTTA-TCATGCCATGTGAC
1 AGTAAATATGTGGATATGTTATTCATGCCATGTGAC
* *
13298413 AATAAATATGTGGGTATG-TATTCATGCCATGTGA
1 AGTAAATATGTGGATATGTTATTCATGCCATGTGA
13298447 TAGTGATTAT
Statistics
Matches: 117, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
34 2 0.02
35 39 0.33
36 74 0.63
37 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.36
Consensus pattern (36 bp):
AGTAAATATGTGGATATGTTATTCATGCCATGTGAC
Found at i:13299039 original size:23 final size:23
Alignment explanation
Indices: 13298936--13299059 Score: 124
Period size: 23 Copynumber: 5.4 Consensus size: 23
13298926 ATTAATGTGC
** **
13298936 AATGTGATAAATGCTTAAATTTT
1 AATGTGATTTATGCTTAAAAGTT
* *
13298959 AATATCATTTATGCTTAAAAGTT
1 AATGTGATTTATGCTTAAAAGTT
* *
13298982 AATGTGATTTATACTTAAAAATT
1 AATGTGATTTATGCTTAAAAGTT
13299005 AATGTGATTTATGCTTAAAAGTT
1 AATGTGATTTATGCTTAAAAGTT
* * **
13299028 AA-GAAGACTTATGCTTAAGTGTT
1 AATG-TGATTTATGCTTAAAAGTT
13299051 AATGTGATT
1 AATGTGATT
13299060 AATGTGTTAA
Statistics
Matches: 81, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
22 1 0.01
23 79 0.98
24 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.42
Consensus pattern (23 bp):
AATGTGATTTATGCTTAAAAGTT
Found at i:13309680 original size:22 final size:22
Alignment explanation
Indices: 13309639--13309680 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
13309629 TGCATTAATG
* *
13309639 AACGGAGAGCACCAAGGTGCTA
1 AACGAAGAGCACAAAGGTGCTA
*
13309661 AACGAAGAGCACAAATGTGC
1 AACGAAGAGCACAAAGGTGC
13309681 AAAATGGATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.40, C:0.21, G:0.29, T:0.10
Consensus pattern (22 bp):
AACGAAGAGCACAAAGGTGCTA
Found at i:13319649 original size:24 final size:24
Alignment explanation
Indices: 13319613--13319671 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
13319603 TTAAACTTTG
*
13319613 TCTGGGCTCGTAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCAAATCAT
*
13319637 TCTTGGCTCGTAAGAGCAAATCAT
1 TCTGGGCTCGTAAGAGCAAATCAT
13319661 TCTGGGCTCGT
1 TCTGGGCTCGT
13319672 GTTGGCTAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCAAATCAT
Found at i:13324910 original size:21 final size:20
Alignment explanation
Indices: 13324883--13324937 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
13324873 TACTAAAACA
13324883 TCACAAAGTTGTAAAAAAAG
1 TCACAAAGTTGTAAAAAAAG
* * *
13324903 TCAGCAAATTTGTAAGAAAAT
1 TCA-CAAAGTTGTAAAAAAAG
*
13324924 TTACAAAGTTGTAA
1 TCACAAAGTTGTAA
13324938 GAAATTAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 13 0.45
21 16 0.55
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.27
Consensus pattern (20 bp):
TCACAAAGTTGTAAAAAAAG
Found at i:13324935 original size:20 final size:20
Alignment explanation
Indices: 13324883--13324941 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
13324873 TACTAAAACA
*
13324883 TCACAAAGTTGTAAAAAAAG
1 TCACAAAGTTGTAAGAAAAG
* *
13324903 TCAGCAAATTTGTAAGAAAAT
1 TCA-CAAAGTTGTAAGAAAAG
*
13324924 TTACAAAGTTGTAAGAAA
1 TCACAAAGTTGTAAGAAA
13324942 TTAGATAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.25
Consensus pattern (20 bp):
TCACAAAGTTGTAAGAAAAG
Found at i:13335718 original size:21 final size:20
Alignment explanation
Indices: 13335694--13335747 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 20
13335684 CTAAAATAAA
13335694 AAAAAACCTAACATAAAGAT
1 AAAAAACCTAACATAAAGAT
*
13335714 GAAAAAACCTAAAATAAAGAT
1 -AAAAAACCTAACATAAAGAT
13335735 AAAAAACCTAACA
1 AAAAAACCTAACA
13335748 ACTGCCCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.67, C:0.15, G:0.06, T:0.13
Consensus pattern (20 bp):
AAAAAACCTAACATAAAGAT
Found at i:13338133 original size:65 final size:65
Alignment explanation
Indices: 13338029--13338156 Score: 168
Period size: 65 Copynumber: 2.0 Consensus size: 65
13338019 TGCTTTTTTT
* * * * * *
13338029 TGAAAAAGTTTGAGGGTCTTTTTTATGCATTTTTAAAGTTTAAATACTCAATTGAGTGCAAAATA
1 TGAAAAAGTTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAATACTCAAGTGAGTGCAAAATA
* *
13338094 TGAAATAA-TTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAGTACTCAAGTGAGTGTAAAA
1 TGAAA-AAGTTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAATACTCAAGTGAGTGCAAAA
13338157 AAAAGTAGGG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
65 52 0.96
66 2 0.04
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.38
Consensus pattern (65 bp):
TGAAAAAGTTTGAAGGCCTTTTTGATGCATTTTGAAAGTTCAAATACTCAAGTGAGTGCAAAATA
Found at i:13338559 original size:11 final size:11
Alignment explanation
Indices: 13338528--13338575 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
13338518 TCACGTTAGC
*
13338528 AAATAATTTTA
1 AAATTATTTTA
13338539 AAATTA--TTA
1 AAATTATTTTA
13338548 AAATTATTTTA
1 AAATTATTTTA
13338559 AAATTAATTTTTA
1 AAATT-A-TTTTA
13338572 AAAT
1 AAAT
13338576 ATAAAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
9 9 0.28
11 13 0.41
12 1 0.03
13 9 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (11 bp):
AAATTATTTTA
Found at i:13338607 original size:40 final size:40
Alignment explanation
Indices: 13338537--13338613 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
13338527 CAAATAATTT
* *
13338537 TAAAATTATTAAAATTATTTTAAAATTAATTTTTAAAATA
1 TAAAATTATTAAAATAATTTTAAAATTAATTTCTAAAATA
**
13338577 TAAAATTATT-AAATAATTTTAATTTCTAATTTCTAAA
1 TAAAATTATTAAAATAATTTTAAAAT-TAATTTCTAAA
13338614 TCTTCTTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 12 0.38
40 20 0.62
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (40 bp):
TAAAATTATTAAAATAATTTTAAAATTAATTTCTAAAATA
Found at i:13343356 original size:18 final size:18
Alignment explanation
Indices: 13343333--13343375 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
13343323 TTTTCAATTA
13343333 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
13343351 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
13343369 TAATTAA
1 TAATTAA
13343376 AAATTTATTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:13344829 original size:9 final size:9
Alignment explanation
Indices: 13344815--13344853 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
13344805 CATATATTCC
13344815 TGTTTGGAT
1 TGTTTGGAT
13344824 TGTTTGGAT
1 TGTTTGGAT
13344833 TGTTTGGAT
1 TGTTTGGAT
* *
13344842 TGCTTGGTT
1 TGTTTGGAT
13344851 TGT
1 TGT
13344854 GGAGATATGG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.08, C:0.03, G:0.33, T:0.56
Consensus pattern (9 bp):
TGTTTGGAT
Found at i:13351028 original size:17 final size:17
Alignment explanation
Indices: 13351006--13351039 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
13350996 AGTTTTTATA
13351006 CCTGATAACAACCTGTT
1 CCTGATAACAACCTGTT
13351023 CCTGATAACAACCTGTT
1 CCTGATAACAACCTGTT
13351040 GACTATGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
CCTGATAACAACCTGTT
Found at i:13353998 original size:23 final size:23
Alignment explanation
Indices: 13353972--13354018 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
13353962 CATCACAAAA
13353972 AAACCGTAAATATCCCCAAGAAC
1 AAACCGTAAATATCCCCAAGAAC
*
13353995 AAACCGTCAATATCCCCAAGAAC
1 AAACCGTAAATATCCCCAAGAAC
13354018 A
1 A
13354019 TTGAACCTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.32, G:0.09, T:0.13
Consensus pattern (23 bp):
AAACCGTAAATATCCCCAAGAAC
Found at i:13358667 original size:28 final size:28
Alignment explanation
Indices: 13358615--13358693 Score: 77
Period size: 28 Copynumber: 2.8 Consensus size: 28
13358605 AAATACAGAA
** * *
13358615 AAAGTGCGAGTTGTCACAATAAAGCTAC
1 AAAGTGCGAACTGTCACAGTGAAGCTAC
* *
13358643 AAAGTGTGAACTGTCACAGTGAAGCTGC
1 AAAGTGCGAACTGTCACAGTGAAGCTAC
* * *
13358671 GAAGTGCGAACTATCAAAGTGAA
1 AAAGTGCGAACTGTCACAGTGAA
13358694 TCTGCGAAGC
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.20
Consensus pattern (28 bp):
AAAGTGCGAACTGTCACAGTGAAGCTAC
Found at i:13358698 original size:28 final size:28
Alignment explanation
Indices: 13358644--13358702 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
13358634 TAAAGCTACA
* * *
13358644 AAGTGTGAACTGTCACAGTGAAGCTGCG
1 AAGTGCGAACTATCAAAGTGAAGCTGCG
*
13358672 AAGTGCGAACTATCAAAGTGAATCTGCG
1 AAGTGCGAACTATCAAAGTGAAGCTGCG
13358700 AAG
1 AAG
13358703 CAACTGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (28 bp):
AAGTGCGAACTATCAAAGTGAAGCTGCG
Found at i:13358843 original size:24 final size:24
Alignment explanation
Indices: 13358798--13358843 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
13358788 ATATTTAGAC
* * * *
13358798 TTTATTAGTATCATAATTTTAGCA
1 TTTATTAGCATAAGAATCTTAGCA
13358822 TTTATTAGCATAAGAATCTTAG
1 TTTATTAGCATAAGAATCTTAG
13358844 TTATTTCCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.46
Consensus pattern (24 bp):
TTTATTAGCATAAGAATCTTAGCA
Found at i:13373421 original size:20 final size:20
Alignment explanation
Indices: 13373396--13373436 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
13373386 ATCTTAGAAT
*
13373396 CCTAAATTTAGAA-CCCAAAC
1 CCTAAATCTA-AATCCCAAAC
13373416 CCTAAATCTAAATCCCAAAC
1 CCTAAATCTAAATCCCAAAC
13373436 C
1 C
13373437 TTTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 2 0.11
20 17 0.89
ACGTcount: A:0.44, C:0.34, G:0.02, T:0.20
Consensus pattern (20 bp):
CCTAAATCTAAATCCCAAAC
Found at i:13373509 original size:28 final size:27
Alignment explanation
Indices: 13373453--13373514 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 27
13373443 TATTGAACAC
* *
13373453 TAAACACCAAACTCATAACTCGTGACCT
1 TAAAC-CCAAACTCATAACTCCTAACCT
13373481 TAAACCCAAACTCATAAC-CCTAACCCCT
1 TAAACCCAAACTCATAACTCCTAA--CCT
13373509 TAAACC
1 TAAACC
13373515 ATGAACATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 3 0.10
27 13 0.43
28 14 0.47
ACGTcount: A:0.40, C:0.37, G:0.03, T:0.19
Consensus pattern (27 bp):
TAAACCCAAACTCATAACTCCTAACCT
Found at i:13382097 original size:18 final size:17
Alignment explanation
Indices: 13382051--13382098 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
13382041 TTGATCGACC
13382051 CGACCCGTTGACTTTGA
1 CGACCCGTTGACTTTGA
* * *
13382068 CTAAGCCATTGACTTTGA
1 C-GACCCGTTGACTTTGA
13382086 TCGACCCGTTGAC
1 -CGACCCGTTGAC
13382099 CGTTGGCTTT
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
17 1 0.04
18 21 0.91
19 1 0.04
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (17 bp):
CGACCCGTTGACTTTGA
Found at i:13382202 original size:31 final size:31
Alignment explanation
Indices: 13382129--13382221 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
13382119 TTTAACTGAC
* * * *
13382129 TTTGACCGTTAACTCTAACTTAACCGTTGAG
1 TTTGACCATTGACTTTAACTTGACCGTTGAG
13382160 TTTGACCATTGACTTTAACTTGACCGTTGAG
1 TTTGACCATTGACTTTAACTTGACCGTTGAG
* *
13382191 TTTGACTATTGACTTTGACTTTGACCGTTGA
1 TTTGACCATTGACTTTAAC-TTGACCGTTGA
13382222 CTTTTTTCGT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
31 44 0.80
32 11 0.20
ACGTcount: A:0.23, C:0.19, G:0.18, T:0.40
Consensus pattern (31 bp):
TTTGACCATTGACTTTAACTTGACCGTTGAG
Found at i:13382213 original size:19 final size:19
Alignment explanation
Indices: 13382155--13382215 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 19
13382145 AACTTAACCG
*
13382155 TTGAGTTTGACCATTGACT
1 TTGACTTTGACCATTGACT
* * *
13382174 TTAAC-TTGACCGTTGAGT
1 TTGACTTTGACCATTGACT
*
13382192 TTGACTATTGA-CTTTGACT
1 TTGACT-TTGACCATTGACT
13382211 TTGAC
1 TTGAC
13382216 CGTTGACTTT
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 15 0.45
19 14 0.42
20 4 0.12
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (19 bp):
TTGACTTTGACCATTGACT
Found at i:13383268 original size:17 final size:17
Alignment explanation
Indices: 13383246--13383281 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13383236 TCTCTTCTAT
*
13383246 TTATTCATTTTCAATTA
1 TTATTCATTATCAATTA
*
13383263 TTATTCATTATGAATTA
1 TTATTCATTATCAATTA
13383280 TT
1 TT
13383282 TTTGGGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.08, G:0.03, T:0.58
Consensus pattern (17 bp):
TTATTCATTATCAATTA
Found at i:13386984 original size:19 final size:18
Alignment explanation
Indices: 13386956--13386995 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
13386946 ATAAAAAATT
* *
13386956 ATTTTTAAAAATTTATAAA
1 ATTTTCAAAAATATA-AAA
13386975 ATTTTCAAAAATATAAAA
1 ATTTTCAAAAATATAAAA
13386993 ATT
1 ATT
13386996 AGTAAATGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTTCAAAAATATAAAA
Found at i:13387454 original size:41 final size:41
Alignment explanation
Indices: 13387400--13387482 Score: 148
Period size: 41 Copynumber: 2.0 Consensus size: 41
13387390 ATATTTAAGT
*
13387400 AATTACATGATGTTTATCATAAAATATTTATACTAATTTTA
1 AATTACATAATGTTTATCATAAAATATTTATACTAATTTTA
*
13387441 AATTTCATAATGTTTATCATAAAATATTTATACTAATTTTA
1 AATTACATAATGTTTATCATAAAATATTTATACTAATTTTA
13387482 A
1 A
13387483 CTAAATTACA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (41 bp):
AATTACATAATGTTTATCATAAAATATTTATACTAATTTTA
Found at i:13390857 original size:112 final size:111
Alignment explanation
Indices: 13390653--13390862 Score: 276
Period size: 112 Copynumber: 1.9 Consensus size: 111
13390643 TGGACGTGTA
*** * *
13390653 TGTTAAATCCTCCCAGGGAAATATGAAAATAGCAATACAACTCAAACAAATATAAGAAGTAATTT
1 TGTTAAATCCTCCCACAAAAATATGAAAATAGCAATACAACTCAAACAAATATAAGAAGTAACTA
* * *
13390718 TAAGATGATTGATTAACTGAACCTGCTCAATTAGCTGTATGTTAAT
66 CAAGATGATTGATCAACTAAACCTGCTCAATTAGCTGTATGTTAAT
** ***
13390764 TGTTAAATCCTCCCACAAAAATATGAAAATAGTGATAACAACTCGGTCAAATATAAGAAGTAACT
1 TGTTAAATCCTCCCACAAAAATATGAAAATAGCAAT-ACAACTCAAACAAATATAAGAAGTAACT
* *
13390829 ACAGGATGATTGATCAACTAAACTTGCTCAATTA
65 ACAAGATGATTGATCAACTAAACCTGCTCAATTA
13390863 CAAATATCTA
Statistics
Matches: 83, Mismatches: 15, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
111 31 0.37
112 52 0.63
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (111 bp):
TGTTAAATCCTCCCACAAAAATATGAAAATAGCAATACAACTCAAACAAATATAAGAAGTAACTA
CAAGATGATTGATCAACTAAACCTGCTCAATTAGCTGTATGTTAAT
Found at i:13394152 original size:5 final size:5
Alignment explanation
Indices: 13394133--13394170 Score: 51
Period size: 5 Copynumber: 7.6 Consensus size: 5
13394123 TATTAAGCTA
*
13394133 AAAAT AAAACG AAAAT AAAAT -AAAT AAAAT AAAAT AAA
1 AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT AAA
13394171 TCTTTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 4 0.14
5 21 0.72
6 4 0.14
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:13394163 original size:14 final size:14
Alignment explanation
Indices: 13394144--13394171 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
13394134 AAATAAAACG
13394144 AAAATAAAATAAAT
1 AAAATAAAATAAAT
13394158 AAAATAAAATAAAT
1 AAAATAAAATAAAT
13394172 CTTTTTATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:13394171 original size:9 final size:10
Alignment explanation
Indices: 13394133--13394170 Score: 51
Period size: 9 Copynumber: 3.8 Consensus size: 10
13394123 TATTAAGCTA
*
13394133 AAAATAAAACG
1 AAAATAAAA-T
13394144 AAAATAAAAT
1 AAAATAAAAT
13394154 -AAATAAAAT
1 AAAATAAAAT
13394163 AAAATAAA
1 AAAATAAA
13394171 TCTTTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 9 0.36
10 7 0.28
11 9 0.36
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:13395660 original size:27 final size:29
Alignment explanation
Indices: 13395618--13395678 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 29
13395608 TTGTACCAAA
* *
13395618 TTTTTTTATATATTTTTTC-TTTTCTTAT
1 TTTTTTTATATATTTTTTCATTTACATAT
*
13395646 TTTTTTTCTAT-TTTTTTCATTTACATAT
1 TTTTTTTATATATTTTTTCATTTACATAT
13395674 TTTTT
1 TTTTT
13395679 GAGACATAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (29 bp):
TTTTTTTATATATTTTTTCATTTACATAT
Found at i:13398660 original size:29 final size:30
Alignment explanation
Indices: 13398616--13398681 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
13398606 CTTGATCTAC
13398616 TTCTCTTGGGTTATTTCCTTTCTTCTTTTT
1 TTCTCTTGGGTTATTTCCTTTCTTCTTTTT
*
13398646 TTCT-TTGGGTTATTTTCTTTCTTCTTTTT
1 TTCTCTTGGGTTATTTCCTTTCTTCTTTTT
*
13398675 TTTTCTT
1 TTCTCTT
13398682 TCTTTTTAGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
29 27 0.82
30 6 0.18
ACGTcount: A:0.03, C:0.17, G:0.09, T:0.71
Consensus pattern (30 bp):
TTCTCTTGGGTTATTTCCTTTCTTCTTTTT
Found at i:13402830 original size:25 final size:24
Alignment explanation
Indices: 13402725--13402832 Score: 114
Period size: 23 Copynumber: 4.5 Consensus size: 24
13402715 CGAAGTACTG
* *
13402725 AACAGAGAGCACATA-AGTGCTGGGT
1 AACAGAGAGCACACACAGTGCT--AT
13402750 AACAGAGAGCACACACAGTGCTAT
1 AACAGAGAGCACACACAGTGCTAT
* * *
13402774 -ACAGAGAGTACACAAAGTACTA-
1 AACAGAGAGCACACACAGTGCTAT
*
13402796 ACCAGAGAGCACACACAGTGCTAAT
1 AACAGAGAGCACACACAGTGCT-AT
13402821 AACAGAGAGCAC
1 AACAGAGAGCAC
13402833 GCTAGTGTTC
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
23 36 0.52
24 2 0.03
25 25 0.36
26 6 0.09
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (24 bp):
AACAGAGAGCACACACAGTGCTAT
Found at i:13414499 original size:5 final size:5
Alignment explanation
Indices: 13414475--13414539 Score: 50
Period size: 5 Copynumber: 13.2 Consensus size: 5
13414465 TCTTTACTGT
*
13414475 TTATG -TATA TTATG -TATG TTATG TTTAATG TTATG TT-TG TATAT-
1 TTATG TTATG TTATG TTATG TTATG -TT-ATG TTATG TTATG T-TATG
13414519 TGTATG -TATG TTATG TTATG T
1 T-TATG TTATG TTATG TTATG T
13414540 ATATTTTTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
4 14 0.29
5 27 0.55
6 5 0.10
7 3 0.06
ACGTcount: A:0.23, C:0.00, G:0.18, T:0.58
Consensus pattern (5 bp):
TTATG
Found at i:13414512 original size:36 final size:36
Alignment explanation
Indices: 13414472--13414575 Score: 101
Period size: 36 Copynumber: 2.9 Consensus size: 36
13414462 GTTTCTTTAC
13414472 TGTTTATGTATATTATGTATGTTATGTTTAATGT-TA-
1 TGTTTATGTATATTATGTATGTTATG-TT-ATGTATAT
13414508 TG-TT-TGTATATTGTATGTATGTTATGTTATGTATATT
1 TGTTTATGTATA-T-TATGTATGTTATGTTATGTATA-T
* * *
13414545 TTTTTATGTATATT-TGTATGTTTTTTTATGT
1 TGTTTATGTATATTATGTATGTTATGTTATGT
13414576 GTTATATTAT
Statistics
Matches: 58, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
34 10 0.17
35 7 0.12
36 30 0.52
37 2 0.03
38 3 0.05
39 6 0.10
ACGTcount: A:0.21, C:0.00, G:0.16, T:0.62
Consensus pattern (36 bp):
TGTTTATGTATATTATGTATGTTATGTTATGTATAT
Found at i:13417383 original size:13 final size:13
Alignment explanation
Indices: 13417346--13417375 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13417336 GATGGTTTTA
13417346 TTTTGTTGGATGG
1 TTTTGTTGGATGG
*
13417359 TTTTGTTAGATGG
1 TTTTGTTGGATGG
13417372 TTTT
1 TTTT
13417376 TATGGATGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.30, T:0.60
Consensus pattern (13 bp):
TTTTGTTGGATGG
Found at i:13418891 original size:3 final size:3
Alignment explanation
Indices: 13418883--13418929 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
13418873 TTTCTAACAG
*
13418883 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
13418930 CTTAAACATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:13426246 original size:40 final size:40
Alignment explanation
Indices: 13426202--13426279 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
13426192 TGATATGTGT
* * * *
13426202 AAGTCTTACAGAAAAGAAGAAAAATCATCTAAACATTCCC
1 AAGTCCTACAGAAAAGAAGAAAAACCAGCCAAACATTCCC
* *
13426242 AAGTCCTATAGAAGAGAAGAAAAACCAGCCAAACATTC
1 AAGTCCTACAGAAAAGAAGAAAAACCAGCCAAACATTC
13426280 TCAAATACCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.50, C:0.21, G:0.13, T:0.17
Consensus pattern (40 bp):
AAGTCCTACAGAAAAGAAGAAAAACCAGCCAAACATTCCC
Found at i:13430717 original size:25 final size:26
Alignment explanation
Indices: 13430631--13430734 Score: 82
Period size: 23 Copynumber: 4.3 Consensus size: 26
13430621 ACTATGTGTA
* *
13430631 CTCTCTTATT-AGCATTGTGTGTGCC
1 CTCTGTTATTCAGCACTGTGTGTGCC
* *
13430656 TTCTG-T-TT-AGCAC-GTTTCGTGCC
1 CTCTGTTATTCAGCACTGTGT-GTGCC
*
13430679 CTC---TATTCAGCACTGTGTGTTCC
1 CTCTGTTATTCAGCACTGTGTGTGCC
*
13430702 CTCTGTTATT-AGCACTTTGTGTGCC
1 CTCTGTTATTCAGCACTGTGTGTGCC
13430727 CTCTGTTA
1 CTCTGTTA
13430735 CCCAACACTT
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
21 1 0.02
22 5 0.08
23 25 0.40
24 4 0.06
25 24 0.38
26 4 0.06
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.43
Consensus pattern (26 bp):
CTCTGTTATTCAGCACTGTGTGTGCC
Found at i:13430726 original size:48 final size:46
Alignment explanation
Indices: 13430611--13430730 Score: 120
Period size: 46 Copynumber: 2.6 Consensus size: 46
13430601 TAGCGCGCGT
* * * * *
13430611 TCTG-ATTAGCACTATGTGTACTCTCTTATTAGCATTGTGTGTGCCT
1 TCTGTATTAGCACTTTGTGTGCCCTC-TATTAGCACTGTGTGTGCCC
* *
13430657 TCTGT-TTAGCACGTTT-CGTGCCCTCTATTCAGCACTGTGTGTTCCC
1 TCTGTATTAGCAC-TTTGTGTGCCCTCTATT-AGCACTGTGTGTGCCC
13430703 TCTGTTATTAGCACTTTGTGTGCCCTCT
1 TCTG-TATTAGCACTTTGTGTGCCCTCT
13430731 GTTACCCAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
45 4 0.07
46 34 0.57
47 6 0.10
48 16 0.27
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.42
Consensus pattern (46 bp):
TCTGTATTAGCACTTTGTGTGCCCTCTATTAGCACTGTGTGTGCCC
Found at i:13436150 original size:6 final size:6
Alignment explanation
Indices: 13436139--13436170 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
13436129 AAAAAAGGAA
13436139 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GA
13436171 GAGGTGTGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (6 bp):
GAAGAT
Found at i:13436527 original size:29 final size:29
Alignment explanation
Indices: 13436472--13436556 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 29
13436462 GTTTACCCTT
* *
13436472 TTTTTGGGCCCTTAAAAGTTGATAAAAAGAA
1 TTTTT-GGCCCTTAAAAATT-AAAAAAAGAA
* *
13436503 TTTTTGGCCTTTAAAAATTAAAAAAATAA
1 TTTTTGGCCCTTAAAAATTAAAAAAAGAA
* *
13436532 -TTTAGACCCCTTAAAAATTAAAAAA
1 TTTTTG-GCCCTTAAAAATTAAAAAA
13436557 CAAAAATTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.09
29 25 0.54
30 12 0.26
31 5 0.11
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.33
Consensus pattern (29 bp):
TTTTTGGCCCTTAAAAATTAAAAAAAGAA
Found at i:13437239 original size:58 final size:55
Alignment explanation
Indices: 13437041--13437247 Score: 184
Period size: 58 Copynumber: 3.6 Consensus size: 55
13437031 AAAAAAAGTT
* *
13437041 TGGTGTCGACCAT-ACCATGGCCGACACCACCTTTATCAGAGAAAAAATAAAATTTTT-
1 TGGTGTCG-CCATGA-CATGGCCGACACCACCTTTATCAGA-TAAAAA-AATATTTTTC
* *
13437098 TGGTGTAGGTCATGACATGGCCGACACCACCTTTATCAGATAAAAAAATATTTTTTC
1 TGGTGT-CGCCATGACATGGCCGACACCACCTTTATCAGATAAAAAAATA-TTTTTC
** * * ** *
13437155 TTAATGTTGCCCATGCCATGATCGACACCACCTTTATCTGATAAAAAAATATCTTTTC
1 -TGGTGTCG-CCATGACATGGCCGACACCACCTTTATCAGATAAAAAAATAT-TTTTC
* *
13437213 ATGGTGTCGCCAATGTCATGGCCGACACCAACTTT
1 -TGGTGTCGCC-ATGACATGGCCGACACCACCTTT
13437248 CCATCCTTTA
Statistics
Matches: 122, Mismatches: 20, Indels: 15
0.78 0.13 0.10
Matches are distributed among these distances:
55 3 0.02
56 10 0.08
57 38 0.31
58 71 0.58
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (55 bp):
TGGTGTCGCCATGACATGGCCGACACCACCTTTATCAGATAAAAAAATATTTTTC
Found at i:13447166 original size:18 final size:19
Alignment explanation
Indices: 13447143--13447187 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
13447133 CCTAAAAAAA
*
13447143 AAAATTAAAGTTGCAA-TG
1 AAAATTAAAGTTGAAATTG
13447161 AAAATTAAAGTTGAAATTG
1 AAAATTAAAGTTGAAATTG
13447180 -AAATTAAA
1 AAAATTAAA
13447188 TTATACTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAATTAAAGTTGAAATTG
Found at i:13447308 original size:37 final size:37
Alignment explanation
Indices: 13447234--13447305 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 37
13447224 TAAGTTGAAA
*
13447234 TTAATTTCAAAATTAAAATACATGTTTAAATTTAAAT
1 TTAACTTCAAAATTAAAATACATGTTTAAATTTAAAT
*
13447271 TTAACTTCAAAA-TAAAATAC-TAGTTTGAATTTAAA
1 TTAACTTCAAAATTAAAATACAT-GTTTAAATTTAAA
13447306 ATTATAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
35 1 0.03
36 20 0.62
37 11 0.34
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.40
Consensus pattern (37 bp):
TTAACTTCAAAATTAAAATACATGTTTAAATTTAAAT
Found at i:13447350 original size:24 final size:24
Alignment explanation
Indices: 13447294--13447360 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
13447284 AAAATACTAG
* ** *
13447294 TTTGAATTTAAAATTATAGTTTATA
1 TTTGAAATTAAAATTA-AACTTACA
13447319 TTTGAAATTAAAATTAAACTTACA
1 TTTGAAATTAAAATTAAACTTACA
*
13447343 TTTGAAATGAAAATTAAA
1 TTTGAAATTAAAATTAAA
13447361 TATGAAATTG
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
24 22 0.59
25 15 0.41
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (24 bp):
TTTGAAATTAAAATTAAACTTACA
Found at i:13447499 original size:23 final size:24
Alignment explanation
Indices: 13447472--13447530 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
13447462 CAATTTTAAA
13447472 TTAAATTGAAATTTCA-ATGAAAT
1 TTAAATTGAAATTTCATATGAAAT
* * *
13447495 TTAAATTTAATTTTCATATGAATT
1 TTAAATTGAAATTTCATATGAAAT
13447519 TTAAA-TGAAATT
1 TTAAATTGAAATT
13447531 GAAATCTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 19 0.63
24 11 0.37
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (24 bp):
TTAAATTGAAATTTCATATGAAAT
Found at i:13447533 original size:17 final size:17
Alignment explanation
Indices: 13447466--13447551 Score: 64
Period size: 17 Copynumber: 4.9 Consensus size: 17
13447456 AACTTACAAT
*
13447466 TTTAAATTAAATTGAAA
1 TTTAAATGAAATTGAAA
* *
13447483 TTTCAATGAAATTTAAA
1 TTTAAATGAAATTGAAA
* *** *
13447500 TTTAATTTTCATATGAAT
1 TTTAAATGAAAT-TGAAA
13447518 TTTAAATGAAATTGAAA
1 TTTAAATGAAATTGAAA
* *
13447535 TCTAAATTGAAAATGAA
1 TTTAAA-TGAAATTGAA
13447552 GTTGAAATCT
Statistics
Matches: 50, Mismatches: 17, Indels: 3
0.71 0.24 0.04
Matches are distributed among these distances:
17 30 0.60
18 20 0.40
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (17 bp):
TTTAAATGAAATTGAAA
Found at i:13447542 original size:24 final size:23
Alignment explanation
Indices: 13447515--13447571 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
13447505 TTTTCATATG
*
13447515 AATTTTAAATGAAATTGAAATCT
1 AATTTAAAATGAAATTGAAATCT
* *
13447538 AAATTGAAAATGAAGTTGAAATCT
1 -AATTTAAAATGAAATTGAAATCT
13447562 AATTTAAAAT
1 AATTTAAAAT
13447572 ATTTAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 9 0.31
24 20 0.69
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.35
Consensus pattern (23 bp):
AATTTAAAATGAAATTGAAATCT
Found at i:13448071 original size:20 final size:20
Alignment explanation
Indices: 13448016--13448091 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 20
13448006 GACCAAATTC
*
13448016 AAATTTAAAAACTATTTAAATTA
1 AAATTTAAAAAATA-TT-AA-TA
*
13448039 AAA-ATAAATAAATATTAATA
1 AAATTTAAA-AAATATTAATA
*
13448059 AAATTTAAAAAAT-TACAATA
1 AAATTTAAAAAATAT-TAATA
*
13448079 ACATTTAAAAAAT
1 AAATTTAAAAAAT
13448092 TATATTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
19 1 0.02
20 25 0.56
21 6 0.13
22 6 0.13
23 7 0.16
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATTTAAAAAATATTAATA
Found at i:13448091 original size:29 final size:28
Alignment explanation
Indices: 13448038--13448092 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
13448028 TATTTAAATT
13448038 AAAAATAAATAAATATTAATAAAATTTA
1 AAAAATAAATAAATATTAATAAAATTTA
13448066 AAAAATTACAATAACAT-TTAA-AAAATT
1 AAAAA-TA-AATAA-ATATTAATAAAATT
13448093 ATATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 5 0.21
29 8 0.33
30 9 0.38
31 2 0.08
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (28 bp):
AAAAATAAATAAATATTAATAAAATTTA
Found at i:13448092 original size:20 final size:20
Alignment explanation
Indices: 13448055--13448093 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
13448045 AATAAATATT
13448055 AATAAAATTTAAAAAATTAC
1 AATAAAATTTAAAAAATTAC
*
13448075 AATAACATTTAAAAAATTA
1 AATAAAATTTAAAAAATTA
13448094 TATTAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AATAAAATTTAAAAAATTAC
Found at i:13448254 original size:16 final size:16
Alignment explanation
Indices: 13448233--13448276 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
13448223 TAATATTTAA
13448233 ATTTAAATTAAAAACT
1 ATTTAAATTAAAAACT
*
13448249 ATTTAAATTAAATACT
1 ATTTAAATTAAAAACT
*
13448265 ATTCAAATTAAA
1 ATTTAAATTAAA
13448277 GTGTTGATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTTAAATTAAAAACT
Found at i:13448379 original size:16 final size:16
Alignment explanation
Indices: 13448358--13448388 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13448348 AAATTAAAAA
13448358 TAAATAAATAATAATT
1 TAAATAAATAATAATT
*
13448374 TAAATAAATATTAAT
1 TAAATAAATAATAAT
13448389 AAAATTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATAAATAATAATT
Found at i:13448380 original size:20 final size:20
Alignment explanation
Indices: 13448355--13448398 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 20
13448345 TTTAAATTAA
13448355 AAATAAATA-AATAATAATTT
1 AAATAAATATAATAA-AATTT
13448375 AAATAAATATTAATAAAATTT
1 AAATAAATA-TAATAAAATTT
13448396 AAA
1 AAA
13448399 AATTACAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 8 0.36
22 5 0.23
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATAAATATAATAAAATTT
Found at i:13448611 original size:17 final size:17
Alignment explanation
Indices: 13448565--13448611 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
13448555 TAATATTTAA
* *
13448565 ATTCAAATTAAAAAAGT
1 ATTCAAATTAAAATACT
*
13448582 ATTTAAATT-AAATACT
1 ATTCAAATTAAAATACT
13448598 ATTCAAATTAAAAT
1 ATTCAAATTAAAAT
13448612 GTTGATGTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTCAAATTAAAATACT
Found at i:13449878 original size:9 final size:10
Alignment explanation
Indices: 13449858--13450012 Score: 52
Period size: 9 Copynumber: 14.8 Consensus size: 10
13449848 GGGGTAAGAT
*
13449858 ATATTTTCAA
1 ATATTTTTAA
13449868 AT-TTTTTAA
1 ATATTTTTAA
*
13449877 ATATTTTT-T
1 ATATTTTTAA
*
13449886 CTATTTTTGAA
1 ATATTTTT-AA
*
13449897 ATATTTTT-T
1 ATATTTTTAA
**
13449906 ATATTTTCGA
1 ATATTTTTAA
*
13449916 AT-TTCTTAAA
1 ATATT-TTTAA
13449926 ATTATATTTTCGAA
1 A-TAT-TTTT--AA
13449940 ATATTTTTTACA
1 ATA-TTTTTA-A
*
13449952 TATATTTTT-T
1 -ATATTTTTAA
*
13449962 ATATTTTGAA
1 ATATTTTTAA
13449972 ATATTTTTTACA
1 ATA-TTTTTA-A
*
13449984 TATATTTTT-T
1 -ATATTTTTAA
*
13449994 ATATTTTCGAA
1 ATATTTT-TAA
13450005 ATATTTTT
1 ATATTTTT
13450013 TAGCTTTTCG
Statistics
Matches: 107, Mismatches: 19, Indels: 38
0.65 0.12 0.23
Matches are distributed among these distances:
9 38 0.36
10 16 0.15
11 21 0.20
12 15 0.14
13 13 0.12
14 4 0.04
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (10 bp):
ATATTTTTAA
Found at i:13449884 original size:11 final size:11
Alignment explanation
Indices: 13449868--13450014 Score: 64
Period size: 11 Copynumber: 13.7 Consensus size: 11
13449858 ATATTTTCAA
13449868 ATTTTTTAAAT
1 ATTTTTTAAAT
*
13449879 ATTTTTT--CT
1 ATTTTTTAAAT
*
13449888 ATTTTTGAAAT
1 ATTTTTTAAAT
13449899 ATTTTTT--AT
1 ATTTTTTAAAT
**
13449908 A-TTTTCGAAT
1 ATTTTTTAAAT
* *
13449918 -TTCTTAAAATT
1 ATTTTTTAAA-T
*
13449929 ATATTTTCGAAAT
1 AT-TTTT-TAAAT
13449942 ATTTTTTACATAT
1 ATTTTTTA-A-AT
13449955 ATTTTTT--AT
1 ATTTTTTAAAT
*
13449964 A-TTTTGAAAT
1 ATTTTTTAAAT
13449974 ATTTTTTACATAT
1 ATTTTTTA-A-AT
13449987 ATTTTTT--AT
1 ATTTTTTAAAT
**
13449996 ATTTTCGAAAT
1 ATTTTTTAAAT
13450007 ATTTTTTA
1 ATTTTTTA
13450015 GCTTTTCGAA
Statistics
Matches: 101, Mismatches: 17, Indels: 36
0.66 0.11 0.23
Matches are distributed among these distances:
8 8 0.08
9 20 0.20
10 10 0.10
11 29 0.29
12 7 0.07
13 24 0.24
14 3 0.03
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (11 bp):
ATTTTTTAAAT
Found at i:13449891 original size:20 final size:20
Alignment explanation
Indices: 13449868--13450014 Score: 84
Period size: 20 Copynumber: 7.0 Consensus size: 20
13449858 ATATTTTCAA
* *
13449868 ATTTTTTAAATATTTTTTCT
1 ATTTTTGAAATATTTTTTAT
13449888 ATTTTTGAAATATTTTTTAT
1 ATTTTTGAAATATTTTTTAT
*
13449908 ATTTTCG-AAT-TTCTTAAAATTAT
1 ATTTTTGAAATATT-TT----TTAT
*
13449931 ATTTTCGAAATATTTTTTACAT
1 ATTTTTGAAATATTTTTT--AT
** **
13449953 ATATTTT-TTATATTTTGAAAT
1 AT-TTTTGAAATATTTT-TTAT
*
13449974 ATTTTTTACATATATTTTTTAT
1 ATTTTTGA-A-ATATTTTTTAT
*
13449996 ATTTTCGAAATATTTTTTA
1 ATTTTTGAAATATTTTTTA
13450015 GCTTTTCGAA
Statistics
Matches: 99, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
18 2 0.02
19 5 0.05
20 40 0.40
21 5 0.05
22 19 0.19
23 21 0.21
24 5 0.05
25 2 0.02
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (20 bp):
ATTTTTGAAATATTTTTTAT
Done.