Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 4 of 206
Found at i:1081967 original size:21 final size:20
Alignment explanation
Indices: 1081936--1081976 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
1081926 AAAAAATATA
1081936 ATTTTTTTAATTCTTTGAAT
1 ATTTTTTTAATTCTTTGAAT
*
1081956 ATTTTTTATAATTTTTTGAAT
1 ATTTTTT-TAATTCTTTGAAT
1081977 TTTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (20 bp):
ATTTTTTTAATTCTTTGAAT
Found at i:1083908 original size:12 final size:14
Alignment explanation
Indices: 1083881--1083912 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1083871 TTATTTTTTA
1083881 TTTTTAAAATACTT
1 TTTTTAAAATACTT
1083895 TTTTTAAAA-A-TT
1 TTTTTAAAATACTT
1083907 TTTTTA
1 TTTTTA
1083913 TTTTAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 1 0.06
14 9 0.50
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTAAAATACTT
Found at i:1083916 original size:18 final size:18
Alignment explanation
Indices: 1083895--1083947 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 18
1083885 TAAAATACTT
1083895 TTTTTAAAAATTTTTTTA
1 TTTTTAAAAATTTTTTTA
1083913 -TTTTAAAATATTTTTTTTA
1 TTTTTAAAA-A-TTTTTTTA
*
1083932 TTTTT-TAAATTTTTTT
1 TTTTTAAAAATTTTTTT
1083948 TGGTGTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 15 0.48
18 2 0.06
19 10 0.32
20 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTAAAAATTTTTTTA
Found at i:1083926 original size:16 final size:16
Alignment explanation
Indices: 1083875--1083927 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
1083865 ATGTATTTAT
1083875 TTTTTATTTTTAAAATA
1 TTTTTA-TTTTAAAATA
* * *
1083892 CTTTT-TTTAAAAATT
1 TTTTTATTTTAAAATA
1083907 TTTTTATTTTAAAATA
1 TTTTTATTTTAAAATA
1083923 TTTTT
1 TTTTT
1083928 TTTATTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
15 12 0.41
16 13 0.45
17 4 0.14
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTTTATTTTAAAATA
Found at i:1083930 original size:14 final size:14
Alignment explanation
Indices: 1083881--1083931 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 14
1083871 TTATTTTTTA
1083881 TTTTTAAAATACTTT
1 TTTTTAAAATA-TTT
* *
1083896 TTTTAAAAATTTTTT
1 TTTTTAAAA-TATTT
1083911 TATTTTAAAATATTT
1 T-TTTTAAAATATTT
1083926 TTTTTA
1 TTTTTA
1083932 TTTTTTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 5 0.17
15 17 0.57
16 8 0.27
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTTTAAAATATTT
Found at i:1083946 original size:20 final size:19
Alignment explanation
Indices: 1083896--1083948 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
1083886 AAAATACTTT
1083896 TTTTAAAA-A-TTTTTTTA
1 TTTTAAAATATTTTTTTTA
1083913 TTTTAAAATATTTTTTTTA
1 TTTTAAAATATTTTTTTTA
*
1083932 TTTTTTAAAT-TTTTTTT
1 -TTTTAAAATATTTTTTT
1083949 GGTGTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 8 0.25
18 1 0.03
19 15 0.47
20 8 0.25
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTAAAATATTTTTTTTA
Found at i:1085603 original size:59 final size:59
Alignment explanation
Indices: 1085534--1085652 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
1085524 TTTATAAATA
1085534 ATAATGGTAATCATAATTAATATATCAATAAATAAAATTTTATATTAAATATAATAATT
1 ATAATGGTAATCATAATTAATATATCAATAAATAAAATTTTATATTAAATATAATAATT
1085593 ATAATGGTAATCATAATTAATATATCAATAAATAAAATTTTATATTAAATATAATAATT
1 ATAATGGTAATCATAATTAATATATCAATAAATAAAATTTTATATTAAATATAATAATT
1085652 A
1 A
1085653 CAATTTTAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (59 bp):
ATAATGGTAATCATAATTAATATATCAATAAATAAAATTTTATATTAAATATAATAATT
Found at i:1085631 original size:21 final size:19
Alignment explanation
Indices: 1085548--1085652 Score: 51
Period size: 17 Copynumber: 5.5 Consensus size: 19
1085538 TGGTAATCAT
1085548 AATTAATATATCAATAAATAA
1 AATTAAT-TAT-AATAAATAA
* *
1085569 AATT--TTATATTAAATAT
1 AATTAATTATAATAAATAA
* *
1085586 AA-TAATTATAATGGTAATCAT
1 AATTAATTATAAT--AAAT-AA
1085607 AATTAATATATCAATAAATAA
1 AATTAAT-TAT-AATAAATAA
* *
1085628 AATT--TTATATTAAATAT
1 AATTAATTATAATAAATAA
1085645 AA-TAATTA
1 AATTAATTA
1085653 CAATTTTAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 23
0.68 0.08 0.24
Matches are distributed among these distances:
16 2 0.03
17 18 0.27
18 15 0.23
19 2 0.03
20 3 0.05
21 13 0.20
22 7 0.11
23 3 0.05
24 3 0.05
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (19 bp):
AATTAATTATAATAAATAA
Found at i:1090260 original size:30 final size:31
Alignment explanation
Indices: 1090224--1090287 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
1090214 TATAAAATGG
*
1090224 TCATTGAACTA-TTGAAAGTTTTTATTTAAA
1 TCATTGAACTATTTAAAAGTTTTTATTTAAA
*
1090254 TCATTGACCTATTTAAAAGTTTTTATTTAAA
1 TCATTGAACTATTTAAAAGTTTTTATTTAAA
1090285 TCA
1 TCA
1090288 CTTGGATGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 10 0.32
31 21 0.68
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (31 bp):
TCATTGAACTATTTAAAAGTTTTTATTTAAA
Found at i:1091993 original size:3 final size:3
Alignment explanation
Indices: 1091987--1092016 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1091977 AGAAGAAGAA
1091987 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1092017 ATTGTGGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:1092566 original size:25 final size:25
Alignment explanation
Indices: 1092502--1092568 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 25
1092492 CCACAAAATT
1092502 AGAAGTTTATAATTTAATTTCTTAAA
1 AGAA-TTTATAATTTAATTTCTTAAA
* * *
1092528 AGAATTTAAAATTTTATTTCTCTCAA
1 AGAATTTATAATTTAATTTCT-TAAA
*
1092554 A-AATTTATGATTTAA
1 AGAATTTATAATTTAA
1092569 AATGAGGTTC
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 26 0.76
26 8 0.24
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (25 bp):
AGAATTTATAATTTAATTTCTTAAA
Found at i:1107864 original size:17 final size:17
Alignment explanation
Indices: 1107842--1107883 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1107832 TATTAAAAAT
1107842 ATAATTTTATCATTT-TA
1 ATAATTTTATC-TTTGTA
1107859 ATAATTTATATCTTTGTA
1 ATAATTT-TATCTTTGTA
1107877 A-AATTTT
1 ATAATTTT
1107884 TAAAAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 1 0.04
17 15 0.65
18 7 0.30
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (17 bp):
ATAATTTTATCTTTGTA
Found at i:1117425 original size:20 final size:21
Alignment explanation
Indices: 1117387--1117425 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1117377 AAAGATGATA
**
1117387 ATTTTTTTCTTCAACTTTCAC
1 ATTTTTTTCCACAACTTTCAC
1117408 ATTTTTTTCCACAA-TTTC
1 ATTTTTTTCCACAACTTTC
1117426 TTGAATCTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.21, C:0.23, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTTTCCACAACTTTCAC
Found at i:1124483 original size:2 final size:2
Alignment explanation
Indices: 1124440--1124464 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1124430 TTTGTTAGAT
1124440 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1124465 TGAATAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1126047 original size:18 final size:18
Alignment explanation
Indices: 1126020--1126055 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
1126010 TCTTTTTTCT
1126020 TTTTAGTTTTAC-TTTAA
1 TTTTAGTTTTACATTTAA
1126037 TTTTAGCTTTTACATTTAA
1 TTTTAG-TTTTACATTTAA
1126056 AACTTATGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.25, C:0.08, G:0.06, T:0.61
Consensus pattern (18 bp):
TTTTAGTTTTACATTTAA
Found at i:1138673 original size:142 final size:141
Alignment explanation
Indices: 1138397--1138677 Score: 456
Period size: 142 Copynumber: 2.0 Consensus size: 141
1138387 ATTTGATACC
* * *
1138397 TTAAGCTAAGTTCATTAGAACTAGCCTAGAATTTCAAAAATTAGGCACGGCATAGCCAGCAAATC
1 TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAGCAAATC
* *
1138462 AGTTCTTAACCTCTCATTCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCAAT
66 AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCAAC
1138527 TTCAATTAACT
131 TTCAATTAACT
* *
1138538 TTAAGCTAAGTTCAGTTAAAACTAGCCTAGAGTTTCAAAAAATAGGCACTACATAGCCAAG-AAA
1 TTAAGCTAAGTTCA-TTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCC-AGCAAA
* *
1138602 TCAGTTCTTAACCTCTCATCCGCCATGATTCAGTTTGATACCTTAAGCTAAGTTCAATCAGTTCA
64 TCAGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCA
1138667 ACTTCAATTAA
129 ACTTCAATTAA
1138678 AACTAGCTTA
Statistics
Matches: 129, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
141 14 0.11
142 113 0.88
143 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.31
Consensus pattern (141 bp):
TTAAGCTAAGTTCATTAAAACTAGCCTAGAATTTCAAAAAATAGGCACGACATAGCCAGCAAATC
AGTTCTTAACCTCTCATCCGCCATGACTCAATTTGATACCTTAAGCTAAGTTCAATCAGTTCAAC
TTCAATTAACT
Found at i:1139533 original size:23 final size:22
Alignment explanation
Indices: 1139499--1139541 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1139489 TTATCTTAAT
1139499 ATTTTTAAATGTTTATAAATTTA
1 ATTTTTAAATG-TTATAAATTTA
*
1139522 ATTTTTATATGTTATAAATT
1 ATTTTTAAATGTTATAAATT
1139542 AGATAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (22 bp):
ATTTTTAAATGTTATAAATTTA
Found at i:1142231 original size:6 final size:6
Alignment explanation
Indices: 1142220--1142284 Score: 130
Period size: 6 Copynumber: 10.8 Consensus size: 6
1142210 CTCTAAACAG
1142220 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA TACATA
1142268 TACATA TACATA TACAT
1 TACATA TACATA TACAT
1142285 GAAGGTATAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 59 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
TACATA
Found at i:1147037 original size:2 final size:2
Alignment explanation
Indices: 1147030--1147056 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1147020 ATGAATTTGC
1147030 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 A
1147057 AGAATCTGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1147927 original size:26 final size:26
Alignment explanation
Indices: 1147889--1147940 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1147879 TTACTATGAA
1147889 AATAATAAAGGTTAAAATACAAACACT
1 AATAATAAAGGTTAAAAT-CAAACACT
* *
1147916 AATAA-AAAGGTTGAAATCTAACACT
1 AATAATAAAGGTTAAAATCAAACACT
1147941 TAGACAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 11 0.48
27 5 0.22
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.23
Consensus pattern (26 bp):
AATAATAAAGGTTAAAATCAAACACT
Found at i:1149931 original size:14 final size:16
Alignment explanation
Indices: 1149906--1149943 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1149896 TCAAAATTCA
1149906 AAAAATACATT-AATT
1 AAAAATACATTAAATT
1149921 AAAAATA-ATTAAATT
1 AAAAATACATTAAATT
1149936 -AAAATACA
1 AAAAATACA
1149944 AAAACAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATACATTAAATT
Found at i:1151477 original size:19 final size:20
Alignment explanation
Indices: 1151453--1151496 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1151443 ATCAATCAAC
1151453 AAATAAATAAA-AT-TAATAA
1 AAATAAA-AAATATATAATAA
*
1151472 AAATAAAAAATATATATTAA
1 AAATAAAAAATATATAATAA
1151492 AAATA
1 AAATA
1151497 TAATCTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 3 0.14
19 9 0.41
20 10 0.45
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAATAAAAAATATATAATAA
Found at i:1151493 original size:13 final size:13
Alignment explanation
Indices: 1151477--1151512 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1151467 AATAAAAATA
1151477 AAAAATATATAT-T
1 AAAAATATA-ATCT
1151490 AAAAATATAATCT
1 AAAAATATAATCT
1151503 AAAAATATAA
1 AAAAATATAA
1151513 ATATATGTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 2 0.09
13 20 0.91
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAATATAATCT
Found at i:1164119 original size:121 final size:121
Alignment explanation
Indices: 1163950--1164213 Score: 293
Period size: 121 Copynumber: 2.2 Consensus size: 121
1163940 ACTTGCTAAG
* * * *
1163950 CTCAACCCATAAAAAATCAAACCTTAGGCAAGAGATTTTTGAATTTGGGTCGGATCGA-ACTAGC
1 CTCAACCCAT-AAAAATCAAACATTAGGCAAGAAACTTTTGAATTTGGGTCAGATC-ATACTAGC
* * *
1164014 TTAAATTCGAATTAAACATTCCCATTGATTGAAATACTTTCCTAACCTTTTAAGTCTGAT
64 TTAAATTCGAATTAAACATTCCCATTAATTGAAATACTCT-CTAACCCTTTAAGT-TGAT
* * * *
1164074 C-CTAACCCATAAAAATCAAACATTA-G-ACGAAACTTTTGAATTTGGGTTATATCATATTAGCT
1 CTC-AACCCATAAAAATCAAACATTAGGCAAGAAACTTTTGAATTTGGGTCAGATCATACTAGCT
* * * * *
1164136 TGAATTCGAATTAGATATTCTCATTAATTGAAATACTCTCTAACCCTTTAAGTTTAT
65 TAAATTCGAATTAAACATTCCCATTAATTGAAATACTCTCTAACCCTTTAAGTTGAT
**
1164193 CTCAACTTATAAAAATCAAAC
1 CTCAACCCATAAAAATCAAAC
1164214 TTTGAATAAA
Statistics
Matches: 119, Mismatches: 18, Indels: 11
0.80 0.12 0.07
Matches are distributed among these distances:
119 20 0.17
120 15 0.13
121 60 0.50
122 1 0.01
123 15 0.13
124 8 0.07
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (121 bp):
CTCAACCCATAAAAATCAAACATTAGGCAAGAAACTTTTGAATTTGGGTCAGATCATACTAGCTT
AAATTCGAATTAAACATTCCCATTAATTGAAATACTCTCTAACCCTTTAAGTTGAT
Found at i:1164237 original size:121 final size:121
Alignment explanation
Indices: 1164010--1164243 Score: 269
Period size: 121 Copynumber: 1.9 Consensus size: 121
1164000 CGGATCGAAC
* * *
1164010 TAGCTTAAATTCGAATTAAACATTCCCATTGATTGAAATACTTTCCTAACCTTTTAAGTCTGATC
1 TAGCTTAAATTCGAATTAAACATTCCCATTAATTGAAATACTCTCCTAACCCTTTAAGTCTGATC
** *
1164075 CTAACCCATAAAAATCAAACATTAGACGAAACTTTTGAATTTGGGTTATATCATAT
66 CTAACCCATAAAAATCAAACATTAGAAAAAACTTTTAAATTTGGGTTATATCATAT
* * * * *
1164131 TAGCTTGAATTCGAATTAGATATTCTCATTAATTGAAATACTCT-CTAACCCTTTAAGT-TTAT-
1 TAGCTTAAATTCGAATTAAACATTCCCATTAATTGAAATACTCTCCTAACCCTTTAAGTCTGATC
** * *
1164193 CTCAACTTATAAAAATCAAAC-TTTGAATAAAAGATTTTTAAATTTGGGTTA
66 CT-AACCCATAAAAATCAAACATTAG-A-AAAA-ACTTTTAAATTTGGGTTA
1164244 ATTCAGACAG
Statistics
Matches: 94, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
118 5 0.05
119 20 0.21
120 15 0.16
121 54 0.57
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.38
Consensus pattern (121 bp):
TAGCTTAAATTCGAATTAAACATTCCCATTAATTGAAATACTCTCCTAACCCTTTAAGTCTGATC
CTAACCCATAAAAATCAAACATTAGAAAAAACTTTTAAATTTGGGTTATATCATAT
Found at i:1166771 original size:14 final size:15
Alignment explanation
Indices: 1166752--1166780 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1166742 CATATTAATA
1166752 ATATATAATA-AAAT
1 ATATATAATATAAAT
1166766 ATATATAATATAAAT
1 ATATATAATATAAAT
1166781 CAGTTAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
ATATATAATATAAAT
Found at i:1171819 original size:6 final size:6
Alignment explanation
Indices: 1171810--1171834 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1171800 GCTGAAGCTA
1171810 GCAATG GCAATG GCAATG GCAATG G
1 GCAATG GCAATG GCAATG GCAATG G
1171835 TTGCTCCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.36, T:0.16
Consensus pattern (6 bp):
GCAATG
Found at i:1181314 original size:17 final size:18
Alignment explanation
Indices: 1181275--1181315 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
1181265 TTTTATAAAT
1181275 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGATA
1181293 TGTGAATTA-ATATTGA-A
1 TGTGAATTATAT-TTGATA
1181310 TGTGAA
1 TGTGAA
1181316 AGGAAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.44
Consensus pattern (18 bp):
TGTGAATTATATTTGATA
Found at i:1181566 original size:23 final size:23
Alignment explanation
Indices: 1181539--1181659 Score: 165
Period size: 23 Copynumber: 5.3 Consensus size: 23
1181529 AGTGTTATTG
*
1181539 ATCAGTGGTAGCTTTGGCTACA-
1 ATCAGTGGTAGCTTCGGCTACAT
* *
1181561 ATTCAGTGGTAGCTACGGTTACAT
1 A-TCAGTGGTAGCTTCGGCTACAT
1181585 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* **
1181608 TTCAGTGGTAGCAAC-GCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1181630 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
1181653 ATCAGTG
1 ATCAGTG
1181660 TGGCATTTAT
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
22 20 0.24
23 64 0.75
24 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:1181644 original size:45 final size:46
Alignment explanation
Indices: 1181539--1181659 Score: 190
Period size: 45 Copynumber: 2.7 Consensus size: 46
1181529 AGTGTTATTG
* * * *
1181539 ATCAGTGGTAGCTTTGGCTACAATTCAGTGGTAGCTACGGTTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCAACGGCTACAT
1181585 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCAAC-GCTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCAACGGCTACAT
*
1181630 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
1181660 TGGCATTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
45 35 0.50
46 35 0.50
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCAACGGCTACAT
Found at i:1185731 original size:26 final size:26
Alignment explanation
Indices: 1185702--1185754 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
1185692 TATTTATAAC
* *
1185702 TTTTAAAAAATTAAATTAAAATTTTA
1 TTTTAAAAAATCAAAATAAAATTTTA
** *
1185728 TTTTTTAAAATCAAAATACAATTTTA
1 TTTTAAAAAATCAAAATAAAATTTTA
1185754 T
1 T
1185755 CATTATTAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TTTTAAAAAATCAAAATAAAATTTTA
Found at i:1186121 original size:22 final size:23
Alignment explanation
Indices: 1186068--1186123 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
1186058 TTTAATTAAA
* * *
1186068 ATTAAAATTAAAATTATTTTTTT
1 ATTAAAATTAAAACTATATTGTT
*
1186091 AATAAAATTAAAACTA-ATTGTT
1 ATTAAAATTAAAACTATATTGTT
1186113 ATTAAAATTAA
1 ATTAAAATTAA
1186124 TTGTTAGTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
ATTAAAATTAAAACTATATTGTT
Found at i:1186136 original size:16 final size:16
Alignment explanation
Indices: 1186099--1186138 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
1186089 TTAATAAAAT
* *
1186099 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
1186115 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
1186131 TAAAATTA
1 TAAAATTA
1186139 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:1186201 original size:59 final size:59
Alignment explanation
Indices: 1186127--1186253 Score: 236
Period size: 59 Copynumber: 2.2 Consensus size: 59
1186117 AAATTAATTG
*
1186127 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGA
1 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGA
*
1186186 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGA
1 TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGA
1186245 TTAGTAAAA
1 TTAGTAAAA
1186254 CAAACTTGAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (59 bp):
TTAGTAAAATTATCAAATTATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGA
Found at i:1188287 original size:31 final size:31
Alignment explanation
Indices: 1188249--1188322 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
1188239 AAAAAAGATT
1188249 AGGTACCAAATTAAGAAAAAGAGTCAAGTTC
1 AGGTACCAAATTAAGAAAAAGAGTCAAGTTC
* * * * *
1188280 AGGTACCAAATTAGGAATACGTGTCAAGTTT
1 AGGTACCAAATTAAGAAAAAGAGTCAAGTTC
*
1188311 GGGTACCAAATT
1 AGGTACCAAATT
1188323 GGACCAAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.24
Consensus pattern (31 bp):
AGGTACCAAATTAAGAAAAAGAGTCAAGTTC
Found at i:1188375 original size:31 final size:30
Alignment explanation
Indices: 1188252--1188379 Score: 91
Period size: 31 Copynumber: 4.2 Consensus size: 30
1188242 AAAGATTAGG
* *
1188252 TACCAAATTAAGAAAAAGAGTCAAGTTCAGG
1 TACCAAATT-AGAAAAAGTGTCAAGTTCAGA
* * ** *
1188283 TACCAAATTAGGAATACGTGTCAAGTTTGGG
1 TACCAAATTA-GAAAAAGTGTCAAGTTCAGA
* ** *
1188314 TACCAAATTGGACCAAAA---AAAAGTTTAGA
1 TACCAAATTAGA--AAAAGTGTCAAGTTCAGA
1188343 TACCAAATTAGAAAAACGTGTCAAGTTCAGA
1 TACCAAATTAGAAAAA-GTGTCAAGTTCAGA
1188374 TACCAA
1 TACCAA
1188380 GTGTCATAAA
Statistics
Matches: 74, Mismatches: 16, Indels: 14
0.71 0.15 0.13
Matches are distributed among these distances:
27 4 0.05
29 18 0.24
30 3 0.04
31 47 0.64
32 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.23
Consensus pattern (30 bp):
TACCAAATTAGAAAAAGTGTCAAGTTCAGA
Found at i:1189215 original size:30 final size:29
Alignment explanation
Indices: 1189175--1189238 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
1189165 TTTTGTTAAA
* * *
1189175 AATATTTTATTTTAAAATTTATATAAT-ATG
1 AATATATTATTTCAAAA-ATAT-TAATAATG
1189205 AATATATTATTTCAAAAATATTAATAATG
1 AATATATTATTTCAAAAATATTAATAATG
1189234 AATAT
1 AATAT
1189239 GGGTAGAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 11 0.37
30 15 0.50
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (29 bp):
AATATATTATTTCAAAAATATTAATAATG
Found at i:1196917 original size:108 final size:107
Alignment explanation
Indices: 1196776--1196979 Score: 329
Period size: 108 Copynumber: 1.9 Consensus size: 107
1196766 AAAGCTACCA
* * *
1196776 TCTTTACTCGTCGGTGATAAAAAAGACAAAATTGAACAATTAGATGACCCAAAAAATATTTGCTA
1 TCTTTACTCGTCGATGATAAAAAAGACAAAATTGAACAATTAGATGACCAAAAAAATATTTACTA
1196841 ACAAGATGACCAAAATTTTTTTTTACTAATAGCTAGATAACC
66 ACAAGATGACCAAAATTTTTTTTTACTAATAGCTAGATAACC
* *
1196883 TCTTTAC-CTGTCGATGATCAAAAAAGACAGAATTGAACAGTTAGATGACCAAAAAAATATTTAC
1 TCTTTACTC-GTCGATGAT-AAAAAAGACAAAATTGAACAATTAGATGACCAAAAAAATATTTAC
*
1196947 TAACTAGATGACCAAAATTTTTTTTTACTAATA
64 TAACAAGATGACCAAAATTTTTTTTTACTAATA
1196980 ACTGGAAAAC
Statistics
Matches: 89, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
106 1 0.01
107 15 0.17
108 73 0.82
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (107 bp):
TCTTTACTCGTCGATGATAAAAAAGACAAAATTGAACAATTAGATGACCAAAAAAATATTTACTA
ACAAGATGACCAAAATTTTTTTTTACTAATAGCTAGATAACC
Found at i:1203343 original size:14 final size:14
Alignment explanation
Indices: 1203326--1203352 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1203316 ATGTCACACC
1203326 AAAAATTTAATAAA
1 AAAAATTTAATAAA
1203340 AAAAATTTAATAA
1 AAAAATTTAATAA
1203353 TTGGACCTAA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAAAATTTAATAAA
Found at i:1205487 original size:19 final size:21
Alignment explanation
Indices: 1205448--1205487 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1205438 CTGATGATTA
1205448 AATATATATGATGTAACAAAG
1 AATATATATGATGTAACAAAG
1205469 AATATATATGAT-TAA-AAAG
1 AATATATATGATGTAACAAAG
1205488 CTTACTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.21
20 3 0.16
21 12 0.63
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (21 bp):
AATATATATGATGTAACAAAG
Found at i:1206585 original size:2 final size:2
Alignment explanation
Indices: 1206578--1206605 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1206568 AAATTCATGA
1206578 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1206606 TTAAAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1207080 original size:2 final size:2
Alignment explanation
Indices: 1207073--1207127 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1207063 ACCCTTGATA
1207073 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1207115 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
1207128 ANNNNNNNNN
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1210917 original size:18 final size:18
Alignment explanation
Indices: 1210894--1210929 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1210884 AAAATTAATT
1210894 ATTAAAAATTAAACAAAA
1 ATTAAAAATTAAACAAAA
1210912 ATTAAAAATTAAACAAAA
1 ATTAAAAATTAAACAAAA
1210930 TAAAATCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (18 bp):
ATTAAAAATTAAACAAAA
Found at i:1225017 original size:2 final size:2
Alignment explanation
Indices: 1225010--1225044 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1225000 AATCAAGAGG
*
1225010 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1225045 CTCAATGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1225899 original size:137 final size:136
Alignment explanation
Indices: 1225702--1226091 Score: 514
Period size: 137 Copynumber: 2.8 Consensus size: 136
1225692 AAAATCGAAA
* * * * * * *
1225702 ATTAGTAGAGAAGAGAGAACAACTTCGAACGCTGGGAACCACTTCAAAGTTATCGAAATTCGATC
1 ATTAGCAGAGAAGAGAGAACAATTTCG-ACGCTCGTAATCACTACAAAGCTATCGAAATTCGATC
* * *
1225767 AAACGAACTTCATAATTCGGCTATAAAACAACCATCCATCACCCAAAAACAAAATAA-AAATTCA
65 AAACGAACTTCATAATTCGACTATAAAACAACCATCCATCA--CAAAAAAAAAAAAAGAAATTCA
1225831 AAAGCAAAG
128 AAAGCAAAG
* *
1225840 GTTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTCCAAAGCTATCGAAATTCGATCA
1 ATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTCGATCA
*
1225905 AACGAACTTTCATAATTCGACTATAAAACAACGATCCATCACAAAAAAAAAAAAAGAAATTCAAA
66 AACGAAC-TTCATAATTCGACTATAAAACAACCATCCATCACAAAAAAAAAAAAAGAAATTCAAA
1225970 AGCAAAG
130 AGCAAAG
* * * *
1225977 ATTAGCAGAGCAGAGAGAACAATTTCGACGCTCGTAATCACTACAAATCTATCTAAATTTGATCA
1 ATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTCGATCA
* * * * *
1226042 AACGAACTTGCATAA-CCAGACTATTAAACAACGATCTATCACCAAAAAAA
66 AACGAACTT-CATAATTC-GACTATAAAACAACCATCCATCACAAAAAAAA
1226092 TTCAAACAAC
Statistics
Matches: 226, Mismatches: 22, Indels: 9
0.88 0.09 0.04
Matches are distributed among these distances:
136 15 0.07
137 156 0.69
138 55 0.24
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.20
Consensus pattern (136 bp):
ATTAGCAGAGAAGAGAGAACAATTTCGACGCTCGTAATCACTACAAAGCTATCGAAATTCGATCA
AACGAACTTCATAATTCGACTATAAAACAACCATCCATCACAAAAAAAAAAAAAGAAATTCAAAA
GCAAAG
Found at i:1228070 original size:22 final size:21
Alignment explanation
Indices: 1228032--1228091 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
1228022 GTGACCATTG
* **
1228032 AAATTTTGAATTTAATTTTTTT
1 AAATTTT-AATTCAATTAATTT
1228054 AAATTTTAATCTCAATTAATTT
1 AAATTTTAAT-TCAATTAATTT
1228076 AAATATTTAATT-AATT
1 AAAT-TTTAATTCAATT
1228092 GATACTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 7 0.21
22 20 0.61
23 6 0.18
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (21 bp):
AAATTTTAATTCAATTAATTT
Found at i:1228114 original size:2 final size:2
Alignment explanation
Indices: 1228107--1228132 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1228097 TTAAATTGTA
1228107 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1228133 CTGAATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1233358 original size:6 final size:7
Alignment explanation
Indices: 1233338--1233366 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1233328 AAATCTAAAA
1233338 TAATTTT
1 TAATTTT
1233345 TAATTTT
1 TAATTTT
1233352 TAATTTT
1 TAATTTT
1233359 TAATTTT
1 TAATTTT
1233366 T
1 T
1233367 CAAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TAATTTT
Found at i:1233413 original size:7 final size:7
Alignment explanation
Indices: 1233401--1233427 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1233391 ATATGATACA
1233401 TTTAGGG
1 TTTAGGG
1233408 TTTAGGG
1 TTTAGGG
1233415 TTTAGGG
1 TTTAGGG
1233422 TTTAGG
1 TTTAGG
1233428 ATGATACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
TTTAGGG
Found at i:1237207 original size:17 final size:17
Alignment explanation
Indices: 1237175--1237208 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1237165 ATCATTGAAT
*
1237175 TATATTATTGCCCTTAA
1 TATATTATTGACCTTAA
*
1237192 TATATTATTGATCTTAA
1 TATATTATTGACCTTAA
1237209 GCTTAATTAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.50
Consensus pattern (17 bp):
TATATTATTGACCTTAA
Found at i:1244638 original size:2 final size:2
Alignment explanation
Indices: 1244592--1244625 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1244582 TTAAAAACTT
1244592 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1244626 AACAAATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1246115 original size:15 final size:15
Alignment explanation
Indices: 1246080--1246129 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1246070 ATACGAACCA
1246080 AAATA-ATA-AAATAT
1 AAATATATATAAAT-T
*
1246094 AATTATAT-TAAATT
1 AAATATATATAAATT
1246108 AGAATATATATAAATT
1 A-AATATATATAAATT
1246124 AAATAT
1 AAATAT
1246130 CAAATTTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
14 6 0.20
15 17 0.57
16 7 0.23
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (15 bp):
AAATATATATAAATT
Found at i:1251258 original size:31 final size:31
Alignment explanation
Indices: 1251222--1251281 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
1251212 CTTTTAACCC
*
1251222 CTAAATTT-GATAATTACATTCATTTTGGTAT
1 CTAAATTTAG-TAATTACATTCAATTTGGTAT
*
1251253 CTAAATTTAGTAATTAGATTCAATTTGGT
1 CTAAATTTAGTAATTACATTCAATTTGGT
1251282 CATTGATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 25 0.96
32 1 0.04
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (31 bp):
CTAAATTTAGTAATTACATTCAATTTGGTAT
Found at i:1255123 original size:31 final size:32
Alignment explanation
Indices: 1255088--1255148 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
1255078 CATGTTAAGT
1255088 ACATGTGTCCATAATCTTGTA-CATTTGGTTA
1 ACATGTGTCCATAATCTTGTATCATTTGGTTA
*
1255119 ACATGTGTCCATACTCTTGTATCATTTGGT
1 ACATGTGTCCATAATCTTGTATCATTTGGT
1255149 AAGGTGAGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 20 0.71
32 8 0.29
ACGTcount: A:0.23, C:0.18, G:0.16, T:0.43
Consensus pattern (32 bp):
ACATGTGTCCATAATCTTGTATCATTTGGTTA
Found at i:1257946 original size:18 final size:18
Alignment explanation
Indices: 1257912--1257959 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
1257902 GACTATTTGC
* * *
1257912 CACATTTGGATTGTCCAC
1 CACATTTGGACTCTCCAA
*
1257930 CATATTTGGACTCTCCAA
1 CACATTTGGACTCTCCAA
1257948 CACATTTGGACT
1 CACATTTGGACT
1257960 GTGTGCCGCC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.27, G:0.15, T:0.33
Consensus pattern (18 bp):
CACATTTGGACTCTCCAA
Found at i:1258802 original size:6 final size:6
Alignment explanation
Indices: 1258791--1258860 Score: 131
Period size: 6 Copynumber: 11.7 Consensus size: 6
1258781 AAAGCAGAAT
1258791 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
*
1258839 AAAAGA AGAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAA
1258861 AGGACTCCAC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 62 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:1269762 original size:2 final size:2
Alignment explanation
Indices: 1269750--1269780 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1269740 CTTTTTCTTT
*
1269750 TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1269781 TTTTTTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.48, T:0.48
Consensus pattern (2 bp):
TG
Found at i:1270693 original size:50 final size:49
Alignment explanation
Indices: 1270631--1270728 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 49
1270621 TAGTAAAATA
1270631 TAATTTTTATTTTCATTAAAAGTAAACATAATATTAATAAAAAAATTTAC
1 TAATTTTTATTTTCATTAAAAGTAAACATAATATTAAT-AAAAAATTTAC
1270681 TAATTTTTATTTTCATTAAAAGTAAACATAATATTAATAAAAAATTTA
1 TAATTTTTATTTTCATTAAAAGTAAACATAATATTAATAAAAAATTTA
1270729 AATCTTATGA
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 10 0.21
50 38 0.79
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (49 bp):
TAATTTTTATTTTCATTAAAAGTAAACATAATATTAATAAAAAATTTAC
Found at i:1290362 original size:22 final size:22
Alignment explanation
Indices: 1290337--1290378 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1290327 CCTAATCACA
1290337 ACCTACTACCACTAAGTAACAT
1 ACCTACTACCACTAAGTAACAT
*
1290359 ACCTACTACCACTAATTAAC
1 ACCTACTACCACTAAGTAAC
1290379 TTGTACAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.33, G:0.02, T:0.24
Consensus pattern (22 bp):
ACCTACTACCACTAAGTAACAT
Found at i:1296388 original size:35 final size:35
Alignment explanation
Indices: 1296342--1296413 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1296332 ACCTTCCACT
1296342 GTTTTTGTGCAGCCAAAGCAAACAGGAGCTTTATG
1 GTTTTTGTGCAGCCAAAGCAAACAGGAGCTTTATG
1296377 GTTTTTGTGCAGCCAAAGCAAACAGGAGCTTTATG
1 GTTTTTGTGCAGCCAAAGCAAACAGGAGCTTTATG
1296412 GT
1 GT
1296414 GTCCAGCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (35 bp):
GTTTTTGTGCAGCCAAAGCAAACAGGAGCTTTATG
Found at i:1301809 original size:24 final size:23
Alignment explanation
Indices: 1301743--1301816 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 23
1301733 AAAAAGGGGT
*
1301743 GATAAATAATAATGAAATAATAATA
1 GATAAATAA-AATG-AATAATAATG
*
1301768 GATAACA-AAATATCAATAATAATG
1 GATAA-ATAAA-ATGAATAATAATG
1301792 GCATAAATAAAATGAATAACTAATG
1 G-ATAAATAAAATGAATAA-TAATG
1301817 AAAGAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
24 19 0.46
25 21 0.51
26 1 0.02
ACGTcount: A:0.59, C:0.05, G:0.09, T:0.26
Consensus pattern (23 bp):
GATAAATAAAATGAATAATAATG
Found at i:1314835 original size:17 final size:17
Alignment explanation
Indices: 1314815--1314869 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
1314805 ACTAAAATAT
1314815 TCATTCTATTAACAAAA
1 TCATTCTATTAACAAAA
*
1314832 TCATATC-ATTAA-AATAT
1 TCAT-TCTATTAACAA-AA
1314849 TCATTCTATTAACAAAA
1 TCATTCTATTAACAAAA
1314866 TCAT
1 TCAT
1314870 AAAAAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 4 0.12
17 24 0.75
18 4 0.12
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.38
Consensus pattern (17 bp):
TCATTCTATTAACAAAA
Found at i:1314845 original size:34 final size:34
Alignment explanation
Indices: 1314797--1314870 Score: 130
Period size: 34 Copynumber: 2.2 Consensus size: 34
1314787 CCTTTATTGG
1314797 ATCATACCACTAAAATATTCATTCTATTAACAAA
1 ATCATACCACTAAAATATTCATTCTATTAACAAA
* *
1314831 ATCATATCATTAAAATATTCATTCTATTAACAAA
1 ATCATACCACTAAAATATTCATTCTATTAACAAA
1314865 ATCATA
1 ATCATA
1314871 AAAAACTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (34 bp):
ATCATACCACTAAAATATTCATTCTATTAACAAA
Found at i:1315194 original size:34 final size:36
Alignment explanation
Indices: 1315147--1315215 Score: 90
Period size: 34 Copynumber: 2.0 Consensus size: 36
1315137 TGGAAAAAAT
* *
1315147 ATTTTATTGAAAACATA-TAAATTTAA-TTTAATTTA
1 ATTTTATTAAAAACATAGT-AACTTAATTTTAATTTA
1315182 ATTTT-TTAAAAACATAGTAACTTAATTTTAATTT
1 ATTTTATTAAAAACATAGTAACTTAATTTTAATTT
1315216 TGAATAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.49
Consensus pattern (36 bp):
ATTTTATTAAAAACATAGTAACTTAATTTTAATTTA
Found at i:1330460 original size:17 final size:17
Alignment explanation
Indices: 1330438--1330470 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1330428 GCCCAATTTA
*
1330438 ACTAATGTTTTATGAAC
1 ACTAATGTTTAATGAAC
1330455 ACTAATGTTTAATGAA
1 ACTAATGTTTAATGAA
1330471 TAAACAACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (17 bp):
ACTAATGTTTAATGAAC
Found at i:1335352 original size:11 final size:11
Alignment explanation
Indices: 1335353--1335381 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1335343 TTTCTTCTTC
1335353 TTCTTCTCCAT
1 TTCTTCTCCAT
1335364 TTCTTCTCCAT
1 TTCTTCTCCAT
1335375 TTCTTCT
1 TTCTTCT
1335382 ACTGCCCAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.34, G:0.00, T:0.59
Consensus pattern (11 bp):
TTCTTCTCCAT
Found at i:1335738 original size:25 final size:25
Alignment explanation
Indices: 1335683--1335739 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
1335673 ATATATATAC
* * *
1335683 AAAATAATGTTAACATTAAATAAAT
1 AAAATTATATTAACATTAAATAAAA
* *
1335708 ATAATTATATTAATATTAAATAAAA
1 AAAATTATATTAACATTAAATAAAA
1335733 AAAATTA
1 AAAATTA
1335740 ATCTCCCTCT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAATTATATTAACATTAAATAAAA
Found at i:1335862 original size:2 final size:2
Alignment explanation
Indices: 1335855--1335884 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1335845 ACCTCCTACA
1335855 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1335885 TTGTTTGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1338751 original size:2 final size:2
Alignment explanation
Indices: 1338744--1338770 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1338734 ACAATAACAA
1338744 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 A
1338771 AATTCCAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1340084 original size:31 final size:32
Alignment explanation
Indices: 1340046--1340108 Score: 119
Period size: 31 Copynumber: 2.0 Consensus size: 32
1340036 GGATCATGAG
1340046 TTGATTTCACAAGGGGTTC-AAAGTTCTTGAA
1 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1340077 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1 TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
1340109 CAATCCCCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 19 0.61
32 12 0.39
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (32 bp):
TTGATTTCACAAGGGGTTCAAAAGTTCTTGAA
Found at i:1340716 original size:21 final size:17
Alignment explanation
Indices: 1340678--1340712 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1340668 TATAAGAATG
1340678 TTTATTGAATGGAAATA
1 TTTATTGAATGGAAATA
1340695 TTTATTGAATGGAAATA
1 TTTATTGAATGGAAATA
1340712 T
1 T
1340713 ATATAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (17 bp):
TTTATTGAATGGAAATA
Found at i:1340905 original size:6 final size:6
Alignment explanation
Indices: 1340894--1340959 Score: 114
Period size: 6 Copynumber: 11.0 Consensus size: 6
1340884 GAGGATTTAA
* *
1340894 TATATG TATATG TATATG TACATG TATATG TATATG TATATG TACATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1340942 TATATG TATATG TATATG
1 TATATG TATATG TATATG
1340960 AATCTTACTC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (6 bp):
TATATG
Found at i:1340926 original size:24 final size:24
Alignment explanation
Indices: 1340894--1340959 Score: 132
Period size: 24 Copynumber: 2.8 Consensus size: 24
1340884 GAGGATTTAA
1340894 TATATGTATATGTATATGTACATG
1 TATATGTATATGTATATGTACATG
1340918 TATATGTATATGTATATGTACATG
1 TATATGTATATGTATATGTACATG
1340942 TATATGTATATGTATATG
1 TATATGTATATGTATATG
1340960 AATCTTACTC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (24 bp):
TATATGTATATGTATATGTACATG
Found at i:1344534 original size:6 final size:6
Alignment explanation
Indices: 1344523--1344552 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
1344513 TCGTCAATCA
*
1344523 CCGTTG CCGTTG CCGTTG CCGTTT CCGTTG
1 CCGTTG CCGTTG CCGTTG CCGTTG CCGTTG
1344553 ATACCTCCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.33, G:0.30, T:0.37
Consensus pattern (6 bp):
CCGTTG
Found at i:1345792 original size:21 final size:21
Alignment explanation
Indices: 1345766--1345820 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
1345756 AACAGCGGTG
*
1345766 GCGGTGAGATTAGTTACTGTA
1 GCGGTGAGATTAGGTACTGTA
* *
1345787 GCGGTGAGATTGGGTATTGTA
1 GCGGTGAGATTAGGTACTGTA
*
1345808 GCAGTGAGATTAG
1 GCGGTGAGATTAG
1345821 AAACAGCGGT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.07, G:0.38, T:0.31
Consensus pattern (21 bp):
GCGGTGAGATTAGGTACTGTA
Found at i:1346098 original size:33 final size:34
Alignment explanation
Indices: 1346031--1346098 Score: 93
Period size: 33 Copynumber: 2.0 Consensus size: 34
1346021 AATAAAATTT
* *
1346031 AAATATTTTTAACTTATATTAATAATAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
* *
1346065 AAATATATTTAAATTAT-TTTATATTAAATAATA
1 AAATATATTTAAATTATATTAATAATAAATAATA
1346098 A
1 A
1346099 TTAAACTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (34 bp):
AAATATATTTAAATTATATTAATAATAAATAATA
Found at i:1353734 original size:24 final size:24
Alignment explanation
Indices: 1353707--1353753 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1353697 TTAATTTCCG
1353707 AGTGATAACATAAT-ACAATTTTAA
1 AGTG-TAACATAATCACAATTTTAA
* *
1353731 AGTGTCACATCATCACAATTTTA
1 AGTGTAACATAATCACAATTTTA
1353754 CATTTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.34
Consensus pattern (24 bp):
AGTGTAACATAATCACAATTTTAA
Found at i:1354837 original size:29 final size:27
Alignment explanation
Indices: 1354801--1354855 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 27
1354791 AATATATTTG
1354801 TTTTTTTAATTTTAAAATACTTTTTAAT
1 TTTTTTTAATTTTAAAAT-CTTTTTAAT
*
1354829 TTTTATTTAATTTTAAAATTTTTTTAA
1 TTTT-TTTAATTTTAAAATCTTTTTAA
1354856 AATACTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTTTAATTTTAAAATCTTTTTAAT
Found at i:1354853 original size:11 final size:11
Alignment explanation
Indices: 1354839--1354939 Score: 79
Period size: 11 Copynumber: 9.4 Consensus size: 11
1354829 TTTTATTTAA
1354839 TTTTAAAATTT
1 TTTTAAAATTT
*
1354850 TTTTAAAATACT
1 TTTTAAAAT-TT
1354862 TTTTAAAA-TT
1 TTTTAAAATTT
1354872 TTTT-AAA---
1 TTTTAAAATTT
*
1354879 TTTTAAAATAT
1 TTTTAAAATTT
1354890 TTTTAAAATACTT
1 TTTTAAAAT--TT
*
1354903 TTTTTAAA-TT
1 TTTTAAAATTT
1354913 TTTTAAAATTT
1 TTTTAAAATTT
**
1354924 TTAAAATAATTT
1 TTTTAA-AATTT
1354936 TTTT
1 TTTT
1354940 GTATTTATTT
Statistics
Matches: 72, Mismatches: 9, Indels: 17
0.73 0.09 0.17
Matches are distributed among these distances:
7 4 0.06
8 3 0.04
9 3 0.04
10 14 0.19
11 24 0.33
12 16 0.22
13 8 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:1354860 original size:40 final size:40
Alignment explanation
Indices: 1354810--1354937 Score: 168
Period size: 40 Copynumber: 3.1 Consensus size: 40
1354800 GTTTTTTTAA
* * *
1354810 TTTTAAAATACTTTTT-AATTTTTATTTAATTTTAAAATTT
1 TTTTAAAATACTTTTTAAAATTTT-TTAAATTTTAAAATAT
1354850 TTTTAAAATACTTTTTAAAATTTTTTAAATTTTAAAATAT
1 TTTTAAAATACTTTTTAAAATTTTTTAAATTTTAAAATAT
*
1354890 TTTTAAAATACTTTTTTTAAATTTTTTAAAATTTTTAAAATAAT
1 TTTTAAAATAC-TTTTTAAAATTTTTT-AAA-TTTTAAAAT-AT
1354934 TTTT
1 TTTT
1354938 TTGTATTTAT
Statistics
Matches: 79, Mismatches: 4, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
40 41 0.52
41 20 0.25
42 3 0.04
43 9 0.11
44 6 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (40 bp):
TTTTAAAATACTTTTTAAAATTTTTTAAATTTTAAAATAT
Found at i:1354866 original size:29 final size:28
Alignment explanation
Indices: 1354803--1354867 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
1354793 TATATTTGTT
**
1354803 TTTTTAATTTTAAAATACTTTTTAATTT
1 TTTTTAATTTTAAAATACTTTTTAATAC
*
1354831 TTATTTAATTTTAAAAT-TTTTTTAAAATAC
1 TT-TTTAATTTTAAAATACTTTTT--AATAC
1354861 TTTTTAA
1 TTTTTAA
1354868 AATTTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
28 7 0.23
29 19 0.61
30 5 0.16
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTTTAATTTTAAAATACTTTTTAATAC
Found at i:1354906 original size:32 final size:32
Alignment explanation
Indices: 1354849--1354939 Score: 111
Period size: 32 Copynumber: 2.9 Consensus size: 32
1354839 TTTTAAAATT
1354849 TTTTTAAAATACTTTTT-AAA-A-TTTTTTAAA
1 TTTTTAAAATA-TTTTTAAAATATTTTTTTAAA
1354879 -TTTTAAAATATTTTTAAAATACTTTTTTTAAA
1 TTTTTAAAATATTTTTAAAATA-TTTTTTTAAA
*
1354911 TTTTTTAAA-ATTTTTAAAATAATTTTTTT
1 TTTTTAAAATATTTTTAAAAT-ATTTTTTT
1354940 GTATTTATTT
Statistics
Matches: 54, Mismatches: 1, Indels: 10
0.83 0.02 0.15
Matches are distributed among these distances:
28 5 0.09
29 13 0.24
30 1 0.02
32 27 0.50
33 8 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (32 bp):
TTTTTAAAATATTTTTAAAATATTTTTTTAAA
Found at i:1354929 original size:9 final size:9
Alignment explanation
Indices: 1354861--1354930 Score: 59
Period size: 9 Copynumber: 7.1 Consensus size: 9
1354851 TTTAAAATAC
1354861 TTTTTAAAA
1 TTTTTAAAA
*
1354870 TTTTTTAAA
1 TTTTTAAAA
*
1354879 TTTTAAAATA
1 TTTTTAAA-A
1354889 TTTTTAAAATA
1 TTTTT-AAA-A
*
1354900 CTTTTTTTAAAT
1 ---TTTTTAAAA
1354912 TTTTTAAAA
1 TTTTTAAAA
1354921 TTTTTAAAA
1 TTTTTAAAA
1354930 T
1 T
1354931 AATTTTTTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
9 32 0.64
10 5 0.10
11 5 0.10
13 3 0.06
14 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:1356040 original size:16 final size:16
Alignment explanation
Indices: 1356007--1356054 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1355997 AGATGACTAT
*
1356007 ATAAAAAATTTTAATAA
1 ATAAAAAA-TATAATAA
*
1356024 ATAAAAAATATATTAA
1 ATAAAAAATATAATAA
1356040 ATTAAAATAATATAA
1 A-TAAAA-AATATAA
1356055 ATATTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 7 0.27
17 13 0.50
18 6 0.23
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAAAAAATATAATAA
Found at i:1356393 original size:44 final size:44
Alignment explanation
Indices: 1356327--1356417 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
1356317 TTTTCATATA
* * *
1356327 AATGCACTATTAGTCTTTCGTTACTATTTAACATTGGAGTGATC
1 AATGCACTATTAGTCCTCCGTTACTATTTAACAGTGGAGTGATC
1356371 AATGCA-TCATTAGTCCTCCGTTACTATTTAACAGTGGAGTGATC
1 AATGCACT-ATTAGTCCTCCGTTACTATTTAACAGTGGAGTGATC
1356415 AAT
1 AAT
1356418 TTGTTCAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
43 1 0.02
44 42 0.98
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (44 bp):
AATGCACTATTAGTCCTCCGTTACTATTTAACAGTGGAGTGATC
Found at i:1357940 original size:45 final size:45
Alignment explanation
Indices: 1357875--1357965 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
1357865 GGTTTAACCA
*
1357875 CCTCCATGTTATCCACATGAATCAACACTATCTAA-AGTCTTCATT
1 CCTCCATGTTATCCACATGAATAAACACTATCTAACA-TCTTCATT
*
1357920 CCTCCATGTTATCCATATGAATAAACACTATCTAACATCTTCATT
1 CCTCCATGTTATCCACATGAATAAACACTATCTAACATCTTCATT
1357965 C
1 C
1357966 GTTTAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 42 0.98
46 1 0.02
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (45 bp):
CCTCCATGTTATCCACATGAATAAACACTATCTAACATCTTCATT
Found at i:1365896 original size:31 final size:31
Alignment explanation
Indices: 1365834--1365899 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1365824 AACTGCCCAA
*
1365834 TGACTTAAATAAAAACTTTTCAATAGTTCAG
1 TGACTTAAATAAAAACTTTTCAATAGCTCAG
* *
1365865 TGACTTAAATGAAAAC-TTTCGAATTGCTCAG
1 TGACTTAAATAAAAACTTTTC-AATAGCTCAG
1365896 TGAC
1 TGAC
1365900 CATTTTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (31 bp):
TGACTTAAATAAAAACTTTTCAATAGCTCAG
Found at i:1370454 original size:14 final size:14
Alignment explanation
Indices: 1370416--1370459 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1370406 AACTTTATTC
1370416 TTAACAAATATTTGAA
1 TTAAC-AATATTT-AA
1370432 TT-A-AATATTTAA
1 TTAACAATATTTAA
1370444 TTAACAATATTTAA
1 TTAACAATATTTAA
1370458 TT
1 TT
1370460 TATAATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.15
13 8 0.31
14 11 0.42
15 1 0.04
16 2 0.08
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (14 bp):
TTAACAATATTTAA
Found at i:1371342 original size:28 final size:27
Alignment explanation
Indices: 1371290--1371342 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1371280 TTCGAATTAT
* *
1371290 TTTAAAAAAAATCATTTAACTCCTAAA
1 TTTAAAAAAAATCAATTAAATCCTAAA
1371317 TTTAAAAAAAATCAATTAAATACCTA
1 TTTAAAAAAAATCAATTAAAT-CCTA
1371343 CATCAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (27 bp):
TTTAAAAAAAATCAATTAAATCCTAAA
Found at i:1380368 original size:25 final size:24
Alignment explanation
Indices: 1380340--1380395 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 24
1380330 GCCATAAAAA
1380340 GGGAAGCT-CAAATGAGCCATGTAAC
1 GGGAAGCTCCAAA-GAGCCAT-TAAC
* *
1380365 GGGAAGTTCCAGAGAGCCATTAAC
1 GGGAAGCTCCAAAGAGCCATTAAC
*
1380389 GAGAAGC
1 GGGAAGC
1380396 CAGGAAGGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 9 0.35
25 14 0.54
26 3 0.12
ACGTcount: A:0.36, C:0.20, G:0.30, T:0.14
Consensus pattern (24 bp):
GGGAAGCTCCAAAGAGCCATTAAC
Found at i:1380475 original size:27 final size:25
Alignment explanation
Indices: 1380443--1380492 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
1380433 GAGAGCTAAA
1380443 TAATCGGAAAGCTCATGAAAGAGCCTT
1 TAATCGGAAAGCTC-TG-AAGAGCCTT
*
1380470 TAATCGGGAAGCTCTGAAGAGCC
1 TAATCGGAAAGCTCTGAAGAGCC
1380493 ATATATCGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.32
26 2 0.09
27 13 0.59
ACGTcount: A:0.34, C:0.20, G:0.26, T:0.20
Consensus pattern (25 bp):
TAATCGGAAAGCTCTGAAGAGCCTT
Found at i:1380500 original size:25 final size:26
Alignment explanation
Indices: 1380411--1380497 Score: 74
Period size: 26 Copynumber: 3.4 Consensus size: 26
1380401 AGGTTCAAGT
*
1380411 GAGCCA-AT-ATCGGGAAGCT-TCGGA
1 GAGCCATATAATCGGGAAGCTCT-GAA
* * *
1380435 GAGCTAAATAATCGGAAAGCTCATGAAA
1 GAGCCATATAATCGGGAAGCTC-TG-AA
*
1380463 GAGCC-TTTAATCGGGAAGCTCTGAA
1 GAGCCATATAATCGGGAAGCTCTGAA
1380488 GAGCCATATA
1 GAGCCATATA
1380498 TCGAGTCGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
24 5 0.10
25 9 0.18
26 15 0.31
27 14 0.29
28 6 0.12
ACGTcount: A:0.36, C:0.18, G:0.26, T:0.20
Consensus pattern (26 bp):
GAGCCATATAATCGGGAAGCTCTGAA
Found at i:1381492 original size:17 final size:17
Alignment explanation
Indices: 1381462--1381500 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1381452 AAAATATGAT
1381462 ATTTTCATTATTTTATC
1 ATTTTCATTATTTTATC
*
1381479 ATTTATCATT-TTTTATT
1 ATTT-TCATTATTTTATC
1381496 ATTTT
1 ATTTT
1381501 TACTTTCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 14 0.70
18 5 0.25
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (17 bp):
ATTTTCATTATTTTATC
Found at i:1382903 original size:2 final size:2
Alignment explanation
Indices: 1382835--1382885 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
1382825 TGATTTTTCA
*
1382835 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1382877 AT AT AT AT A
1 AT AT AT AT A
1382886 AGATAAGGGC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1384483 original size:43 final size:43
Alignment explanation
Indices: 1384422--1384514 Score: 125
Period size: 43 Copynumber: 2.1 Consensus size: 43
1384412 AAAATCAACG
*
1384422 CATTAAGAGAGAGGAAGTGGATGAAGTGGAACCACC-ATTGACA
1 CATTAAGAGAGAGGAAGTGGACGAAG-GGAACCACCGATTGACA
* * *
1384465 CATTAAGGGAGAGGAAGTGGACGAAGGGAACCGCCGTTTTGACA
1 CATTAAGAGAGAGGAAGTGGACGAAGGGAACCACCG-ATTGACA
1384509 CATTAA
1 CATTAA
1384515 CTAGTACCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
42 8 0.18
43 24 0.55
44 12 0.27
ACGTcount: A:0.37, C:0.15, G:0.31, T:0.17
Consensus pattern (43 bp):
CATTAAGAGAGAGGAAGTGGACGAAGGGAACCACCGATTGACA
Found at i:1385196 original size:19 final size:19
Alignment explanation
Indices: 1385161--1385236 Score: 77
Period size: 19 Copynumber: 4.1 Consensus size: 19
1385151 CTTTTAAAAA
*
1385161 TATAAAT-TTTGGAATTTT
1 TATAAATATTTTGAATTTT
1385179 TATAAATATTTTGAATTTT
1 TATAAATATTTTGAATTTT
* * *
1385198 AAAAAATATTTTAAATTTT
1 TATAAATATTTTGAATTTT
1385217 TGA-ATAATATTTTG-ATTTT
1 T-ATA-AATATTTTGAATTTT
1385236 T
1 T
1385237 TTTTTGTAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
18 7 0.14
19 33 0.67
20 9 0.18
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:1385332 original size:9 final size:9
Alignment explanation
Indices: 1385318--1385347 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1385308 ACATCAATCT
1385318 ATTATTCGA
1 ATTATTCGA
1385327 ATTATTCGA
1 ATTATTCGA
*
1385336 GTTATTCGA
1 ATTATTCGA
1385345 ATT
1 ATT
1385348 GTCAAATTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.30, C:0.10, G:0.13, T:0.47
Consensus pattern (9 bp):
ATTATTCGA
Found at i:1385419 original size:2 final size:2
Alignment explanation
Indices: 1385412--1385443 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1385402 TAACACGCCA
1385412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1385444 TGGCATGATA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1389733 original size:31 final size:31
Alignment explanation
Indices: 1389698--1389756 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
1389688 TAAAAGCCGG
*
1389698 TGACTT-AATTAAAAACTTTTGAATAATTCAA
1 TGACTTAAATT-AAAACTTTCGAATAATTCAA
*
1389729 TGACTTAAATTAAAACTTTCGGATAATT
1 TGACTTAAATTAAAACTTTCGAATAATT
1389757 TAGTGACCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 21 0.84
32 4 0.16
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.39
Consensus pattern (31 bp):
TGACTTAAATTAAAACTTTCGAATAATTCAA
Found at i:1408893 original size:2 final size:2
Alignment explanation
Indices: 1408881--1408914 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1408871 AAGAATGCAT
*
1408881 TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1408915 AATTATTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1420487 original size:24 final size:24
Alignment explanation
Indices: 1420458--1420508 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
1420448 AATATTGACT
*
1420458 CTAACTGCTTTCTGCATGAAATGA
1 CTAACTACTTTCTGCATGAAATGA
1420482 CTAACTACTTTCTGCATGAAATGA
1 CTAACTACTTTCTGCATGAAATGA
1420506 CTA
1 CTA
1420509 TTGAGGAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (24 bp):
CTAACTACTTTCTGCATGAAATGA
Found at i:1421845 original size:32 final size:31
Alignment explanation
Indices: 1421809--1421875 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 31
1421799 TTTTTTTTTG
1421809 AATTAA-TCGAATTAAGCTA-TTTAATTCTTTCA
1 AATTAACTCGAA-TAAG-TAGTTTAATT-TTTCA
*
1421841 AATTAACTTGAATAAGTAGTTTAATTTTTCA
1 AATTAACTCGAATAAGTAGTTTAATTTTTCA
1421872 AATT
1 AATT
1421876 CGAGTTGAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 11 0.34
32 17 0.53
33 4 0.12
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.45
Consensus pattern (31 bp):
AATTAACTCGAATAAGTAGTTTAATTTTTCA
Found at i:1422061 original size:21 final size:20
Alignment explanation
Indices: 1422031--1422090 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
1422021 TCTGAATTCC
*
1422031 AAAA-TTAAATTTTAT-TTA
1 AAAATTTAAATTATATGTTA
1422049 AAATTATTTAAA-TATATGTTA
1 AAA--ATTTAAATTATATGTTA
1422070 AAAATTTAAATTA-A-GTTA
1 AAAATTTAAATTATATGTTA
1422088 AAA
1 AAA
1422091 TAATAGCTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
18 10 0.28
19 8 0.22
20 7 0.19
21 11 0.31
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (20 bp):
AAAATTTAAATTATATGTTA
Found at i:1422089 original size:18 final size:19
Alignment explanation
Indices: 1422054--1422090 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
1422044 ATTTAAAATT
*
1422054 ATTTAAATATATGTTAAAA
1 ATTTAAATATAAGTTAAAA
1422073 ATTTAAAT-TAAGTTAAAA
1 ATTTAAATATAAGTTAAAA
1422091 TAATAGCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTTAAATATAAGTTAAAA
Found at i:1422231 original size:5 final size:5
Alignment explanation
Indices: 1422221--1422246 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1422211 ATTTTACCCA
1422221 GGCCC GGCCC GGCCC GGCCC GGCCC G
1 GGCCC GGCCC GGCCC GGCCC GGCCC G
1422247 TTTTTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.58, G:0.42, T:0.00
Consensus pattern (5 bp):
GGCCC
Found at i:1422318 original size:11 final size:11
Alignment explanation
Indices: 1422298--1422404 Score: 56
Period size: 11 Copynumber: 10.4 Consensus size: 11
1422288 CAAAAATTAA
1422298 AAAAAGTATTTT
1 AAAAA-TATTTT
1422310 AAAAATATTTT
1 AAAAATATTTT
1422321 --AAA-A--TT
1 AAAAATATTTT
* * *
1422327 AAAAAAAATTA
1 AAAAATATTTT
1422338 AAAAAGTATTTT
1 AAAAA-TATTTT
1422350 AAAAA-ATTTT
1 AAAAATATTTT
1422360 ---AA-ATTTT
1 AAAAATATTTT
*
1422367 AAAAACT-TTTA
1 AAAAA-TATTTT
1422378 AAAAAGTATTTT
1 AAAAA-TATTTT
*
1422390 AAAAGTATTTT
1 AAAAATATTTT
1422401 AAAA
1 AAAA
1422405 TTAAAAAATA
Statistics
Matches: 75, Mismatches: 8, Indels: 25
0.69 0.07 0.23
Matches are distributed among these distances:
6 2 0.03
7 7 0.09
8 4 0.05
9 4 0.05
10 7 0.09
11 31 0.41
12 20 0.27
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:1422344 original size:40 final size:40
Alignment explanation
Indices: 1422271--1422412 Score: 187
Period size: 40 Copynumber: 3.5 Consensus size: 40
1422261 ACCAAAAATT
1422271 TATTTTAAAAATTAAAACAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-AAA-AAAAATT-AAAAAAGTATTTTAAAAA
1422315 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
* *** *
1422355 -ATTTTAAATTTTAAAAACTTTTAAAAAAGTATTTTAAAAG
1 TATTTTAAA-ATTAAAAAAAATTAAAAAAGTATTTTAAAAA
1422395 TATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
1422413 TAAAAAATAA
Statistics
Matches: 89, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
39 8 0.09
40 51 0.57
41 15 0.17
42 3 0.03
43 6 0.07
44 6 0.07
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:1422358 original size:10 final size:10
Alignment explanation
Indices: 1422305--1422382 Score: 51
Period size: 10 Copynumber: 8.1 Consensus size: 10
1422295 TAAAAAAAGT
1422305 ATTTTAAAAA
1 ATTTTAAAAA
1422315 TATTTT--AAA
1 -ATTTTAAAAA
*
1422324 A-TTAAAAAA
1 ATTTTAAAAA
* *
1422333 AATTAAAAAA
1 ATTTTAAAAA
1422343 GTATTTTAAAAA
1 --ATTTTAAAAA
1422355 ATTTT---AA
1 ATTTTAAAAA
1422362 ATTTTAAAAA
1 ATTTTAAAAA
*
1422372 CTTTTAAAAA
1 ATTTTAAAAA
1422382 A
1 A
1422383 GTATTTTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
7 9 0.17
8 1 0.02
9 7 0.13
10 24 0.44
11 5 0.09
12 8 0.15
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (10 bp):
ATTTTAAAAA
Found at i:1422367 original size:17 final size:17
Alignment explanation
Indices: 1422345--1422379 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1422335 TTAAAAAAGT
1422345 ATTTTAAAAAATTTTAA
1 ATTTTAAAAAATTTTAA
*
1422362 ATTTTAAAAACTTTTAA
1 ATTTTAAAAAATTTTAA
1422379 A
1 A
1422380 AAAGTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
ATTTTAAAAAATTTTAA
Found at i:1422859 original size:23 final size:23
Alignment explanation
Indices: 1422833--1422907 Score: 69
Period size: 23 Copynumber: 3.1 Consensus size: 23
1422823 AATCTTTTTG
1422833 TTTTTTAATTATTTGTGTTTCCA
1 TTTTTTAATTATTTGTGTTTCCA
* * * ***
1422856 TTTTAATCAAATTTTTTGTTTTTGTT
1 TTTT--T-TAATTATTTGTGTTTCCA
1422882 TTTTTTAATTATTTGTGTTTCCA
1 TTTTTTAATTATTTGTGTTTCCA
1422905 TTT
1 TTT
1422908 GAACCAACCT
Statistics
Matches: 37, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
23 19 0.51
24 1 0.03
25 1 0.03
26 16 0.43
ACGTcount: A:0.17, C:0.07, G:0.08, T:0.68
Consensus pattern (23 bp):
TTTTTTAATTATTTGTGTTTCCA
Found at i:1422868 original size:26 final size:25
Alignment explanation
Indices: 1422839--1422907 Score: 61
Period size: 24 Copynumber: 2.8 Consensus size: 25
1422829 TTTGTTTTTT
1422839 AATTATTTGTGTTTCCATTTTAATCA
1 AATTATTTGTGTTTCCATTTT-ATCA
*** * **
1422865 AATT-TTT-TGTTTTTGTTTTTTTT
1 AATTATTTGTGTTTCCATTTTATCA
1422888 AATTATTTGTGTTTCCATTT
1 AATTATTTGTGTTTCCATTT
1422908 GAACCAACCT
Statistics
Matches: 32, Mismatches: 9, Indels: 5
0.70 0.20 0.11
Matches are distributed among these distances:
23 5 0.16
24 12 0.38
25 11 0.34
26 4 0.12
ACGTcount: A:0.19, C:0.07, G:0.09, T:0.65
Consensus pattern (25 bp):
AATTATTTGTGTTTCCATTTTATCA
Found at i:1422893 original size:49 final size:52
Alignment explanation
Indices: 1422833--1422963 Score: 178
Period size: 49 Copynumber: 2.5 Consensus size: 52
1422823 AATCTTTTTG
* *
1422833 TTTTTTAATTATTTGTGTTTCCATTTTAATCAAATTTTTTG-TTTT-TG-TT
1 TTTTTTAATTATTTGTGTTTCCATTTTAACCAAACTTTTTGTTTTTATGCTT
* *
1422882 TTTTTTAATTATTTGTGTTTCCATTTGAACCAACCTTTTTGTTTTTATGCTT
1 TTTTTTAATTATTTGTGTTTCCATTTTAACCAAACTTTTTGTTTTTATGCTT
1422934 TTTTTTAAGATTTATTTGTGTTTCCATTTT
1 TTTTTT-A-A-TTATTTGTGTTTCCATTTT
1422964 TAAAACAATG
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
49 37 0.52
50 4 0.06
51 2 0.03
52 8 0.11
53 1 0.01
54 1 0.01
55 18 0.25
ACGTcount: A:0.18, C:0.09, G:0.09, T:0.64
Consensus pattern (52 bp):
TTTTTTAATTATTTGTGTTTCCATTTTAACCAAACTTTTTGTTTTTATGCTT
Found at i:1423796 original size:20 final size:20
Alignment explanation
Indices: 1423768--1423807 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
1423758 GTAAAATATC
*
1423768 TAATGGTCATTTTCTATTCT
1 TAATAGTCATTTTCTATTCT
1423788 TAATAGTCATTTTCTATTCT
1 TAATAGTCATTTTCTATTCT
1423808 CACATTATCA
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:0.23, C:0.15, G:0.07, T:0.55
Consensus pattern (20 bp):
TAATAGTCATTTTCTATTCT
Found at i:1424134 original size:28 final size:25
Alignment explanation
Indices: 1424097--1424150 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
1424087 TATTAAATCC
* *
1424097 AAACTTAAGTACTTAATTGAGACAAAAA
1 AAACTCAAGTA-TCAATT-AGA-AAAAA
1424125 AAACTCAAGTATCAATTAGAAAAAA
1 AAACTCAAGTATCAATTAGAAAAAA
1424150 A
1 A
1424151 GTACTAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 6 0.25
26 3 0.12
27 5 0.21
28 10 0.42
ACGTcount: A:0.57, C:0.11, G:0.09, T:0.22
Consensus pattern (25 bp):
AAACTCAAGTATCAATTAGAAAAAA
Found at i:1429984 original size:40 final size:40
Alignment explanation
Indices: 1429911--1430033 Score: 167
Period size: 40 Copynumber: 3.0 Consensus size: 40
1429901 ACCAAAAATT
*
1429911 TATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT-TAA-AAAAATT-AAAAAAGTATTTTAAAAA
1429955 TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
* *
1429995 -AATTTAAAATTTAAAAAATTTAATAAAAGTATTTTAAAA
1 TATTTTAAAATTTAAAAAAATTAA-AAAAGTATTTTAAAA
1430034 TTAAAAAATA
Statistics
Matches: 75, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
39 21 0.28
40 33 0.44
41 7 0.09
42 2 0.03
43 6 0.08
44 6 0.08
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
TATTTTAAAATTTAAAAAAATTAAAAAAGTATTTTAAAAA
Found at i:1429999 original size:11 final size:10
Alignment explanation
Indices: 1429961--1430022 Score: 53
Period size: 9 Copynumber: 6.3 Consensus size: 10
1429951 AAAATATTTT
1429961 AAAATTTAAA
1 AAAATTTAAA
1429971 AAAA-TTAAA
1 AAAATTTAAA
1429980 AAAGTATTTTAAA
1 AAA--A-TTTAAA
1429993 AAAATTT---
1 AAAATTTAAA
1430000 AAAATTT-AA
1 AAAATTTAAA
1430009 AAAATTTAATA
1 AAAATTTAA-A
1430020 AAA
1 AAA
1430023 GTATTTTAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
7 7 0.16
9 15 0.34
10 8 0.18
11 6 0.14
13 8 0.18
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:1430003 original size:29 final size:29
Alignment explanation
Indices: 1429971--1430041 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
1429961 AAAATTTAAA
1429971 AAAATTAAAAAAGTATTTTAA-AAAA-A-TTT
1 AAAATTAAAAAA--A-TTTAATAAAAGATTTT
*
1430000 AAAATTTAAAAAATTTAATAAAAGTATTTT
1 AAAATTAAAAAAATTTAATAAAAG-ATTTT
1430030 AAAATTAAAAAA
1 AAAATTAAAAAA
1430042 TAAAAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 5 0.14
27 5 0.14
29 12 0.33
30 14 0.39
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (29 bp):
AAAATTAAAAAAATTTAATAAAAGATTTT
Found at i:1433094 original size:15 final size:16
Alignment explanation
Indices: 1433076--1433106 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1433066 AATTTACTTG
1433076 AATAAAATAAA-ATTT
1 AATAAAATAAATATTT
1433091 AATAAAATAAATATTT
1 AATAAAATAAATATTT
1433107 TGGTCAGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AATAAAATAAATATTT
Found at i:1433099 original size:20 final size:19
Alignment explanation
Indices: 1433050--1433101 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
1433040 AAAAAGAGAA
1433050 TAATAAATATAAATAAAATT
1 TAATAAATA-AAATAAAATT
* *
1433070 TACTTGAATAAAATAAAATT
1 TA-ATAAATAAAATAAAATT
1433090 TAATAAAATAAA
1 TAAT-AAATAAA
1433102 TATTTTGGTC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 1 0.04
20 20 0.77
21 5 0.19
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
TAATAAATAAAATAAAATT
Found at i:1439566 original size:31 final size:31
Alignment explanation
Indices: 1439498--1439559 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
1439488 TGGTCATTTG
*
1439498 AACTATTCGAAAGTTTTCATTTAAGTCACTA
1 AACTATTCAAAAGTTTTCATTTAAGTCACTA
* *
1439529 AACTATTCAAAAGTTTTTATTTACGTCACTA
1 AACTATTCAAAAGTTTTCATTTAAGTCACTA
1439560 GGCTATTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.40
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTCATTTAAGTCACTA
Done.