Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 98 of 198
Found at i:31492390 original size:21 final size:20
Alignment explanation
Indices: 31492374--31492410 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
31492364 TGTTTTTAAT
*
31492374 AAATAAATA-AAAATTTTTA
1 AAATAAAAATAAAATTTTTA
31492393 AAATAAAAATAAAATTTT
1 AAATAAAAATAAAATTTT
31492411 ATGTTTTTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATAAAAATAAAATTTTTA
Found at i:31495643 original size:29 final size:28
Alignment explanation
Indices: 31495609--31495785 Score: 133
Period size: 29 Copynumber: 6.1 Consensus size: 28
31495599 CAAAGTCTTT
31495609 CCACAAAGGTGTCCTTTTAACAGAGATAG
1 CCACAAAGGT-TCCTTTTAACAGAGATAG
*
31495638 CCACAAAGGCATCCTTTTAACAGAGATAG
1 CCACAAAGG-TTCCTTTTAACAGAGATAG
* * * * *
31495667 CCACAAAAGCTTCCTTATAACAAATATGG
1 CCAC-AAAGGTTCCTTTTAACAGAGATAG
* *
31495696 CGACATAGGCGTT-CTTTTAACAGAGATAG
1 CCACA-AAG-GTTCCTTTTAACAGAGATAG
* * * *
31495725 CCACATAGGCTTCCTTATAGCAGAGATTG
1 CCACAAAGG-TTCCTTTTAACAGAGATAG
* **
31495754 CCACAAGGGCATT-CTTTTAATTGAGATAG
1 CCACAAAGG--TTCCTTTTAACAGAGATAG
31495783 CCA
1 CCA
31495786 TAAATACATC
Statistics
Matches: 113, Mismatches: 28, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
27 1 0.01
28 4 0.04
29 100 0.88
30 8 0.07
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.25
Consensus pattern (28 bp):
CCACAAAGGTTCCTTTTAACAGAGATAG
Found at i:31495682 original size:58 final size:58
Alignment explanation
Indices: 31495620--31495785 Score: 197
Period size: 58 Copynumber: 2.9 Consensus size: 58
31495610 CACAAAGGTG
* *
31495620 TCCTTTTAACAGAGATAGCCACAAAGGCATCCTTTTAACAGAGATAGCCACAAAAGCT
1 TCCTTATAACAGAGATAGCCACAAAGGCATTCTTTTAACAGAGATAGCCACAAAAGCT
* * * * * * * *
31495678 TCCTTATAACAAATATGGCGACATAGGCGTTCTTTTAACAGAGATAGCCACATAGGCT
1 TCCTTATAACAGAGATAGCCACAAAGGCATTCTTTTAACAGAGATAGCCACAAAAGCT
* * * **
31495736 TCCTTATAGCAGAGATTGCCACAAGGGCATTCTTTTAATTGAGATAGCCA
1 TCCTTATAACAGAGATAGCCACAAAGGCATTCTTTTAACAGAGATAGCCA
31495786 TAAATACATC
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
58 88 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (58 bp):
TCCTTATAACAGAGATAGCCACAAAGGCATTCTTTTAACAGAGATAGCCACAAAAGCT
Found at i:31508205 original size:43 final size:41
Alignment explanation
Indices: 31508092--31508212 Score: 127
Period size: 43 Copynumber: 2.9 Consensus size: 41
31508082 AAAATGCAAT
* * *
31508092 GCACCAAGGTTGCCGATTGTGTCCGAGGCTCCCGTACATCCAA
1 GCACCAAGGTT-CCGATAGTGT-CGAGGCTCCTGCACATCCAA
* * *
31508135 GCACC-AGGTGCCGATAGTGTTTGAGGCTCCTGCACATCCGA
1 GCACCAAGGTTCCGATAGTG-TCGAGGCTCCTGCACATCCAA
*
31508176 GCCACCAAGGTTCCGATGGTGCTCGAGGCTCCTGCAC
1 G-CACCAAGGTTCCGATAGTG-TCGAGGCTCCTGCAC
31508213 GACTGAGGGC
Statistics
Matches: 65, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
41 25 0.38
42 9 0.14
43 31 0.48
ACGTcount: A:0.19, C:0.32, G:0.28, T:0.21
Consensus pattern (41 bp):
GCACCAAGGTTCCGATAGTGTCGAGGCTCCTGCACATCCAA
Found at i:31513102 original size:11 final size:11
Alignment explanation
Indices: 31513075--31513112 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
31513065 ACAATTGAAT
31513075 ATTTCATTTCAC
1 ATTTCATTTC-C
31513087 ATTTCATTTCC
1 ATTTCATTTCC
31513098 ATTTC-TTATCC
1 ATTTCATT-TCC
31513109 ATTT
1 ATTT
31513113 TCCATTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 2 0.08
11 13 0.52
12 10 0.40
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTCATTTCC
Found at i:31514613 original size:50 final size:50
Alignment explanation
Indices: 31514538--31514637 Score: 155
Period size: 50 Copynumber: 2.0 Consensus size: 50
31514528 AATTAAAAAG
* * **
31514538 CCATATTGTGTAAGACCATAGCTGGTGGGCTATGGTGTCATATGGAAATA
1 CCATATCGTGTAAGACCATAACTGGTGGGCTATGGCATCATATGGAAATA
*
31514588 CCATATCGTGTAAGACCATAACTGGTGGGTTATGGCATCATATGGAAATA
1 CCATATCGTGTAAGACCATAACTGGTGGGCTATGGCATCATATGGAAATA
31514638 TCTAAAGGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (50 bp):
CCATATCGTGTAAGACCATAACTGGTGGGCTATGGCATCATATGGAAATA
Found at i:31519863 original size:26 final size:26
Alignment explanation
Indices: 31519824--31519899 Score: 116
Period size: 26 Copynumber: 2.9 Consensus size: 26
31519814 CAAATTTCTG
*
31519824 TAAAAGGATACCTTCGTGGCTATCCC
1 TAAAAGGATGCCTTCGTGGCTATCCC
* *
31519850 TAAAAGGATGCCTTTGTGGCTATCCT
1 TAAAAGGATGCCTTCGTGGCTATCCC
*
31519876 TGAAAGGATGCCTTCGTGGCTATC
1 TAAAAGGATGCCTTCGTGGCTATC
31519900 TCTTTTAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (26 bp):
TAAAAGGATGCCTTCGTGGCTATCCC
Found at i:31519923 original size:29 final size:29
Alignment explanation
Indices: 31519824--31520081 Score: 174
Period size: 29 Copynumber: 9.2 Consensus size: 29
31519814 CAAATTTCTG
* * *
31519824 TAAAAGGATACCTTCGTGGCTATC-C--C
1 TAAAAGGAAACCTTTGTGGCTATCTCTTT
**
31519850 TAAAAGGATGCCTTTGTGGCTATC-C--T
1 TAAAAGGAAACCTTTGTGGCTATCTCTTT
* ** *
31519876 TGAAAGGATGCCTTCGTGGCTATCTCTTT
1 TAAAAGGAAACCTTTGTGGCTATCTCTTT
* * *
31519905 TAAAAGGAATCATTTGTGGCTATCTCTAT
1 TAAAAGGAAACCTTTGTGGCTATCTCTTT
* * *
31519934 TAAAAGGAAGCCTTTGTGGCGATCTCTGT
1 TAAAAGGAAACCTTTGTGGCTATCTCTTT
* * *
31519963 TAAAA-GAAACCTTCGTGTCTATCTTTTT
1 TAAAAGGAAACCTTTGTGGCTATCTCTTT
* * * **
31519991 TAAAAGGAAGCCTTTGAGGCAATCTCAGT
1 TAAAAGGAAACCTTTGTGGCTATCTCTTT
** **
31520020 T-AAAGGAAACCTTCATCACTATCT-TTGT
1 TAAAAGGAAACCTTTGTGGCTATCTCTT-T
* * *
31520048 TAAAAGGAAGCCTTTGTGGCCATCTCTAT
1 TAAAAGGAAACCTTTGTGGCTATCTCTTT
31520077 TAAAA
1 TAAAA
31520082 AAATGCCTTT
Statistics
Matches: 180, Mismatches: 45, Indels: 11
0.76 0.19 0.05
Matches are distributed among these distances:
26 45 0.25
27 1 0.01
28 40 0.22
29 93 0.52
30 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (29 bp):
TAAAAGGAAACCTTTGTGGCTATCTCTTT
Found at i:31520005 original size:57 final size:57
Alignment explanation
Indices: 31519878--31520081 Score: 219
Period size: 57 Copynumber: 3.6 Consensus size: 57
31519868 GCTATCCTTG
* * * * * * * * *
31519878 AAAGGATGCCTTCGTGGCTATCTCTTTTAAAAGGAATCATTTGTGGCTATCTCTATTA
1 AAAGGAAGCCTTTGTGGCAATCTCTGTTAAAA-GAAACCTTCGTGACTATCTTTATTA
* * *
31519936 AAAGGAAGCCTTTGTGGCGATCTCTGTTAAAAGAAACCTTCGTGTCTATCTTTTTTA
1 AAAGGAAGCCTTTGTGGCAATCTCTGTTAAAAGAAACCTTCGTGACTATCTTTATTA
* * * * * *
31519993 AAAGGAAGCCTTTGAGGCAATCTCAGTTAAAGGAAACCTTCATCACTATCTTTGTTA
1 AAAGGAAGCCTTTGTGGCAATCTCTGTTAAAAGAAACCTTCGTGACTATCTTTATTA
* *
31520050 AAAGGAAGCCTTTGTGGCCATCTCTATTAAAA
1 AAAGGAAGCCTTTGTGGCAATCTCTGTTAAAA
31520082 AAATGCCTTT
Statistics
Matches: 123, Mismatches: 23, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
57 95 0.77
58 28 0.23
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (57 bp):
AAAGGAAGCCTTTGTGGCAATCTCTGTTAAAAGAAACCTTCGTGACTATCTTTATTA
Found at i:31520016 original size:86 final size:84
Alignment explanation
Indices: 31519850--31520032 Score: 208
Period size: 86 Copynumber: 2.2 Consensus size: 84
31519840 TGGCTATCCC
* * * ** *
31519850 TAAAAGGATGCCTTTGTGGCTATCCTTGAAAGGATGCCTTCGTGGCTATCTCTTTTAAAAGGAAT
1 TAAAAGGAAGCCTTTGTGGCGATCCTTGAAAAGAAACCTTCGTGGCTATCTCTTTTAAAAGGAAG
* *
31519915 CATTTGTGGCTATCTCTA-T
66 CATTTGAGGCAATCTC-AGT
* * *
31519934 TAAAAGGAAGCCTTTGTGGCGATCTCTGTTAAAAGAAACCTTCGTGTCTATCTTTTTTAAAAGGA
1 TAAAAGGAAGCCTTTGTGGCGATC-CT-TGAAAAGAAACCTTCGTGGCTATCTCTTTTAAAAGGA
*
31519999 AGCCTTTGAGGCAATCTCAGT
64 AGCATTTGAGGCAATCTCAGT
*
31520020 T-AAAGGAAACCTT
1 TAAAAGGAAGCCTT
31520033 CATCACTATC
Statistics
Matches: 83, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
84 22 0.27
85 14 0.17
86 47 0.57
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (84 bp):
TAAAAGGAAGCCTTTGTGGCGATCCTTGAAAAGAAACCTTCGTGGCTATCTCTTTTAAAAGGAAG
CATTTGAGGCAATCTCAGT
Found at i:31520080 original size:86 final size:87
Alignment explanation
Indices: 31519878--31520081 Score: 216
Period size: 86 Copynumber: 2.4 Consensus size: 87
31519868 GCTATCCTTG
* * * *
31519878 AAAGGATGCCTTCGTGGCTATCTCTTTTAAAAGGAATCATTTGTGGCTATCTCTATTAAAAGGAA
1 AAAGGAAGCCTTCGTGGCTATCTCTTTTAAAAGGAAGCATTTGAGGCAATCTCTATTAAAAGGAA
* ** **
31519943 GCCTTTGTGGCGATCTCTGTTA
66 ACCTTCATCACGATCTCTGTTA
* * * *
31519965 AAA-GAAACCTTCGTGTCTATCTTTTTTAAAAGGAAGCCTTTGAGGCAATCTC-AGTT-AAAGGA
1 AAAGGAAGCCTTCGTGGCTATCTCTTTTAAAAGGAAGCATTTGAGGCAATCTCTA-TTAAAAGGA
* *
31520027 AACCTTCATCACTATCTTTGTTA
65 AACCTTCATCACGATCTCTGTTA
* * *
31520050 AAAGGAAGCCTTTGTGGCCATCTCTATTAAAA
1 AAAGGAAGCCTTCGTGGCTATCTCTTTTAAAA
31520082 AAATGCCTTT
Statistics
Matches: 94, Mismatches: 21, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
85 26 0.28
86 65 0.69
87 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (87 bp):
AAAGGAAGCCTTCGTGGCTATCTCTTTTAAAAGGAAGCATTTGAGGCAATCTCTATTAAAAGGAA
ACCTTCATCACGATCTCTGTTA
Found at i:31521993 original size:7 final size:7
Alignment explanation
Indices: 31521983--31522012 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
31521973 GAGTTTAGGA
*
31521983 TTCAAGG
1 TTCATGG
31521990 TTCATGG
1 TTCATGG
31521997 TTCATGG
1 TTCATGG
31522004 TTCATGG
1 TTCATGG
31522011 TT
1 TT
31522013 TGAGTTTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.17, C:0.13, G:0.27, T:0.43
Consensus pattern (7 bp):
TTCATGG
Found at i:31522077 original size:20 final size:20
Alignment explanation
Indices: 31522030--31522085 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
31522020 GAGGTTTAGG
* *
31522030 GTTTGGGTTCAAGGTTCGAG
1 GTTTGGGTTCGAGGTTCGAA
31522050 GTTTGGGTTCGA-GTTCGAA
1 GTTTGGGTTCGAGGTTCGAA
*
31522069 GTTTAGGGTTCGGGGTT
1 GTTT-GGGTTCGAGGTT
31522086 TAGTATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 10 0.32
20 18 0.58
21 3 0.10
ACGTcount: A:0.12, C:0.09, G:0.41, T:0.38
Consensus pattern (20 bp):
GTTTGGGTTCGAGGTTCGAA
Found at i:31526373 original size:21 final size:21
Alignment explanation
Indices: 31526349--31526415 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
31526339 GTTACTGGGG
**
31526349 TGGGTCAAATAGAAGTGATTT
1 TGGGTCAAGCAGAAGTGATTT
31526370 TGGGT-AGAGCAGAAGTGATTT
1 TGGGTCA-AGCAGAAGTGATTT
31526391 TGGGTCAAGCAGAAGTGATTT
1 TGGGTCAAGCAGAAGTGATTT
31526412 TGGG
1 TGGG
31526416 GTTGACCCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.28, C:0.06, G:0.36, T:0.30
Consensus pattern (21 bp):
TGGGTCAAGCAGAAGTGATTT
Found at i:31526746 original size:5 final size:5
Alignment explanation
Indices: 31526736--31526761 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
31526726 TACAAGCATC
31526736 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
31526762 ACTATAGTAA
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:31532499 original size:33 final size:33
Alignment explanation
Indices: 31532448--31532521 Score: 121
Period size: 33 Copynumber: 2.2 Consensus size: 33
31532438 TTCAGGGGGC
* *
31532448 TTACCTTTAAGAGTAGGAAAACAAAGTTCGGTT
1 TTACCTTTAAGAGAAGGAAAACAAAGTTCAGTT
*
31532481 TTACCTTTAGGAGAAGGAAAACAAAGTTCAGTT
1 TTACCTTTAAGAGAAGGAAAACAAAGTTCAGTT
31532514 TTACCTTT
1 TTACCTTT
31532522 TCCATTTAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (33 bp):
TTACCTTTAAGAGAAGGAAAACAAAGTTCAGTT
Found at i:31533425 original size:28 final size:29
Alignment explanation
Indices: 31533390--31533457 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
31533380 CTTCATTTTC
**
31533390 TTTCAATTTTTT-TCAA-CATCTTTTTCTT
1 TTTCAATTTTTTCTCAATC-TCAATTTCTT
31533418 TTTCAATTTTTTTCTCAATCTCAATTTCTT
1 TTTCAA-TTTTTTCTCAATCTCAATTTCTT
31533448 TTTCAATTTT
1 TTTCAATTTT
31533458 CTTTTCTTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 6 0.17
29 10 0.29
30 18 0.51
31 1 0.03
ACGTcount: A:0.19, C:0.18, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTCAATTTTTTCTCAATCTCAATTTCTT
Found at i:31533441 original size:18 final size:18
Alignment explanation
Indices: 31533420--31533454 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
31533410 TTTTTCTTTT
31533420 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
31533438 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
31533455 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:31533510 original size:21 final size:21
Alignment explanation
Indices: 31533468--31533522 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
31533458 CTTTTCTTCA
* * *
31533468 TTTTCTTTTTATTTTATCTCT
1 TTTTCTTTTTCTCTCATCTCT
*
31533489 TTTTCTTTTTCTCTCATTTCT
1 TTTTCTTTTTCTCTCATCTCT
*
31533510 TTTT-TTCTTCTCT
1 TTTTCTTTTTCTCT
31533523 AAATTTCATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTCTTTTTCTCTCATCTCT
Found at i:31533528 original size:21 final size:21
Alignment explanation
Indices: 31533486--31533529 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
31533476 TTATTTTATC
* *
31533486 TCTTTTTCTTTTTCTCTCATT
1 TCTTTTTCTTCTTCTCTAATT
31533507 TCTTTTT-TTCTTCTCTAAATT
1 TCTTTTTCTTCTTCTCT-AATT
31533528 TC
1 TC
31533530 ATTCAAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.09, C:0.23, G:0.00, T:0.68
Consensus pattern (21 bp):
TCTTTTTCTTCTTCTCTAATT
Found at i:31552611 original size:24 final size:24
Alignment explanation
Indices: 31552566--31552611 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31552556 AATTTGGTTT
*
31552566 GTTTATTTTAATTAATTGTATTAG
1 GTTTATTTTAATTAATTATATTAG
*
31552590 GTTTA-TTTAACTTAGTTATATT
1 GTTTATTTTAA-TTAATTATATT
31552612 TAATCTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.28, C:0.02, G:0.11, T:0.59
Consensus pattern (24 bp):
GTTTATTTTAATTAATTATATTAG
Found at i:31553328 original size:45 final size:45
Alignment explanation
Indices: 31553264--31553353 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
31553254 AAAAATGACA
*
31553264 TCACATCTTTTTTGCAACTGGAGGAGGAAACTCTATATGAAGCTT
1 TCACATCTTTTTTGCAACTGGAGGAGGAAACGCTATATGAAGCTT
31553309 TCACATCTTTTTTGCAACTGGAGGAGGAAACGCTATATGAAGCTT
1 TCACATCTTTTTTGCAACTGGAGGAGGAAACGCTATATGAAGCTT
31553354 GGGAACGATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (45 bp):
TCACATCTTTTTTGCAACTGGAGGAGGAAACGCTATATGAAGCTT
Found at i:31567790 original size:31 final size:31
Alignment explanation
Indices: 31567752--31567813 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
31567742 AGGCAAATTA
*
31567752 CAAGAGTAATTGAATCGTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
31567783 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
31567814 AAAATTATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:31574080 original size:31 final size:31
Alignment explanation
Indices: 31574042--31574134 Score: 159
Period size: 31 Copynumber: 3.0 Consensus size: 31
31574032 AGGCAAATTA
31574042 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
*
31574073 CAAGAGTAATTGAATCCTAATGAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
* *
31574104 CAAGTGTAATTGAGTCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
31574135 AAAATTATCT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 58 1.00
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:31586000 original size:55 final size:55
Alignment explanation
Indices: 31585920--31586056 Score: 193
Period size: 55 Copynumber: 2.5 Consensus size: 55
31585910 ATTTCCCACA
* * * *
31585920 AATATTGCTTCTTTTGGATCGATTGTTTTTATGTTTAAATCGATTGTCATGTTGG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATAGATTGTCATGTTAG
* * * *
31585975 AATACTGCTTCTTTTAAATCAATTGTTTATATGTTTAAATAGATTTTCATGTTAG
1 AATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATAGATTGTCATGTTAG
*
31586030 AATATTGCTTCATTTGAATCGATTGTT
1 AATATTGCTTCTTTTGAATCGATTGTT
31586057 ATGGTGGAAT
Statistics
Matches: 70, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 70 1.00
ACGTcount: A:0.26, C:0.09, G:0.15, T:0.50
Consensus pattern (55 bp):
AATATTGCTTCTTTTGAATCGATTGTTTATATGTTTAAATAGATTGTCATGTTAG
Found at i:31586133 original size:94 final size:95
Alignment explanation
Indices: 31585983--31586215 Score: 337
Period size: 94 Copynumber: 2.5 Consensus size: 95
31585973 GGAATACTGC
* * *
31585983 TTCTTTTAAATCAATTGTTTATATGTTTAAATAGATT-TTCATGTTAGAATATTGCTTCATTTGA
1 TTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTT-ATGTTAGAATACTGCTTCATTTGA
*
31586047 ATCGATTGTTATGGTGGAATACTG-ATTCTT
65 ATCGATAGTTATGGTGGAATACTGCATTCTT
* * *
31586077 ATTCTTTTGAATC-ATTTTTTATATGTTTAAATCGATTGTTATGTTGGAATACTGCTTCTTTTGA
1 -TTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTAGAATACTGCTTCATTTGA
*
31586141 ATCGATAGTTATGGTGGAATACTGCTTTCTT
65 ATCGATAGTTATGGTGGAATACTGCATTCTT
* *
31586172 TTCTTTTGAATCGATTGTTTGTATGTTTAAATCGATTGTTATGT
1 TTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGT
31586216 AGCTTGTCTA
Statistics
Matches: 125, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
94 78 0.62
95 47 0.38
ACGTcount: A:0.24, C:0.09, G:0.16, T:0.50
Consensus pattern (95 bp):
TTCTTTTGAATCAATTGTTTATATGTTTAAATCGATTGTTATGTTAGAATACTGCTTCATTTGAA
TCGATAGTTATGGTGGAATACTGCATTCTT
Found at i:31586152 original size:34 final size:35
Alignment explanation
Indices: 31586106--31586173 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 35
31586096 TATATGTTTA
* *
31586106 AATCGATTGTTATGTTGGAATACTGC-TTCTTTTG
1 AATCGATAGTTATGGTGGAATACTGCTTTCTTTTG
31586140 AATCGATAGTTATGGTGGAATACTGCTTTCTTTT
1 AATCGATAGTTATGGTGGAATACTGCTTTCTTTT
31586174 CTTTTGAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 24 0.77
35 7 0.23
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.46
Consensus pattern (35 bp):
AATCGATAGTTATGGTGGAATACTGCTTTCTTTTG
Found at i:31586632 original size:17 final size:17
Alignment explanation
Indices: 31586612--31586649 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
31586602 AACCTAAAAA
31586612 AATTAATAATTATAGTT
1 AATTAATAATTATAGTT
**
31586629 AATTTTTAATTATAGTT
1 AATTAATAATTATAGTT
31586646 AATT
1 AATT
31586650 TTATTGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (17 bp):
AATTAATAATTATAGTT
Found at i:31586650 original size:17 final size:17
Alignment explanation
Indices: 31586618--31586651 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31586608 AAAAAATTAA
31586618 TAATTATAGTTAATTTT
1 TAATTATAGTTAATTTT
31586635 TAATTATAGTTAATTTT
1 TAATTATAGTTAATTTT
31586652 ATTGTATTTA
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:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (17 bp):
TAATTATAGTTAATTTT
Found at i:31587785 original size:6 final size:6
Alignment explanation
Indices: 31587771--31587802 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
31587761 TAATTATAAA
31587771 TTATA- TTATAT TTATAT TTATAT TTATAT TTA
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTA
31587803 CAAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTATAT
Found at i:31589571 original size:3 final size:3
Alignment explanation
Indices: 31589563--31589610 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
31589553 AAGGACACAA
* * * *
31589563 ATT ATT ATT ATT ATC ATT ACT ATT ACT ATT ATT ATT AAAT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
31589609 AT
1 AT
31589611 CTTCTTTTAG
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
3 34 0.94
4 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:31589770 original size:24 final size:24
Alignment explanation
Indices: 31589734--31589780 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
31589724 TCAATAGATC
31589734 AATGGAAAAATAACAAAAAATTAT
1 AATGGAAAAATAACAAAAAATTAT
*
31589758 AATGGAAACATAACAAAAAATTA
1 AATGGAAAAATAACAAAAAATTA
31589781 CAAATAAACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.66, C:0.06, G:0.09, T:0.19
Consensus pattern (24 bp):
AATGGAAAAATAACAAAAAATTAT
Found at i:31590250 original size:22 final size:24
Alignment explanation
Indices: 31590225--31590278 Score: 87
Period size: 22 Copynumber: 2.4 Consensus size: 24
31590215 AGAAAAGTAG
31590225 TGATTTTTTAAAACAAA-A-AATT
1 TGATTTTTTAAAACAAAGAGAATT
31590247 TGATTTTTTAAAACAAAGAGAATT
1 TGATTTTTTAAAACAAAGAGAATT
31590271 TG-TTTTTT
1 TGATTTTTT
31590279 CAACTATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.57
23 7 0.23
24 6 0.20
ACGTcount: A:0.41, C:0.04, G:0.09, T:0.46
Consensus pattern (24 bp):
TGATTTTTTAAAACAAAGAGAATT
Found at i:31598967 original size:40 final size:39
Alignment explanation
Indices: 31598923--31599015 Score: 109
Period size: 40 Copynumber: 2.4 Consensus size: 39
31598913 CTTAATACAA
* * *
31598923 CTATTTTCATATAA-TCGATTCATATAATCATTTCGTATAT
1 CTATTTTCATATAACT-GATTCAT-TAACCATTCCATATAT
* *
31598963 CTATTTCCATATAACTGATTCATTTACCATTCCATATAT
1 CTATTTTCATATAACTGATTCATTAACCATTCCATATAT
31599002 CTA-TTTCATATAAC
1 CTATTTTCATATAAC
31599016 CATTTCATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
38 10 0.22
39 15 0.33
40 20 0.43
41 1 0.02
ACGTcount: A:0.32, C:0.19, G:0.03, T:0.45
Consensus pattern (39 bp):
CTATTTTCATATAACTGATTCATTAACCATTCCATATAT
Found at i:31599009 original size:25 final size:26
Alignment explanation
Indices: 31598967--31599019 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
31598957 GTATATCTAT
*
31598967 TTCCATATAACTGATTCAT-TTACCA
1 TTCCATATAACTGATTCATATAACCA
*
31598992 TTCCATATATCT-ATTTCATATAACCA
1 TTCCATATAACTGA-TTCATATAACCA
31599018 TT
1 TT
31599020 TCATTTTACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 1 0.04
25 16 0.67
26 7 0.29
ACGTcount: A:0.32, C:0.23, G:0.02, T:0.43
Consensus pattern (26 bp):
TTCCATATAACTGATTCATATAACCA
Found at i:31599013 original size:13 final size:13
Alignment explanation
Indices: 31598927--31599023 Score: 58
Period size: 13 Copynumber: 7.5 Consensus size: 13
31598917 ATACAACTAT
*
31598927 TTTCATATAATCGA
1 TTTCATAT-ATCTA
31598941 -TTCATATAATC-A
1 TTTCATAT-ATCTA
*
31598953 TTTCGTATATCTA
1 TTTCATATATCTA
*
31598966 TTTCCATATAACTGA
1 TTT-CATATATCT-A
* *
31598981 -TTCATTTA-CCA
1 TTTCATATATCTA
*
31598992 TTCCATATATCTA
1 TTTCATATATCTA
* *
31599005 TTTCATATAACCA
1 TTTCATATATCTA
31599018 TTTCAT
1 TTTCAT
31599024 TTTACACATT
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
11 1 0.02
12 11 0.17
13 44 0.67
14 9 0.14
15 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.45
Consensus pattern (13 bp):
TTTCATATATCTA
Found at i:31599028 original size:39 final size:40
Alignment explanation
Indices: 31598923--31599033 Score: 106
Period size: 40 Copynumber: 2.8 Consensus size: 40
31598913 CTTAATACAA
* * * *
31598923 CTATTTTCATATAA-TCGATTCATATA-ATCATTTCGTATAT
1 CTATTTCCATATAACTC-ATTCATTTACA-CATTCCATATAT
*
31598963 CTATTTCCATATAACTGATTCATTTAC-CATTCCATATAT
1 CTATTTCCATATAACTCATTCATTTACACATTCCATATAT
31599002 CTATTT-CATATAAC-CATTTCATTTTACACATT
1 CTATTTCCATATAACTCA-TTCA-TTTACACATT
31599034 TAGCACATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
37 1 0.02
38 12 0.20
39 21 0.35
40 25 0.42
41 1 0.02
ACGTcount: A:0.32, C:0.20, G:0.03, T:0.46
Consensus pattern (40 bp):
CTATTTCCATATAACTCATTCATTTACACATTCCATATAT
Found at i:31601303 original size:24 final size:24
Alignment explanation
Indices: 31601275--31601343 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
31601265 ACACTCCACA
*
31601275 TTGTGGCCAAGCCACTCAATAGCG
1 TTGTGGCCAAGCCACTCAATAACG
* *
31601299 TTGTGGTCAAGCCACTCAATAATG
1 TTGTGGCCAAGCCACTCAATAACG
* **
31601323 TTCTAACCAAGCCACTCAATA
1 TTGTGGCCAAGCCACTCAATA
31601344 TTGCAGATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (24 bp):
TTGTGGCCAAGCCACTCAATAACG
Found at i:31601410 original size:39 final size:39
Alignment explanation
Indices: 31601330--31601421 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 39
31601320 ATGTTCTAAC
* * * ** **
31601330 CAAGCCACTCAATATTGCAGATAAGCTGCATGTTGTTGT
1 CAAGCCACTCAATATCGCAGACAAGCTACACCTTGCGGT
31601369 CAAGCCACTCAATATCGCAGACAAGCTACACCTTGCGGT
1 CAAGCCACTCAATATCGCAGACAAGCTACACCTTGCGGT
**
31601408 CAAGATACTCAATA
1 CAAGCCACTCAATA
31601422 ATGTTGTGGC
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (39 bp):
CAAGCCACTCAATATCGCAGACAAGCTACACCTTGCGGT
Found at i:31602865 original size:9 final size:9
Alignment explanation
Indices: 31602851--31602876 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
31602841 ATATTTATAA
31602851 CTCATAAAC
1 CTCATAAAC
31602860 CTCATAAAC
1 CTCATAAAC
31602869 CTCATAAA
1 CTCATAAA
31602877 TAAAATCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (9 bp):
CTCATAAAC
Found at i:31603292 original size:16 final size:15
Alignment explanation
Indices: 31603250--31603292 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
31603240 CTAATTCAAG
31603250 CATATATCACA-TAA
1 CATATATCACATTAA
31603264 CATATATTC-CATTAA
1 CATATA-TCACATTAA
31603279 TCATATATCACATT
1 -CATATATCACATT
31603293 TCACACATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.32
15 7 0.28
16 10 0.40
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (15 bp):
CATATATCACATTAA
Found at i:31605390 original size:50 final size:49
Alignment explanation
Indices: 31605327--31605511 Score: 171
Period size: 50 Copynumber: 3.7 Consensus size: 49
31605317 TATTAGAGGA
* * *
31605327 CCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCT
1 CCCA-GTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGA--ACT
* *
31605379 CCC-GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACT
1 CCCAGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACT
* * * *
31605427 CCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAAGAG-ACAT
1 CCCA-GTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAAC-T
* * *
31605476 CCCATGTAAAACCATGTTTGGGACATGGCTTTGGCA
1 CCCA-GTAAGACCATGTCTGGGACATGGCATTGGCA
31605512 TGTTATTATC
Statistics
Matches: 114, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
48 8 0.07
49 37 0.32
50 66 0.58
52 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (49 bp):
CCCAGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAACT
Found at i:31610666 original size:56 final size:50
Alignment explanation
Indices: 31610570--31610816 Score: 203
Period size: 50 Copynumber: 4.8 Consensus size: 50
31610560 ATTTGGGTAA
* * *
31610570 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
31610626 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * *
31610676 AGAGGTCTCC-CGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATA
1 AGAGGTC-CCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * * *
31610726 AGAACTCTCATGTAAGACCATATCTAGGATATGTCATTGGCA--GTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * *
31610775 AAACATCCCATGTAAGACCATGTTTGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
31610817 TGTTATTATC
Statistics
Matches: 157, Mismatches: 31, Indels: 13
0.78 0.15 0.06
Matches are distributed among these distances:
48 1 0.01
49 35 0.22
50 75 0.48
51 2 0.01
53 3 0.02
55 1 0.01
56 40 0.25
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:31614987 original size:38 final size:38
Alignment explanation
Indices: 31614932--31615004 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 38
31614922 ACCCGGATGA
** *
31614932 ATGGAATATGTGCTACTAT-AAGCCTCTGATAGAATGTC
1 ATGGAATATGTAATACTATGAA-CCTATGATAGAATGTC
31614970 ATGGAATATGTAATACTATGAACCTATGATAGAAT
1 ATGGAATATGTAATACTATGAACCTATGATAGAAT
31615005 ATCTCATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
38 29 0.94
39 2 0.06
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.32
Consensus pattern (38 bp):
ATGGAATATGTAATACTATGAACCTATGATAGAATGTC
Found at i:31617631 original size:24 final size:21
Alignment explanation
Indices: 31617602--31617646 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
31617592 ATTTAACCCG
31617602 TCTTCAAAACGAACACACATTTCT
1 TCTTC-AAACG-ACACA-ATTTCT
*
31617626 TCTTCAGACGACACAATTTCT
1 TCTTCAAACGACACAATTTCT
31617647 CGAGTATACT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 6 0.30
22 5 0.25
23 4 0.20
24 5 0.25
ACGTcount: A:0.33, C:0.29, G:0.07, T:0.31
Consensus pattern (21 bp):
TCTTCAAACGACACAATTTCT
Found at i:31627061 original size:27 final size:25
Alignment explanation
Indices: 31627006--31627064 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
31626996 AGGCTTACCC
* *
31627006 ATATTATTTTTAAAAATATATATTT
1 ATATTATTTTTAAAAATATATAATA
* *
31627031 ATATTATTTTTAATTTAATATTTAATA
1 ATATTATTTTTAA--AAATATATAATA
31627058 ATATTAT
1 ATATTAT
31627065 ATATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 13 0.46
27 15 0.54
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
ATATTATTTTTAAAAATATATAATA
Found at i:31627070 original size:24 final size:24
Alignment explanation
Indices: 31627043--31627094 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
31627033 ATTATTTTTA
*
31627043 ATTTAATATTTAATAATATTATAT
1 ATTTAATATTTAATAAAATTATAT
** * *
31627067 ATTTTTTATTTATTAAAATTTTAT
1 ATTTAATATTTAATAAAATTATAT
31627091 ATTT
1 ATTT
31627095 TGTCAAAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTAATATTTAATAAAATTATAT
Found at i:31627095 original size:24 final size:24
Alignment explanation
Indices: 31627049--31627095 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
31627039 TTTAATTTAA
*
31627049 TATTTAATAATATTATATATTTTT
1 TATTTAATAAAATTATATATTTTT
* *
31627073 TATTTATTAAAATTTTATATTTT
1 TATTTAATAAAATTATATATTTT
31627096 GTCAAAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TATTTAATAAAATTATATATTTTT
Found at i:31628358 original size:20 final size:20
Alignment explanation
Indices: 31628318--31628358 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
31628308 ATTATTTTTT
*
31628318 AAAATTATAAAAAATATATA
1 AAAATTATAAAAAATAAATA
31628338 AAAATTATAAATAAA-AAATA
1 AAAATTATAAA-AAATAAATA
31628358 A
1 A
31628359 TGTCCAGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (20 bp):
AAAATTATAAAAAATAAATA
Found at i:31628686 original size:92 final size:92
Alignment explanation
Indices: 31628584--31628761 Score: 231
Period size: 90 Copynumber: 1.9 Consensus size: 92
31628574 ACCAATTTAG
* *
31628584 TTAGAAAAATTATCGAAATGTCATTCCT-TAA-TTAAAAT-ATTTTATATTATTCTAGATTATTT
1 TTAGAAAAATTA-CGAAA-AT-A-TCCTATAATTTAAAATAATTTT-TATTATTCTAGAGTATTT
31628646 TAGTAT-TTTT-ATTTCAACAAAAACATTTGA
61 TAGTATATTTTCATTTCAACAAAAACATTTGA
* *
31628676 TTAGAGAAATTACGAAAATATCCTATAATTTAAAATAATTTTTATTATTCTAGGGTATTTTAGTA
1 TTAGAAAAATTACGAAAATATCCTATAATTTAAAATAATTTTTATTATTCTAGAGTATTTTAGTA
*
31628741 TATTTTCATTTCAATAAAAAC
66 TATTTTCATTTCAACAAAAAC
31628762 TAATAACAAT
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
88 4 0.05
89 4 0.05
90 30 0.39
91 14 0.18
92 24 0.32
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.44
Consensus pattern (92 bp):
TTAGAAAAATTACGAAAATATCCTATAATTTAAAATAATTTTTATTATTCTAGAGTATTTTAGTA
TATTTTCATTTCAACAAAAACATTTGA
Found at i:31630276 original size:19 final size:19
Alignment explanation
Indices: 31630226--31630278 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
31630216 CTAAACCCAC
31630226 ATTCAATTTAAATAATTAAA
1 ATTCAATTTAAA-AATTAAA
*
31630246 ATT-ATTTTTAAAAATT-AA
1 ATTCA-ATTTAAAAATTAAA
31630264 ATTCAATTATAAAAA
1 ATTCAATT-TAAAAA
31630279 CATGTTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 7 0.25
19 12 0.43
20 9 0.32
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
ATTCAATTTAAAAATTAAA
Found at i:31631041 original size:45 final size:45
Alignment explanation
Indices: 31630977--31631068 Score: 184
Period size: 45 Copynumber: 2.0 Consensus size: 45
31630967 AGAATCTGAG
31630977 TATAGAGATGAAAATTTCAGGCATCCTGGGAATCTGATTGAAGAT
1 TATAGAGATGAAAATTTCAGGCATCCTGGGAATCTGATTGAAGAT
31631022 TATAGAGATGAAAATTTCAGGCATCCTGGGAATCTGATTGAAGAT
1 TATAGAGATGAAAATTTCAGGCATCCTGGGAATCTGATTGAAGAT
31631067 TA
1 TA
31631069 ACGATTTGTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.36, C:0.11, G:0.24, T:0.29
Consensus pattern (45 bp):
TATAGAGATGAAAATTTCAGGCATCCTGGGAATCTGATTGAAGAT
Found at i:31632384 original size:17 final size:19
Alignment explanation
Indices: 31632362--31632399 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
31632352 GGTCAGCTTA
31632362 CATGTTTAAC-T-CATATG
1 CATGTTTAACTTACATATG
31632379 CATGTTTAACTTACATATG
1 CATGTTTAACTTACATATG
31632398 CA
1 CA
31632400 ATGATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (19 bp):
CATGTTTAACTTACATATG
Found at i:31634120 original size:44 final size:44
Alignment explanation
Indices: 31634027--31634121 Score: 113
Period size: 44 Copynumber: 2.1 Consensus size: 44
31634017 ATAGAAGCGT
* * *
31634027 AATGAAATAGAGGCGTAATAGCAATTTAATTGTTTGGTTGAATGT
1 AATGGAATAGAGGCGTAATAGCAATTT-ATTGTTTGATTGAATGG
*
31634072 AATGGAATAGAGGCGTAATAG-TATTCT-TGTGTTTGATTGAATGG
1 AATGGAATAGAGGCGTAATAGCAATT-TAT-TGTTTGATTGAATGG
31634116 AATGGA
1 AATGGA
31634122 GGTGTAATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
43 1 0.02
44 22 0.50
45 21 0.48
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATAGCAATTTATTGTTTGATTGAATGG
Found at i:31634233 original size:20 final size:22
Alignment explanation
Indices: 31634208--31634267 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 22
31634198 TGTTTTGTTA
*
31634208 TAAAAT-TTTAATA-AGATTAT
1 TAAAATATATAATATAGATTAT
31634228 TAAAATAATATAATATAGATTAT
1 TAAAAT-ATATAATATAGATTAT
31634251 TAAAATAATATAATATA
1 TAAAAT-ATATAATATA
31634268 AATATTTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 6 0.17
22 6 0.17
23 24 0.67
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (22 bp):
TAAAATATATAATATAGATTAT
Found at i:31634251 original size:23 final size:23
Alignment explanation
Indices: 31634216--31634267 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
31634206 TATAAAATTT
31634216 TAATA-AGATTATTAAAATAATA
1 TAATATAGATTATTAAAATAATA
31634238 TAATATAGATTATTAAAATAATA
1 TAATATAGATTATTAAAATAATA
31634261 TAATATA
1 TAATATA
31634268 AATATTTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 5 0.17
23 24 0.83
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (23 bp):
TAATATAGATTATTAAAATAATA
Found at i:31634695 original size:11 final size:11
Alignment explanation
Indices: 31634676--31634730 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
31634666 AGGATTATTA
*
31634676 TTAAAAATAAT
1 TTAATAATAAT
31634687 TTAATAATAA-
1 TTAATAATAAT
*
31634697 ATAATAAATAAT
1 TTAAT-AATAAT
* *
31634709 TTAATCATATT
1 TTAATAATAAT
31634720 TTAAT-ATAAT
1 TTAATAATAAT
31634730 T
1 T
31634731 ATTATTAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
10 9 0.25
11 23 0.64
12 4 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAATAATAAT
Found at i:31636934 original size:40 final size:39
Alignment explanation
Indices: 31636890--31637028 Score: 129
Period size: 40 Copynumber: 3.5 Consensus size: 39
31636880 CTAAAGCCTA
* *
31636890 CTAGGCACTATGCCCGATA-ATTACACCGACACGAAGCTTG
1 CTAGGCATTAGGCCCGATAGA-TACACCGACACGAAGC-TG
* * *
31636930 CTAGGCATTAAGCCCGATAGATAC-CCTGGCACAAAGCCTG
1 CTAGGCATTAGGCCCGATAGATACACC-GACACGAAG-CTG
* * *
31636970 CTAGGCATTAGGCCCAATAGATATACTGACACGAAGACTG
1 CTAGGCATTAGGCCCGATAGATACACCGACACGAAG-CTG
**
31637010 CTAGGCAGAAGGCCCGATA
1 CTAGGCATTAGGCCCGATA
31637029 CATTACAGTA
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
39 2 0.02
40 76 0.94
41 3 0.04
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (39 bp):
CTAGGCATTAGGCCCGATAGATACACCGACACGAAGCTG
Found at i:31648642 original size:47 final size:47
Alignment explanation
Indices: 31648588--31648682 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
31648578 ATGCAGGAAA
31648588 AGGCACGTCCTTAGAACAAGAAGGAATAGTCTTGATTAACGGAACAC
1 AGGCACGTCCTTAGAACAAGAAGGAATAGTCTTGATTAACGGAACAC
31648635 AGGCACGTCCTTAGAACAAGAAGGAATAGTCTTGATTAACGGAACAC
1 AGGCACGTCCTTAGAACAAGAAGGAATAGTCTTGATTAACGGAACAC
31648682 A
1 A
31648683 CGTGGGTACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (47 bp):
AGGCACGTCCTTAGAACAAGAAGGAATAGTCTTGATTAACGGAACAC
Found at i:31659160 original size:40 final size:40
Alignment explanation
Indices: 31659134--31659215 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
31659124 GAGTCATCTA
31659134 CAATTCAATTTGGCTTTTATTAGATAACATCATATACTAT
1 CAATTCAATTTGGCTTTTATTAGATAACATCATATACTAT
31659174 CAATTCAATTTGGCTTTTATTAGATAACATCATATACTAT
1 CAATTCAATTTGGCTTTTATTAGATAACATCATATACTAT
31659214 CA
1 CA
31659216 CATTAAGCCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.41
Consensus pattern (40 bp):
CAATTCAATTTGGCTTTTATTAGATAACATCATATACTAT
Found at i:31659621 original size:51 final size:51
Alignment explanation
Indices: 31659553--31659710 Score: 280
Period size: 51 Copynumber: 3.1 Consensus size: 51
31659543 ATCACATTTA
*
31659553 TCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
31659604 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* * *
31659655 TCACTAGTCACTGATCATATAAGTGTAGCTAAAGTTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
31659706 TCACT
1 TCACT
31659711 GATCAGAAGT
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 103 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:31663123 original size:22 final size:22
Alignment explanation
Indices: 31663098--31663183 Score: 102
Period size: 22 Copynumber: 3.8 Consensus size: 22
31663088 TATTAAACAA
31663098 AGAGCACTAAAGTGCTATACAG
1 AGAGCACTAAAGTGCTATACAG
31663120 AGAGCAC-AAATGTGCTATACAG
1 AGAGCACTAAA-GTGCTATACAG
* *
31663142 AGAGCACTAATGTGCTAATAAGCGG
1 AGAGCACTAAAGTGCT-AT-A-CAG
*
31663167 AGAGCACTAACGTGCTA
1 AGAGCACTAAAGTGCTA
31663184 GAAATCAGAG
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.05
22 30 0.54
23 4 0.07
24 2 0.04
25 17 0.30
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (22 bp):
AGAGCACTAAAGTGCTATACAG
Found at i:31663194 original size:25 final size:25
Alignment explanation
Indices: 31663098--31663242 Score: 109
Period size: 25 Copynumber: 6.3 Consensus size: 25
31663088 TATTAAACAA
*
31663098 AGAGCACTAAAGTGCT-AT-A-CAG
1 AGAGCACTAACGTGCTAATAATCAG
* *
31663120 AGAGCACAAATGTGCT-AT-A-CAG
1 AGAGCACTAACGTGCTAATAATCAG
* * *
31663142 AGAGCACTAATGTGCTAATAAGCGG
1 AGAGCACTAACGTGCTAATAATCAG
31663167 AGAGCACTAACGTGCTAGA-AATCAG
1 AGAGCACTAACGTGCTA-ATAATCAG
*
31663192 AGAG------CGTGCTAGTAATCAG
1 AGAGCACTAACGTGCTAATAATCAG
* *
31663211 AGAGTACTGACGTGCTAATAATCAG
1 AGAGCACTAACGTGCTAATAATCAG
31663236 AGAGCAC
1 AGAGCAC
31663243 GCTAAACTCC
Statistics
Matches: 102, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
19 17 0.17
22 35 0.34
23 2 0.02
24 1 0.01
25 46 0.45
26 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.19
Consensus pattern (25 bp):
AGAGCACTAACGTGCTAATAATCAG
Found at i:31663201 original size:19 final size:19
Alignment explanation
Indices: 31663177--31663214 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
31663167 AGAGCACTAA
31663177 CGTGCTAGAAATCAGAGAG
1 CGTGCTAGAAATCAGAGAG
*
31663196 CGTGCTAGTAATCAGAGAG
1 CGTGCTAGAAATCAGAGAG
31663215 TACTGACGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (19 bp):
CGTGCTAGAAATCAGAGAG
Found at i:31664374 original size:51 final size:51
Alignment explanation
Indices: 31664306--31664463 Score: 280
Period size: 51 Copynumber: 3.1 Consensus size: 51
31664296 ATCACATTTA
*
31664306 TCACTTGTCACTGATCAGATAAGTGTAACTAAAGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* *
31664357 TCACTTGTCATTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTAG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
*
31664408 TCACTTGTTACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
31664459 TCACT
1 TCACT
31664464 GATCAGAAGT
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 101 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.32
Consensus pattern (51 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:31668041 original size:38 final size:34
Alignment explanation
Indices: 31667983--31668052 Score: 86
Period size: 38 Copynumber: 1.9 Consensus size: 34
31667973 CAACATCTTG
31667983 AAATTTTTTTATTTTTATTTCAATTTTTCAATTT
1 AAATTTTTTTATTTTTATTTCAATTTTTCAATTT
**
31668017 AAATTTCTTTTAGTTATTTCATTTCCTTTTTTCAAT
1 AAATTT-TTTTA-TT-TTT-ATTTCAATTTTTCAAT
31668053 AAACTACAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 6 0.20
35 5 0.17
36 2 0.07
37 3 0.10
38 14 0.47
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.64
Consensus pattern (34 bp):
AAATTTTTTTATTTTTATTTCAATTTTTCAATTT
Found at i:31670093 original size:43 final size:43
Alignment explanation
Indices: 31670022--31670107 Score: 109
Period size: 43 Copynumber: 2.0 Consensus size: 43
31670012 TTTTATCTTA
* * * * *
31670022 GAAAAAATAATTTAAAAAGAGGAAAAGATAATCTTGGGTTGTT
1 GAAAAAAGAATTGAAAAAGAGCAAAAGATAAACATGGGTTGTT
**
31670065 GAAAAAAGAATTGAAAAAGAGCTGAAGATAAACATGGGTTGTT
1 GAAAAAAGAATTGAAAAAGAGCAAAAGATAAACATGGGTTGTT
31670108 TGTTTTACCT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.49, C:0.03, G:0.23, T:0.24
Consensus pattern (43 bp):
GAAAAAAGAATTGAAAAAGAGCAAAAGATAAACATGGGTTGTT
Found at i:31677109 original size:16 final size:16
Alignment explanation
Indices: 31677084--31677131 Score: 78
Period size: 16 Copynumber: 3.0 Consensus size: 16
31677074 ATTCAATCCA
*
31677084 AAAATCATATTTTTGC
1 AAAATTATATTTTTGC
31677100 AAAATTATATTTTTGC
1 AAAATTATATTTTTGC
*
31677116 AAAATTATACTTTTGC
1 AAAATTATATTTTTGC
31677132 TCCTATAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (16 bp):
AAAATTATATTTTTGC
Found at i:31680291 original size:40 final size:40
Alignment explanation
Indices: 31680239--31680452 Score: 158
Period size: 40 Copynumber: 5.5 Consensus size: 40
31680229 AATCATTGTT
*
31680239 GGTTTATTCGACTAGTGCTGGGCACACATTTGATATCGTC
1 GGTTTATCCGACTAGTGCTGGGCACACATTTGATATCGTC
* * * * * *
31680279 GGTTTATCCGACTAGCGCTAGGCGCA-A-CTCAT-T-GTT
1 GGTTTATCCGACTAGTGCTGGGCACACATTTGATATCGTC
* * * * *
31680315 GGTTTATCCGACTAGAGCTGGGCACA-A---AACATTGTT
1 GGTTTATCCGACTAGTGCTGGGCACACATTTGATATCGTC
* * ** *
31680351 GATTTATCGGACTAGTTTTGGGAACACATTTGATATCGTC
1 GGTTTATCCGACTAGTGCTGGGCACACATTTGATATCGTC
* * * *
31680391 AGTTTATCTGACAAGTGCTGGGCACACATTTGATATCATC
1 GGTTTATCCGACTAGTGCTGGGCACACATTTGATATCGTC
*
31680431 GGTTTATCC-ATCTAGCGCTGGG
1 GGTTTATCCGA-CTAGTGCTGGG
31680453 TGAAAAACTG
Statistics
Matches: 133, Mismatches: 34, Indels: 14
0.73 0.19 0.08
Matches are distributed among these distances:
34 1 0.01
35 1 0.01
36 49 0.37
37 2 0.02
38 3 0.02
39 2 0.02
40 75 0.56
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (40 bp):
GGTTTATCCGACTAGTGCTGGGCACACATTTGATATCGTC
Found at i:31680325 original size:36 final size:36
Alignment explanation
Indices: 31680203--31680365 Score: 148
Period size: 36 Copynumber: 4.4 Consensus size: 36
31680193 GTATTTTTCA
*
31680203 GTTTAGCCGACTAGCGCTGGGTGCA-AAATCATTGTTG
1 GTTTATCCGACTAGCGCT-GG-GCACAAATCATTGTTG
* * * * *
31680240 GTTTATTCGACTAGTGCTGGGCACACATTTGATATCGTCG
1 GTTTATCCGACTAGCGCTGGGCACA-A-ATCAT-T-GTTG
* * *
31680280 GTTTATCCGACTAGCGCTAGGCGCAACTCATTGTTG
1 GTTTATCCGACTAGCGCTGGGCACAAATCATTGTTG
* *
31680316 GTTTATCCGACTAGAGCTGGGCACAAAACATTGTTG
1 GTTTATCCGACTAGCGCTGGGCACAAATCATTGTTG
* *
31680352 ATTTATCGGACTAG
1 GTTTATCCGACTAG
31680366 TTTTGGGAAC
Statistics
Matches: 101, Mismatches: 20, Indels: 11
0.77 0.15 0.08
Matches are distributed among these distances:
35 3 0.03
36 49 0.49
37 17 0.17
38 6 0.06
39 2 0.02
40 24 0.24
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (36 bp):
GTTTATCCGACTAGCGCTGGGCACAAATCATTGTTG
Found at i:31680572 original size:24 final size:24
Alignment explanation
Indices: 31680545--31680591 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
31680535 ATTGAAGAAG
*
31680545 GTTGAAAAGGATATAAATGAAAAT
1 GTTGAAAAAGATATAAATGAAAAT
*
31680569 GTTGAAAAAGATATCAATGAAAA
1 GTTGAAAAAGATATAAATGAAAA
31680592 GGTCAGTGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.19, T:0.23
Consensus pattern (24 bp):
GTTGAAAAAGATATAAATGAAAAT
Found at i:31681705 original size:11 final size:11
Alignment explanation
Indices: 31681689--31681721 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
31681679 TTAGTATTCA
31681689 TGAGATATGAT
1 TGAGATATGAT
31681700 TGAGATATGAT
1 TGAGATATGAT
31681711 TGAGATATGAT
1 TGAGATATGAT
31681722 ATTGTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.27, T:0.36
Consensus pattern (11 bp):
TGAGATATGAT
Found at i:31690383 original size:17 final size:17
Alignment explanation
Indices: 31690361--31690399 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
31690351 ATTAAAAGTG
31690361 TGCATACTATAATAGTT
1 TGCATACTATAATAGTT
* * *
31690378 TGCATATTGTTATAGTT
1 TGCATACTATAATAGTT
31690395 TGCAT
1 TGCAT
31690400 GAAATAATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (17 bp):
TGCATACTATAATAGTT
Found at i:31693265 original size:17 final size:16
Alignment explanation
Indices: 31693243--31693304 Score: 54
Period size: 17 Copynumber: 3.7 Consensus size: 16
31693233 TTCGCTAGGT
31693243 GATACTATCCACCAGGA
1 GATACTATCCACCA-GA
* *
31693260 GATACTATTCGCCA-A
1 GATACTATCCACCAGA
*
31693275 TTGATACTATCCGCCAGA
1 --GATACTATCCACCAGA
31693293 TGATACTATCCA
1 -GATACTATCCA
31693305 TCATGCAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
15 1 0.03
17 36 0.95
18 1 0.03
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (16 bp):
GATACTATCCACCAGA
Found at i:31695257 original size:265 final size:266
Alignment explanation
Indices: 31694773--31695294 Score: 773
Period size: 265 Copynumber: 2.0 Consensus size: 266
31694763 ACTTACTTAT
* *
31694773 TTTATCTTCCCTTCTTAGGACCACCGAAGAAATAAAAAAATCTTCAATGGCTACGTCAGAGGATA
1 TTTATCTTCCCTTCTTAGGACCACCGAAGAAATAAAAAAACCTTCAATGACTACGTCAGAGGATA
*
31694838 CATACTGTGTGAGGCTTCTAGTGTTTTTGTATTATACATGACAAATGAAGGTGGCAACAAGGCTT
66 CATACTGTGTGAGGCTTCTAGTGATTTTGTATTATACATGACAAATGAAGGTGGCAACAAGGCTT
* * * * * *
31694903 GAAATTTGAAGAACAATATGTTGTAACTAAAAATGCATTCGTCAAACTGTGTTCTTTCCTTAAAT
131 GAAATTTAAAGAACAATATGTTGAAACAAAAAAAGCATTCGTCAAACTATGTTATTTCCTTAAAT
* *
31694968 CTTTACAAAGAATTTTTATGTTTTAAAAG-TTTTGGGTTCTTAAGCTTAAATGTTTTATATACTT
196 ATTTACAAAGAATTTTTATGTTTTAAAAGTTTTTGGGTCCTTAAGCTTAAATGTTTTATATACTT
31695032 GCTCTG
261 GCTCTG
** **
31695038 TTTATCTTCCCTTCTTAGGACCATTGAAGAAATAAAGGAACCTTCAATGACTACG-CTAGAGGAT
1 TTTATCTTCCCTTCTTAGGACCACCGAAGAAATAAAAAAACCTTCAATGACTACGTC-AGAGGAT
* * * **
31695102 ACATATTGTGTGAGGCTTCTAGTGATTTTGTATTATGCATGACAAATGAGGGTGGGGACAAGGCT
65 ACATACTGTGTGAGGCTTCTAGTGATTTTGTATTATACATGACAAATGAAGGTGGCAACAAGGCT
* * *
31695167 TGAAATTTAAAGAACAATATTTTGAAACAAAAAAAGTATTTGTCAAACTATGTTATTTCCTTAAA
130 TGAAATTTAAAGAACAATATGTTGAAACAAAAAAAGCATTCGTCAAACTATGTTATTTCCTTAAA
*
31695232 TATTTATAATA-AAGTTTTT-TGTTTTAAAAGTTTTTGGGTCCTTAAGCTTAAATGTTTTATATA
195 TATTTACAA-AGAA-TTTTTATGTTTTAAAAGTTTTTGGGTCCTTAAGCTTAAATGTTTTATATA
31695295 TTACTACTAT
Statistics
Matches: 229, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
264 1 0.00
265 191 0.83
266 37 0.16
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (266 bp):
TTTATCTTCCCTTCTTAGGACCACCGAAGAAATAAAAAAACCTTCAATGACTACGTCAGAGGATA
CATACTGTGTGAGGCTTCTAGTGATTTTGTATTATACATGACAAATGAAGGTGGCAACAAGGCTT
GAAATTTAAAGAACAATATGTTGAAACAAAAAAAGCATTCGTCAAACTATGTTATTTCCTTAAAT
ATTTACAAAGAATTTTTATGTTTTAAAAGTTTTTGGGTCCTTAAGCTTAAATGTTTTATATACTT
GCTCTG
Found at i:31696452 original size:17 final size:17
Alignment explanation
Indices: 31696418--31696452 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
31696408 CTTAAGAACA
* *
31696418 AAAGAAAGAATTATGAG
1 AAAGAAAGAATGAAGAG
31696435 AAAGAAAGAATGAAGAG
1 AAAGAAAGAATGAAGAG
31696452 A
1 A
31696453 GGAAGATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (17 bp):
AAAGAAAGAATGAAGAG
Found at i:31702099 original size:20 final size:19
Alignment explanation
Indices: 31702050--31702105 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 19
31702040 CTTGCAAAAT
31702050 TGTGACTATGTGATGTGGAA
1 TGTGAC-ATGTGATGTGGAA
* *
31702070 TGAGTA-ATGTGATGTGTTAA
1 TGTG-ACATGTGATGTG-GAA
31702090 TGTGACATGTGATGTG
1 TGTGACATGTGATGTG
31702106 CAACTGTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 11 0.37
20 18 0.60
21 1 0.03
ACGTcount: A:0.25, C:0.04, G:0.34, T:0.38
Consensus pattern (19 bp):
TGTGACATGTGATGTGGAA
Found at i:31702113 original size:20 final size:19
Alignment explanation
Indices: 31702050--31702113 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
31702040 CTTGCAAAAT
*
31702050 TGTGACTATGTGATGTGGAA
1 TGTGAC-ATGTGATGTGCAA
* *
31702070 TGAGTA-ATGTGATGTGTTAA
1 TGTG-ACATGTGATGTG-CAA
31702090 TGTGACATGTGATGTGCAA
1 TGTGACATGTGATGTGCAA
31702109 CTGTG
1 -TGTG
31702114 TTAGCTATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 13 0.36
20 22 0.61
21 1 0.03
ACGTcount: A:0.25, C:0.06, G:0.33, T:0.36
Consensus pattern (19 bp):
TGTGACATGTGATGTGCAA
Found at i:31704500 original size:42 final size:42
Alignment explanation
Indices: 31704435--31704560 Score: 145
Period size: 42 Copynumber: 3.0 Consensus size: 42
31704425 GAGGTGTGAT
*
31704435 TTCGTGTAAGACACTGTCTGGGACATTGGCATCGATATGA-GA
1 TTCGTGTAAGAC-CTGTTTGGGACATTGGCATCGATATGATGA
*
31704477 TTACGTGTTAGACCTGTTTGGGACATTGGCA-CTG-TAT-ATGA
1 TT-CGTGTAAGACCTGTTTGGGACATTGGCATC-GATATGATGA
**
31704518 TTCGTGTAAGACCCTGTTTGGGACAGAGGCATCGATATG-TGA
1 TTCGTGTAAGA-CCTGTTTGGGACATTGGCATCGATATGATGA
31704560 T
1 T
31704561 AACATGTAAG
Statistics
Matches: 72, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
40 9 0.12
41 26 0.36
42 28 0.39
43 9 0.12
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (42 bp):
TTCGTGTAAGACCTGTTTGGGACATTGGCATCGATATGATGA
Found at i:31704542 original size:41 final size:41
Alignment explanation
Indices: 31704435--31704555 Score: 140
Period size: 41 Copynumber: 2.9 Consensus size: 41
31704425 GAGGTGTGAT
* *
31704435 TTCGTGTAAGACACTGTCTGGGACATTGGCATCGATATGAGA
1 TTCGTGTAAGACCCTGTTTGGGACATTGGCATCGATAT-AGA
*
31704477 TTACGTGTTAGA-CCTGTTTGGGACATTGGCA-CTG-TATATGA
1 TT-CGTGTAAGACCCTGTTTGGGACATTGGCATC-GATATA-GA
**
31704518 TTCGTGTAAGACCCTGTTTGGGACAGAGGCATCGATAT
1 TTCGTGTAAGACCCTGTTTGGGACATTGGCATCGATAT
31704556 GTGATAACAT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
40 9 0.13
41 26 0.39
42 24 0.36
43 8 0.12
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (41 bp):
TTCGTGTAAGACCCTGTTTGGGACATTGGCATCGATATAGA
Found at i:31704590 original size:83 final size:83
Alignment explanation
Indices: 31704435--31704601 Score: 192
Period size: 83 Copynumber: 2.0 Consensus size: 83
31704425 GAGGTGTGAT
** * * * * * *
31704435 TTCGTGTAAGACACTGTCTGGGACATTGGCATCGATATGAGATTACGTGTTAGACCTGTTTGGGA
1 TTCGTGTAAGACACTGTCTGGGACAGAGGCATCGATATGAGATAACATGTAAGACCTATCTGAGA
31704500 CATTGGCACTGTATATGA
66 CATTGGCACTGTATATGA
* * *
31704518 TTCGTGTAAGACCCTGTTTGGGACAGAGGCATCGATATGTGATAACATGTAAGACCATATCTGAG
1 TTCGTGTAAGACACTGTCTGGGACAGAGGCATCGATATGAGATAACATGTAAGACC-TATCTGAG
* * *
31704583 ATA-TGGCATTGTATGTGA
65 ACATTGGCACTGTATATGA
31704601 T
1 T
31704602 ATATGTGTTT
Statistics
Matches: 69, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
83 62 0.90
84 7 0.10
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (83 bp):
TTCGTGTAAGACACTGTCTGGGACAGAGGCATCGATATGAGATAACATGTAAGACCTATCTGAGA
CATTGGCACTGTATATGA
Found at i:31704798 original size:13 final size:13
Alignment explanation
Indices: 31704780--31704807 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
31704770 GAGAAAAATG
31704780 ATTGTATATGTGT
1 ATTGTATATGTGT
31704793 ATTGTATATGTGT
1 ATTGTATATGTGT
31704806 AT
1 AT
31704808 GAGATTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.21, T:0.54
Consensus pattern (13 bp):
ATTGTATATGTGT
Found at i:31706051 original size:23 final size:23
Alignment explanation
Indices: 31706008--31706052 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
31705998 TTTGACATAA
* *
31706008 TGCTAGTTTGGTATCTATTTTCT
1 TGCTAGTTTGATACCTATTTTCT
31706031 TGCTAGTTTCGATACCT-TTTTC
1 TGCTAGTTT-GATACCTATTTTC
31706053 CAAAAATATC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.13, C:0.18, G:0.16, T:0.53
Consensus pattern (23 bp):
TGCTAGTTTGATACCTATTTTCT
Found at i:31711580 original size:151 final size:151
Alignment explanation
Indices: 31711303--31711605 Score: 419
Period size: 151 Copynumber: 2.0 Consensus size: 151
31711293 TTAGAGATCT
* * *
31711303 ATGTGAAATTGTGAATAAAGTGGATTCAGGCGCTGGTCATAAGTTCTACCAGTGGCTGGGTATAC
1 ATGTGAAACTGTGAATAAAGTGAATTCAGGCGCTAGTCATAAGTTCTACCAGTGGCTGGGTATAC
* * * * * ** *
31711368 CGGCATATGTTGCAGATACCTGATAACTTGTGTGAGCAGGACTGAGTAGTTACGGATGACTGACA
66 CGGCATATGCTGCAGATACCTGACAACTTGTGTGAGAAGCACTGAGTAGTGACAAAAGACTGACA
* *
31711433 ACTTGTGTGAGCAGGCCCGTG
131 ACTTGTATGAGCAGACCCGTG
* *
31711454 ATGTGAAACTGTGATTAAAGTGAATTCAGGTGCTAGT-ATTAAGTTCTACCAGTGGCTGGGTATA
1 ATGTGAAACTGTGAATAAAGTGAATTCAGGCGCTAGTCA-TAAGTTCTACCAGTGGCTGGGTATA
* * *
31711518 CCGGCATATGCTGCGGATACCTGACAGCTTGTGTGAGAAGCACTGAGTAGTGCCAAAAGACTGAC
65 CCGGCATATGCTGCAGATACCTGACAACTTGTGTGAGAAGCACTGAGTAGTGACAAAAGACTGAC
*
31711583 AGCTTGTATGAGCAGACCCGTG
130 AACTTGTATGAGCAGACCCGTG
31711605 A
1 A
31711606 AAGTGAATAG
Statistics
Matches: 132, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
150 1 0.01
151 131 0.99
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.26
Consensus pattern (151 bp):
ATGTGAAACTGTGAATAAAGTGAATTCAGGCGCTAGTCATAAGTTCTACCAGTGGCTGGGTATAC
CGGCATATGCTGCAGATACCTGACAACTTGTGTGAGAAGCACTGAGTAGTGACAAAAGACTGACA
ACTTGTATGAGCAGACCCGTG
Found at i:31716999 original size:22 final size:22
Alignment explanation
Indices: 31716952--31716996 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
31716942 ATGCAATCTT
*
31716952 AGATATGATATGCAATCTTAGA
1 AGATATGATATGCAATATTAGA
* *
31716974 AGATATGATTTTGTAATATTAGA
1 AGATATGA-TATGCAATATTAGA
31716997 GATTTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
AGATATGATATGCAATATTAGA
Found at i:31717244 original size:23 final size:23
Alignment explanation
Indices: 31717200--31717244 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31717190 TCTTGTTTTG
* *
31717200 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
*
31717223 TTGATTTGTATATTATTGATTT
1 TTGATTTGTATATAATTGATTT
31717245 CAAATCTCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.00, G:0.13, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:31717736 original size:23 final size:22
Alignment explanation
Indices: 31717706--31717749 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
31717696 ATAATTCAAA
*
31717706 TACATATATATGTTTCTTATATG
1 TACATATATATATTT-TTATATG
31717729 TACATATATATATTTTTATAT
1 TACATATATATATTTTTATAT
31717750 TTTATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.34, C:0.07, G:0.05, T:0.55
Consensus pattern (22 bp):
TACATATATATATTTTTATATG
Found at i:31717929 original size:3 final size:3
Alignment explanation
Indices: 31717923--31717951 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
31717913 TTTATTTATC
31717923 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31717952 GTTCTTGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31722021 original size:11 final size:11
Alignment explanation
Indices: 31722005--31722032 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
31721995 AGATCCAATT
31722005 AAAAAAAACCA
1 AAAAAAAACCA
31722016 AAAAAAAACCA
1 AAAAAAAACCA
31722027 AAAAAA
1 AAAAAA
31722033 TTAAAAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACCA
Found at i:31722052 original size:20 final size:20
Alignment explanation
Indices: 31722029--31722067 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31722019 AAAAACCAAA
*
31722029 AAAATTAAAAAATCAAAATC
1 AAAATTAAAAAATAAAAATC
31722049 AAAATTAAAAAATAAAAAT
1 AAAATTAAAAAATAAAAAT
31722068 GACAAAAAGA
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:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (20 bp):
AAAATTAAAAAATAAAAATC
Found at i:31723488 original size:44 final size:44
Alignment explanation
Indices: 31723439--31723821 Score: 549
Period size: 44 Copynumber: 8.7 Consensus size: 44
31723429 GATACTAGTT
* **
31723439 CTATCTCCCTAGAAAGCAGTGGAATAGGTTGAAGATTGTAAGTC
1 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTC
**
31723483 CTATCTCCCTGGAAAGCAGTGGAATAGGTTGAAGATTGTAAGTC
1 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTC
*
31723527 CTATCTCCCTTGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTC
1 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTC
* * *
31723571 CTATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTATGAGTC
1 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTC
* *
31723615 CTATCTCCCTGGTCAGTAGTAGAATAGGTTGAAGATTGTAAGTC
1 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTC
*
31723659 CTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAA-TC
1 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTC
*
31723703 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAATATTGTGAA-TC
1 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTC
*
31723747 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAATATTGTGAA-TC
1 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGT-AAGTC
* * *
31723791 CTATCTCTCTGAG-CAACAGTGGAGTAGGTTG
1 CTATCTCCCTG-GTCAGCAGTGGAATAGGTTG
31723822 GAAATTACAT
Statistics
Matches: 316, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
44 313 0.99
45 3 0.01
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (44 bp):
CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTGTAAGTC
Found at i:31723878 original size:132 final size:132
Alignment explanation
Indices: 31723439--31723884 Score: 411
Period size: 132 Copynumber: 3.4 Consensus size: 132
31723429 GATACTAGTT
** * * ** * **
31723439 CTATCTCCCTAGAAAGCAGTGGAATAGGTTGAAGATTG-TAAGTCCTATCTCCCTGGAAAGCAGT
1 CTATCTCCCTAGTCAGCAGTGGAACAGATTGAAGACGGCGAA-TCCTATCTCCCTGGTCAGCAGT
* * *
31723503 GGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTTGTCAGCAGTGGAATAGGTTGAAGATTGTA-
65 AGAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGTCAACAGTGGAATAGGTTGAAGATTG-AC
*
31723567 AGTC
129 AATC
* * * * **** * *
31723571 CTATCTCCCTGGTCAACAGTGGAATAGGTTGAAGATTATGAGTCCTATCTCCCTGGTCAGTAGTA
1 CTATCTCCCTAGTCAGCAGTGGAACAGATTGAAGACGGCGAATCCTATCTCCCTGGTCAGCAGTA
* **
31723636 GAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGTCAGCAGTGGAATAGGTTGAAGATTGTGAA
66 GAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGTCAACAGTGGAATAGGTTGAAGATTGACAA
31723701 TC
131 TC
* * * * ** * *
31723703 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAATATTGTGAATCCTATCTCCCTGGTCAGCAGTG
1 CTATCTCCCTAGTCAGCAGTGGAACAGATTGAAGACGGCGAATCCTATCTCCCTGGTCAGCAGTA
* * *
31723768 GAATAGGTTGAATATTGTGAA-TCCTATCTCTCTGAG-CAACAGTGGAGTAGGTTGGAA-ATT-A
66 GAATAGGTTGAAGATTGT-AAGTCCTATCTCCCT-AGTCAACAGTGGAATAGGTT-GAAGATTGA
31723829 CATATC
128 CA-ATC
* * * *
31723835 TTATCTCCCTAAG-CAGTAGTGGAGCAGATTGAAGACGGCGAATCTTATCT
1 CTATCTCCCT-AGTCAGCAGTGGAACAGATTGAAGACGGCGAATCCTATCT
31723885 TCCCAAGGTA
Statistics
Matches: 270, Mismatches: 37, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
131 1 0.00
132 260 0.96
133 9 0.03
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (132 bp):
CTATCTCCCTAGTCAGCAGTGGAACAGATTGAAGACGGCGAATCCTATCTCCCTGGTCAGCAGTA
GAATAGGTTGAAGATTGTAAGTCCTATCTCCCTAGTCAACAGTGGAATAGGTTGAAGATTGACAA
TC
Found at i:31723880 original size:44 final size:44
Alignment explanation
Indices: 31723832--31724130 Score: 141
Period size: 44 Copynumber: 6.8 Consensus size: 44
31723822 GAAATTACAT
*
31723832 ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGGCGA
* * * ** *
31723876 ATCTTATCTTCCC-AAG--GTAGTAGGAAAGCAAATTTAAG-CCACTA
1 ATCTTATC-TCCCTAAGCAGTAGT-GG--AGTAGATTGAAGACGGCGA
** * * * ** **
31723920 GCCTTATCTCCCTGAGTAGCAGTGGAGTA-AGTTGAAGATTGTAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGA-TTGAAGACGGCGA
* * * * ***
31723964 ACCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAAATTAC-A
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGGCGA
* * *
31724007 GATCTTATATCCCTAAGCAGTAGTGGAGTAGATCGAATACGGCGA
1 -ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGGCGA
* * ** *
31724052 ATCTTATCTTCCC-AAGGTAGTAG-GGAAGTAGATTTAAG-CCACTA
1 ATCTTATC-TCCCTAA-GCAGTAGTGG-AGTAGATTGAAGACGGCGA
** *
31724096 GCCTTATCTCCCTGAGCAGTAGTGGAGTAG-TTGAA
1 ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAA
31724131 AATTACAGAT
Statistics
Matches: 193, Mismatches: 45, Indels: 36
0.70 0.16 0.13
Matches are distributed among these distances:
42 10 0.05
43 30 0.16
44 113 0.59
45 36 0.19
46 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
ATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGGCGA
Found at i:31723926 original size:88 final size:87
Alignment explanation
Indices: 31723834--31724130 Score: 282
Period size: 88 Copynumber: 3.4 Consensus size: 87
31723824 AATTACATAT
*
31723834 CTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAG
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAG
* *
31723899 GAAAGCAAATTTAAGCCACTAGC
66 G-AAGTAGATTTAAGCCACTAGC
* * * ** ** * *
31723922 CTTATCTCCCTGAGTAGCAGTGGAGTA-AGTTGAAGATTGTAAACCTTATC-TCCCTAAGCAGCA
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGA-TTGAAGACGGCGAATCTTATCTTCCC-AAG--GTA
* * *** *
31723985 GT-GG-AGTAGGTTGAAAATTAC-AGAT
62 GTAGGAAGTAGATT-TAAGCCACTAG-C
* * *
31724010 CTTATATCCCTAAGCAGTAGTGGAGTAGATCGAATACGGCGAATCTTATCTTCCCAAGGTAGTAG
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGGCGAATCTTATCTTCCCAAGGTAGTA-
31724075 GGAAGTAGATTTAAGCCACTAGC
65 GGAAGTAGATTTAAGCCACTAGC
*
31724098 CTTATCTCCCTGAGCAGTAGTGGAGTAG-TTGAA
1 CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAA
31724131 AATTACAGAT
Statistics
Matches: 158, Mismatches: 39, Indels: 25
0.71 0.18 0.11
Matches are distributed among these distances:
86 4 0.03
87 16 0.10
88 118 0.75
89 16 0.10
90 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (87 bp):
CTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGACGGCGAATCTTATCTTCCCAAGGTAGTAG
GAAGTAGATTTAAGCCACTAGC
Found at i:31723930 original size:176 final size:176
Alignment explanation
Indices: 31723748--31724130 Score: 567
Period size: 176 Copynumber: 2.2 Consensus size: 176
31723738 TTGTGAATCC
* * * * *
31723748 TATCTCCCTG-GTCAGCAGTGGAATAGGTTGAATATTGTGAATCC-TATCTCTCTGAGCAACAGT
1 TATCTCCCTGAGTCAGCAGTGGAGTA-GTTGAAGATTGT-AAACCTTATCTCCCTAAGCAACAGT
* * * *
31723811 GGAGTAGGTTGGAAATTACATATCTTATCTCCCTAAGCAGTAGTGGAGCAGATTGAAGACGGCGA
64 GGAGTAGGTTGAAAATTACAGATCTTATATCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGA
31723876 ATCTTATCTTCCCAAGGTAGTAGGAAAGCAAATTTAAGCCACTAGCCT
129 ATCTTATCTTCCCAAGGTAGTAGGAAAGCAAATTTAAGCCACTAGCCT
*
31723924 TATCTCCCTGAGT-AGCAGTGGAGTAAGTTGAAGATTGTAAACCTTATCTCCCTAAGCAGCAGTG
1 TATCTCCCTGAGTCAGCAGTGGAGT-AGTTGAAGATTGTAAACCTTATCTCCCTAAGCAACAGTG
* *
31723988 GAGTAGGTTGAAAATTACAGATCTTATATCCCTAAGCAGTAGTGGAGTAGATCGAATACGGCGAA
65 GAGTAGGTTGAAAATTACAGATCTTATATCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAA
* * *
31724053 TCTTATCTTCCCAAGGTAGTAGGGAAGTAGATTTAAGCCACTAGCCT
130 TCTTATCTTCCCAAGGTAGTAGGAAAGCAAATTTAAGCCACTAGCCT
*
31724100 TATCTCCCTGAG-CAGTAGTGGAGTAGTTGAA
1 TATCTCCCTGAGTCAGCAGTGGAGTAGTTGAA
31724131 AATTACAGAT
Statistics
Matches: 187, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
175 11 0.06
176 173 0.93
177 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (176 bp):
TATCTCCCTGAGTCAGCAGTGGAGTAGTTGAAGATTGTAAACCTTATCTCCCTAAGCAACAGTGG
AGTAGGTTGAAAATTACAGATCTTATATCCCTAAGCAGTAGTGGAGCAGATCGAAGACGGCGAAT
CTTATCTTCCCAAGGTAGTAGGAAAGCAAATTTAAGCCACTAGCCT
Found at i:31725139 original size:23 final size:23
Alignment explanation
Indices: 31725095--31725139 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
31725085 TCTTATTTTG
* *
31725095 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
31725118 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
31725140 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:31725499 original size:37 final size:37
Alignment explanation
Indices: 31725423--31725499 Score: 86
Period size: 37 Copynumber: 2.1 Consensus size: 37
31725413 CATACATACG
*
31725423 TTTTATAATATATACATATACGTACACATTTTTTAATT
1 TTTTATAATATATACATATACG-ACACATTTTATAATT
* *
31725461 TTTTATAA-ATATATATATAC-ACATACTTTTATATATT
1 TTTTATAATATATACATATACGACACA-TTTTATA-ATT
31725498 TT
1 TT
31725500 CTATGTTTCA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
35 4 0.12
36 6 0.18
37 16 0.47
38 8 0.24
ACGTcount: A:0.38, C:0.09, G:0.01, T:0.52
Consensus pattern (37 bp):
TTTTATAATATATACATATACGACACATTTTATAATT
Found at i:31725626 original size:2 final size:2
Alignment explanation
Indices: 31725619--31725650 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
31725609 TTATATGTAC
*
31725619 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31725651 TTTATAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:31725830 original size:3 final size:3
Alignment explanation
Indices: 31725822--31725856 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
31725812 TTTATTTATC
*
31725822 TTA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31725857 GTTGTTCTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31727227 original size:35 final size:35
Alignment explanation
Indices: 31727161--31727228 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
31727151 GACAACATTG
* * ***
31727161 AATTAAAATTTTAAAAAAATTTAATGTTTTAAAGA
1 AATTAAAAATATAAAAAAATTTAAAAATTTAAAGA
31727196 AATTAAAAATATAAAAAAATTTAAAAATTTAAA
1 AATTAAAAATATAAAAAAATTTAAAAATTTAAA
31727229 ATTATTGAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (35 bp):
AATTAAAAATATAAAAAAATTTAAAAATTTAAAGA
Found at i:31732152 original size:6 final size:6
Alignment explanation
Indices: 31732143--31732168 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31732133 CCATGAAGAT
31732143 GATGAC GATGAC GATGAC GATGAC GA
1 GATGAC GATGAC GATGAC GATGAC GA
31732169 AGAGGGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.35, T:0.15
Consensus pattern (6 bp):
GATGAC
Found at i:31736307 original size:23 final size:23
Alignment explanation
Indices: 31736251--31736295 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
31736241 AGGCCCGCCC
*
31736251 AAATTATTTTAATTATTTTTAAA
1 AAATTATTTAAATTATTTTTAAA
31736274 AAATTATTTAAATTATTTTTAA
1 AAATTATTTAAATTATTTTTAA
31736296 TTTAATATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AAATTATTTAAATTATTTTTAAA
Found at i:31744966 original size:21 final size:20
Alignment explanation
Indices: 31744929--31744967 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
31744919 TCCAATAACA
**
31744929 CACCAATAATGTGGTCAAGC
1 CACCAATAATGCAGTCAAGC
31744949 CACCAGATAATGCAGTCAA
1 CACCA-ATAATGCAGTCAA
31744968 CCTGCCAGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (20 bp):
CACCAATAATGCAGTCAAGC
Found at i:31745178 original size:35 final size:35
Alignment explanation
Indices: 31745139--31745264 Score: 130
Period size: 35 Copynumber: 3.6 Consensus size: 35
31745129 AATTTGAATA
* * *
31745139 GGCATGCATAACATGCGATTCAGAAACAATATAGT
1 GGCATGCTTAACATGCGAATCAGAAACAATATAAT
* * *
31745174 GGCATGCTTACCATGCAAATCA-AACACAATTTAAT
1 GGCATGCTTAACATGCGAATCAGAA-ACAATATAAT
* **
31745209 GACATGCTTAACATATGAATCAGAAA-AAGTAATAAT
1 GGCATGCTTAACATGCGAATCAGAAACAA-T-ATAAT
31745245 GGCATGCTTAACATGCGAAT
1 GGCATGCTTAACATGCGAAT
31745265 ATGAATATCA
Statistics
Matches: 72, Mismatches: 15, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
34 4 0.06
35 45 0.62
36 23 0.32
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.25
Consensus pattern (35 bp):
GGCATGCTTAACATGCGAATCAGAAACAATATAAT
Found at i:31749316 original size:43 final size:43
Alignment explanation
Indices: 31749242--31749389 Score: 197
Period size: 43 Copynumber: 3.4 Consensus size: 43
31749232 TGTCCCAGAC
* ** *
31749242 ATGGTCTTACATGGAAATCTCGTATAAATGCCAATAACCCAGCT
1 ATGGTCTTACA-CGAAATCTCAAATCAATGCCAATAACCCAGCT
*
31749286 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAACCCAGCT
1 ATGGTCTTACACGAAATCTCAAATCAATGCCAATAACCCAGCT
* * ** *
31749329 ATGGTCTCACATGAAATCTCAAATCAATGCCAATAGTCTAGCT
1 ATGGTCTTACACGAAATCTCAAATCAATGCCAATAACCCAGCT
31749372 ATGGTCTTACACGAAATC
1 ATGGTCTTACACGAAATC
31749390 ACACCTCGAA
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
43 80 0.88
44 11 0.12
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.26
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCAATGCCAATAACCCAGCT
Found at i:31749602 original size:61 final size:63
Alignment explanation
Indices: 31749533--31749660 Score: 188
Period size: 61 Copynumber: 2.1 Consensus size: 63
31749523 TATATATATA
* * * *
31749533 TATATCCATATACGAATCAAATTCAGCAATGTAT-ATCTACATACAAATC-AATTCGGTAATG
1 TATATCCATATACAAATCAAATTCAGCAATGTATAAACCACATACAAATCAAATTCGGCAATG
* *
31749594 TATATCCATATACAAATCAAATTCGGCAATGTATAAACCATATACAAATCAAATTCGGCAATG
1 TATATCCATATACAAATCAAATTCAGCAATGTATAAACCACATACAAATCAAATTCGGCAATG
31749657 TATA
1 TATA
31749661 AAACATATAC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
61 32 0.54
62 12 0.20
63 15 0.25
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (63 bp):
TATATCCATATACAAATCAAATTCAGCAATGTATAAACCACATACAAATCAAATTCGGCAATG
Found at i:31749640 original size:32 final size:31
Alignment explanation
Indices: 31749533--31749671 Score: 172
Period size: 32 Copynumber: 4.5 Consensus size: 31
31749523 TATATATATA
* * *
31749533 TATATCCATATACGAATCAAATTCAGCAATG
1 TATAACCATATACAAATCAAATTCGGCAATG
* * * *
31749564 TATATCTACATACAAATC-AATTCGGTAATG
1 TATAACCATATACAAATCAAATTCGGCAATG
*
31749594 TATATCCATATACAAATCAAATTCGGCAATG
1 TATAACCATATACAAATCAAATTCGGCAATG
31749625 TATAAACCATATACAAATCAAATTCGGCAATG
1 TAT-AACCATATACAAATCAAATTCGGCAATG
*
31749657 TATAAAACATATACA
1 TAT-AACCATATACA
31749672 TTTAAATTCA
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
30 26 0.27
31 29 0.30
32 41 0.43
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.29
Consensus pattern (31 bp):
TATAACCATATACAAATCAAATTCGGCAATG
Found at i:31749895 original size:30 final size:29
Alignment explanation
Indices: 31749838--31749895 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
31749828 AAATCCATTT
*
31749838 AATTTCACATTTTACACTTTAGCCCCTAA
1 AATTTCACATTTTACAATTTAGCCCCTAA
* * *
31749867 AATTTTACATTTTCTCAATTTAGTCCCTA
1 AATTTCACATTTT-ACAATTTAGCCCCTA
31749896 TTTCAAAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.43
Consensus pattern (29 bp):
AATTTCACATTTTACAATTTAGCCCCTAA
Found at i:31753961 original size:9 final size:9
Alignment explanation
Indices: 31753949--31753994 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
31753939 GAATTATTCG
*
31753949 AATCGAGTT
1 AATCGAATT
31753958 AATCGAATT
1 AATCGAATT
31753967 AATCGAATT
1 AATCGAATT
*
31753976 AATCGAATC
1 AATCGAATT
31753985 AATTCGAATT
1 AA-TCGAATT
31753995 TTTTCTTTCG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
9 27 0.82
10 6 0.18
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (9 bp):
AATCGAATT
Found at i:31754053 original size:9 final size:9
Alignment explanation
Indices: 31754036--31754073 Score: 67
Period size: 9 Copynumber: 4.2 Consensus size: 9
31754026 TAAATTTTCG
31754036 AATTCGAAT
1 AATTCGAAT
*
31754045 AACTCGAAT
1 AATTCGAAT
31754054 AATTCGAAT
1 AATTCGAAT
31754063 AATTCGAAT
1 AATTCGAAT
31754072 AA
1 AA
31754074 AAACTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:31754118 original size:29 final size:29
Alignment explanation
Indices: 31754078--31754136 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
31754068 GAATAAAAAC
*
31754078 TATATTTTTTATTTTTAAAATATACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
31754107 TATATTTTTTATTTTTAAAATACACTACA
1 TATATTTTTTATTTTTAAAATACACTACA
31754136 T
1 T
31754137 TTAAAACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.08, G:0.00, T:0.54
Consensus pattern (29 bp):
TATATTTTTTATTTTTAAAATACACTACA
Found at i:31755724 original size:5 final size:5
Alignment explanation
Indices: 31755716--31755763 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
31755706 CGAACAAATA
* *
31755716 ATTCG ATTCG ATTCG ATTCG ATCTCT ATCTC- ACTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG AT-TCG AT-TCG ATTCG ATTCG ATTCG AT
31755764 AAAACTTCAA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
4 2 0.05
5 29 0.76
6 7 0.18
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.40
Consensus pattern (5 bp):
ATTCG
Found at i:31756994 original size:23 final size:22
Alignment explanation
Indices: 31756954--31756997 Score: 70
Period size: 23 Copynumber: 2.0 Consensus size: 22
31756944 AAATTATAAA
*
31756954 ATATAAAAATATATATATGTAC
1 ATATAAAAAAATATATATGTAC
31756976 ATATAAGAAAAATATATATGTA
1 ATATAA-AAAAATATATATGTA
31756998 TGTGAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (22 bp):
ATATAAAAAAATATATATGTAC
Found at i:31757000 original size:27 final size:26
Alignment explanation
Indices: 31756958--31757021 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
31756948 TATAAAATAT
31756958 AAAAATATATA-TATGT-ACA-TATAA
1 AAAAATATATATTATGTGA-ATTATAA
31756982 GAAAAATATATATGTATGTGAATTATAA
1 -AAAAATATATAT-TATGTGAATTATAA
*
31757010 AAATATATATAT
1 AAAAATATATAT
31757022 AAATATACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 11 0.32
27 17 0.50
28 6 0.18
ACGTcount: A:0.55, C:0.02, G:0.08, T:0.36
Consensus pattern (26 bp):
AAAAATATATATTATGTGAATTATAA
Found at i:31757025 original size:12 final size:12
Alignment explanation
Indices: 31757005--31757075 Score: 52
Period size: 12 Copynumber: 5.7 Consensus size: 12
31756995 GTATGTGAAT
*
31757005 TATAAAAATATA
1 TATATAAATATA
31757017 TATATAAATATACA
1 TATATAAATAT--A
* * *
31757031 TATTTTAATATG
1 TATATAAATATA
*
31757043 TAATATATATATA
1 T-ATATAAATATA
* *
31757056 TATATAAGTATG
1 TATATAAATATA
31757068 TATATAAA
1 TATATAAA
31757076 ATTATGAAAC
Statistics
Matches: 44, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
12 26 0.59
13 8 0.18
14 10 0.23
ACGTcount: A:0.52, C:0.01, G:0.04, T:0.42
Consensus pattern (12 bp):
TATATAAATATA
Found at i:31757734 original size:23 final size:22
Alignment explanation
Indices: 31757691--31757748 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
31757681 AAAGGGTATC
* *
31757691 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
31757712 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
31757735 TGCATATCATATCT
1 TACAAATCATATCT
31757749 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:31758385 original size:44 final size:44
Alignment explanation
Indices: 31758291--31758416 Score: 130
Period size: 44 Copynumber: 2.8 Consensus size: 44
31758281 GAGATCCATC
* * * *
31758291 ATTCTAATCCACTCCACTACAACTTCAGGGAGAT-AGGATTGGTTT
1 ATTC-AATCTACTCCACTGCAACCTCAGGGAGATAAGAATT-GTTT
* *
31758336 CTTCAATCTATTCCACTGCAACCTCAGGGAGATAAGAATT-TCTT
1 ATTCAATCTACTCCACTGCAACCTCAGGGAGATAAGAATTGT-TT
* * *
31758380 ATTCAATTTGCTCCACTGCAACCTCGGGGAGATAAGA
1 ATTCAATCTACTCCACTGCAACCTCAGGGAGATAAGA
31758417 CTGGATGCGA
Statistics
Matches: 68, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
43 1 0.01
44 59 0.87
45 8 0.12
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.29
Consensus pattern (44 bp):
ATTCAATCTACTCCACTGCAACCTCAGGGAGATAAGAATTGTTT
Found at i:31758581 original size:45 final size:45
Alignment explanation
Indices: 31758517--31759680 Score: 1409
Period size: 45 Copynumber: 25.9 Consensus size: 45
31758507 TACTTCTGTC
*
31758517 TTCGATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGCTATT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* * * *
31758562 TTCGATCTACTTCGCTGCCAATATAGGAAGACAAGATCCGTTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* * * * * * *
31758607 TTCGATCCACTTTGCTACCAATATAGGAAGCCCAGATCTGTTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* * ** *
31758653 TT-GATCTACTTCGCTGCTAATACAGGAAGAAAAGATCTATTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* * *
31758697 TTCGATCTACTTCACTACCAATATAGGAAGACAAGATCTGCTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* * *
31758743 TT-GATCTACCTCGCTGCCGATACAGGAAGACAAGATCTGTTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* *
31758788 TT-GATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* *
31758833 TT-GATCTACTTCGCTGCCAGTACAGGAAGACAAGATCTGTTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* * * *
31758878 TT-GATCTACTTCACTGCCAATATAGGAAGACAAGATCTGTTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* *
31758922 TTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATAT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* * *
31758968 TT-GATCTACTTCGCTGCCAATACAGGAAGATAAGATCTGTTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* *
31759012 TTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGCTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* * * *
31759058 TT-GATCTACTTCGCTGCCAGTACGGGAAGACAAGATCTGTTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* * * *
31759102 TTAGATCTACTTCGCTACCAATATAGGAAGATAAGATCTGCTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* * * *
31759148 TT-GATCTACTTTGCTGCCAATACAGGAAGATAAGATCTGTTATA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* * * *
31759192 TTCGATCTACATCGCTACCAATATAGGAAGATAAGATCTGCTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* * * *
31759238 TT-GATCTACTTTGCTGCCAATACAGGAAGATAAGATCTGTTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* * *
31759282 TTCGATCTACTTCACTACCAATATAGGAAGACAAGATCTGCTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* *
31759328 TT-GATCTTCTTCGCTGCCAGTACAGGAAGACAAGATCTGCTATT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* * *
31759372 TTCGATCTACTTAGCTGCCAATACAGGAAGACAAGATTTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* * *
31759417 TTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTACTATA
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* *
31759462 TTCAATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
*
31759507 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATC
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
* * * * *
31759552 TTCGATCTACTTCACTACTAATACAAGAAGACAAGATCTGGTATCT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTAT-T
* * *
31759598 TT-GATCTACTTC-ATGCCAATACAGGAAGACAAGATTTG-TTTT
1 TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
31759640 CTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG
1 -TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTG
31759681 TTCTCTGCAG
Statistics
Matches: 964, Mismatches: 137, Indels: 36
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.00
43 4 0.00
44 46 0.05
45 897 0.93
46 16 0.02
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (45 bp):
TTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATT
Found at i:31761220 original size:63 final size:62
Alignment explanation
Indices: 31761101--31761220 Score: 143
Period size: 63 Copynumber: 1.9 Consensus size: 62
31761091 TTCCTTTATT
** * * * * *
31761101 TATTTTTTAGACTCAAAGTGCCCTTTGCGGGTTTTCACCTCGGTGTTGTTTTCTTTTTTCCC
1 TATTTTTTAGACTCAAAGCACCCTTTGCGGATTTTCACCTCGATCTTGTCTCCTTTTTTCCC
*
31761163 TATTTTTTAGGACTCAAAGCACCCTTTGCGGATTTTCACCTTGATCCTT-TCTCCTTTT
1 TATTTTTTA-GACTCAAAGCACCCTTTGCGGATTTTCACCTCGAT-CTTGTCTCCTTTT
31761221 AGGTACTTCT
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
62 9 0.19
63 37 0.77
64 2 0.04
ACGTcount: A:0.14, C:0.24, G:0.15, T:0.47
Consensus pattern (62 bp):
TATTTTTTAGACTCAAAGCACCCTTTGCGGATTTTCACCTCGATCTTGTCTCCTTTTTTCCC
Found at i:31762110 original size:10 final size:10
Alignment explanation
Indices: 31762089--31762118 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
31762079 TGGCCTCTCA
31762089 TTTTTCTATTC
1 TTTTTCT-TTC
31762100 TTTTTCTTTC
1 TTTTTCTTTC
31762110 TTTTTCTTT
1 TTTTTCTTT
31762119 TTTCATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 12 0.63
11 7 0.37
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTC
Done.