Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 7 of 171
Found at i:2871556 original size:55 final size:55
Alignment explanation
Indices: 2871465--2871683 Score: 237
Period size: 55 Copynumber: 3.9 Consensus size: 55
2871455 TAACAATCTC
* * * * * *
2871465 TTCAAAAGAAGCAATATTTCAATATGACCATTGATTTAAACATATAAATAATTGA
1 TTCAAAAGAAGCAGTATTCCAACATAACAATTGATTTAAACATATAAACAATTGA
* * *
2871520 TTCAAAAGAAGTAGTATTCCAATATAACAATCGATTTAAACATATAAACAATTGA
1 TTCAAAAGAAGCAGTATTCCAACATAACAATTGATTTAAACATATAAACAATTGA
* *
2871575 TTCAAAAGAAGAAGCAGTATTCCACCAT---AATTGATTTAAACATATAAACAATTAA
1 TTC--AA-AAGAAGCAGTATTCCAACATAACAATTGATTTAAACATATAAACAATTGA
* * * *
2871630 TTCAAAAGGAGTAGTATTTCAACATAACAATTGATTTAAAGAATAATAAACAAT
1 TTCAAAAGAAGCAGTATTCCAACATAACAATTGATTTAAA-CAT-ATAAACAAT
2871684 ATTCCACCAT
Statistics
Matches: 139, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
52 16 0.12
53 2 0.01
55 91 0.65
56 2 0.01
57 11 0.08
58 17 0.12
ACGTcount: A:0.49, C:0.12, G:0.10, T:0.30
Consensus pattern (55 bp):
TTCAAAAGAAGCAGTATTCCAACATAACAATTGATTTAAACATATAAACAATTGA
Found at i:2871606 original size:89 final size:89
Alignment explanation
Indices: 2871514--2871967 Score: 298
Period size: 89 Copynumber: 5.0 Consensus size: 89
2871504 ACATATAAAT
* * * *
2871514 AATTGATTCAAAAGAAGTAGTATTCCAATATAACAATCGATTTAAACATATAAACAATTGATTCA
1 AATTAATTCAAAAGAAGCACTATTCCAATATGACAATCGATTTAAACATATAAACAATTGATTCA
2871579 AAAGAAGAAGCAGTATTCCACCAT-
66 AAA-AAGAAGCAGTATTCCACCATA
* * * * * * * * * *
2871603 AATTGATTTAAACATATAAACAATTAATT-CAA-AAG-GAGTAGTATTTCAAC--AT-AACAATT
1 AATT-AATTCAA-A-AGAAGC-ACT-ATTCCAATATGACAATCG-ATTTAAACATATAAACAATT
* * * *
2871662 GATTTAAAGAATAATAAACAATATTCCACCATAA
60 GA-TTCAA-AA-AAGAAGCAGTATTCCACCAT-A
* ** * * * * *
2871696 CAACCT-ATTCAAAAGAAATAATATTTCAACATGACAATTGATTTAAACATATAAACAATTAATT
1 -AA-TTAATTCAAAAGAAGCACTATTCCAATATGACAATCGATTTAAACATATAAACAATTGATT
* * *
2871760 TAAAAGCAGAAGCAGTATTCCACAATA
64 CAAAA-AAGAAGCAGTATTCCACCATA
* * * *
2871787 GCAATTAATTCAAAAGAAGCAGTATTCCAATTTGACAATTGATTTAAACATATAAATAATTGATT
1 --AATTAATTCAAAAGAAGCACTATTCCAATATGACAATCGATTTAAACATATAAACAATTGATT
* *
2871852 C--AAAAGAAGTAGTATTTCACCATAA
64 CAAAAAAGAAGCAGTATTCCACCAT-A
* * * *
2871877 CAATCAATTCAAAAGTAGCACTATTCCAATTTGACAATCGATTTAAACATATAAACAATTTATTC
1 -AATTAATTCAAAAGAAGCACTATTCCAATATGACAATCGATTTAAACATATAAACAATTGATTC
* * *
2871942 AAAAAAAAAACAGTATTCCAACATA
65 AAAAAAGAAGCAGTATTCCACCATA
2871967 A
1 A
2871968 CAATCGATTC
Statistics
Matches: 280, Mismatches: 62, Indels: 46
0.72 0.16 0.12
Matches are distributed among these distances:
89 92 0.33
90 19 0.07
91 55 0.20
92 85 0.30
93 15 0.05
94 13 0.05
95 1 0.00
ACGTcount: A:0.48, C:0.14, G:0.09, T:0.29
Consensus pattern (89 bp):
AATTAATTCAAAAGAAGCACTATTCCAATATGACAATCGATTTAAACATATAAACAATTGATTCA
AAAAAGAAGCAGTATTCCACCATA
Found at i:2871799 original size:92 final size:90
Alignment explanation
Indices: 2871683--2871980 Score: 321
Period size: 89 Copynumber: 3.3 Consensus size: 90
2871673 TAATAAACAA
* * * ** * **
2871683 TATTCCACCATAACAACCTATTCAAAAGAAATAATATTTCAACATGACAATTGATTTAAACATAT
1 TATTCCACAATAACAATCAATTCAAAAGAAGCAATATTCCAATTTGACAATTGATTTAAACATAT
2871748 AAACAATTAATTTAAAAGCAGAAGCAG
66 AAACAATTAATTTAAAA--AGAAGCAG
* * *
2871775 TATTCCACAATAGCAATTAATTCAAAAGAAGCAGTATTCCAATTTGACAATTGATTTAAACATAT
1 TATTCCACAATAACAATCAATTCAAAAGAAGCAATATTCCAATTTGACAATTGATTTAAACATAT
* * * *
2871840 AAATAATTGA-TTCAAAAGAAGTAG
66 AAACAATTAATTTAAAAAGAAGCAG
* * * * *
2871864 TATTTCACCATAACAATCAATTCAAAAGTAGCACTATTCCAATTTGACAATCGATTTAAACATAT
1 TATTCCACAATAACAATCAATTCAAAAGAAGCAATATTCCAATTTGACAATTGATTTAAACATAT
* * * *
2871929 AAACAATTTATTCAAAAAAAAAACAG
66 AAACAATTAATT-TAAAAAGAAGCAG
*
2871955 TATTCCA-ACATAACAATCGATTCAAA
1 TATTCCACA-ATAACAATCAATTCAAA
2871981 TTTAAACATA
Statistics
Matches: 171, Mismatches: 32, Indels: 7
0.81 0.15 0.03
Matches are distributed among these distances:
89 73 0.43
90 1 0.01
91 35 0.20
92 62 0.36
ACGTcount: A:0.48, C:0.16, G:0.08, T:0.29
Consensus pattern (90 bp):
TATTCCACAATAACAATCAATTCAAAAGAAGCAATATTCCAATTTGACAATTGATTTAAACATAT
AAACAATTAATTTAAAAAGAAGCAG
Found at i:2873565 original size:5 final size:5
Alignment explanation
Indices: 2873555--2873584 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
2873545 AAATATATAT
2873555 GCTTG GCTTG GCTTG GCTTG GCTTG GCTTG
1 GCTTG GCTTG GCTTG GCTTG GCTTG GCTTG
2873585 ATGATACTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.20, G:0.40, T:0.40
Consensus pattern (5 bp):
GCTTG
Found at i:2874081 original size:16 final size:16
Alignment explanation
Indices: 2874060--2874122 Score: 65
Period size: 16 Copynumber: 3.9 Consensus size: 16
2874050 CACTGAAATT
*
2874060 AAATAGAATTGTAATG
1 AAATAGAATTGTAATA
* *
2874076 AAATAGGATTATAATA
1 AAATAGAATTGTAATA
*
2874092 AAATA-AAGTTGTAACA
1 AAATAGAA-TTGTAATA
*
2874108 AAATAGAGTTGTAAT
1 AAATAGAATTGTAAT
2874123 GGAATAAAGT
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
15 1 0.03
16 35 0.95
17 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.16, T:0.30
Consensus pattern (16 bp):
AAATAGAATTGTAATA
Found at i:2874104 original size:32 final size:32
Alignment explanation
Indices: 2874060--2874138 Score: 81
Period size: 32 Copynumber: 2.5 Consensus size: 32
2874050 CACTGAAATT
*
2874060 AAATAGAA-TTGTAATGAAATAG-GATTATAATA
1 AAATA-AAGTTGTAATAAAATAGAG-TTATAATA
* * *
2874092 AAATAAAGTTGTAACAAAATAGAGTTGTAATG
1 AAATAAAGTTGTAATAAAATAGAGTTATAATA
*
2874124 GAATAAAGTTGTAAT
1 AAATAAAGTTGTAAT
2874139 CAGTAATTCA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.05
32 36 0.92
33 1 0.03
ACGTcount: A:0.51, C:0.01, G:0.18, T:0.30
Consensus pattern (32 bp):
AAATAAAGTTGTAATAAAATAGAGTTATAATA
Found at i:2874393 original size:21 final size:21
Alignment explanation
Indices: 2874298--2874398 Score: 55
Period size: 21 Copynumber: 4.9 Consensus size: 21
2874288 ATTATTATTG
**
2874298 TTATTAAATATAATAGGATTA
1 TTATTAAATATAATATAATTA
* *
2874319 TTATTAAATATAATTTAATAA
1 TTATTAAATATAATATAATTA
** * *
2874340 AAATGATA-ATAA-ATAATT-
1 TTATTAAATATAATATAATTA
* * * *
2874358 TAATCATATTTTAATATAATTA
1 TTATTA-AATATAATATAATTA
*
2874380 TTATTAAATATAATTTAAT
1 TTATTAAATATAATATAAT
2874399 AAAATTTTTA
Statistics
Matches: 56, Mismatches: 20, Indels: 8
0.67 0.24 0.10
Matches are distributed among these distances:
18 4 0.07
19 4 0.07
20 7 0.12
21 37 0.66
22 4 0.07
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (21 bp):
TTATTAAATATAATATAATTA
Found at i:2874406 original size:37 final size:36
Alignment explanation
Indices: 2874352--2874441 Score: 101
Period size: 37 Copynumber: 2.4 Consensus size: 36
2874342 ATGATAATAA
* *
2874352 ATAATTTAATCATATTTTAATATAATTATTATTAAAT
1 ATAATTTAATAAAATTTTAATATAATTATT-TTAAAT
* *
2874389 ATAATTTAATAAAATTTTTAATTTAATTATTTTATAT
1 ATAATTTAATAAAA-TTTTAATATAATTATTTTAAAT
2874426 A-AATTTATATTAAAAT
1 ATAATTTA-A-TAAAAT
2874442 ATTTTAAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
36 6 0.13
37 20 0.43
38 20 0.43
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (36 bp):
ATAATTTAATAAAATTTTAATATAATTATTTTAAAT
Found at i:2874417 original size:38 final size:37
Alignment explanation
Indices: 2874352--2874448 Score: 108
Period size: 38 Copynumber: 2.6 Consensus size: 37
2874342 ATGATAATAA
* *
2874352 ATAATTTAATCATA-TTTTAATATAATTATTATTAAAT
1 ATAATTTAATAAAATTTTTAATATAATTATT-TTAAAT
* *
2874389 ATAATTTAATAAAATTTTTAATTTAATTATTTTATAT
1 ATAATTTAATAAAATTTTTAATATAATTATTTTAAAT
2874426 A-AATTTATATTAAAATATTTTAA
1 ATAATTTA-A-TAAAAT-TTTTAA
2874449 ATATTTTTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
36 6 0.12
37 19 0.37
38 21 0.40
39 6 0.12
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (37 bp):
ATAATTTAATAAAATTTTTAATATAATTATTTTAAAT
Found at i:2874422 original size:26 final size:27
Alignment explanation
Indices: 2874353--2874448 Score: 85
Period size: 26 Copynumber: 3.7 Consensus size: 27
2874343 TGATAATAAA
*
2874353 TAATTTAATCATATTTTAATATAATTAT
1 TAATTTAAT-ATATTTTAATAAAATTAT
* * *
2874381 T-ATTAAATATAATTTAATAAAATTTT
1 TAATTTAATATATTTTAATAAAATTAT
*
2874407 TAATTTAAT-TATTTTATATAAATTTA-
1 TAATTTAATATATTTTA-ATAAAATTAT
*
2874433 T-A-TTAAAATATTTTAA
1 TAATTTAATATATTTTAA
2874449 ATATTTTTTT
Statistics
Matches: 56, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
24 5 0.09
25 8 0.14
26 23 0.41
27 19 0.34
28 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (27 bp):
TAATTTAATATATTTTAATAAAATTAT
Found at i:2876834 original size:3 final size:3
Alignment explanation
Indices: 2876828--2876854 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2876818 TTGTTTTTTT
2876828 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
2876855 ACTATCCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2882393 original size:21 final size:21
Alignment explanation
Indices: 2882369--2882408 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
2882359 CTTCCACCTC
* *
2882369 CACCTCCACCACGGCCACCCT
1 CACCCCCACCACCGCCACCCT
*
2882390 CACCCCCACCCCCGCCACC
1 CACCCCCACCACCGCCACC
2882409 ACCAAAGGCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.70, G:0.07, T:0.05
Consensus pattern (21 bp):
CACCCCCACCACCGCCACCCT
Found at i:2891580 original size:16 final size:17
Alignment explanation
Indices: 2891548--2891579 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2891538 TATTTGATTC
2891548 ATTATAATTTATTTTTT
1 ATTATAATTTATTTTTT
2891565 ATTA-AATTT-TTTTTT
1 ATTATAATTTATTTTTT
2891580 TTTTCAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
ATTATAATTTATTTTTT
Found at i:2895632 original size:25 final size:25
Alignment explanation
Indices: 2895597--2895649 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 25
2895587 ACTACATATA
*
2895597 TTTTAT-TTTAAAAAATTGAAAACTT
1 TTTTATATTAAAAAAATTG-AAACTT
2895622 TTTTATATTAAAAAAAATTGAAACTT
1 TTTTATATT-AAAAAAATTGAAACTT
2895648 TT
1 TT
2895650 ATCCAGAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 6 0.24
26 10 0.40
27 9 0.36
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (25 bp):
TTTTATATTAAAAAAATTGAAACTT
Found at i:2914915 original size:210 final size:210
Alignment explanation
Indices: 2914547--2914939 Score: 664
Period size: 210 Copynumber: 1.9 Consensus size: 210
2914537 TTTATGTATA
* *
2914547 TATTTATTATAATTTTTAGCTTTTAGTGTATAGCATGCTTATATGTAACAATACATTATCTATAA
1 TATTTATTAGAATTTTTAGCTTTTAGTATATAGCATGCTTATATGTAACAATACATTATCTATAA
*
2914612 TTCCACTATTTACTTATGTGTTAATTTTAAAACTGTCCACTTAAGTCATAGTCACAAATTATTTA
66 TTCCACTATTTACTTATGTGTTAATTTCAAAACTGTCCACTTAAGTCATAGTCACAAATTATTTA
2914677 TATCTTGAGCTACAAAATTCGCAATTAAGATCCACTTGATGTT-TTTGAAACTATATATAGCATG
131 TATCTTGAGCTACAAAATTCGCAATTAAGATCCACTTGAT-TTCTTTGAAACTATATATAGCATG
2914741 CTTATATAGCATAAAT
195 CTTATATAGCATAAAT
2914757 TATTTATTAGAATTTTTAGCTTTTAGTATATAGCATGCTTATATGTAACAATACATTATCTATAA
1 TATTTATTAGAATTTTTAGCTTTTAGTATATAGCATGCTTATATGTAACAATACATTATCTATAA
* * * *
2914822 TTCCACTATTTATTTATGTTTTAATTTCAAAGCTGTCCACTTGAGTCATAGTCACTAAATTATTT
66 TTCCACTATTTACTTATGTGTTAATTTCAAAACTGTCCACTTAAGTCATAGTCAC-AAATTATTT
* * *
2914887 ATATCTTGAGTTACAGAATTCG-AATTAAGATCCGCTTGATTTCTTTGAAACTA
130 ATATCTTGAGCTACAAAATTCGCAATTAAGATCCACTTGATTTCTTTGAAACTA
2914940 GACTCAAATA
Statistics
Matches: 171, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
209 2 0.01
210 140 0.82
211 29 0.17
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (210 bp):
TATTTATTAGAATTTTTAGCTTTTAGTATATAGCATGCTTATATGTAACAATACATTATCTATAA
TTCCACTATTTACTTATGTGTTAATTTCAAAACTGTCCACTTAAGTCATAGTCACAAATTATTTA
TATCTTGAGCTACAAAATTCGCAATTAAGATCCACTTGATTTCTTTGAAACTATATATAGCATGC
TTATATAGCATAAAT
Found at i:2915758 original size:11 final size:10
Alignment explanation
Indices: 2915733--2915797 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
2915723 TTGTCAAGAA
*
2915733 TTTCTTCCTT
1 TTTCTTCCAT
2915743 TTTCTTCTCAT
1 TTTCTTC-CAT
*
2915754 TTTC-TCCAC
1 TTTCTTCCAT
*
2915763 TTTCATTCCTT
1 TTTC-TTCCAT
2915774 TTTCTTCTCAT
1 TTTCTTC-CAT
*
2915785 TTT-TTCCAC
1 TTTCTTCCAT
2915794 TTTC
1 TTTC
2915798 ACCTACTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 11 0.25
10 15 0.34
11 18 0.41
ACGTcount: A:0.08, C:0.31, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTCTTCCAT
Found at i:2915775 original size:31 final size:31
Alignment explanation
Indices: 2915733--2915798 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
2915723 TTGTCAAGAA
2915733 TTTC-TTCCTTTTTCTTCTCATTTTCTCCAC
1 TTTCATTCCTTTTTCTTCTCATTTTCTCCAC
*
2915763 TTTCATTCCTTTTTCTTCTCATTTTTTCCAC
1 TTTCATTCCTTTTTCTTCTCATTTTCTCCAC
2915794 TTTCA
1 TTTCA
2915799 CCTACTATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTCATTCCTTTTTCTTCTCATTTTCTCCAC
Found at i:2918191 original size:3 final size:3
Alignment explanation
Indices: 2918173--2918205 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2918163 TTACTATTTA
*
2918173 ATT AGT ATT A-T ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
2918206 ACTAATTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:2925245 original size:41 final size:40
Alignment explanation
Indices: 2925197--2925297 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
2925187 TCGACCTCGA
** *
2925197 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
2925237 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
2925275 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
2925298 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:2926507 original size:319 final size:319
Alignment explanation
Indices: 2925928--2926568 Score: 1219
Period size: 319 Copynumber: 2.0 Consensus size: 319
2925918 ATATGTAATG
2925928 GAATGATTATGATTTAGGTGAATTTGAGTATAAATTGCTTTGATTGCTAGTTGAAATTGCAGGGA
1 GAATGATTATGATTTAGGTGAATTTGAGTATAAATTGCTTTGATTGCTAGTTGAAATTGCAGGGA
*
2925993 AGGTTAGATGTCTATAAAAAGGGTTATATCGCGTTTGAAATAAAAATTTACTAAAAATCTTTGGA
66 AGGTTAGATGTCTATAAAAAGGGTTATATCGCGTTTGAAATAAAAATTTACTAAAAATCTGTGGA
2926058 ACATCAAAATAAGTCCTAATGTCCTTTTAATACATATTTTAAGTCTCGAGGGTCCATTTAAGGTA
131 ACATCAAAATAAGTCCTAATGTCCTTTTAATACATATTTTAAGTCTCGAGGGTCCATTTAAGGTA
*
2926123 ATTTTATGATTATTTTATAGTATGATCATTAATTATCTATTTATTATTTGTAAGATTATCCGATA
196 ATTTTATGATTATTTTATAGTATGATCATTAATTATCTATTTATTATTTGCAAGATTATCCGATA
* *
2926188 TGTCTGGTAATACCCTGTAACCCTATTTCGGTGACGGTTTAGGGTTAAGGGGTGTTACA
261 TGTCTGGTAATACCCTGTAACCCTATTTCAGTGACGATTTAGGGTTAAGGGGTGTTACA
*
2926247 GAATGATTATGATTTAGGTGAATTTGAGTATAAATTGCTTTGGTTGCTAGTTGAAATTGCAGGGA
1 GAATGATTATGATTTAGGTGAATTTGAGTATAAATTGCTTTGATTGCTAGTTGAAATTGCAGGGA
*
2926312 AGGTTAGATGTCTATAAAAGGGGTTATATCGCGTTTGAAATAAAAATTTACTAAAAATCTGTGGA
66 AGGTTAGATGTCTATAAAAAGGGTTATATCGCGTTTGAAATAAAAATTTACTAAAAATCTGTGGA
2926377 ACATCAAAATAAGTCCTAATGTCCTTTTAATACATATTTTAAGTCTCGAGGGTCCATTTAAGGTA
131 ACATCAAAATAAGTCCTAATGTCCTTTTAATACATATTTTAAGTCTCGAGGGTCCATTTAAGGTA
2926442 ATTTTATGATTATTTTATAGTATGATCATTAATTATCTATTTATTATTTGCAAGATTATCCGATA
196 ATTTTATGATTATTTTATAGTATGATCATTAATTATCTATTTATTATTTGCAAGATTATCCGATA
*
2926507 TGTCTGGTAATACCCTGTAACCCTGTTTCAGTGACGATTTAGGGTTAAGGGGTGTTACA
261 TGTCTGGTAATACCCTGTAACCCTATTTCAGTGACGATTTAGGGTTAAGGGGTGTTACA
2926566 GAA
1 GAA
2926569 CATATTCTCT
Statistics
Matches: 315, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
319 315 1.00
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (319 bp):
GAATGATTATGATTTAGGTGAATTTGAGTATAAATTGCTTTGATTGCTAGTTGAAATTGCAGGGA
AGGTTAGATGTCTATAAAAAGGGTTATATCGCGTTTGAAATAAAAATTTACTAAAAATCTGTGGA
ACATCAAAATAAGTCCTAATGTCCTTTTAATACATATTTTAAGTCTCGAGGGTCCATTTAAGGTA
ATTTTATGATTATTTTATAGTATGATCATTAATTATCTATTTATTATTTGCAAGATTATCCGATA
TGTCTGGTAATACCCTGTAACCCTATTTCAGTGACGATTTAGGGTTAAGGGGTGTTACA
Found at i:2926785 original size:11 final size:11
Alignment explanation
Indices: 2926769--2926816 Score: 62
Period size: 11 Copynumber: 4.3 Consensus size: 11
2926759 CCATTTTCTA
*
2926769 AATAAAATAAT
1 AATAAAATATT
2926780 AAT-AAATATTT
1 AATAAAATA-TT
2926791 AAGTAAAATATT
1 AA-TAAAATATT
2926803 AATAAAATATT
1 AATAAAATATT
2926814 AAT
1 AAT
2926817 TAATTAATTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
10 5 0.15
11 18 0.55
12 5 0.15
13 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (11 bp):
AATAAAATATT
Found at i:2928943 original size:14 final size:14
Alignment explanation
Indices: 2928924--2928951 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2928914 TAGCTCTCTC
2928924 TCTCTATATATAGA
1 TCTCTATATATAGA
2928938 TCTCTATATATAGA
1 TCTCTATATATAGA
2928952 GAGAGATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TCTCTATATATAGA
Found at i:2941820 original size:3 final size:3
Alignment explanation
Indices: 2941812--2941868 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
2941802 CGACAAACAC
*
2941812 CTT CTT CTT CGT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2941860 CTT CTT CTT
1 CTT CTT CTT
2941869 TTCCTCTGAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:2942387 original size:26 final size:26
Alignment explanation
Indices: 2942358--2942411 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
2942348 TAAATTTTAG
* *
2942358 AATTAATAATCTT-ATTTTACTATTAA
1 AATTAA-AATATTCATTGTACTATTAA
*
2942384 AATTAAAATATTCATTGTACTTTTAA
1 AATTAAAATATTCATTGTACTATTAA
2942410 AA
1 AA
2942412 AATATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (26 bp):
AATTAAAATATTCATTGTACTATTAA
Found at i:2966856 original size:153 final size:152
Alignment explanation
Indices: 2966578--2966860 Score: 401
Period size: 153 Copynumber: 1.9 Consensus size: 152
2966568 TAGTCACTCT
**
2966578 AGTTTCAATTCAGTCATTCAACTTTTGAAAAATAACAAAACAGTCACTAACATTATCGAAAAGTG
1 AGTTTCAATTCAGTCATTCAACTTTCAAAAAATAACAAAACAGTCACTAACATTATCGAAAAGTG
* * *
2966643 ACAAATCAGTCACCCATTAACATTTTCCATTATAGACCTAACGAGAAAGGTGACGTGGCCAAGTA
66 ACAAATCAATCACCCATTAACATTTTCCACTAAAGACCTAACGAGAAAGGTGACGTGGCC-AGTA
2966708 ACTTCCCACATTGGATGAGATAA
130 ACTTCCCACATTGGATGAGATAA
* *
2966731 AGTTTCAATTCAGTCACTT-AACTTTCAAAAAATAACAAATCAGTCACTAACATTATGGAAAAGT
1 AGTTTCAATTCAGTCA-TTCAACTTTCAAAAAATAACAAAACAGTCACTAACATTATCGAAAAGT
* * * * *
2966795 GACAAATCAATCACTCATTTATATTTTTCGCTACAAG-CCTAACGAGACAA-GTGACGTGGCCAG
65 GACAAATCAATCACCCATTAACATTTTCCACTA-AAGACCTAACGAGA-AAGGTGACGTGGCCAG
2966858 TAA
128 TAA
2966861 ATTAGTTGAT
Statistics
Matches: 115, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
152 5 0.04
153 104 0.90
154 6 0.05
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (152 bp):
AGTTTCAATTCAGTCATTCAACTTTCAAAAAATAACAAAACAGTCACTAACATTATCGAAAAGTG
ACAAATCAATCACCCATTAACATTTTCCACTAAAGACCTAACGAGAAAGGTGACGTGGCCAGTAA
CTTCCCACATTGGATGAGATAA
Found at i:2981941 original size:3 final size:3
Alignment explanation
Indices: 2981928--2981964 Score: 65
Period size: 3 Copynumber: 12.0 Consensus size: 3
2981918 GTTCATGTAC
2981928 CTT CTTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT C-TT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
2981965 TTTGTATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:2993607 original size:22 final size:23
Alignment explanation
Indices: 2993582--2993628 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
2993572 TTTAAAAAAA
2993582 TATTTATATT-ATTT-TAATTTTT
1 TATTTAT-TTAATTTATAATTTTT
*
2993604 TAT-TATTTAATTTATTATTTTT
1 TATTTATTTAATTTATAATTTTT
2993626 TAT
1 TAT
2993629 ATAATCATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 2 0.09
21 7 0.32
22 13 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (23 bp):
TATTTATTTAATTTATAATTTTT
Found at i:2993609 original size:16 final size:16
Alignment explanation
Indices: 2993583--2993627 Score: 60
Period size: 15 Copynumber: 3.0 Consensus size: 16
2993573 TTAAAAAAAT
2993583 ATTTA-TATTATTTTA
1 ATTTATTATTATTTTA
*
2993598 ATTTTTTATTA-TTTA
1 ATTTATTATTATTTTA
2993613 ATTTATTATT-TTTTA
1 ATTTATTATTATTTTA
2993628 TATAATCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 21 0.81
16 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTATTATTATTTTA
Found at i:3013325 original size:15 final size:15
Alignment explanation
Indices: 3013305--3013353 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
3013295 TTTTTTTGTA
3013305 TTCATTGATGCTTTG
1 TTCATTGATGCTTTG
3013320 TTCATTG-T--TTT-
1 TTCATTGATGCTTTG
3013331 TTCAATTTGATGCTTTG
1 TTC-A-TTGATGCTTTG
3013348 TTCATT
1 TTCATT
3013354 ATTTTATTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
11 3 0.11
12 4 0.14
13 3 0.11
14 2 0.07
15 9 0.32
16 4 0.14
17 3 0.11
ACGTcount: A:0.14, C:0.12, G:0.14, T:0.59
Consensus pattern (15 bp):
TTCATTGATGCTTTG
Found at i:3016052 original size:37 final size:38
Alignment explanation
Indices: 3015952--3016054 Score: 91
Period size: 37 Copynumber: 2.7 Consensus size: 38
3015942 GACCTTGAGT
* **
3015952 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGAGC
** * ** *
3015993 CGATGAGGTACTGGATACCACTTTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
3016030 CGATGAGACACTGGGTGTCACTTTA
1 CGATGAGACACTGGGTGTCACTTTA
3016055 TTGTTTCGAA
Statistics
Matches: 48, Mismatches: 14, Indels: 4
0.73 0.21 0.06
Matches are distributed among these distances:
37 20 0.42
38 14 0.29
41 14 0.29
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.31
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAGC
Found at i:3020041 original size:24 final size:25
Alignment explanation
Indices: 3020014--3020069 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
3020004 TTAAGACAAC
*
3020014 AATTCAGATGACAA-CTAA-GCATAT
1 AATTCAGATAACAATCTAATGCAT-T
* *
3020038 AATTCAAATAACAATTTAATGCATT
1 AATTCAGATAACAATCTAATGCATT
3020063 AATTCAG
1 AATTCAG
3020070 TAGTTTCCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 12 0.46
25 10 0.38
26 4 0.15
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.30
Consensus pattern (25 bp):
AATTCAGATAACAATCTAATGCATT
Found at i:3022203 original size:3 final size:3
Alignment explanation
Indices: 3022195--3022234 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
3022185 ATTTAGTTAC
* * *
3022195 ATA ATA ATA ATA ATA ATA ATA ATG ATG ATA ATG ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3022235 CTAGTTACTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3028422 original size:6 final size:6
Alignment explanation
Indices: 3028411--3028443 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3028401 AGGATACAAC
3028411 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTG
1 TTGGGT TTGGGT TTGGGT TTGGGT TTGGGT TTG
3028444 AGTGAGAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TTGGGT
Found at i:3028766 original size:21 final size:21
Alignment explanation
Indices: 3028740--3028781 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3028730 TAATATCATA
*
3028740 TTAATAATTTTATTTTAAATT
1 TTAATAATTTTATTTAAAATT
*
3028761 TTAATATTTTTATTTAAAATT
1 TTAATAATTTTATTTAAAATT
3028782 ATTATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTAATAATTTTATTTAAAATT
Found at i:3028793 original size:22 final size:22
Alignment explanation
Indices: 3028738--3028806 Score: 86
Period size: 22 Copynumber: 3.2 Consensus size: 22
3028728 TTTAATATCA
* *
3028738 TATTAATAATTTTATTTTAAAT
1 TATTAATATTTTTATTTAAAAT
3028760 T-TTAATATTTTTATTTAAAAT
1 TATTAATATTTTTATTTAAAAT
* **
3028781 TATTATTATTTTTAAATAAAAT
1 TATTAATATTTTTATTTAAAAT
3028803 TATT
1 TATT
3028807 GAGATGACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
21 19 0.46
22 22 0.54
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TATTAATATTTTTATTTAAAAT
Found at i:3034029 original size:27 final size:29
Alignment explanation
Indices: 3033995--3034051 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
3033985 CGCATATGAA
3033995 TTTTTTTT-CA-CATCAAATTCAGTGTTT
1 TTTTTTTTCCATCATCAAATTCAGTGTTT
*
3034022 TTTTTTTTGCCATCATCGAATTCAGTGTTT
1 TTTTTTTT-CCATCATCAAATTCAGTGTTT
3034052 AATTTAGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 8 0.31
29 2 0.08
30 16 0.62
ACGTcount: A:0.19, C:0.16, G:0.11, T:0.54
Consensus pattern (29 bp):
TTTTTTTTCCATCATCAAATTCAGTGTTT
Found at i:3034592 original size:16 final size:16
Alignment explanation
Indices: 3034545--3034593 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
3034535 TAACCCGATA
3034545 AAATAATAACATGTAAA-
1 AAATAAT-ACAT-TAAAT
* *
3034562 AAATAATAAAATAAAT
1 AAATAATACATTAAAT
3034578 AAATAATACATTAAAT
1 AAATAATACATTAAAT
3034594 TAAAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 4 0.15
16 16 0.59
17 7 0.26
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (16 bp):
AAATAATACATTAAAT
Found at i:3034601 original size:20 final size:20
Alignment explanation
Indices: 3034558--3034609 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
3034548 TAATAACATG
*
3034558 TAAAAAATAA-TAAAATAAA
1 TAAATAATAATTAAAATAAA
*
3034577 TAAATAATACATTAAATTAAA
1 TAAATAATA-ATTAAAATAAA
3034598 -AAATAATAATTA
1 TAAATAATAATTA
3034610 TCTAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 12 0.41
20 9 0.31
21 8 0.28
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAATAATAATTAAAATAAA
Found at i:3034787 original size:13 final size:12
Alignment explanation
Indices: 3034725--3034787 Score: 56
Period size: 12 Copynumber: 5.1 Consensus size: 12
3034715 AAATTTGTTA
3034725 AAAAAATAAATT
1 AAAAAATAAATT
* *
3034737 GAAAAA-AAATA
1 AAAAAATAAATT
**
3034748 AAAAAATTGATGGT
1 AAAAAATAAAT--T
3034762 AAAAAATAAATT
1 AAAAAATAAATT
3034774 AAAAAATACAATT
1 AAAAAATA-AATT
3034787 A
1 A
3034788 TAACCATTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
11 9 0.23
12 16 0.41
13 5 0.13
14 9 0.23
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (12 bp):
AAAAAATAAATT
Found at i:3043045 original size:2 final size:2
Alignment explanation
Indices: 3043030--3043069 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
3043020 TTTTTGTAGA
3043030 AT AT A- AT A- 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
3043070 TTTCATGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3046071 original size:246 final size:246
Alignment explanation
Indices: 3045637--3046104 Score: 785
Period size: 246 Copynumber: 1.9 Consensus size: 246
3045627 TATCATATAT
*
3045637 TCATATTGACAAGAAGTTGTTCCTCGAGTGATGACAAATAGCTATAGATCTTTCCAGTATTATTT
1 TCATATTGACAAGAAGTTGTTCCTCGACTGATGACAAATAGCTATAGATCTTTCCAGTATTATTT
* *
3045702 CAACATTTTGCCAGTGGAGTTTCGGCAGTTTAATCTTCTACTATTTCATCTTCATTCAAAAAGGA
66 CAACATTTTGCCAGTGGAGTGTCGACAGTTTAATCTTCTACTATTTCATCTTCATTCAAAAAGGA
* * *
3045767 GAATATTGCCTATTTCTATGGTTTGAGACCAAGAAGCTGCCTCGTTGAGTAACCACAGCTATGTC
131 CAATATTGCATATTTCTATGATTTGAGACCAAGAAGCTGCCTCGTTGAGTAACCACAGCTATGTC
3045832 TGAAGCTAAAATTTGAAAAGTAACTAATGACAAAAGCAGACCAAATAAGTA
196 TGAAGCTAAAATTTGAAAAGTAACTAATGACAAAAGCAGACCAAATAAGTA
* *
3045883 TCATATTGACAATAAGTTGTTCCTCGACTGATGACAAATAGCTATAGATCTTTCCAGTTTTATTT
1 TCATATTGACAAGAAGTTGTTCCTCGACTGATGACAAATAGCTATAGATCTTTCCAGTATTATTT
* * *
3045948 CAACATTTTGCCAGTGGAGTGTCTATAGTTTAATCTTCTACTATTTTATCTTCATTCAAAAAGGA
66 CAACATTTTGCCAGTGGAGTGTCGACAGTTTAATCTTCTACTATTTCATCTTCATTCAAAAAGGA
* *
3046013 CATTATTGCATATTTCTATGATTTGAGACCAAGAAGCTGCCAT-GTTGAGTAACCACAGCTCTGT
131 CAATATTGCATATTTCTATGATTTGAGACCAAGAAGCTGCC-TCGTTGAGTAACCACAGCTATGT
* *
3046077 CTGAAGCTAAATTTTGAATAGTAACTAA
195 CTGAAGCTAAAATTTGAAAAGTAACTAA
3046105 GCATGGATTC
Statistics
Matches: 206, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
246 205 1.00
247 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Consensus pattern (246 bp):
TCATATTGACAAGAAGTTGTTCCTCGACTGATGACAAATAGCTATAGATCTTTCCAGTATTATTT
CAACATTTTGCCAGTGGAGTGTCGACAGTTTAATCTTCTACTATTTCATCTTCATTCAAAAAGGA
CAATATTGCATATTTCTATGATTTGAGACCAAGAAGCTGCCTCGTTGAGTAACCACAGCTATGTC
TGAAGCTAAAATTTGAAAAGTAACTAATGACAAAAGCAGACCAAATAAGTA
Found at i:3046457 original size:65 final size:65
Alignment explanation
Indices: 3046384--3046511 Score: 222
Period size: 65 Copynumber: 2.0 Consensus size: 65
3046374 CGATGGAACA
3046384 GGAAAAAATGGA-TGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAACAAC
1 GGAAAAAAT-GATTGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAACAAC
3046448 T
65 T
**
3046449 GGAAAAAATGATTGACACCCATTCTTGATTGTAATGTTCTTTTAAGGATAATTCGACAAACAA
1 GGAAAAAATGATTGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAACAA
3046512 GGAGGAAATT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 2 0.03
65 58 0.97
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (65 bp):
GGAAAAAATGATTGACACCCATTCTTGATTACAATGTTCTTTTAAGGATAATTCGACAAACAACT
Found at i:3050382 original size:20 final size:20
Alignment explanation
Indices: 3050354--3050391 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3050344 TTTAATTATT
*
3050354 TTAGCTTAATTAACTTAAAC
1 TTAGCTTAATTAAATTAAAC
*
3050374 TTAGTTTAATTAAATTAA
1 TTAGCTTAATTAAATTAA
3050392 GCTATTCGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAGCTTAATTAAATTAAAC
Found at i:3057191 original size:105 final size:108
Alignment explanation
Indices: 3057045--3057247 Score: 288
Period size: 108 Copynumber: 1.9 Consensus size: 108
3057035 CGAACTTAAA
*
3057045 TTTTTCGGTTAATTCTGTCAGTTAATATAATTAATCAAAATTTATAT-T-T-TTTTTATTTTTGA
1 TTTTTCGGTTAATTCGGTCAGTTAATATAATTAATCAAAATTTATATATATATTTTTATTTTTGA
* *
3057107 TTAAGACAAATATAAAACATATAAAAATTTAACTGAACCGAAT
66 TTAAAACAAATATAAAACATATAAAAAATTAACTGAACCGAAT
** * *
3057150 TTTTTCGGTTAATTCGGTTGGTTAATCA-AATTGATCGAAATTTATATATATATTTTTATTTTTG
1 TTTTTCGGTTAATTCGGTCAGTTAAT-ATAATTAATCAAAATTTATATATATATTTTTATTTTTG
* *
3057214 GTTAAAACAAGTATAAAACATATAAAAAATTAAC
65 ATTAAAACAAATATAAAACATATAAAAAATTAAC
3057248 CGAATGATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
105 40 0.47
106 2 0.02
107 1 0.01
108 42 0.49
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.43
Consensus pattern (108 bp):
TTTTTCGGTTAATTCGGTCAGTTAATATAATTAATCAAAATTTATATATATATTTTTATTTTTGA
TTAAAACAAATATAAAACATATAAAAAATTAACTGAACCGAAT
Found at i:3082316 original size:21 final size:22
Alignment explanation
Indices: 3082264--3082316 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
3082254 ATGATGAAAT
3082264 TATA-AATTAATATAAAATAAA
1 TATATAATTAATATAAAATAAA
* *
3082285 TCTATATTTAATATATAAA-AAA
1 TATATAATTAATATA-AAATAAA
3082307 -ATATAATTAA
1 TATATAATTAA
3082317 ATTTCAACCC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 11 0.42
22 12 0.46
23 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
TATATAATTAATATAAAATAAA
Found at i:3082537 original size:99 final size:100
Alignment explanation
Indices: 3082378--3082559 Score: 285
Period size: 99 Copynumber: 1.8 Consensus size: 100
3082368 CCATGAACAT
3082378 GTTTCTTTGATTCTTTTTTATCATTCATTTGTTGTGTTTTATATTGATTTAATTTTATATTATAA
1 GTTTCTTTGATTCTTTTTTATCATTCATTTGTTGTGTTTTATATTGATTTAATTTTATATTATAA
3082443 CTAACCATACATCAATTTGTACATGCCGTGAACGG
66 CTAACCATACATCAATTTGTACATGCCGTGAACGG
* * **
3082478 GTTT-TTTTATTCTTTTTTATCATTCATTTGTTGTGTTTTATATTTATTTGGTTTTATATTATAA
1 GTTTCTTTGATTCTTTTTTATCATTCATTTGTTGTGTTTTATATTGATTTAATTTTATATTATAA
* * **
3082542 TTGACCATTGATCAATTT
66 CTAACCATACATCAATTT
3082560 ATACTTGAAC
Statistics
Matches: 74, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
99 70 0.95
100 4 0.05
ACGTcount: A:0.23, C:0.10, G:0.11, T:0.55
Consensus pattern (100 bp):
GTTTCTTTGATTCTTTTTTATCATTCATTTGTTGTGTTTTATATTGATTTAATTTTATATTATAA
CTAACCATACATCAATTTGTACATGCCGTGAACGG
Found at i:3082602 original size:3 final size:3
Alignment explanation
Indices: 3082594--3082638 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3082584 TGTTGTATTT
3082594 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3082639 TTTTTAGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3090099 original size:23 final size:24
Alignment explanation
Indices: 3090054--3090100 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
3090044 AATATTTGAT
3090054 ATTTGAACTTAACACTTTTTTTTA
1 ATTTGAACTTAACACTTTTTTTTA
* *
3090078 ATTTGTACTTAA-ATTTTTTTTTA
1 ATTTGAACTTAACACTTTTTTTTA
3090101 TCTAATTTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.60
Consensus pattern (24 bp):
ATTTGAACTTAACACTTTTTTTTA
Found at i:3090162 original size:30 final size:30
Alignment explanation
Indices: 3090095--3090163 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
3090085 CTTAAATTTT
3090095 TTTTTATCTAATTTGGTACTCAAACTTGACA
1 TTTTT-TCTAATTTGGTACTCAAACTTGACA
**
3090126 CGTTTTCTAATTTGGTAC-CTAAACTTGACA
1 TTTTTTCTAATTTGGTACTC-AAACTTGACA
3090156 TTTTTTCT
1 TTTTTTCT
3090164 TAAAGTTGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 1 0.03
30 29 0.88
31 3 0.09
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.48
Consensus pattern (30 bp):
TTTTTTCTAATTTGGTACTCAAACTTGACA
Found at i:3091122 original size:31 final size:30
Alignment explanation
Indices: 3091084--3091183 Score: 86
Period size: 31 Copynumber: 3.4 Consensus size: 30
3091074 AAAAAAATTT
3091084 AAGTACCAAATTGAGAAAAAGTGTTAAGTTC
1 AAGTACCAAATTGAGAAAAAGTG-TAAGTTC
*
3091115 AAGTACCAAATTGGGTAAAAA----AAGTT-
1 AAGTACCAAATTGAG-AAAAAGTGTAAGTTC
* *
3091141 TAGATACCAAATT-AAAAAAATGTGTCAAGTTC
1 AAG-TACCAAATTGAGAAAAA-GTGT-AAGTTC
3091173 AAGTACCAAAT
1 AAGTACCAAAT
3091184 ATTATATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 18
0.71 0.06 0.23
Matches are distributed among these distances:
25 5 0.09
26 2 0.04
27 14 0.25
31 27 0.49
32 7 0.13
ACGTcount: A:0.48, C:0.11, G:0.16, T:0.25
Consensus pattern (30 bp):
AAGTACCAAATTGAGAAAAAGTGTAAGTTC
Found at i:3091171 original size:58 final size:59
Alignment explanation
Indices: 3091057--3091183 Score: 179
Period size: 58 Copynumber: 2.2 Consensus size: 59
3091047 GTTCAAGTAC
* *
3091057 GTACCAAATTGGGTCCAAAAAAAATTTAAGTACCAAATTGAGAAAAAGTGTTAAGTTCAA
1 GTACCAAATTGGGT-CAAAAAAAATTTAAGTACCAAATTGAAAAAAAGTGTCAAGTTCAA
*
3091117 GTACCAAATTGGGT-AAAAAAAGTTT-AGATACCAAATT-AAAAAAATGTGTCAAGTTCAA
1 GTACCAAATTGGGTCAAAAAAAATTTAAG-TACCAAATTGAAAAAAA-GTGTCAAGTTCAA
3091175 GTACCAAAT
1 GTACCAAAT
3091184 ATTATATTAA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
57 8 0.13
58 40 0.65
60 14 0.23
ACGTcount: A:0.47, C:0.12, G:0.16, T:0.25
Consensus pattern (59 bp):
GTACCAAATTGGGTCAAAAAAAATTTAAGTACCAAATTGAAAAAAAGTGTCAAGTTCAA
Found at i:3093140 original size:9 final size:9
Alignment explanation
Indices: 3093116--3093174 Score: 51
Period size: 9 Copynumber: 7.1 Consensus size: 9
3093106 GATGATGATT
3093116 ATAATTTTAAA
1 ATAATTTT--A
3093127 ATAATTTTA
1 ATAATTTTA
3093136 ATAATTTT-
1 ATAATTTTA
3093144 AT-ATTTTA
1 ATAATTTTA
3093152 A-AA----A
1 ATAATTTTA
3093156 ATAATTTTA
1 ATAATTTTA
3093165 ATAATTTTA
1 ATAATTTTA
3093174 A
1 A
3093175 AATCATTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 5 0.12
8 4 0.10
9 20 0.49
11 8 0.20
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
ATAATTTTA
Found at i:3093141 original size:20 final size:20
Alignment explanation
Indices: 3093116--3093182 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
3093106 GATGATGATT
3093116 ATAATTTTAAAATAATTTT--A
1 ATAATTTT--AATAATTTTAAA
3093136 ATAATTTT-AT-ATTTTAAAAA
1 ATAATTTTAATAATTTT--AAA
3093156 ATAATTTTAATAATTTTAAA
1 ATAATTTTAATAATTTTAAA
*
3093176 ATCATTT
1 ATAATTT
3093183 GCTGATATAG
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
16 5 0.12
17 2 0.05
20 26 0.65
21 2 0.05
22 5 0.12
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATTTTAATAATTTTAAA
Found at i:3093740 original size:12 final size:12
Alignment explanation
Indices: 3093723--3093747 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3093713 CATTATATTA
3093723 TGAAGTAAAATT
1 TGAAGTAAAATT
3093735 TGAAGTAAAATT
1 TGAAGTAAAATT
3093747 T
1 T
3093748 TATTCATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TGAAGTAAAATT
Found at i:3105794 original size:2 final size:2
Alignment explanation
Indices: 3105787--3105811 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3105777 AAGGTATTAA
3105787 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 A
3105812 GTTTACCTTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3116104 original size:44 final size:44
Alignment explanation
Indices: 3116041--3116127 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
3116031 TTAAGTTAAA
3116041 AATTCAATATACCAAAATAGATATTAACAATAACATATAATTCT
1 AATTCAATATACCAAAATAGATATTAACAATAACATATAATTCT
3116085 AATTCAATATACCAAAATAGATATTAACAATAACATATAATTC
1 AATTCAATATACCAAAATAGATATTAACAATAACATATAATTC
3116128 AGGAATACAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (44 bp):
AATTCAATATACCAAAATAGATATTAACAATAACATATAATTCT
Found at i:3127566 original size:18 final size:18
Alignment explanation
Indices: 3127533--3127567 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3127523 CATTAATGAT
3127533 TCATCAATCAATTCATCG
1 TCATCAATCAATTCATCG
3127551 TCAT-AATCAATATCATC
1 TCATCAATCAAT-TCATC
3127568 ATCCTCGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (18 bp):
TCATCAATCAATTCATCG
Found at i:3135092 original size:5 final size:5
Alignment explanation
Indices: 3135078--3135115 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
3135068 ACAATATCTC
*
3135078 TTTCT TTTCT CTTCT TTTCT TTTCT TTTCTT TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTC-T TTTCT TT
3135116 GGCTCCTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:3135094 original size:10 final size:10
Alignment explanation
Indices: 3135074--3135107 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
3135064 GTAAACAATA
3135074 TCTCTTTCTTT
1 TCTC-TTCTTT
3135085 TCTCTTCTTT
1 TCTCTTCTTT
*
3135095 TCTTTTCTTT
1 TCTCTTCTTT
3135105 TCT
1 TCT
3135108 TTTTCTTTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (10 bp):
TCTCTTCTTT
Found at i:3136593 original size:23 final size:22
Alignment explanation
Indices: 3136549--3136593 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
3136539 TTGCGGTGGA
*
3136549 AAGATAAATAAAAATATGAGGT
1 AAGATAAATAAAAATATAAGGT
*
3136571 AAGATAAATACAAAATTTAAGGT
1 AAGATAAATA-AAAATATAAGGT
3136594 TTAAAACTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.58, C:0.02, G:0.16, T:0.24
Consensus pattern (22 bp):
AAGATAAATAAAAATATAAGGT
Found at i:3152176 original size:21 final size:21
Alignment explanation
Indices: 3152150--3152192 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3152140 ATCAAATAAA
* *
3152150 AATAAAACAATATTTATTGTT
1 AATAAAACAAAAATTATTGTT
*
3152171 AATAAAATAAAAATTATTGTT
1 AATAAAACAAAAATTATTGTT
3152192 A
1 A
3152193 GAAGGGTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (21 bp):
AATAAAACAAAAATTATTGTT
Found at i:3157913 original size:111 final size:111
Alignment explanation
Indices: 3157719--3157940 Score: 426
Period size: 111 Copynumber: 2.0 Consensus size: 111
3157709 TCTTTATGGA
3157719 GTGGATTTTATCTGATATGAGATTCAAATGGCATACTGCTCTTATACTGCAGTTTTTGGAATTTT
1 GTGGATTTTATCTGATATGAGATTCAAATGGCATACTGCTCTTATACTGCAGTTTTTGGAATTTT
*
3157784 TGTATCATCTTTAGACACTTGCTATTTAACAAAAATTAATTTCAAT
66 TGTATCAACTTTAGACACTTGCTATTTAACAAAAATTAATTTCAAT
3157830 GTGGATTTTATCTGATATGAGATTCAAATGGCATACTGCTCTTATACTGCAGTTTTTGGAATTTT
1 GTGGATTTTATCTGATATGAGATTCAAATGGCATACTGCTCTTATACTGCAGTTTTTGGAATTTT
*
3157895 TGTATCAAGTTTAGACACTTGCTATTTAACAAAAATTAATTTCAAT
66 TGTATCAACTTTAGACACTTGCTATTTAACAAAAATTAATTTCAAT
3157941 TTCTTTTCTT
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (111 bp):
GTGGATTTTATCTGATATGAGATTCAAATGGCATACTGCTCTTATACTGCAGTTTTTGGAATTTT
TGTATCAACTTTAGACACTTGCTATTTAACAAAAATTAATTTCAAT
Found at i:3171835 original size:30 final size:30
Alignment explanation
Indices: 3171765--3171834 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 30
3171755 TTCAATTATT
3171765 AAATATAAAAATATTTTTTTTATAAAATTA
1 AAATATAAAAATATTTTTTTTATAAAATTA
3171795 AAATATAAAAATA-TTTTTTTATAAAATTA
1 AAATATAAAAATATTTTTTTTATAAAATTA
3171824 AAATATAAAAA
1 AAATATAAAAA
3171835 AATAAATTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAATATAAAAATATTTTTTTTATAAAATTA
Found at i:3172084 original size:14 final size:14
Alignment explanation
Indices: 3172065--3172108 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
3172055 AAAACATATT
3172065 TTAAATATAAATAA
1 TTAAATATAAATAA
3172079 TTAAATATAAATAA
1 TTAAATATAAATAA
*
3172093 TTATATTATAAATAA
1 TTA-AATATAAATAA
3172108 T
1 T
3172109 AACATCATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAATATAAATAA
Found at i:3183451 original size:17 final size:18
Alignment explanation
Indices: 3183419--3183453 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3183409 ACTTTAATAA
*
3183419 TTAATTTTATTATCACTG
1 TTAATTTAATTATCACTG
3183437 TTAATTTAATT-TCACTG
1 TTAATTTAATTATCACTG
3183454 AAATTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.29, C:0.11, G:0.06, T:0.54
Consensus pattern (18 bp):
TTAATTTAATTATCACTG
Found at i:3184255 original size:16 final size:16
Alignment explanation
Indices: 3184234--3184272 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
3184224 ATATTAAAAA
3184234 AATATA-AATACATATT
1 AATATATAAT-CATATT
3184250 AATATATAATCATATT
1 AATATATAATCATATT
3184266 AATATAT
1 AATATAT
3184273 TTAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATATAATCATATT
Found at i:3184635 original size:22 final size:22
Alignment explanation
Indices: 3184581--3184643 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
3184571 TACTTTTTAA
*
3184581 AAAATAATAAATATGTAAATTATT
1 AAAATAATAAA-AT-TATATTATT
*
3184605 AAAATAATAAAATTATATTTTT
1 AAAATAATAAAATTATATTATT
* *
3184627 ACAATAATAAAAATATA
1 AAAATAATAAAATTATA
3184644 CAATTTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 22 0.63
23 2 0.06
24 11 0.31
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (22 bp):
AAAATAATAAAATTATATTATT
Found at i:3196302 original size:21 final size:21
Alignment explanation
Indices: 3196278--3196321 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
3196268 AAAGTGAGAC
3196278 CTGAAAGTAAAGCTCGAGCTT
1 CTGAAAGTAAAGCTCGAGCTT
3196299 CTGAAAGTAAAGCTCGAGCTT
1 CTGAAAGTAAAGCTCGAGCTT
3196320 CT
1 CT
3196322 TCCTCAAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (21 bp):
CTGAAAGTAAAGCTCGAGCTT
Found at i:3198336 original size:21 final size:21
Alignment explanation
Indices: 3198306--3198349 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
3198296 TCTTAATTTT
3198306 AAATCTAAA-CCTAAACACTA
1 AAATCTAAACCCTAAACACTA
*
3198326 AAATCATAAACCCTAAGCACTA
1 AAATC-TAAACCCTAAACACTA
3198348 AA
1 AA
3198350 CTTAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 4 0.19
22 12 0.57
ACGTcount: A:0.55, C:0.25, G:0.02, T:0.18
Consensus pattern (21 bp):
AAATCTAAACCCTAAACACTA
Found at i:3224095 original size:18 final size:17
Alignment explanation
Indices: 3224052--3224096 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
3224042 TTTGTTTAGT
3224052 AATGTTTTTATCTCAAA
1 AATGTTTTTATCTCAAA
* *
3224069 AGTGTTTTTTGTCTCAAA
1 AATG-TTTTTATCTCAAA
*
3224087 AATGCTTTTA
1 AATGTTTTTA
3224097 AAAAACAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (17 bp):
AATGTTTTTATCTCAAA
Found at i:3225031 original size:23 final size:23
Alignment explanation
Indices: 3225001--3225061 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 23
3224991 GTTAAAATGA
3225001 TTTTAATTATATTTTTTAGTTTT
1 TTTTAATTATATTTTTTAGTTTT
* *
3225024 TTTTAATTA-A-CTTTTGGTTTT
1 TTTTAATTATATTTTTTAGTTTT
*
3225045 TTTTCAA-TATGTTTTTT
1 TTTT-AATTATATTTTTT
3225062 TAATAGAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
21 15 0.48
22 3 0.10
23 13 0.42
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (23 bp):
TTTTAATTATATTTTTTAGTTTT
Found at i:3229054 original size:18 final size:20
Alignment explanation
Indices: 3229028--3229066 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 20
3229018 GCAAAAAATC
*
3229028 AAATTAAAA-AAAA-TAAAA
1 AAATAAAAACAAAACTAAAA
3229046 AAATAAAAACAAAACTAAAA
1 AAATAAAAACAAAACTAAAA
3229066 A
1 A
3229067 TATATGGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.82, C:0.05, G:0.00, T:0.13
Consensus pattern (20 bp):
AAATAAAAACAAAACTAAAA
Found at i:3229937 original size:15 final size:15
Alignment explanation
Indices: 3229919--3229964 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
3229909 GAACCATTCA
*
3229919 AAAATTAAAAAAATT
1 AAAATTATAAAAATT
*
3229934 AAAATTATCAAAA-T
1 AAAATTATAAAAATT
3229948 -AAATTATAAAAATT
1 AAAATTATAAAAATT
3229962 AAA
1 AAA
3229965 TCCACAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 13 0.50
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAATTATAAAAATT
Found at i:3229953 original size:13 final size:14
Alignment explanation
Indices: 3229920--3229965 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 14
3229910 AACCATTCAA
*
3229920 AAATTAAAAAAATT
1 AAATTATAAAAATT
*
3229934 AAAATTATCAAAA-T
1 -AAATTATAAAAATT
3229948 AAATTATAAAAATT
1 AAATTATAAAAATT
3229962 AAAT
1 AAAT
3229966 CCACAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 11 0.41
14 6 0.22
15 10 0.37
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATTATAAAAATT
Found at i:3232977 original size:32 final size:32
Alignment explanation
Indices: 3232913--3232977 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
3232903 TTTAATGAGT
* * *
3232913 AATAGTGTAGTTTACTCTTAATTTGATATAAA
1 AATAGTGTAGCTTACTCTTAACTTAATATAAA
*
3232945 AATAGTGTAGCTTACTCTTAACTTAATGTAAA
1 AATAGTGTAGCTTACTCTTAACTTAATATAAA
3232977 A
1 A
3232978 GAATTAAGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.40
Consensus pattern (32 bp):
AATAGTGTAGCTTACTCTTAACTTAATATAAA
Found at i:3239673 original size:23 final size:23
Alignment explanation
Indices: 3239646--3239845 Score: 169
Period size: 23 Copynumber: 9.2 Consensus size: 23
3239636 CTAGCGCGCG
3239646 CTCTGATTAGCACTTTGTGTGCT
1 CTCTGATTAGCACTTTGTGTGCT
3239669 CTCTGATTAGCACTTTGTGTG--
1 CTCTGATTAGCACTTTGTGTGCT
* *
3239690 CTC-----AGTACTTTGTGTACT
1 CTCTGATTAGCACTTTGTGTGCT
*
3239708 CTCTGATTAGCACTGTGTGTGCT
1 CTCTGATTAGCACTTTGTGTGCT
* * *
3239731 CTCTGTTTAGCACGTCT-CGTGCT
1 CTCTGATTAGCAC-TTTGTGTGCT
**
3239754 CTCTGTTATTAGCACTGCGTGTGCT
1 CTCTG--ATTAGCACTTTGTGTGCT
3239779 CTCTGATTAGCACTTTGTGTG--
1 CTCTGATTAGCACTTTGTGTGCT
* *
3239800 CTC-----AGTACTTTGTGTACT
1 CTCTGATTAGCACTTTGTGTGCT
*
3239818 CTCTGTTTAGCACTTTGTGTGCT
1 CTCTGATTAGCACTTTGTGTGCT
3239841 CTCTG
1 CTCTG
3239846 TTGCCCAACA
Statistics
Matches: 141, Mismatches: 18, Indels: 36
0.72 0.09 0.18
Matches are distributed among these distances:
16 22 0.16
18 6 0.04
21 6 0.04
23 87 0.62
24 3 0.02
25 17 0.12
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.42
Consensus pattern (23 bp):
CTCTGATTAGCACTTTGTGTGCT
Found at i:3239711 original size:39 final size:39
Alignment explanation
Indices: 3239657--3239731 Score: 132
Period size: 39 Copynumber: 1.9 Consensus size: 39
3239647 TCTGATTAGC
* *
3239657 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTTGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
3239696 ACTTTGTGTACTCTCTGATTAGCACTGTGTGTGCTC
1 ACTTTGTGTACTCTCTGATTAGCACTGTGTGTGCTC
3239732 TCTGTTTAGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (39 bp):
ACTTTGTGTACTCTCTGATTAGCACTGTGTGTGCTCAGT
Found at i:3239801 original size:48 final size:46
Alignment explanation
Indices: 3239696--3239802 Score: 135
Period size: 48 Copynumber: 2.3 Consensus size: 46
3239686 TGTGCTCAGT
* * *
3239696 ACTTTGTGTACTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGC
1 ACTTTGTGTGCTCTCTGATTAGCACTGCGTGTGCTCTCTGATTAGC
* *
3239742 ACGTCT-CGTGCTCTCTGTTATTAGCACTGCGTGTGCTCTCTGATTAGC
1 AC-TTTGTGTGCTCTCTG--ATTAGCACTGCGTGTGCTCTCTGATTAGC
3239790 ACTTTGTGTGCTC
1 ACTTTGTGTGCTC
3239803 AGTACTTTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
46 11 0.22
47 4 0.08
48 35 0.70
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.41
Consensus pattern (46 bp):
ACTTTGTGTGCTCTCTGATTAGCACTGCGTGTGCTCTCTGATTAGC
Found at i:3246144 original size:25 final size:23
Alignment explanation
Indices: 3246098--3246323 Score: 221
Period size: 23 Copynumber: 10.3 Consensus size: 23
3246088 ACACTAGCGC
3246098 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
3246121 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
3246144 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
3246160 ACTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* * *
3246183 GCTCTCTGTTTAGCACGTCT-CGT
1 GCTCTCTGATTAGCAC-TTTGTGT
**
3246206 GCTCTCTGTTATTAGCACTGCGTGT
1 GCTCTCTG--ATTAGCACTTTGTGT
3246231 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
3246254 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
*
3246277 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
* *
3246293 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTTGTGT
3246316 GCTCTCTG
1 GCTCTCTG
3246324 TTGCCCAGCA
Statistics
Matches: 167, Mismatches: 18, Indels: 36
0.76 0.08 0.16
Matches are distributed among these distances:
16 22 0.13
18 6 0.04
21 6 0.04
23 113 0.68
24 3 0.02
25 17 0.10
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.42
Consensus pattern (23 bp):
GCTCTCTGATTAGCACTTTGTGT
Found at i:3246166 original size:39 final size:39
Alignment explanation
Indices: 3246112--3246319 Score: 173
Period size: 39 Copynumber: 4.9 Consensus size: 39
3246102 TCTGATTAGC
3246112 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
* * *
3246151 ACTTTGTGTACTCTCTGATTAGCACTGTGTGTGCTCTCTGTTT
1 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTG--CTCAG--T
** * ** *
3246194 AGCACGTCTCGTGCTCTCTGTTATTAGCACTGCGTGTGCTCTCTGATTAGC
1 A-C-TTTGT-GTGCTCTCTG--ATTAGCACTTTGTGTG--CTC-----AGT
3246245 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
3246284 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTC
3246320 TCTGTTGCCC
Statistics
Matches: 137, Mismatches: 18, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
39 67 0.49
41 4 0.03
43 2 0.01
44 4 0.03
45 2 0.01
46 23 0.17
48 30 0.22
49 2 0.01
50 1 0.01
51 1 0.01
53 1 0.01
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (39 bp):
ACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:3246175 original size:62 final size:62
Alignment explanation
Indices: 3246099--3246323 Score: 283
Period size: 62 Copynumber: 3.5 Consensus size: 62
3246089 CACTAGCGCG
3246099 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA
1 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA
* * * *
3246161 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCTCGTGCT-CTCTGTTA-TTAGCAC
1 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCAC-T-TTGTG-TGCTCAG-TACTT-----
*
3246224 TGCGTGTG
57 T--GTGTA
3246232 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA
1 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA
*
3246294 CTCTCTGTTTAGCACTTTGTGTGCTCTCTG
1 CTCTCTGATTAGCACTTTGTGTGCTCTCTG
3246324 TTGCCCAGCA
Statistics
Matches: 139, Mismatches: 11, Indels: 26
0.79 0.06 0.15
Matches are distributed among these distances:
62 69 0.50
63 1 0.01
64 11 0.08
65 3 0.02
68 3 0.02
69 11 0.08
70 1 0.01
71 40 0.29
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.43
Consensus pattern (62 bp):
CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTTTGTGTA
Found at i:3246231 original size:48 final size:46
Alignment explanation
Indices: 3246161--3246280 Score: 161
Period size: 48 Copynumber: 2.6 Consensus size: 46
3246151 ACTTTGTGTA
*
3246161 CTCTCTGATTAGCACTGTGTGTGCTCTCTGTTTAGCACGTCT-CGTG
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCAC-TCTGCGTG
* * *
3246207 CTCTCTGTTATTAGCACTGCGTGTGCTCTCTGATTAGCACTTTGTGTG
1 CTCTCTG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTCTGCGTG
*
3246255 CTCTCTGATTAGCACTTTGTGTGCTC
1 CTCTCTGATTAGCACTGTGTGTGCTC
3246281 AGTACTTTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
46 24 0.37
47 2 0.03
48 39 0.60
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.41
Consensus pattern (46 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTCTGCGTG
Found at i:3246324 original size:23 final size:23
Alignment explanation
Indices: 3246279--3246372 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
3246269 CTTTGTGTGC
*
3246279 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
3246302 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
3246325 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
3246350 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
3246372 T
1 T
3246373 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:3247730 original size:48 final size:43
Alignment explanation
Indices: 3247674--3247850 Score: 165
Period size: 46 Copynumber: 3.7 Consensus size: 43
3247664 CGAAGTACTG
3247674 AACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACA-AAGTGCT----AACAGAGAGCACACACAGTGCTA
*
3247722 AACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAG--CACAAAGTGCTAA-CAGAGAGCACACACAGTGCT-A
* *
3247769 TAACAGAGAGCACGAGACGTGCTAAACAGAAAGCACACACAGTGCTA
1 -AACAGAGAGCAC-A-AAGTGCT-AACAGAGAGCACACACAGTGCTA
* *
3247816 AACAAAGAGCACGAGACGTGCTAAACAGAGAGCAC
1 AACAGAGAGCAC-A-AAGTGCT-AACAGAGAGCAC
3247851 GCTAGTGTTC
Statistics
Matches: 115, Mismatches: 6, Indels: 18
0.83 0.04 0.13
Matches are distributed among these distances:
45 2 0.02
46 56 0.49
47 3 0.03
48 42 0.37
49 8 0.07
50 4 0.03
ACGTcount: A:0.44, C:0.23, G:0.24, T:0.10
Consensus pattern (43 bp):
AACAGAGAGCACAAAGTGCTAACAGAGAGCACACACAGTGCTA
Found at i:3247774 original size:71 final size:68
Alignment explanation
Indices: 3247651--3247851 Score: 194
Period size: 71 Copynumber: 2.9 Consensus size: 68
3247641 TAAACGGAAC
* * *
3247651 AAACAGAGAGTAC-CGAAGTACTGAACAGAGAGCACATA-AGTGCTGGGCAACAGAGAGCAC-AC
1 AAACAGAGAGTACACAAAGTACT-AACAGAGAGCACACACAGTGCT---AAACAGAGAGCACGAC
3247713 ACAGTGCT
62 AC-GTGCT
*
3247721 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGA
1 AAACAGAGAGTACACAAAGTACTAA-CAGAGAGCACACACAGTGCT-A-AACAGAGAGCACGACA
3247786 CGTGCT
63 CGTGCT
* * * * * *
3247792 AAACAGAAAGCACACACAGTGCTAAACAAAGAGCACGAGAC-GTGCTAAACAGAGAGCACG
1 AAACAGAGAGTACACAAAGTACT-AACAGAGAGCAC-ACACAGTGCTAAACAGAGAGCACG
3247852 CTAGTGTTCC
Statistics
Matches: 113, Mismatches: 11, Indels: 15
0.81 0.08 0.11
Matches are distributed among these distances:
69 13 0.12
70 16 0.14
71 70 0.62
72 14 0.12
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (68 bp):
AAACAGAGAGTACACAAAGTACTAACAGAGAGCACACACAGTGCTAAACAGAGAGCACGACACGT
GCT
Found at i:3247851 original size:23 final size:23
Alignment explanation
Indices: 3247699--3247850 Score: 182
Period size: 23 Copynumber: 6.5 Consensus size: 23
3247689 AGTGCTGGGC
3247699 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
3247722 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
*
3247745 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
3247769 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
*
3247793 AACAGAAAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
3247816 AACAAAGAGCACGAGAC-GTGCTA
1 AACAGAGAGCAC-ACACAGTGCTA
3247839 AACAGAGAGCAC
1 AACAGAGAGCAC
3247851 GCTAGTGTTC
Statistics
Matches: 109, Mismatches: 15, Indels: 10
0.81 0.11 0.07
Matches are distributed among these distances:
22 3 0.03
23 82 0.75
24 5 0.05
25 16 0.15
26 3 0.03
ACGTcount: A:0.45, C:0.23, G:0.22, T:0.10
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:3251005 original size:2 final size:2
Alignment explanation
Indices: 3251000--3251033 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3250990 GGGGGGGCTA
3251000 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
3251034 GAATCCAAGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3279886 original size:12 final size:12
Alignment explanation
Indices: 3279869--3279894 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3279859 TAGCTCATCA
3279869 TTTATTTTTTTT
1 TTTATTTTTTTT
3279881 TTTATTTTTTTT
1 TTTATTTTTTTT
3279893 TT
1 TT
3279895 ATGTTTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTATTTTTTTT
Found at i:3279901 original size:12 final size:11
Alignment explanation
Indices: 3279869--3279902 Score: 50
Period size: 11 Copynumber: 2.9 Consensus size: 11
3279859 TAGCTCATCA
3279869 TTTATTTTTTTT
1 TTTA-TTTTTTT
3279881 TTTATTTTTTT
1 TTTATTTTTTT
3279892 TTTATGTTTTT
1 TTTAT-TTTTT
3279903 ACAACTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (11 bp):
TTTATTTTTTT
Found at i:3287455 original size:22 final size:22
Alignment explanation
Indices: 3287427--3287475 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
3287417 CACATTTTAA
3287427 TTTTTTA-TATACATTTTAGAAC
1 TTTTTTATTATA-ATTTTAGAAC
* *
3287449 TTTTTTATTATAATTTTTGAAG
1 TTTTTTATTATAATTTTAGAAC
3287471 TTTTT
1 TTTTT
3287476 GAGTTCTGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (22 bp):
TTTTTTATTATAATTTTAGAAC
Found at i:3287629 original size:19 final size:20
Alignment explanation
Indices: 3287587--3287629 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
3287577 GAACATTTTA
*
3287587 ATTA-TTTTTGAAAAAAACT
1 ATTATTTTTTGAAAAAAACC
*
3287606 TTTATTTTTTG-AAAAAACC
1 ATTATTTTTTGAAAAAAACC
3287625 ATTAT
1 ATTAT
3287630 GGATTTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (20 bp):
ATTATTTTTTGAAAAAAACC
Found at i:3295229 original size:196 final size:197
Alignment explanation
Indices: 3294831--3295233 Score: 461
Period size: 196 Copynumber: 2.1 Consensus size: 197
3294821 GATGTATCTG
* * *
3294831 AAATGATAAAGTTTTTTTAACATTAATTTTATTATAAGTTCTTATCATATATGTTATTTTTGATA
1 AAATGATAAAGTTTTTTTAACATTAATCTTATTATAAGTTCTTATCATATATGCTATTTTGGATA
* * * * ** * * *
3294896 CAATACTTAGAATTATCTATAGTCCCTCCCCAACTTTTAAATAGGAGGATAATGTACTTTACCGT
66 CAATACTTAAAACTATCTATAATCACTCCCCAACCCTTAAATAAGAGGATAATGGACTTTACCGC
* * * * ** * * * * *
3294961 ACTCGAACCCATGTTCTCTTGTATTAACAATAATGTCGATAACAATCGAGCTAAAATTCAATCGG
131 ACACAAACCCATGTCCTCCTACACTAACAATAATATCGATAACAATCGAGCTAAAACTAAATCGA
3295026 TA
196 TA
* *
3295028 AAATGATAAAGTTTTTTTAACATTAATCTTATTATAAGTTTTTATCATATTTGCTATTTTGGATA
1 AAATGATAAAGTTTTTTTAACATTAATCTTATTATAAGTTCTTATCATATATGCTATTTTGGATA
* * * * *
3295093 TAATA-TTAAAACTA-CTCATAATTATTCTCCAACCCTTAAATAAGAGGATAATGGACTTTAGCG
66 CAATACTTAAAACTATCT-ATAATCACTCCCCAACCCTTAAATAAGAGGATAATGGACTTTACCG
* * * *
3295156 CACACAAACTC-TCGTCCTCCTACACTGACAATAATATCGATAACAATCGAGTTAAGACTAAATC
130 CACACAAACCCAT-GTCCTCCTACACTAACAATAATATCGATAACAATCGAGCTAAAACTAAATC
3295220 GATA
194 GATA
3295224 AAATGATAAA
1 AAATGATAAA
3295234 ATTAAATTAA
Statistics
Matches: 170, Mismatches: 34, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
195 3 0.02
196 103 0.61
197 64 0.38
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (197 bp):
AAATGATAAAGTTTTTTTAACATTAATCTTATTATAAGTTCTTATCATATATGCTATTTTGGATA
CAATACTTAAAACTATCTATAATCACTCCCCAACCCTTAAATAAGAGGATAATGGACTTTACCGC
ACACAAACCCATGTCCTCCTACACTAACAATAATATCGATAACAATCGAGCTAAAACTAAATCGA
TA
Found at i:3309193 original size:10 final size:9
Alignment explanation
Indices: 3309180--3309262 Score: 69
Period size: 10 Copynumber: 8.6 Consensus size: 9
3309170 TAATACCCAT
3309180 AAAATTATTA
1 AAAATTA-TA
3309190 AAAATTATA
1 AAAATTATA
*
3309199 AAGAAATATA
1 AA-AATTATA
3309209 AAAATTAT-
1 AAAATTATA
3309217 AAAATATATA
1 AAAAT-TATA
* *
3309227 GAAATATAAAA
1 -AAA-ATTATA
3309238 AAAATTATAA
1 AAAATTAT-A
3309248 AAAATTTATA
1 AAAA-TTATA
3309258 AAAAT
1 AAAAT
3309263 GTAAAGAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
8 5 0.08
9 16 0.27
10 28 0.47
11 9 0.15
12 2 0.03
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (9 bp):
AAAATTATA
Found at i:3309212 original size:19 final size:18
Alignment explanation
Indices: 3309188--3309261 Score: 76
Period size: 19 Copynumber: 3.8 Consensus size: 18
3309178 ATAAAATTAT
3309188 TAAAAATTATAAAGAAATA
1 TAAAAATTATAAA-AAATA
*
3309207 TAAAAATTATAAAATATA
1 TAAAAATTATAAAAAATA
* *
3309225 TAGAAATATAAAAAAAATTA
1 TAAAAAT-TATAAAAAA-TA
3309245 TAAAAAATTTATAAAAA
1 T-AAAAA-TTATAAAAA
3309262 TGTAAAGAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 10 0.22
19 20 0.44
20 3 0.07
21 11 0.24
22 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAAATTATAAAAAATA
Found at i:3309224 original size:26 final size:29
Alignment explanation
Indices: 3309180--3309238 Score: 88
Period size: 26 Copynumber: 2.1 Consensus size: 29
3309170 TAATACCCAT
3309180 AAAATTATTAAAAATTATAAAGAAATATA
1 AAAATTATTAAAAATTATAAAGAAATATA
*
3309209 AAAATTA-T-AAAA-TATATAGAAATATA
1 AAAATTATTAAAAATTATAAAGAAATATA
3309235 AAAA
1 AAAA
3309239 AAATTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 17 0.59
27 4 0.14
28 1 0.03
29 7 0.24
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (29 bp):
AAAATTATTAAAAATTATAAAGAAATATA
Found at i:3309272 original size:10 final size:10
Alignment explanation
Indices: 3309195--3309277 Score: 52
Period size: 10 Copynumber: 8.6 Consensus size: 10
3309185 TATTAAAAAT
3309195 TATAAAGAAA
1 TATAAAGAAA
3309205 TAT-AA-AAA
1 TATAAAGAAA
*
3309213 T-TATA-AAA
1 TATAAAGAAA
*
3309221 TATATAGAAA
1 TATAAAGAAA
*
3309231 TATAAAAAAAA
1 TAT-AAAGAAA
3309242 TTATAAA-AAA
1 -TATAAAGAAA
*
3309252 TTTATAA-AAA
1 TATA-AAGAAA
*
3309262 TGTAAAGAAA
1 TATAAAGAAA
3309272 TATAAA
1 TATAAA
3309278 ATTCGTAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
7 1 0.02
8 9 0.15
9 11 0.18
10 28 0.47
11 8 0.13
12 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (10 bp):
TATAAAGAAA
Found at i:3309441 original size:20 final size:20
Alignment explanation
Indices: 3309418--3309456 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3309408 TTAACAGATC
3309418 TTTTTAATG-TATTTTATAAT
1 TTTTTAATGAT-TTTTATAAT
*
3309438 TTTTTTATGATTTTTATAA
1 TTTTTAATGATTTTTATAA
3309457 AAATTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTTTAATGATTTTTATAAT
Found at i:3309464 original size:41 final size:40
Alignment explanation
Indices: 3309418--3309496 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 40
3309408 TTAACAGATC
* *
3309418 TTTTTAATGTATTTTATAATTTTTTTATGATTTTTATAAAAA
1 TTTTAAAT-TATTTTAT-AGTTTTTTATGATTTTTATAAAAA
* *
3309460 TTTTACAATTTTTTTATAGTTTTTTATTATTTTTATA
1 TTTTA-AATTATTTTATAGTTTTTTATGATTTTTATA
3309497 TTTGTTCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
41 18 0.56
42 11 0.34
43 3 0.09
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (40 bp):
TTTTAAATTATTTTATAGTTTTTTATGATTTTTATAAAAA
Found at i:3309536 original size:28 final size:28
Alignment explanation
Indices: 3309493--3309566 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 28
3309483 TTATTATTTT
*
3309493 TATATTTGTTCTATTTTTAATAAAATTTAA
1 TATATTT-TTATATTTTTAATAAAA-TTAA
*
3309523 -ATATTTTTATATTTTTATTAAAATTAA
1 TATATTTTTATATTTTTAATAAAATTAA
* *
3309550 TTTTTTTTTATATTTTT
1 TATATTTTTATATTTTT
3309567 TAATTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 4 0.10
28 29 0.74
29 6 0.15
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (28 bp):
TATATTTTTATATTTTTAATAAAATTAA
Found at i:3309911 original size:105 final size:105
Alignment explanation
Indices: 3309726--3309920 Score: 270
Period size: 105 Copynumber: 1.8 Consensus size: 105
3309716 TGCAAAAAAA
* ** * *
3309726 AAGTAGGAGCTTAATTGCCTTTTTTGAAAAAAGTTTGAGAGCTTTTTTTTATGTATTTTGAAAGT
1 AAGTAGGAGCATAATTGCCTTTTTTGAAAAAAAATTGAGAGC-TTTTTTTATATATTGTGAAAGT
*
3309791 TCAAGTATTTAATTGAGTGGAAAAAAAAGGTAAGAGCTTAATT
65 TCAAGTATTAAATTGAGT--AAAAAAAAGGTAAGAGCTTAATT
*
3309834 AAGTAGGAGCATAATTG-TTTTTTTGAAAAAAAATTGAG-GAC-TTTTTTATATATTGTGAAAGT
1 AAGTAGGAGCATAATTGCCTTTTTTGAAAAAAAATTGAGAG-CTTTTTTTATATATTGTGAAAGT
3309896 TCAAGTATTAAATTGAGTAAAAAAA
65 TCAAGTATTAAATTGAGTAAAAAAA
3309921 TAAAAACTTA
Statistics
Matches: 79, Mismatches: 7, Indels: 7
0.85 0.08 0.08
Matches are distributed among these distances:
103 7 0.09
105 36 0.46
106 1 0.01
107 19 0.24
108 16 0.20
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (105 bp):
AAGTAGGAGCATAATTGCCTTTTTTGAAAAAAAATTGAGAGCTTTTTTTATATATTGTGAAAGTT
CAAGTATTAAATTGAGTAAAAAAAAGGTAAGAGCTTAATT
Found at i:3311171 original size:6 final size:6
Alignment explanation
Indices: 3311162--3311188 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3311152 TATGTAAATG
3311162 TCATCT TCATCT TCATCT TCATCT TCA
1 TCATCT TCATCT TCATCT TCATCT TCA
3311189 CGGTCACGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.33, G:0.00, T:0.48
Consensus pattern (6 bp):
TCATCT
Found at i:3312876 original size:6 final size:6
Alignment explanation
Indices: 3312865--3312905 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
3312855 AAAACAATAT
3312865 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
3312906 TTTAAGCTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.51, C:0.15, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAC
Found at i:3327739 original size:6 final size:6
Alignment explanation
Indices: 3327730--3327758 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
3327720 AGAAATTTAA
3327730 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
3327759 AGTGGGTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:3333510 original size:6 final size:6
Alignment explanation
Indices: 3333499--3333534 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
3333489 TCCCTTGAAG
3333499 AACAGA AACAGA AACAGA AACAGA AACAGA AACAGA
1 AACAGA AACAGA AACAGA AACAGA AACAGA AACAGA
3333535 GAGTTTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.17, G:0.17, T:0.00
Consensus pattern (6 bp):
AACAGA
Found at i:3340953 original size:23 final size:23
Alignment explanation
Indices: 3340927--3341051 Score: 112
Period size: 23 Copynumber: 5.4 Consensus size: 23
3340917 AGCACGTCTC
*
3340927 GTGCTCTCTGATTAGCGCTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
3340950 GTGCTTTCTGATTAGTACTTTGT
1 GTGCTCTCTGATTAGCACTTTGT
* * *
3340973 GTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGT
* *
3340996 GTGCTCTCTGTTGCCTAGCAC-TTAT
1 GTGCTCTCTGAT---TAGCACTTTGT
*
3341021 GTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATTAGCACTTTGT
*
3341042 GTACTCTCTG
1 GTGCTCTCTG
3341052 CTTGTTCCGT
Statistics
Matches: 84, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
21 14 0.17
22 2 0.02
23 49 0.58
24 1 0.01
25 12 0.14
26 6 0.07
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.45
Consensus pattern (23 bp):
GTGCTCTCTGATTAGCACTTTGT
Found at i:3341039 original size:21 final size:21
Alignment explanation
Indices: 3340906--3341051 Score: 96
Period size: 23 Copynumber: 6.4 Consensus size: 21
3340896 ACACTAGCGC
*
3340906 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGTTTAGCAC-T-TTGT
* *
3340929 GCTCTCTGATTAGCGCTTTGTGT
1 GCTCTCTGTTTAGCAC-TT-TGT
* * *
3340952 GCTTTCTGATTAGTACTTTGT
1 GCTCTCTGTTTAGCACTTTGT
3340973 GTACTCTCTGTTTAGCACTGTGTGT
1 G--CTCTCTGTTTAGCACT-T-TGT
3340998 GCTCTCTGTTGCCTAGCACTTATGT
1 GCTCTCTGTT---TAGCACTT-TGT
*
3341023 GCTCTCTG-TTAGTACTTTGGT
1 GCTCTCTGTTTAGCACTTT-GT
*
3341044 ACTCTCTG
1 GCTCTCTG
3341052 CTTGTTCCGT
Statistics
Matches: 101, Mismatches: 13, Indels: 20
0.75 0.10 0.15
Matches are distributed among these distances:
20 1 0.01
21 20 0.20
22 3 0.03
23 52 0.51
24 2 0.02
25 16 0.16
26 7 0.07
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (21 bp):
GCTCTCTGTTTAGCACTTTGT
Found at i:3341046 original size:69 final size:69
Alignment explanation
Indices: 3340907--3341051 Score: 181
Period size: 69 Copynumber: 2.1 Consensus size: 69
3340897 CACTAGCGCG
* * *
3340907 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCGCTTTGTGTGCTTTCTGATTAGTACTTTG
1 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
3340972 TGTA
66 TGTA
* *
3340976 CTCTCTGTTTAGCACTGTGT-GTGCTCTCTGTTGCCTAGCAC-TTATGTGCTCTCTG-TTAGTAC
1 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGAT---TAGCACTTTATGTGCTCTCTGATTAGTAC
3341038 TTTG-GTA
62 TTTGTGTA
3341045 CTCTCTG
1 CTCTCTG
3341052 CTTGTTCCGT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
69 36 0.54
70 14 0.21
71 12 0.18
72 5 0.07
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (69 bp):
CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTTTATGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:3341838 original size:19 final size:19
Alignment explanation
Indices: 3341814--3341850 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3341804 ATATTACACA
*
3341814 TAAAAAAAATTATATTTAC
1 TAAAAAAAATCATATTTAC
*
3341833 TAAAAATAATCATATTTA
1 TAAAAAAAATCATATTTA
3341851 TAATAATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAAAATCATATTTAC
Found at i:3343947 original size:22 final size:23
Alignment explanation
Indices: 3343922--3343965 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
3343912 TAAAATGTTT
3343922 TAAAAA-TAAAAATAATTTTTTC
1 TAAAAAGTAAAAATAATTTTTTC
* *
3343944 TAAAAAGTAAAGATGATTTTTT
1 TAAAAAGTAAAAATAATTTTTT
3343966 TTGTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (23 bp):
TAAAAAGTAAAAATAATTTTTTC
Found at i:3347275 original size:28 final size:31
Alignment explanation
Indices: 3347243--3347301 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
3347233 TTATAATAGT
3347243 AAAA-TTATAATTTTTAGAG-GA-TTAAATA
1 AAAATTTATAATTTTTAGAGTGACTTAAATA
3347271 AAAATTTTATAATTTTTAGAGTGACTTAAAT
1 AAAA-TTTATAATTTTTAGAGTGACTTAAAT
3347302 TGTAATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 4 0.15
30 15 0.56
31 2 0.07
32 6 0.22
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (31 bp):
AAAATTTATAATTTTTAGAGTGACTTAAATA
Found at i:3348180 original size:62 final size:59
Alignment explanation
Indices: 3347925--3348427 Score: 360
Period size: 61 Copynumber: 8.3 Consensus size: 59
3347915 GAAAAAAAAA
* * *
3347925 TTGGTGTTGGTCATGCAAT-AGCCGACACCCCTTTTTTATCTGATAAAAAAATTT-AATTTT
1 TTGGTGTTGGCCATGCAATGA-CCGACACTCC-TTTTT-TCAGATAAAAAAATTTAAATTTT
* ***
3347985 TTGGGTGTTGGTCATGCAATGGTTGACACTCCCTTTTTGTCAGAT-AAAAAATTT-AATTTT
1 TT-GGTGTTGGCCATGCAATGACCGACACT-CCTTTTT-TCAGATAAAAAAATTTAAATTTT
* * ** * * * *
3348045 TTGATGTTAGCCATATAATGACCGATACTCCTATTTATCTGATAAAAAAA-TCAAATTTT
1 TTGGTGTTGGCCATGCAATGACCGACACTCCT-TTTTTCAGATAAAAAAATTTAAATTTT
* * *
3348104 TGGGTGTTGACCATGCAAT-AGCCGACAACTTCTTTTTTCAGATAAAAAAATTTCAAAATTTT
1 TTGGTGTTGGCCATGCAATGA-CCGAC-ACTCCTTTTTTCAGATAAAAAAATTT--AAATTTT
* *
3348166 TTGGTGTTGGCCATGCAATGACCGACAC-CCTATTTTTCTAGATAAAAAATTTTAAAATATT
1 TTGGTGTTGGCCATGCAATGACCGACACTCCT-TTTTTC-AGATAAAAAAATTT-AAATTTT
* **
3348227 TTGGTGTTGGCCATGCCATGACCGACACTCCCTTTTTGTCAGAT-AAAAAATTCGAATTTT
1 TTGGTGTTGGCCATGCAATGACCGACACT-CCTTTTT-TCAGATAAAAAAATTTAAATTTT
* ** * * * * * *
3348287 TTTGTGTTGATCATGCCATGATCGACACCTTCTTTTTTATCTGGTAAAAAAA-TTAATTTTT
1 TTGGTGTTGGCCATGCAATGACCGACA-C-TCCTTTTT-TCAGATAAAAAAATTTAAATTTT
* * * * * ** * *
3348348 TTTGTGTTGGCAATACAATGATCGATAC-CCTCTTTTTGTGAAATAAAAAATTCAAATTTTTT
1 TTGGTGTTGGCCATGCAATGACCGACACTCCT-TTTTTCAGATA-AAAAAATTTAAA--TTTT
3348410 TTGGTGTTGGCCATGCAA
1 TTGGTGTTGGCCATGCAA
3348428 ATTTGATTTT
Statistics
Matches: 353, Mismatches: 65, Indels: 48
0.76 0.14 0.10
Matches are distributed among these distances:
58 16 0.05
59 75 0.21
60 59 0.17
61 119 0.34
62 78 0.22
63 6 0.02
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (59 bp):
TTGGTGTTGGCCATGCAATGACCGACACTCCTTTTTTCAGATAAAAAAATTTAAATTTT
Found at i:3348358 original size:121 final size:120
Alignment explanation
Indices: 3347936--3348427 Score: 432
Period size: 121 Copynumber: 4.1 Consensus size: 120
3347926 TGGTGTTGGT
* * *
3347936 CATGCAAT-AGCCGACACCCCTTTTTTATCTGATAAAAAAATTTAATTTTTTGGGTGTTGGTCAT
1 CATGCAATGA-CCGACACCTCTTTTTTATCTGATAAAAAAA-TTAAATTTTTGGGTGTTGGCCAT
*** *
3348000 GCAATGGTTGACACTCCCTTTTTGTCAGATAAAAAATT-TAA-TTTTTTGATGTT-AGC
64 GCAATGACCGACACTCCCTTTTTGTCAGATAAAAAATTCAAATTTTTTTG-TGTTGA-C
** * * * * *
3348056 CATATAATGACCGATA-CTCCTATTTATCTGATAAAAAAATCAAATTTTTGGGTGTTGACCATGC
1 CATGCAATGACCGACACCTCTTTTTTATCTGATAAAAAAATTAAATTTTTGGGTGTTGGCCATGC
* * *
3348120 AAT-AGCCGACAACT-TCTTTTT-TCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGC
66 AATGA-CCGAC-ACTCCCTTTTTGTCAGAT-AAAAAA-TTC-AAATTTTTTTGTGTTGAC
* *
3348177 CATGCAATGACCGACACC-CTATTTT-TCTAGATAAAAAATTTTAAAATATTTT-GGTGTTGGCC
1 CATGCAATGACCGACACCTCTTTTTTATCT-GATAAAAAA-ATT-AAAT-TTTTGGGTGTTGGCC
* * *
3348239 ATGCCATGACCGACACTCCCTTTTTGTCAGATAAAAAATTCGAATTTTTTTGTGTTGAT
62 ATGCAATGACCGACACTCCCTTTTTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGAC
* * * * ** * *
3348298 CATGCCATGATCGACACCTTCTTTTTTATCTGGTAAAAAAATTAATTTTTTTTGTGTTGGCAATA
1 CATGCAATGACCGACACC-TCTTTTTTATCTGATAAAAAAATTAAATTTTTGGGTGTTGGCCATG
* * * * *
3348363 CAATGATCGATAC-CCTCTTTTTGTGAAATAAAAAATTCAAATTTTTTTTGGTGTTGGC
65 CAATGACCGACACTCC-CTTTTTGTCAGATAAAAAATTCAAA-TTTTTTT-GTGTTGAC
3348421 CATGCAA
1 CATGCAA
3348428 ATTTGATTTT
Statistics
Matches: 298, Mismatches: 50, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
117 6 0.02
118 39 0.13
119 25 0.08
120 20 0.07
121 109 0.37
122 23 0.08
123 62 0.21
124 14 0.05
ACGTcount: A:0.30, C:0.16, G:0.15, T:0.39
Consensus pattern (120 bp):
CATGCAATGACCGACACCTCTTTTTTATCTGATAAAAAAATTAAATTTTTGGGTGTTGGCCATGC
AATGACCGACACTCCCTTTTTGTCAGATAAAAAATTCAAATTTTTTTGTGTTGAC
Found at i:3376034 original size:111 final size:111
Alignment explanation
Indices: 3375747--3376316 Score: 827
Period size: 111 Copynumber: 5.1 Consensus size: 111
3375737 GTGAGTGGGC
* * * * *
3375747 CTGCTGCTGCCGAACCAGCTGGCCATTCCGGGCAGGACCTGTGCCTTGAGCATTTGACTGCTCAT
1 CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
* * * *
3375812 ATCGAGGCGAGCCCATGTTTGATACACTTCCATTTC-CATGAAAGTT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCA-TTCGCATGAAAATT
* * * * *
3375858 AGGATGCTGCTGCTGAACCAGCTGACCATTCCAGGCAGGACCTGTGCCTTGAGCATATGTCTGCT
1 ---CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCT
* * *
3375923 CATATCGAGGTGATCCCATGTTCGATACAGTTCCGTTCACATGAAAATT
63 CATATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
* *
3375972 CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATACGAATGCTCAT
1 CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
*
3376037 ATCGAGGTGATCCCATGTTTGGTACAGTTCCATTCGCATGAAAATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
* * *
3376083 CTGCTGCTGATGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATACGAATGCTCAT
1 CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
*
3376148 ATCGAGGTGATCCCATGTTTGGTACAGTTCCATTCGCATGAAAATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
* ** * *
3376194 CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCATGACCCATACCTTGAACATATGACTGCTCAT
1 CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
*
3376259 ATCGAGGTGATCCCATGTTAGATACAGTTCCATTCGCATGAAAATT
66 ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
3376305 CTGCTGCTGCTG
1 CTGCTGCTGCTG
3376317 CTGCTGAATT
Statistics
Matches: 421, Mismatches: 34, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
111 323 0.77
113 3 0.01
114 95 0.23
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.28
Consensus pattern (111 bp):
CTGCTGCTGCTGAACCATCTGGCCATTCCAGGCAGGACCTGTCCCTTGAGCATATGACTGCTCAT
ATCGAGGTGATCCCATGTTTGATACAGTTCCATTCGCATGAAAATT
Found at i:3381942 original size:24 final size:23
Alignment explanation
Indices: 3381915--3381974 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
3381905 TCATTAATAT
3381915 TGTTCATGAACATGCTCAATTATA
1 TGTTCATGAACATGCTCAATTA-A
* **
3381939 TGTTCATGAACATGTTCGTTTAA
1 TGTTCATGAACATGCTCAATTAA
3381962 TGTTCATGAACAT
1 TGTTCATGAACAT
3381975 ATTCGATTAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGCTCAATTAA
Found at i:3381968 original size:23 final size:23
Alignment explanation
Indices: 3381915--3381984 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
3381905 TCATTAATAT
* *
3381915 TGTTCATGAACATGCTCAATTATA
1 TGTTCATGAACATGTTCGATTA-A
*
3381939 TGTTCATGAACATGTTCGTTTAA
1 TGTTCATGAACATGTTCGATTAA
*
3381962 TGTTCATGAACATATTCGATTAA
1 TGTTCATGAACATGTTCGATTAA
3381985 ATTAAATGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.40
Consensus pattern (23 bp):
TGTTCATGAACATGTTCGATTAA
Found at i:3382793 original size:6 final size:6
Alignment explanation
Indices: 3382784--3382816 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
3382774 AGCACCGCCA
3382784 CCCCCT CCCCCT CCCCCT CCCCCT CCCCCT CCC
1 CCCCCT CCCCCT CCCCCT CCCCCT CCCCCT CCC
3382817 GAGCTCTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.00, C:0.85, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCCCT
Found at i:3389527 original size:24 final size:26
Alignment explanation
Indices: 3389494--3389545 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
3389484 CCATTTAATA
*
3389494 ATTTATTAAAG-GTTTT-AAATCTGTT
1 ATTTATTAAAGAATTTTAAAATCT-TT
3389519 ATTT-TTAAAGAATTTTAAAATCTTT
1 ATTTATTAAAGAATTTTAAAATCTTT
3389544 AT
1 AT
3389546 AATTTAACAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 6 0.25
25 12 0.50
26 6 0.25
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.52
Consensus pattern (26 bp):
ATTTATTAAAGAATTTTAAAATCTTT
Found at i:3404400 original size:23 final size:23
Alignment explanation
Indices: 3404368--3404478 Score: 134
Period size: 23 Copynumber: 4.8 Consensus size: 23
3404358 GCTGGGAAAA
3404368 CAGTAAGCACACACAGTGCAAAT
1 CAGTAAGCACACACAGTGCAAAT
* *
3404391 CAGTAGGCACACACAATGCAAAAT
1 CAGTAAGCACACACAGTGC-AAAT
*
3404415 -AGTAAGCACACACAGTGCAAAA
1 CAGTAAGCACACACAGTGCAAAT
* * * *
3404437 CAATAAGCACATATAGTGCGAAT
1 CAGTAAGCACACACAGTGCAAAT
*
3404460 CAGTAAGCACTCACAGTGC
1 CAGTAAGCACACACAGTGC
3404479 TGAACAGTAA
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
22 3 0.04
23 65 0.90
24 4 0.06
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.14
Consensus pattern (23 bp):
CAGTAAGCACACACAGTGCAAAT
Found at i:3404486 original size:23 final size:22
Alignment explanation
Indices: 3404365--3404490 Score: 126
Period size: 23 Copynumber: 5.5 Consensus size: 22
3404355 AGTGCTGGGA
3404365 AAACAGTAAGCACACACAGTGC
1 AAACAGTAAGCACACACAGTGC
* *
3404387 AAATCAGTAGGCACACACAATGC
1 AAA-CAGTAAGCACACACAGTGC
*
3404410 AAAATAGTAAGCACACACAGTGC
1 -AAACAGTAAGCACACACAGTGC
* * *
3404433 AAAACAATAAGCACATATAGTGC
1 -AAACAGTAAGCACACACAGTGC
* *
3404456 GAATCAGTAAGCACTCACAGTGC
1 -AAACAGTAAGCACACACAGTGC
*
3404479 TGAACAGTAAGC
1 -AAACAGTAAGC
3404491 GTGCTAATGT
Statistics
Matches: 84, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
22 3 0.04
23 78 0.93
24 3 0.04
ACGTcount: A:0.44, C:0.23, G:0.18, T:0.14
Consensus pattern (22 bp):
AAACAGTAAGCACACACAGTGC
Found at i:3407581 original size:19 final size:19
Alignment explanation
Indices: 3407539--3407582 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
3407529 ATTTAAAGAG
3407539 GTATAAATCTTAAAATTAT
1 GTATAAATCTTAAAATTAT
* *
3407558 ATATAAAT-TTTAAATTGAT
1 GTATAAATCTTAAAATT-AT
3407577 GTATAA
1 GTATAA
3407583 TTATGTACGT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (19 bp):
GTATAAATCTTAAAATTAT
Done.