Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 4 of 204
Found at i:1426199 original size:3 final size:3
Alignment explanation
Indices: 1426193--1426232 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
1426183 AATGATGATA
* * *
1426193 ATC ATC ATC ATC ATC ATC ATC ATC ACC ACC ATC ACC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1426233 CCTTCTCTTC
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:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (3 bp):
ATC
Found at i:1430916 original size:57 final size:56
Alignment explanation
Indices: 1430814--1430923 Score: 125
Period size: 57 Copynumber: 1.9 Consensus size: 56
1430804 TTTAACTATT
* *
1430814 TTTTAAATTTTAAAAAAATATTTTTTATAAATTTTATACATTTAAATAATTTTAATGA
1 TTTTAAATTTTAAAAAAATAATCTTTATAAATTTTATACATTT-AA-AATTTTAATGA
* * * *
1430872 TTTTAAATTTT-TAAAATTAATCTTTATAACTTTTTTA-ATTTTAAAATTTTAA
1 TTTTAAATTTTAAAAAAATAATCTTTATAAATTTTATACA-TTTAAAATTTTAA
1430924 AAAATTAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
55 8 0.18
56 3 0.07
57 23 0.51
58 11 0.24
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.55
Consensus pattern (56 bp):
TTTTAAATTTTAAAAAAATAATCTTTATAAATTTTATACATTTAAAATTTTAATGA
Found at i:1440238 original size:32 final size:33
Alignment explanation
Indices: 1440197--1440265 Score: 131
Period size: 32 Copynumber: 2.1 Consensus size: 33
1440187 GTGAGCCGAT
1440197 TGTTTAGTTCTTAAGAAATAATATATTTGCAC-
1 TGTTTAGTTCTTAAGAAATAATATATTTGCACA
1440229 TGTTTAGTTCTTAAGAAATAATATATTTGCACA
1 TGTTTAGTTCTTAAGAAATAATATATTTGCACA
1440262 TGTT
1 TGTT
1440266 ATTTATTACA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (33 bp):
TGTTTAGTTCTTAAGAAATAATATATTTGCACA
Found at i:1444571 original size:16 final size:16
Alignment explanation
Indices: 1444543--1444608 Score: 56
Period size: 16 Copynumber: 4.5 Consensus size: 16
1444533 GGAATCAGTT
1444543 ATATT-AATGTTATTTA
1 ATATTAAAT-TTATTTA
*
1444559 ATTTTAAATTTATTTA
1 ATATTAAATTTATTTA
1444575 ATATTAAA---A--TA
1 ATATTAAATTTATTTA
*
1444586 ATATTAAA-ATATTTA
1 ATATTAAATTTATTTA
1444601 ATATTAAA
1 ATATTAAA
1444609 ATAATACAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
11 10 0.23
13 2 0.05
15 10 0.23
16 18 0.42
17 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATATTAAATTTATTTA
Found at i:1454975 original size:24 final size:24
Alignment explanation
Indices: 1454948--1454995 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1454938 ATTGAAATGG
1454948 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
1454972 ATTGAATTTATATTGATTGAATTT
1 ATTGAATTTATATTGATTGAATTT
1454996 GTATATATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 3 0.14
24 14 0.64
25 5 0.23
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:1458740 original size:2 final size:2
Alignment explanation
Indices: 1458733--1458772 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1458723 ATGATTCTTA
1458733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1458773 TACATTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1461100 original size:2 final size:2
Alignment explanation
Indices: 1461093--1461125 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1461083 CACCGGTAAT
1461093 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1461126 TCTTTGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1463081 original size:25 final size:23
Alignment explanation
Indices: 1463041--1463099 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 23
1463031 CTAATATTTA
* *
1463041 TATTTTTTTATCAATTT-AGTCTT
1 TATTTTTTTATAAATTTGACT-TT
1463064 TATTTTTTTAGTTAAATTTGACTTT
1 TATTTTTTTA--TAAATTTGACTTT
1463089 TAATTTTTTTA
1 T-ATTTTTTTA
1463100 AAAAGAGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 10 0.33
25 9 0.30
26 11 0.37
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (23 bp):
TATTTTTTTATAAATTTGACTTT
Found at i:1467546 original size:167 final size:167
Alignment explanation
Indices: 1467270--1467751 Score: 919
Period size: 167 Copynumber: 2.9 Consensus size: 167
1467260 CGTGAGCGGC
*
1467270 TGCCCTGAAGGTCTAGTTCACAAAGATGGAAGTGCCTCAAGCGCACGTGGGTGTAGCCCAAGTGA
1 TGCCCTGAAGGTCTAGTTCACAAAGATGGAAGTGCCTCAAGCGTACGTGGGTGTAGCCCAAGTGA
1467335 ACCATCTTCCTCAACAAGTGACTTATATGCCATAGATCAGGCGTTCGAATTCCACCAGGGTGAGA
66 ACCATCTTCCTCAACAAGTGACTTATATGCCATAGATCAGGCGTTCGAATTCCACCAGGGTGAGA
1467400 TGCTCACATCCCCTTGGCGAGTTCACAAAGATGGAAG
131 TGCTCACATCCCCTTGGCGAGTTCACAAAGATGGAAG
*
1467437 TGCCCTGAAGGTCTAGTTCACAAAGATGGAAGTGTCTCAAGCGTACGTGGGTGTAGCCCAAGTGA
1 TGCCCTGAAGGTCTAGTTCACAAAGATGGAAGTGCCTCAAGCGTACGTGGGTGTAGCCCAAGTGA
1467502 ACCATCTTCCTCAACAAGTGACTTATATGCCATAGATCAGGCGTTCGAATTCCACCAGGGTGAGA
66 ACCATCTTCCTCAACAAGTGACTTATATGCCATAGATCAGGCGTTCGAATTCCACCAGGGTGAGA
*
1467567 TGCTCACATCCACTTGGCGAGTTCACAAAGATGGAAG
131 TGCTCACATCCCCTTGGCGAGTTCACAAAGATGGAAG
1467604 TGCCCTGAAGGTCTAGTTCACAAAGATGGAAGTGCCTCAAGCGTACGTGGGTGTAGCCCAAGTGA
1 TGCCCTGAAGGTCTAGTTCACAAAGATGGAAGTGCCTCAAGCGTACGTGGGTGTAGCCCAAGTGA
* *
1467669 ACCATCTTCCTCAACAAGTAACTTATATGCCATAGATCAGCCGTTCGAATTCCACCAGGGTGAGA
66 ACCATCTTCCTCAACAAGTGACTTATATGCCATAGATCAGGCGTTCGAATTCCACCAGGGTGAGA
1467734 TGCTCACATCCCCTTGGC
131 TGCTCACATCCCCTTGGC
1467752 AAGTAGCTAC
Statistics
Matches: 308, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
167 308 1.00
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.23
Consensus pattern (167 bp):
TGCCCTGAAGGTCTAGTTCACAAAGATGGAAGTGCCTCAAGCGTACGTGGGTGTAGCCCAAGTGA
ACCATCTTCCTCAACAAGTGACTTATATGCCATAGATCAGGCGTTCGAATTCCACCAGGGTGAGA
TGCTCACATCCCCTTGGCGAGTTCACAAAGATGGAAG
Found at i:1470896 original size:20 final size:21
Alignment explanation
Indices: 1470871--1470915 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
1470861 ATATAACTTT
*
1470871 AAAAAA-TAGTAATATTATAA
1 AAAAAACTAATAATATTATAA
*
1470891 AAAAAACCTAATGATATTATAA
1 AAAAAA-CTAATAATATTATAA
1470913 AAA
1 AAA
1470916 TTATAAACTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
22 15 0.71
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAAACTAATAATATTATAA
Found at i:1471510 original size:19 final size:19
Alignment explanation
Indices: 1471435--1471513 Score: 67
Period size: 19 Copynumber: 4.2 Consensus size: 19
1471425 CATCCTTTAA
1471435 TTAA-ATTTTTAAAA-ATT
1 TTAATATTTTTAAAATATT
* * *
1471452 TAAATATATTCAAAATATT
1 TTAATATTTTTAAAATATT
*
1471471 TTTAT-TCTTTTAAAATGATT
1 TTAATAT-TTTTAAAAT-ATT
1471491 TTAATGATTTTTAAAA-ATT
1 TTAAT-ATTTTTAAAATATT
1471510 TTAA
1 TTAA
1471514 AAATTAATTA
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
17 3 0.06
18 9 0.19
19 20 0.42
20 7 0.15
21 8 0.17
22 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (19 bp):
TTAATATTTTTAAAATATT
Found at i:1472706 original size:31 final size:31
Alignment explanation
Indices: 1472662--1472727 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1472652 GTTGTTTTGG
* *
1472662 ATATTAAAATAAATATCGAAACTAAACTAAA
1 ATATCAAAATAAATATCAAAACTAAACTAAA
* * *
1472693 ATATCAAATTAAATATTAAAATTAAACTAAA
1 ATATCAAAATAAATATCAAAACTAAACTAAA
1472724 ATAT
1 ATAT
1472728 TTAACGATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.61, C:0.08, G:0.02, T:0.30
Consensus pattern (31 bp):
ATATCAAAATAAATATCAAAACTAAACTAAA
Found at i:1477196 original size:150 final size:150
Alignment explanation
Indices: 1476920--1477222 Score: 579
Period size: 150 Copynumber: 2.0 Consensus size: 150
1476910 TTAAACGTAT
* *
1476920 TGAGAATAGCTCTACGGTTAAGGAAACTGCTGGAAACTACTGCAATGAAGACAGTGAGGATTTAA
1 TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
*
1476985 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTGAGGGAGAA
66 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTAAGGGAGAA
1477050 AGTCCCATGGTTGATGATTC
131 AGTCCCATGGTTGATGATTC
1477070 TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
1 TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
1477135 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTAAGGGAGAA
66 GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTAAGGGAGAA
1477200 AGTCCCATGGTTGATGATTC
131 AGTCCCATGGTTGATGATTC
1477220 TGA
1 TGA
1477223 TCGCCCTCCG
Statistics
Matches: 150, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 150 1.00
ACGTcount: A:0.31, C:0.12, G:0.30, T:0.27
Consensus pattern (150 bp):
TGAGAATAGCTCTAAGGTTAAGGAAACTGCTGGAAACAACTGCAATGAAGACAGTGAGGATTTAA
GTCAAGTTGTTGATTCTTCAGGCTTAGAGGATGTGGTTAGTGGTAGAAGGTCAACTAAGGGAGAA
AGTCCCATGGTTGATGATTC
Found at i:1483353 original size:10 final size:10
Alignment explanation
Indices: 1483338--1483362 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1483328 TCTTTCTTTA
1483338 TTTTTTTATT
1 TTTTTTTATT
1483348 TTTTTTTATT
1 TTTTTTTATT
1483358 TTTTT
1 TTTTT
1483363 AAATTTTCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTATT
Found at i:1483369 original size:18 final size:18
Alignment explanation
Indices: 1483334--1483369 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1483324 GTTTTCTTTC
**
1483334 TTTATTTTTTTATTTTTT
1 TTTATTTTTTTAAATTTT
1483352 TTTATTTTTTTAAATTTT
1 TTTATTTTTTTAAATTTT
1483370 CATGGTTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTATTTTTTTAAATTTT
Found at i:1486723 original size:22 final size:20
Alignment explanation
Indices: 1486697--1486737 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1486687 CAAATATAAA
*
1486697 TTCATCTCATCTTGTATGTGGC
1 TTCATC-CATCTGGTA-GTGGC
1486719 TTCATCCATCTGGTAGTGG
1 TTCATCCATCTGGTAGTGG
1486738 AACATGTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 8 0.44
22 6 0.33
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.41
Consensus pattern (20 bp):
TTCATCCATCTGGTAGTGGC
Found at i:1494927 original size:162 final size:162
Alignment explanation
Indices: 1494660--1494984 Score: 607
Period size: 162 Copynumber: 2.0 Consensus size: 162
1494650 TGATTGTCAC
1494660 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
1 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
*
1494725 CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCGGTCTG
66 CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
1494790 GTTTTAAACACAT-ACATGTCTTTGAACACTCA
131 GTTTTAAACACATGA-ATGTCTTTGAACACTCA
1494822 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
1 TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
*
1494887 CTCTCCGTCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
66 CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
*
1494952 GTTTTAAGCACATGAATGTCTTTGAACACTCA
131 GTTTTAAACACATGAATGTCTTTGAACACTCA
1494984 T
1 T
1494985 TTTCGAATTC
Statistics
Matches: 159, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
162 158 0.99
163 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (162 bp):
TGCAAGCTTTGATGGACGCATTCGAACCTACCTCAATTACGGGTTACCAATTCGAGTATAAGAAC
CTCTCCATCCCTAAAGATACAGCAACACAACACATATACGAATATAGGTATAACTGTGCCGTCTG
GTTTTAAACACATGAATGTCTTTGAACACTCA
Found at i:1495912 original size:18 final size:17
Alignment explanation
Indices: 1495876--1495915 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
1495866 TAATAAAAAT
1495876 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
1495893 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
1495908 ATAATTTT
1 ATAATTTT
1495916 TAAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:1506916 original size:18 final size:18
Alignment explanation
Indices: 1506885--1506936 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1506875 TAAATTATAT
*
1506885 TAATCATATTAAAATGAACA
1 TAAT-ATATAAAAAT-AACA
*
1506905 T-ATATATAAAAATAATA
1 TAATATATAAAAATAACA
*
1506922 TAATATCTAAAAATA
1 TAATATATAAAAATA
1506937 TAAAATAAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 4 0.14
18 21 0.75
19 2 0.07
20 1 0.04
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.33
Consensus pattern (18 bp):
TAATATATAAAAATAACA
Found at i:1507050 original size:2 final size:2
Alignment explanation
Indices: 1507043--1507095 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1507033 AAGTAGGCTT
1507043 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1507085 TA TA TA TA TA T
1 TA TA TA TA TA T
1507096 TCTATTTTAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1509061 original size:17 final size:18
Alignment explanation
Indices: 1509036--1509069 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1509026 GCATTTGTAC
*
1509036 AAGT-TTTTTTAATAATG
1 AAGTATTTTATAATAATG
1509053 AAGTATTTTATAATAAT
1 AAGTATTTTATAATAAT
1509070 TTAACTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (18 bp):
AAGTATTTTATAATAATG
Found at i:1509787 original size:22 final size:23
Alignment explanation
Indices: 1509751--1509804 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 23
1509741 AAAAAAAAAG
*
1509751 CCTACT-TTTTTTTGTT-GTTTT
1 CCTACTGTTTTCTTGTTAGTTTT
*
1509772 CCTACTGTTTTCTTGTTATTTTT
1 CCTACTGTTTTCTTGTTAGTTTT
1509795 CC-ACTGTTTT
1 CCTACTGTTTT
1509805 GTTGAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 6 0.21
22 17 0.59
23 6 0.21
ACGTcount: A:0.07, C:0.19, G:0.09, T:0.65
Consensus pattern (23 bp):
CCTACTGTTTTCTTGTTAGTTTT
Found at i:1515029 original size:33 final size:33
Alignment explanation
Indices: 1514992--1515057 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1514982 AGCAGCCATT
*
1514992 GGAGGTCTCTCTGATAGTAGTGAAAGTAGGTGA
1 GGAGGTCTCTCCGATAGTAGTGAAAGTAGGTGA
*
1515025 GGAGGTCTCTCCGATAGTAGTTAAAGTAGGTGA
1 GGAGGTCTCTCCGATAGTAGTGAAAGTAGGTGA
1515058 TAGATGACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.27, C:0.11, G:0.35, T:0.27
Consensus pattern (33 bp):
GGAGGTCTCTCCGATAGTAGTGAAAGTAGGTGA
Found at i:1519831 original size:22 final size:22
Alignment explanation
Indices: 1519806--1519847 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1519796 TGCTTATGTT
* *
1519806 TTACTGTCATTTTGTTATTATA
1 TTACTATCATTTTATTATTATA
*
1519828 TTACTATTATTTTATTATTA
1 TTACTATCATTTTATTATTA
1519848 GTGTTTAGAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (22 bp):
TTACTATCATTTTATTATTATA
Found at i:1527871 original size:11 final size:11
Alignment explanation
Indices: 1527855--1527880 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1527845 ATTTATATTT
1527855 AAAAAAATTAA
1 AAAAAAATTAA
1527866 AAAAAAATTAA
1 AAAAAAATTAA
1527877 AAAA
1 AAAA
1527881 TTCTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (11 bp):
AAAAAAATTAA
Found at i:1527919 original size:10 final size:10
Alignment explanation
Indices: 1527851--1527927 Score: 54
Period size: 10 Copynumber: 7.8 Consensus size: 10
1527841 CAAAATTTAT
1527851 ATTTAAAAAA
1 ATTTAAAAAA
*
1527861 ATTAAAAAAA
1 ATTTAAAAAA
*
1527871 AATT-AAAAA
1 ATTTAAAAAA
1527880 ATTCTAAAAAA
1 ATT-TAAAAAA
* *
1527891 TATATAAAGAA
1 -ATTTAAAAAA
*
1527902 AGTT---AAA
1 ATTTAAAAAA
1527909 ATTTAAAAAA
1 ATTTAAAAAA
1527919 ATTCTAAAA
1 ATT-TAAAA
1527928 TAATAATTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 13
0.68 0.14 0.18
Matches are distributed among these distances:
7 5 0.10
9 7 0.14
10 20 0.40
11 16 0.32
12 2 0.04
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (10 bp):
ATTTAAAAAA
Found at i:1527919 original size:29 final size:28
Alignment explanation
Indices: 1527851--1527921 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
1527841 CAAAATTTAT
1527851 ATTTAAAAAAATTAAAAAAAAATTAAAAA
1 ATTTAAAAAAATTAAAAAAAAATT-AAAA
* *
1527880 ATTCT-AAAAAATATATAAAGAAAGTT-AAA
1 ATT-TAAAAAAAT-TA-AAAAAAAATTAAAA
1527909 ATTTAAAAAAATT
1 ATTTAAAAAAATT
1527922 CTAAAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
28 2 0.06
29 23 0.64
30 3 0.08
31 8 0.22
ACGTcount: A:0.68, C:0.01, G:0.03, T:0.28
Consensus pattern (28 bp):
ATTTAAAAAAATTAAAAAAAAATTAAAA
Found at i:1539282 original size:16 final size:17
Alignment explanation
Indices: 1539261--1539294 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1539251 TACTACTAAA
1539261 AATTTA-TTTTTACTTT
1 AATTTAGTTTTTACTTT
*
1539277 AATTTAGTTTTTATTTT
1 AATTTAGTTTTTACTTT
1539294 A
1 A
1539295 TTTTGGGGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (17 bp):
AATTTAGTTTTTACTTT
Found at i:1549986 original size:62 final size:61
Alignment explanation
Indices: 1549896--1550019 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 61
1549886 GGGGTTTGAA
* * *
1549896 TTTTTTTTTGTATAAGTTAGTCCCTGAACTTGGTAATTGTTCCCA-GATTAGGGCTTGAACT
1 TTTTTTTTTGTATAAGTAAGTCCCTGAACTTGGTAACTATTCCCACG-TTAGGGCTTGAACT
* *
1549957 TTTTTTTTCTGT-TCAAGTAAGTCTCTGAACTTGGTAACTATTCCCACGTTAGGGCTTTAACT
1 TTTTTTTT-TGTAT-AAGTAAGTCCCTGAACTTGGTAACTATTCCCACGTTAGGGCTTGAACT
1550019 T
1 T
1550020 AAAGGTTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
61 9 0.16
62 45 0.82
63 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.44
Consensus pattern (61 bp):
TTTTTTTTTGTATAAGTAAGTCCCTGAACTTGGTAACTATTCCCACGTTAGGGCTTGAACT
Found at i:1553746 original size:33 final size:33
Alignment explanation
Indices: 1553704--1553771 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
1553694 ACAAAACATA
* *
1553704 TACGAAGTTCTCGAATCCTAACTGTTGACCTAG
1 TACGAAGTTCTCGAATCCTAACTCTTGACCAAG
*
1553737 TACGAAGTTCTCGAATTCTAACTCTTGACCAAG
1 TACGAAGTTCTCGAATCCTAACTCTTGACCAAG
1553770 TA
1 TA
1553772 GCATTGGGCG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (33 bp):
TACGAAGTTCTCGAATCCTAACTCTTGACCAAG
Found at i:1555947 original size:123 final size:122
Alignment explanation
Indices: 1555702--1555947 Score: 483
Period size: 123 Copynumber: 2.0 Consensus size: 122
1555692 TGTCAAACAG
1555702 TTGTTACTGTGTCTTAATTTGGGCTCAAAGAAGTACTTATGAGATAGAGCTCTTTCGGAGTTGTA
1 TTGTTACTGTGTCTTAATTTGGGCTCAAAGAAGTACTTATGAGATAGAGCTCTTTCGGAGTTGTA
1555767 ATCTATGAAGACCTTGTTTGCCTTCCACCTGGGTTGTATTCAAAAAAAAAATAAAGT
66 ATCTATGAAGACCTTGTTTGCCTTCCACCTGGGTTGTATTCAAAAAAAAAATAAAGT
1555824 TTGTTACTGTGTCTTAATTTGGGCTCAAAGAAGTACTTATGAGATAGAGCTCTTTCGGGAGTTGT
1 TTGTTACTGTGTCTTAATTTGGGCTCAAAGAAGTACTTATGAGATAGAGCTCTTTC-GGAGTTGT
1555889 AATCTATGAAGACCTTGTTTGCCTTCCACCTGGGTTGTATTCAAAAAAAAAATAAAGT
65 AATCTATGAAGACCTTGTTTGCCTTCCACCTGGGTTGTATTCAAAAAAAAAATAAAGT
1555947 T
1 T
1555948 CAATGTTTTA
Statistics
Matches: 123, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
122 56 0.46
123 67 0.54
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (122 bp):
TTGTTACTGTGTCTTAATTTGGGCTCAAAGAAGTACTTATGAGATAGAGCTCTTTCGGAGTTGTA
ATCTATGAAGACCTTGTTTGCCTTCCACCTGGGTTGTATTCAAAAAAAAAATAAAGT
Found at i:1558627 original size:15 final size:15
Alignment explanation
Indices: 1558607--1558657 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
1558597 AGCCCCCAGA
1558607 ACCACCGAAGGGGTC
1 ACCACCGAAGGGGTC
*
1558622 ACCACCGAAGAGGTC
1 ACCACCGAAGGGGTC
1558637 ACCACCGAAGGGGTC
1 ACCACCGAAGGGGTC
1558652 ACCACC
1 ACCACC
1558658 AAAATTGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.29, C:0.37, G:0.27, T:0.06
Consensus pattern (15 bp):
ACCACCGAAGGGGTC
Found at i:1562008 original size:3 final size:3
Alignment explanation
Indices: 1562000--1562037 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
1561990 TTACACATAA
*
1562000 AAC AAC AAC AAC AGC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1562038 TAATGACAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.32, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1568929 original size:24 final size:24
Alignment explanation
Indices: 1568902--1568958 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
1568892 ATTTTTATGA
*
1568902 TAATAAAATATAATTTTATTATTT
1 TAATAAAATATAATTTTATAATTT
** *
1568926 TAATAATTTATATTTTTATAATTT
1 TAATAAAATATAATTTTATAATTT
1568950 T--TAAAATAT
1 TAATAAAATAT
1568959 TAAATTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
22 6 0.22
24 21 0.78
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TAATAAAATATAATTTTATAATTT
Found at i:1568941 original size:15 final size:16
Alignment explanation
Indices: 1568911--1568949 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
1568901 ATAATAAAAT
1568911 ATAATTTTATTATTTTA
1 ATAA-TTTATTATTTTA
*
1568928 ATAATTTA-TATTTTT
1 ATAATTTATTATTTTA
1568943 ATAATTT
1 ATAATTT
1568950 TTAAAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.62
16 4 0.19
17 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATAATTTATTATTTTA
Found at i:1569138 original size:21 final size:22
Alignment explanation
Indices: 1569112--1569193 Score: 68
Period size: 21 Copynumber: 4.0 Consensus size: 22
1569102 GGCCCATTTT
1569112 TATTTTAAAAAT-TTTAAAAAA
1 TATTTTAAAAATATTTAAAAAA
*
1569133 TATTTTAAAAATATTT--TAAA
1 TATTTTAAAAATATTTAAAAAA
* *
1569153 -A--TTAAAAAAATTAAAAAAA
1 TATTTTAAAAATATTTAAAAAA
* *
1569172 GTATTTTAAAATTATTTTAAAA
1 -TATTTTAAAAATATTTAAAAA
1569194 TAAAAAAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
17 10 0.22
19 4 0.09
20 3 0.07
21 13 0.28
22 3 0.07
23 13 0.28
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.41
Consensus pattern (22 bp):
TATTTTAAAAATATTTAAAAAA
Found at i:1569142 original size:11 final size:11
Alignment explanation
Indices: 1569112--1569153 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
1569102 GGCCCATTTT
1569112 TATTTTAAAAA
1 TATTTTAAAAA
*
1569123 T-TTTAAAAAA
1 TATTTTAAAAA
1569133 TATTTTAAAAA
1 TATTTTAAAAA
1569144 TATTTTAAAA
1 TATTTTAAAA
1569154 TTAAAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:1569177 original size:40 final size:39
Alignment explanation
Indices: 1569116--1569240 Score: 171
Period size: 39 Copynumber: 3.2 Consensus size: 39
1569106 CATTTTTATT
**
1569116 TTAAAAATTTTAAAAAA-TATTTTAAAAATATTTTAAAA
1 TTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
*
1569154 TTAAAAAAATTAAAAAAAGTATTTTAAAATTATTTTAAAA
1 TTAAAAAAATT-AAAAAAGTATTTTAAAAATATTTTAAAA
* * *
1569194 TAAAAAAAATTAAAAAAGTATGTAAAAAATATTTTAAAA
1 TTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
*
1569233 TTTAAAAA
1 TTAAAAAA
1569241 TAAATATATT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
38 9 0.12
39 37 0.49
40 30 0.39
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (39 bp):
TTAAAAAAATTAAAAAAGTATTTTAAAAATATTTTAAAA
Found at i:1569194 original size:11 final size:11
Alignment explanation
Indices: 1569111--1569194 Score: 54
Period size: 11 Copynumber: 8.1 Consensus size: 11
1569101 CGGCCCATTT
1569111 TTATTTTAAAA
1 TTATTTTAAAA
1569122 --ATTTTAAAAA
1 TTATTTT-AAAA
*
1569132 ATATTTTAAAA
1 TTATTTTAAAA
*
1569143 ATATTTTAAAA
1 TTATTTTAAAA
**
1569154 TTA--AAAAAA
1 TTATTTTAAAA
**
1569163 TTA--AAAAAA
1 TTATTTTAAAA
*
1569172 GTATTTTAAAA
1 TTATTTTAAAA
1569183 TTATTTTAAAA
1 TTATTTTAAAA
1569194 T
1 T
1569195 AAAAAAAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
9 20 0.33
10 4 0.07
11 32 0.52
12 5 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
TTATTTTAAAA
Found at i:1570421 original size:19 final size:19
Alignment explanation
Indices: 1570397--1570433 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1570387 AAAAATTAAA
1570397 TTTTAATAATACCATTTTT
1 TTTTAATAATACCATTTTT
1570416 TTTTAATAATACCATTTT
1 TTTTAATAATACCATTTT
1570434 ACTTGTAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTAATAATACCATTTTT
Found at i:1576919 original size:125 final size:124
Alignment explanation
Indices: 1576706--1577045 Score: 452
Period size: 125 Copynumber: 2.7 Consensus size: 124
1576696 GGTCCGAGAA
* * * *
1576706 GAAATAATTTTATTTGACCTTTCTGAGCAAATAGTATAAAATT-ACATATAGCAGGATGCTATTT
1 GAAATAATTTTTTTTGACCTTTCTGAGCAAATAGTAT-AAATTCGCTTCTAGCAGGATGCTATTT
* * * **
1576770 GAGAAGAAATTT-TGAAATTGCGCCCTCATGGATGCGCTCTTGCTACAGTAGGTCATGGAT
65 GAGAAG-AATTTGTAAAATCGCGCCCTCATGGACGCGCAATTGCTACAGTAGGTCATGGAT
*
1576830 GAAATAAATTTTTTTTGACGTTTCTGAGCAAATAGTATAAATTCGCTTCTAGCAGGATGCTATTT
1 GAAAT-AATTTTTTTTGACCTTTCTGAGCAAATAGTATAAATTCGCTTCTAGCAGGATGCTATTT
* * * * *
1576895 GAAAAGAATTTGTAAAATCCCGCCCTCGTGGACGCGGAATTGCTACAGTAGGTCGTGGAT
65 GAGAAGAATTTGTAAAATCGCGCCCTCATGGACGCGCAATTGCTACAGTAGGTCATGGAT
* *
1576955 GAAATAA-TTTTTTTGACCTTTCTGAGCAAATAATATAAAATCGCTTCTAGCAGGATGCTATTTG
1 GAAATAATTTTTTTTGACCTTTCTGAGCAAATAGTATAAATTCGCTTCTAGCAGGATGCTATTTG
* *
1577019 AGAATATTTTGTGAAAATCGCGCCCTC
66 AGAAGAATTTGT-AAAATCGCGCCCTC
1577046 GGGGACGCAC
Statistics
Matches: 190, Mismatches: 22, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
123 63 0.33
124 30 0.16
125 97 0.51
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (124 bp):
GAAATAATTTTTTTTGACCTTTCTGAGCAAATAGTATAAATTCGCTTCTAGCAGGATGCTATTTG
AGAAGAATTTGTAAAATCGCGCCCTCATGGACGCGCAATTGCTACAGTAGGTCATGGAT
Found at i:1577336 original size:21 final size:20
Alignment explanation
Indices: 1577308--1577410 Score: 80
Period size: 21 Copynumber: 4.8 Consensus size: 20
1577298 CGTAAAAGAA
1577308 TTAGGTTAGGGTTTTTAAGT
1 TTAGGTTAGGGTTTTTAAGT
* *
1577328 TTAGGGTTAGGGTTTTCAACTT
1 TTA-GGTTAGGGTTTTTAA-GT
* *
1577350 AATTATGTTATGGTTTTTAAGT
1 --TTAGGTTAGGGTTTTTAAGT
* *
1577372 TTAAGGTTAGGGTTTTCAACTT
1 TT-AGGTTAGGGTTTTTAA-GT
1577394 AATTAGGTTAGGGTTTT
1 --TTAGGTTAGGGTTTT
1577411 CAATTTTTAT
Statistics
Matches: 65, Mismatches: 10, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
20 5 0.08
21 27 0.42
22 3 0.05
23 25 0.38
24 5 0.08
ACGTcount: A:0.22, C:0.04, G:0.25, T:0.49
Consensus pattern (20 bp):
TTAGGTTAGGGTTTTTAAGT
Found at i:1577364 original size:23 final size:23
Alignment explanation
Indices: 1577306--1577413 Score: 109
Period size: 23 Copynumber: 4.9 Consensus size: 23
1577296 TTCGTAAAAG
* *
1577306 AATTAGGTTAGGGTTTTTAA-GT
1 AATTAGGTTAGGGTTTTCAACTT
1577328 --TTAGGGTTAGGGTTTTCAACTT
1 AATTA-GGTTAGGGTTTTCAACTT
* * * *
1577350 AATTATGTTATGGTTTTTAAGTT
1 AATTAGGTTAGGGTTTTCAACTT
*
1577373 --TAAGGTTAGGGTTTTCAACTT
1 AATTAGGTTAGGGTTTTCAACTT
1577394 AATTAGGTTAGGGTTTTCAA
1 AATTAGGTTAGGGTTTTCAA
1577414 TTTTTATCAC
Statistics
Matches: 68, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
20 3 0.04
21 30 0.44
22 1 0.01
23 31 0.46
24 3 0.04
ACGTcount: A:0.25, C:0.05, G:0.24, T:0.46
Consensus pattern (23 bp):
AATTAGGTTAGGGTTTTCAACTT
Found at i:1577369 original size:44 final size:44
Alignment explanation
Indices: 1577306--1577410 Score: 183
Period size: 44 Copynumber: 2.4 Consensus size: 44
1577296 TTCGTAAAAG
*
1577306 AATTAGGTTAGGGTTTTTAAGTTTAGGGTTAGGGTTTTCAACTT
1 AATTAGGTTAGGGTTTTTAAGTTTAAGGTTAGGGTTTTCAACTT
* *
1577350 AATTATGTTATGGTTTTTAAGTTTAAGGTTAGGGTTTTCAACTT
1 AATTAGGTTAGGGTTTTTAAGTTTAAGGTTAGGGTTTTCAACTT
1577394 AATTAGGTTAGGGTTTT
1 AATTAGGTTAGGGTTTT
1577411 CAATTTTTAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.24, C:0.04, G:0.25, T:0.48
Consensus pattern (44 bp):
AATTAGGTTAGGGTTTTTAAGTTTAAGGTTAGGGTTTTCAACTT
Found at i:1577450 original size:25 final size:25
Alignment explanation
Indices: 1577415--1577575 Score: 174
Period size: 25 Copynumber: 6.6 Consensus size: 25
1577405 GGTTTTCAAT
*
1577415 TTTTATCACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
*
1577440 TTTTATTACATCATATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
1577465 TTTTATTACATCAAATAAACTTCTA
1 TTTTATTACATCAAATAAACTTCTA
1577490 TTTTATTACATCAAAT-AA-TATC-A
1 TTTTATTACATCAAATAAACT-TCTA
** * * * *
1577513 --AAATAAC-TCAAAAAAATTTCAA
1 TTTTATTACATCAAATAAACTTCTA
1577535 TTTTTATTACATC-AATAAAACTTCTA
1 -TTTTATTACATCAAAT-AAACTTCTA
1577561 TTTTATTACATCAAA
1 TTTTATTACATCAAA
1577576 CAAAGTTTAA
Statistics
Matches: 113, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
20 5 0.04
21 8 0.07
22 2 0.02
23 2 0.02
24 4 0.04
25 81 0.72
26 11 0.10
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.42
Consensus pattern (25 bp):
TTTTATTACATCAAATAAACTTCTA
Found at i:1578046 original size:18 final size:18
Alignment explanation
Indices: 1578008--1578047 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1577998 GACTCGGAAA
*
1578008 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGAT
* *
1578026 AGGATACATGTAATGGAT
1 AGGATACATATAAGGGAT
1578044 AGGA
1 AGGA
1578048 AATGCACCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.05, G:0.30, T:0.25
Consensus pattern (18 bp):
AGGATACATATAAGGGAT
Found at i:1578902 original size:20 final size:20
Alignment explanation
Indices: 1578865--1578902 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1578855 TTTATTTTTA
*
1578865 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
1578885 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
1578903 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:1579893 original size:51 final size:51
Alignment explanation
Indices: 1579836--1579956 Score: 172
Period size: 51 Copynumber: 2.4 Consensus size: 51
1579826 TTTAAAAAAA
* * * *
1579836 GAAATTGAGAGCAAATTGAAATTAAATATGGGTTTGA-GAGATTTTTGGAAT
1 GAAATTGAGAGAAAATTGAAATTAAATATGGATTT-ATGAGAATTTTGGAAG
* *
1579887 GAAATTGAGAGGAGATTGAAATTAAATATGGATTTATGAGAATTTTGGAAG
1 GAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGGAAG
1579938 GAAATTGAGAGAAAATTGA
1 GAAATTGAGAGAAAATTGA
1579957 GAGGAAATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.02
51 61 0.98
ACGTcount: A:0.42, C:0.01, G:0.26, T:0.31
Consensus pattern (51 bp):
GAAATTGAGAGAAAATTGAAATTAAATATGGATTTATGAGAATTTTGGAAG
Found at i:1579955 original size:11 final size:11
Alignment explanation
Indices: 1579936--1579981 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
1579926 GAATTTTGGA
1579936 AGGAAATTGAG
1 AGGAAATTGAG
*
1579947 AGAAAATTGAG
1 AGGAAATTGAG
1579958 AGGAAATTGAG
1 AGGAAATTGAG
1579969 AGGAAATATGAG
1 AGGAAAT-TGAG
1579981 A
1 A
1579982 TAGGATTTGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
11 27 0.84
12 5 0.16
ACGTcount: A:0.50, C:0.00, G:0.33, T:0.17
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:1592568 original size:2 final size:2
Alignment explanation
Indices: 1592561--1592586 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1592551 AAAACTTCAA
1592561 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
1592587 TAAAATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1593726 original size:24 final size:25
Alignment explanation
Indices: 1593694--1593740 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
1593684 ACCCTAAATA
1593694 TGTCAGTATTAATTCTT-TTGAAGG
1 TGTCAGTATTAATTCTTGTTGAAGG
*
1593718 TGTCAGTATTAATTTTTGTTGAA
1 TGTCAGTATTAATTCTTGTTGAA
1593741 CCTACAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.26, C:0.06, G:0.19, T:0.49
Consensus pattern (25 bp):
TGTCAGTATTAATTCTTGTTGAAGG
Found at i:1594151 original size:14 final size:14
Alignment explanation
Indices: 1594119--1594145 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1594109 GATTATCATT
1594119 CATTAATCAAAATA
1 CATTAATCAAAATA
1594133 CATTAATCAAAAT
1 CATTAATCAAAAT
1594146 TGATTAGTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (14 bp):
CATTAATCAAAATA
Found at i:1597068 original size:32 final size:32
Alignment explanation
Indices: 1597019--1597086 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
1597009 GTATATGAAT
*
1597019 ATTTTATATTTGAAATTTATTTAATAT-CATTC
1 ATTTGATATTTGAAATTT-TTTAATATACATTC
* * *
1597051 ATTTGATATTTGTAATTTTTTTATATACATTT
1 ATTTGATATTTGAAATTTTTTAATATACATTC
1597083 ATTT
1 ATTT
1597087 TTTTTAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 7 0.23
32 24 0.77
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (32 bp):
ATTTGATATTTGAAATTTTTTAATATACATTC
Found at i:1613578 original size:284 final size:284
Alignment explanation
Indices: 1613056--1613607 Score: 883
Period size: 284 Copynumber: 1.9 Consensus size: 284
1613046 GTTTCCCATC
* * * *
1613056 CTAGTCTTGTTTACTTAACAAATACGGCGATCAAAGCCTGATATATTGGAATAAGCATAGAATAA
1 CTAGCCTTGTTTACTCAACAAATACGACGAACAAAGCCTGATATATTGGAATAAGCATAGAATAA
* *
1613121 GAATCTAAACCGCTAGTTATAGCCGTTGTAACGACCGACAATTAAATAAGTCTACCGATCAAATT
66 GAATCTAAACCGATAGTTATAGCCGTTGTAACGACCGACAATTAAATAAGTCCACCGATCAAATT
* *
1613186 TTCAACAAGCATCTTACTCACATATCAATCGGTCATACCGAAAATGCATGATCTACTGCCATAAC
131 TTCAACAAGCATCTTACTCACATATCAATCGATCATACAGAAAATGCATGATCTACTGCCATAAC
1613251 CACTTATAAACCTCAACACGATACATAATCTAAGTTCTTAATTAGGCCAATCAACACTAATTGCC
196 CACTTATAAACCTCAACACGATACATAATCTAAGTTCTTAATTAGGCCAATCAACACTAATTGCC
1613316 AACACATAATCTATAAGTCCTATT
261 AACACATAATCTATAAGTCCTATT
* *
1613340 CTAGCCTTGTTTACTCAA-AATATATGACGAACAAAGCCTGATATGTTGGAATAAGCATAGAATA
1 CTAGCCTTGTTTACTCAACAA-ATACGACGAACAAAGCCTGATATATTGGAATAAGCATAGAATA
* * *
1613404 AGAATCTAAACTGATAGTTATAGCCGTTGTAACGGCCGACAATTAAATAAGTCCACTGATCAAAT
65 AGAATCTAAACCGATAGTTATAGCCGTTGTAACGACCGACAATTAAATAAGTCCACCGATCAAAT
* * *
1613469 TTTCAACAAGCATCTTACTCACATATCGATTGATCATA-AGAAAAATGCATGATCTACTGCCGTA
130 TTTCAACAAGCATCTTACTCACATATCAATCGATCATACAG-AAAATGCATGATCTACTGCCATA
* ** * *
1613533 ACCACTTATAGACCTTGACACGATACATAATCTAGGTTTTTAATTAGGCCAATCAACACTAATTG
194 ACCACTTATAAACCTCAACACGATACATAATCTAAGTTCTTAATTAGGCCAATCAACACTAATTG
1613598 CCAACACATA
259 CCAACACATA
1613608 TCTGAGTTCT
Statistics
Matches: 245, Mismatches: 21, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
283 3 0.01
284 242 0.99
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (284 bp):
CTAGCCTTGTTTACTCAACAAATACGACGAACAAAGCCTGATATATTGGAATAAGCATAGAATAA
GAATCTAAACCGATAGTTATAGCCGTTGTAACGACCGACAATTAAATAAGTCCACCGATCAAATT
TTCAACAAGCATCTTACTCACATATCAATCGATCATACAGAAAATGCATGATCTACTGCCATAAC
CACTTATAAACCTCAACACGATACATAATCTAAGTTCTTAATTAGGCCAATCAACACTAATTGCC
AACACATAATCTATAAGTCCTATT
Found at i:1618029 original size:14 final size:15
Alignment explanation
Indices: 1618006--1618046 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
1617996 AACGTAAGTA
1618006 ATTAAAATATAATAT
1 ATTAAAATATAATAT
*
1618021 -TTCAAATATAA-AT
1 ATTAAAATATAATAT
1618034 ATTAAAATATAAT
1 ATTAAAATATAAT
1618047 CTAAAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAAATATAATAT
Found at i:1621468 original size:14 final size:14
Alignment explanation
Indices: 1621449--1621476 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1621439 TCAAATTCAA
1621449 TAGTTTATGTGCTC
1 TAGTTTATGTGCTC
1621463 TAGTTTATGTGCTC
1 TAGTTTATGTGCTC
1621477 GGCCACTCGG
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:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (14 bp):
TAGTTTATGTGCTC
Found at i:1629459 original size:4 final size:4
Alignment explanation
Indices: 1629450--1629544 Score: 190
Period size: 4 Copynumber: 23.8 Consensus size: 4
1629440 ATCAATTTTA
1629450 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1629498 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA
1629545 CAGACACGCA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 91 1.00
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1637963 original size:21 final size:20
Alignment explanation
Indices: 1637920--1637963 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
1637910 ATAAATATTT
* *
1637920 TTTAACAAATTGAAAATATA
1 TTTAAAAAATTGAAAAAATA
1637940 TTTAAAAAATTGAAATAAATA
1 TTTAAAAAATTGAAA-AAATA
1637961 TTT
1 TTT
1637964 CCCAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTAAAAAATTGAAAAAATA
Found at i:1640328 original size:31 final size:30
Alignment explanation
Indices: 1640290--1640347 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
1640280 ATATTAATAT
1640290 TTAATAGTTGAGTAACTAAAATGAAAAACAA
1 TTAATAGTTGAGTAACTAAAAT-AAAAACAA
*
1640321 TTAATAGTTGAGTGACTAAAATAAAAA
1 TTAATAGTTGAGTAACTAAAATAAAAA
1640348 GAACTGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (30 bp):
TTAATAGTTGAGTAACTAAAATAAAAACAA
Found at i:1646087 original size:14 final size:14
Alignment explanation
Indices: 1646068--1646095 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1646058 CAATTTTTAA
1646068 ATTTTAGTGAAATT
1 ATTTTAGTGAAATT
1646082 ATTTTAGTGAAATT
1 ATTTTAGTGAAATT
1646096 GCTAGCTTTT
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:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
ATTTTAGTGAAATT
Found at i:1652519 original size:24 final size:24
Alignment explanation
Indices: 1652479--1652525 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1652469 AATTAATAAC
*
1652479 GATAAAATTATACTTTAATTTTTT
1 GATAAAATTATAATTTAATTTTTT
1652503 GATAAATATT-TAATTTAATTTTT
1 GATAAA-ATTATAATTTAATTTTT
1652526 AAAATTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (24 bp):
GATAAAATTATAATTTAATTTTTT
Found at i:1657989 original size:2 final size:2
Alignment explanation
Indices: 1657982--1658012 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1657972 TAATCTCGAA
1657982 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1658013 AGATGTCACC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1659438 original size:22 final size:22
Alignment explanation
Indices: 1659413--1659454 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1659403 CAAACGTAAC
*
1659413 AACAAAATAGTGAAATGATAAT
1 AACAAAATAATGAAATGATAAT
*
1659435 AACATAATAATGAAATGATA
1 AACAAAATAATGAAATGATA
1659455 GCAAAACAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.05, G:0.12, T:0.24
Consensus pattern (22 bp):
AACAAAATAATGAAATGATAAT
Found at i:1659741 original size:10 final size:10
Alignment explanation
Indices: 1659694--1659743 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
1659684 TTATATATAG
*
1659694 ATATATATAT
1 ATATACATAT
1659704 ATATACATAT
1 ATATACATAT
1659714 ATAT--ATAT
1 ATATACATAT
*
1659722 ATATATATAT
1 ATATACATAT
*
1659732 ATAAACATAT
1 ATATACATAT
1659742 AT
1 AT
1659744 TTCATCCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 8 0.23
10 27 0.77
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (10 bp):
ATATACATAT
Found at i:1659741 original size:12 final size:12
Alignment explanation
Indices: 1659686--1659743 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
1659676 CTATAATTTT
* *
1659686 ATATATAGATAT
1 ATATATATATAA
1659698 ATATATATATACA
1 ATATATATATA-A
*
1659711 TATATATATATAT
1 -ATATATATATAA
1659724 ATATATATATAA
1 ATATATATATAA
*
1659736 ACATATAT
1 ATATATAT
1659744 TTCATCCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
12 28 0.72
14 11 0.28
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (12 bp):
ATATATATATAA
Found at i:1659743 original size:2 final size:2
Alignment explanation
Indices: 1659685--1659734 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
1659675 TCTATAATTT
* *
1659685 TA TA TA TA GA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1659727 TA TA TA TA
1 TA TA TA TA
1659735 AACATATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1664635 original size:31 final size:31
Alignment explanation
Indices: 1664597--1664659 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1664587 ATGTTTCCTA
*
1664597 ACAAATTGAAAATGTATTAAAATAAATATTT
1 ACAAATTGAAAATGCATTAAAATAAATATTT
1664628 ACAAATTGAAAATGCATTAAAATAAATATTT
1 ACAAATTGAAAATGCATTAAAATAAATATTT
1664659 A
1 A
1664660 TACTTAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.56, C:0.05, G:0.06, T:0.33
Consensus pattern (31 bp):
ACAAATTGAAAATGCATTAAAATAAATATTT
Found at i:1664988 original size:30 final size:30
Alignment explanation
Indices: 1664954--1665016 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
1664944 ACTTAACAAG
1664954 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
* *
1664984 CAAATGCCTTTAAAATATTAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
1665014 CAA
1 CAA
1665017 TAAAATAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:1666068 original size:18 final size:17
Alignment explanation
Indices: 1666045--1666079 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1666035 CATCGTTTAA
1666045 ATTTAAATATTATTTTTT
1 ATTTAAA-ATTATTTTTT
*
1666063 ATTTAAACTTATTTTTT
1 ATTTAAAATTATTTTTT
1666080 GAGATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTAAAATTATTTTTT
Found at i:1666521 original size:18 final size:18
Alignment explanation
Indices: 1666498--1666540 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
1666488 CACGGAGGAA
1666498 GAAGAAGAAGAACCAGAG
1 GAAGAAGAAGAACCAGAG
*
1666516 GAAGAAGAGGAACCAGAG
1 GAAGAAGAAGAACCAGAG
1666534 GAAGAAG
1 GAAGAAG
1666541 GAGTTCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.37, T:0.00
Consensus pattern (18 bp):
GAAGAAGAAGAACCAGAG
Found at i:1673263 original size:29 final size:30
Alignment explanation
Indices: 1673229--1673287 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
1673219 TTTGGCCTAA
* *
1673229 TGTGTAATTTTGTAC-TTAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
1673258 TGTGTAATTTTATACATAAAATTTTGATTT
1 TGTGTAATTTTATACATAAAATTTTGATTT
1673288 GATCCAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 14 0.52
30 13 0.48
ACGTcount: A:0.29, C:0.03, G:0.12, T:0.56
Consensus pattern (30 bp):
TGTGTAATTTTATACATAAAATTTTGATTT
Found at i:1673654 original size:2 final size:2
Alignment explanation
Indices: 1673649--1673680 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1673639 ATTAAAAAAG
1673649 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1673681 AGTAGGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1676742 original size:25 final size:25
Alignment explanation
Indices: 1676690--1676742 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
1676680 AGAAAATATC
*
1676690 ATTAAAATAACATAAAAAAACAATT
1 ATTAAAATAACATAAAAAAACAAAT
1676715 ATTAAAATAACAT-AAAAAACAACAT
1 ATTAAAATAACATAAAAAAACAA-AT
1676740 ATT
1 ATT
1676743 TTTTTTGTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.66, C:0.09, G:0.00, T:0.25
Consensus pattern (25 bp):
ATTAAAATAACATAAAAAAACAAAT
Found at i:1677651 original size:112 final size:109
Alignment explanation
Indices: 1677525--1677796 Score: 357
Period size: 112 Copynumber: 2.5 Consensus size: 109
1677515 TTTTTTTCTT
*
1677525 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACAAAAAAAATAAAAAAAAAATAATTCTGGGTG
1 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAAAATAATTCTGGGTG
*
1677590 CTGGCCTGTCAATGGCCTGCACCCAGTACAAAATTTAAAAAAAAAT-C
66 CTGGCCTGTCAATGGCCGGCACCCAGTA-AAAA---AAAAAAAAATAC
* * *** * ** *
1677637 TTTTTTTTCGTGTCAGAGTCAAATATAAATTTACGAAAAAAATTTTAAAAAATTTTTTTTGGGTG
1 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAAAATAATTCTGGGTG
** ***
1677702 CTGGCCTGTCAATGGCCGGCACCCAGTAGTAAAAAAAATTTTAC
66 CTGGCCTGTCAATGGCCGGCACCCAGTAAAAAAAAAAAAAATAC
1677746 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAA
1 TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAA
1677797 TGTGTTAGAT
Statistics
Matches: 138, Mismatches: 21, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
108 7 0.05
109 47 0.34
111 2 0.01
112 82 0.59
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (109 bp):
TTTTTTTTCGTGTCAGAGTCAGATATAAATATACGAAAAAAATAAAAAAAAAATAATTCTGGGTG
CTGGCCTGTCAATGGCCGGCACCCAGTAAAAAAAAAAAAAATAC
Found at i:1677898 original size:29 final size:29
Alignment explanation
Indices: 1677866--1677954 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 29
1677856 GATGTAGAAA
1677866 AAAAAATTTAAAATAAATTAGATTGAATG
1 AAAAAATTTAAAATAAATTAGATTGAATG
*** * *
1677895 -AAAAA---AAAATGTGTTAGA-TGTAGG
1 AAAAAATTTAAAATAAATTAGATTGAATG
* *
1677919 AAAAAAATTTGAAATAAATGAGATTGAATG
1 -AAAAAATTTAAAATAAATTAGATTGAATG
1677949 AAAAAA
1 AAAAAA
1677955 AATAGGTGTT
Statistics
Matches: 42, Mismatches: 12, Indels: 12
0.64 0.18 0.18
Matches are distributed among these distances:
24 4 0.10
25 10 0.24
26 5 0.12
28 5 0.12
29 14 0.33
30 4 0.10
ACGTcount: A:0.58, C:0.00, G:0.16, T:0.26
Consensus pattern (29 bp):
AAAAAATTTAAAATAAATTAGATTGAATG
Found at i:1677901 original size:55 final size:54
Alignment explanation
Indices: 1677789--1677997 Score: 307
Period size: 54 Copynumber: 3.9 Consensus size: 54
1677779 CGAAAAAAAT
*
1677789 AAAAAAAATGTGTTAGATGTAGGAAAAAAATTTGAAAT-AATGAGATTGAATGA
1 AAAAAAAATGTGTTAGATGTAGAAAAAAAATTTGAAATAAATGAGATTGAATGA
* *
1677842 AAAAAAAA-GTGTTAGATGTAGAAAAAAAAATTTAAAATAAATTAGATTGAATGA
1 AAAAAAAATGTGTTAGATGTAG-AAAAAAAATTTGAAATAAATGAGATTGAATGA
*
1677896 AAAAAAAATGTGTTAGATGTAGGAAAAAAATTTGAAATAAATGAGATTGAATGA
1 AAAAAAAATGTGTTAGATGTAGAAAAAAAATTTGAAATAAATGAGATTGAATGA
* * *
1677950 AAAAAAATAGGTGTTAGATGTATG-AAATAAATTTGAAATCAATGAGAT
1 AAAAAAA-ATGTGTTAGATGTA-GAAAAAAAATTTGAAATAAATGAGAT
1677998 AAAATTTGAA
Statistics
Matches: 142, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
52 13 0.09
53 22 0.15
54 58 0.41
55 48 0.34
56 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (54 bp):
AAAAAAAATGTGTTAGATGTAGAAAAAAAATTTGAAATAAATGAGATTGAATGA
Found at i:1677994 original size:20 final size:21
Alignment explanation
Indices: 1677971--1678009 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1677961 TGTTAGATGT
1677971 ATGAAAT-AAATTTGAAATCA
1 ATGAAATAAAATTTGAAATCA
*
1677991 ATGAGATAAAATTTGAAAT
1 ATGAAATAAAATTTGAAAT
1678010 AAAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (21 bp):
ATGAAATAAAATTTGAAATCA
Found at i:1680046 original size:18 final size:17
Alignment explanation
Indices: 1680009--1680047 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
1679999 TTAAAATGTT
* *
1680009 AAATTAAAAATATTATA
1 AAATTAAAAATATAAAA
1680026 AAATTATAAAATATAAAA
1 AAATTA-AAAATATAAAA
1680044 AAAT
1 AAAT
1680048 CCCAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATTAAAAATATAAAA
Found at i:1680913 original size:31 final size:31
Alignment explanation
Indices: 1680873--1680933 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1680863 TCTTGAATTT
* *
1680873 GACACATTTTCCTAATTTGGTACCTAAACTA
1 GACAAATTTTCCTAAGTTGGTACCTAAACTA
* *
1680904 GACAAATTTTCTTAAGTTGGTACTTAAACT
1 GACAAATTTTCCTAAGTTGGTACCTAAACT
1680934 GTTTGAGGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (31 bp):
GACAAATTTTCCTAAGTTGGTACCTAAACTA
Found at i:1681551 original size:4 final size:4
Alignment explanation
Indices: 1681542--1681567 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1681532 TTAGTTTTAG
1681542 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
1681568 GACAATAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:1681826 original size:31 final size:30
Alignment explanation
Indices: 1681789--1681883 Score: 90
Period size: 31 Copynumber: 3.2 Consensus size: 30
1681779 AAAAAAAAAC
1681789 TTAGGTACCAAATTAGGAAAAAATGTCAAGT
1 TTAGGTACCAAATTAGGAAAAAATGTCAA-T
* * * *
1681820 TCAGGTATCAAATTGGGGAAAAA----AAT
1 TTAGGTACCAAATTAGGAAAAAATGTCAAT
* *
1681846 TTAGGTACCAAATTAAGAAAAATTGTCAAAT
1 TTAGGTACCAAATTAGGAAAAAATGTC-AAT
1681877 TTAGGTA
1 TTAGGTA
1681884 TCGAATTGAG
Statistics
Matches: 49, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
26 18 0.37
27 2 0.04
31 29 0.59
ACGTcount: A:0.45, C:0.08, G:0.19, T:0.27
Consensus pattern (30 bp):
TTAGGTACCAAATTAGGAAAAAATGTCAAT
Found at i:1681859 original size:57 final size:57
Alignment explanation
Indices: 1681780--1681925 Score: 188
Period size: 57 Copynumber: 2.6 Consensus size: 57
1681770 TTAAACCTAA
* * *
1681780 AAAAAAAACTTAGGTACCAAATTAGGAAAAAATGTCAAGTTCAGGTATCAAATTGGG
1 AAAAAAAATTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAGGTATCAAATTGAG
* * * * *
1681837 GAAAAAAATTTAGGTACCAAATTAAGAAAAATTGTCAAATTTAGGTATCGAATTGAG
1 AAAAAAAATTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAGGTATCAAATTGAG
*
1681894 AAAAAAAATTATA--TACCAAATTAGAAAAAAAT
1 AAAAAAAATT-TAGGTACCAAATTAGGAAAAAAT
1681926 ATAGGTTCAA
Statistics
Matches: 76, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
56 16 0.21
57 58 0.76
58 2 0.03
ACGTcount: A:0.52, C:0.08, G:0.15, T:0.25
Consensus pattern (57 bp):
AAAAAAAATTTAGGTACCAAATTAGGAAAAAATGTCAAATTCAGGTATCAAATTGAG
Found at i:1699875 original size:31 final size:31
Alignment explanation
Indices: 1699829--1699899 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
1699819 AGTTACAAAA
*
1699829 AAGTTATTGAATTATTCGA-AGGTTTTTATTT
1 AAGTAATTGAATTATTCGATA-GTTTTTATTT
* *
1699860 AAGTAATTGAGTTATTTGATAGTTTTTATTT
1 AAGTAATTGAATTATTCGATAGTTTTTATTT
*
1699891 AAGTCATTG
1 AAGTAATTG
1699900 GGTTGATGAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.17, T:0.51
Consensus pattern (31 bp):
AAGTAATTGAATTATTCGATAGTTTTTATTT
Found at i:1700877 original size:15 final size:16
Alignment explanation
Indices: 1700854--1700883 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1700844 TTAAATTTTT
1700854 TATATAAAAATAATAA
1 TATATAAAAATAATAA
1700870 TATA-AAAAATAATA
1 TATATAAAAATAATA
1700884 CGGACGGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TATATAAAAATAATAA
Found at i:1706795 original size:2 final size:2
Alignment explanation
Indices: 1706783--1706826 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
1706773 TATGATTTAC
*
1706783 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1706823 AT AT
1 AT AT
1706827 TATCAAAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1706919 original size:19 final size:20
Alignment explanation
Indices: 1706891--1706928 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1706881 CGAAAGGAAA
1706891 AAAAATATATAAATATGTAC
1 AAAAATATATAAATATGTAC
*
1706911 AAAAA-ATATATATATGTA
1 AAAAATATATAAATATGTA
1706929 TATAGATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.61, C:0.03, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAAATATATAAATATGTAC
Found at i:1708838 original size:44 final size:44
Alignment explanation
Indices: 1708778--1708959 Score: 147
Period size: 44 Copynumber: 4.2 Consensus size: 44
1708768 CTTCGATCTG
*
1708778 CTCCACCACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTA
* * * **** * *
1708822 CTCCACTACTGTTTAGGGAGACAAG-GCTGGGGTCTTT-GATCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTATAAT-TTTCAACCTA
* *
1708865 CTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTA
* * * * *
1708909 CTCCACTGCTGAC-CAAGGAGATAAGAT-TCACAATCTTCAACCTA
1 CTCCACTACTG-CTTAGGGAGATAAGATCT-ATAATTTTCAACCTA
*
1708953 TTCCACT
1 CTCCACT
1708960 GCTGACCAGG
Statistics
Matches: 107, Mismatches: 26, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
43 34 0.32
44 72 0.67
45 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTA
Found at i:1708869 original size:87 final size:87
Alignment explanation
Indices: 1708752--1708915 Score: 256
Period size: 87 Copynumber: 1.9 Consensus size: 87
1708742 GCTGACCAGA
* * *
1708752 GAGATAAGGTTGGGGACTTCGATCTGCTCCACCACTGCTTAGGGAGATAAGATCTATAATTTTCA
1 GAGACAAGGCTGGGGACTTCGATCTACTCCACCACTGCTTAGGGAGATAAGATCTATAATTTTCA
1708817 ACCTACTCCACTACTGTTTAGG
66 ACCTACTCCACTACTGTTTAGG
* * * * *
1708839 GAGACAAGGCTGGGGTCTTTGATCTACTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTA
1 GAGACAAGGCTGGGGACTTCGATCTACTCCACCACTGCTTAGGGAGATAAGATCTATAATTTTCA
1708904 ACCTACTCCACT
66 ACCTACTCCACT
1708916 GCTGACCAAG
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 69 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (87 bp):
GAGACAAGGCTGGGGACTTCGATCTACTCCACCACTGCTTAGGGAGATAAGATCTATAATTTTCA
ACCTACTCCACTACTGTTTAGG
Found at i:1708929 original size:87 final size:87
Alignment explanation
Indices: 1708722--1708929 Score: 247
Period size: 87 Copynumber: 2.4 Consensus size: 87
1708712 AGGGATTCAC
* * ** * * *
1708722 AATTTTCAACCTATTTCTTTGCTGACC-AGAGAGATAAGGTTGGGGACTTCGATCTGCTCCACCA
1 AATTTTCAACCTACTCCACTGCTGACCAAG-GAGACAAGGCTGGGGACTTCGATCTACTCCACCA
1708786 CTGCTTAGGGAGATAAGATCTAT
65 CTGCTTAGGGAGATAAGATCTAT
* *** * * * *
1708809 AATTTTCAACCTACTCCACTACTGTTTAGGGAGACAAGGCTGGGGTCTTTGATCTACTCCACTAC
1 AATTTTCAACCTACTCCACTGCTGACCAAGGAGACAAGGCTGGGGACTTCGATCTACTCCACCAC
*
1708874 TGCTTAGGGAGATAAGATCTGT
66 TGCTTAGGGAGATAAGATCTAT
*
1708896 AATTTTTAACCTACTCCACTGCTGACCAAGGAGA
1 AATTTTCAACCTACTCCACTGCTGACCAAGGAGA
1708930 TAAGATTCAC
Statistics
Matches: 98, Mismatches: 22, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
87 97 0.99
88 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (87 bp):
AATTTTCAACCTACTCCACTGCTGACCAAGGAGACAAGGCTGGGGACTTCGATCTACTCCACCAC
TGCTTAGGGAGATAAGATCTAT
Found at i:1709130 original size:45 final size:45
Alignment explanation
Indices: 1709071--1709308 Score: 130
Period size: 45 Copynumber: 5.4 Consensus size: 45
1709061 GCAAGGCTGG
* * * *
1709071 TATCTTCGATCTGCTTCGCTGTTGATGCAGGAAGGCAAAATCTGC
1 TATCTTCAACCTGCTTCGCTGTCGATCCAGGAAGGCAAAATCTGC
* * * * **
1709116 TATCTTCAACCTGCTCCACTG-CAACCCAAGG-AGGC-AAGGCTAG-
1 TATCTTCAACCTGCTTCGCTGTCGATCC-AGGAAGGCAAAATCT-GC
* * * * *
1709159 TATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGG-ATAGATATGC
1 TATCTTCAACCTGCTTCGCTGTCGATCCAGGAAGGCA-AAATCTGC
* * * * * * * ** *
1709204 TATCTTCAACCTGCTCCAC-GACAACCCAGGGATGC-AAGGCTGG
1 TATCTTCAACCTGCTTCGCTGTCGATCCAGGAAGGCAAAATCTGC
* * * * *
1709247 TATCTTCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATCTAC
1 TATCTTCAACCTGCTTCGCTGTCGATCCAGGAAGGCAAAATCTGC
1709292 TATCTTCAACCTGCTTC
1 TATCTTCAACCTGCTTC
1709309 ACTACAACCC
Statistics
Matches: 130, Mismatches: 53, Indels: 20
0.64 0.26 0.10
Matches are distributed among these distances:
43 42 0.32
44 33 0.25
45 55 0.42
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (45 bp):
TATCTTCAACCTGCTTCGCTGTCGATCCAGGAAGGCAAAATCTGC
Found at i:1709173 original size:43 final size:41
Alignment explanation
Indices: 1709038--1709173 Score: 94
Period size: 43 Copynumber: 3.1 Consensus size: 41
1709028 TATTTTTAAC
*
1709038 CTGCTCCACTACAACCAAGGGAGGCAAGGCTGGTATCTTCGAT
1 CTGCTCCACTGCAACCAA-GGAGGCAAGGCT-GTATCTTCGAT
* * * ** ** * *
1709081 CTGCTTCGCTGTTGATGC-AGGAAGGCAAAATCTGCTATCTTCAAC
1 CTGCTCCACTG--CAACCAAGG-AGGC-AAGGCTG-TATCTTCGAT
1709126 CTGCTCCACTGCAACCCAAGGAGGCAAGGCTAGTATCTTCGAT
1 CTGCTCCACTGCAA-CCAAGGAGGCAAGGCT-GTATCTTCGAT
1709169 CTGCT
1 CTGCT
1709174 TCGCTGTCGA
Statistics
Matches: 66, Mismatches: 19, Indels: 16
0.65 0.19 0.16
Matches are distributed among these distances:
43 28 0.42
44 12 0.18
45 26 0.39
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (41 bp):
CTGCTCCACTGCAACCAAGGAGGCAAGGCTGTATCTTCGAT
Found at i:1709417 original size:88 final size:88
Alignment explanation
Indices: 1708988--1709420 Score: 532
Period size: 88 Copynumber: 4.9 Consensus size: 88
1708978 GTTGGGGTCA
* * * * * * *
1708988 TCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGGTATGCTATTTTTAACCTGCTCCACTACAAC
1 TCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATATGCTATCTTCAACCTGCTCCACTGCAAC
*
1709053 CAAGGGAGGCAAGGCTGGTATCT
66 CCAGGGAGGCAAGGCTGGTATCT
* * * *
1709076 TCGATCTGCTTCGCTGTTGATGCAGGAAGGCAAAATCTGCTATCTTCAACCTGCTCCACTGCAAC
1 TCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATATGCTATCTTCAACCTGCTCCACTGCAAC
* *
1709141 CCAAGGAGGCAAGGCTAGTATCT
66 CCAGGGAGGCAAGGCTGGTATCT
*
1709164 TCGATCTGCTTCGCTGTCGATGCAGGAAGG-ATAGATATGCTATCTTCAACCTGCTCCAC-GACA
1 TCGATCTGCTTCGCTGTCGATACAGGAAGGCA-AGATATGCTATCTTCAACCTGCTCCACTG-CA
*
1709227 ACCCAGGGATGCAAGGCTGGTATCT
64 ACCCAGGGAGGCAAGGCTGGTATCT
* * * *
1709252 TCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATCTACTATCTTCAACCTGCTTCACTACAAC
1 TCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATATGCTATCTTCAACCTGCTCCACTGCAAC
* * *
1709317 CCAGGTATGCAAGGCTGGTATTT
66 CCAGGGAGGCAAGGCTGGTATCT
* * * *
1709340 TCGATCTGTTTCGCCT-TC-AGTACATGAAGGCAAGATATGTTATTTTCAACCTGCTCCACTGCA
1 TCGATCTGCTTCG-CTGTCGA-TACAGGAAGGCAAGATATGCTATCTTCAACCTGCTCCACTGCA
** *
1709403 AATCAGGAAGGCAAGGCT
64 ACCCAGGGAGGCAAGGCT
1709421 TTGTGATTTC
Statistics
Matches: 302, Mismatches: 37, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
87 3 0.01
88 296 0.98
89 3 0.01
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (88 bp):
TCGATCTGCTTCGCTGTCGATACAGGAAGGCAAGATATGCTATCTTCAACCTGCTCCACTGCAAC
CCAGGGAGGCAAGGCTGGTATCT
Found at i:1715012 original size:31 final size:29
Alignment explanation
Indices: 1714974--1715034 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 29
1714964 TTTAAAAGTA
*
1714974 AATAAATTAATTTTTATTCGTAAAATTAAAT
1 AATAAATTAATTTTCATT--TAAAATTAAAT
1715005 AATAAATTAATTTTCATTTAAAATTAAAT
1 AATAAATTAATTTTCATTTAAAATTAAAT
1715034 A
1 A
1715035 TTTTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (29 bp):
AATAAATTAATTTTCATTTAAAATTAAAT
Found at i:1727870 original size:19 final size:19
Alignment explanation
Indices: 1727820--1727871 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1727810 TTTTATATTA
*
1727820 TTAAATTTAATTATTATCC
1 TTAAACTTAATTATTATCC
*
1727839 TTAATACAT-ATTATTAAT-C
1 TTAA-ACTTAATTATT-ATCC
1727858 TTAAACTTAATTAT
1 TTAAACTTAATTAT
1727872 ATCTTGAGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.11
19 20 0.74
20 4 0.15
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAACTTAATTATTATCC
Found at i:1731459 original size:37 final size:37
Alignment explanation
Indices: 1731409--1731486 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
1731399 AATCTGTATC
1731409 AAACCCATAAAAAGTCTGTTCAGACCCATACTTTAAA
1 AAACCCATAAAAAGTCTGTTCAGACCCATACTTTAAA
1731446 AAACCCATAAAAAGTCTGTTCAGACCCATACTTTAAA
1 AAACCCATAAAAAGTCTGTTCAGACCCATACTTTAAA
1731483 AAAC
1 AAAC
1731487 AATTTTAATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.45, C:0.24, G:0.08, T:0.23
Consensus pattern (37 bp):
AAACCCATAAAAAGTCTGTTCAGACCCATACTTTAAA
Found at i:1731537 original size:2 final size:2
Alignment explanation
Indices: 1731521--1731554 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1731511 TCAAAAGATC
* *
1731521 AT AT AT GT AT GT 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
1731555 CAATCAAACG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1731967 original size:31 final size:31
Alignment explanation
Indices: 1731894--1731967 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
1731884 TAATTTGCTC
* * *
1731894 AATTTTAGTCCCTATGTTTTTTGAATTAGTC
1 AATTTTAGTCCTTATGCTTTTTGAATTAGTA
1731925 AATTTTAGTCCTTATGCTTTTTGAATTA-TAA
1 AATTTTAGTCCTTATGCTTTTTGAATTAGT-A
1731956 AATTTTAGTCCT
1 AATTTTAGTCCT
1731968 GACTTGGTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 1 0.03
31 38 0.97
ACGTcount: A:0.26, C:0.12, G:0.11, T:0.51
Consensus pattern (31 bp):
AATTTTAGTCCTTATGCTTTTTGAATTAGTA
Found at i:1753228 original size:10 final size:12
Alignment explanation
Indices: 1753204--1753228 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1753194 AAAGATTAAA
1753204 ATATCATTTTAT
1 ATATCATTTTAT
1753216 ATATCATTTTAT
1 ATATCATTTTAT
1753228 A
1 A
1753229 ATTTAAAGTA
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:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATCATTTTAT
Found at i:1754605 original size:7 final size:7
Alignment explanation
Indices: 1754590--1754620 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1754580 TTTAGGACTA
1754590 AAATTTC
1 AAATTTC
*
1754597 AAATCTC
1 AAATTTC
1754604 AAATTTC
1 AAATTTC
1754611 AAATTTC
1 AAATTTC
1754618 AAA
1 AAA
1754621 AAGCATAGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (7 bp):
AAATTTC
Found at i:1766747 original size:21 final size:20
Alignment explanation
Indices: 1766717--1766778 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
1766707 GTCATAATAA
*
1766717 AAAAACATATTAATTAATTAT
1 AAAAATATATTAATTAATT-T
* *
1766738 AAAAATATATAAATATTATTT
1 AAAAATATATTAAT-TAATTT
*
1766759 AAAAATA-ATTAAATAATTT
1 AAAAATATATTAATTAATTT
1766778 A
1 A
1766779 TATTTTATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 6 0.18
20 4 0.12
21 20 0.59
22 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAATATATTAATTAATTT
Found at i:1774744 original size:16 final size:14
Alignment explanation
Indices: 1774725--1774758 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
1774715 TTGACTAGAC
1774725 AAAATATTGTAAGAAA
1 AAAATATT-TAA-AAA
1774741 AAAATATTTAAAAA
1 AAAATATTTAAAAA
1774755 AAAA
1 AAAA
1774759 GACACTGTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
15 3 0.17
16 8 0.44
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (14 bp):
AAAATATTTAAAAA
Found at i:1774756 original size:15 final size:16
Alignment explanation
Indices: 1774725--1774758 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1774715 TTGACTAGAC
*
1774725 AAAATATTGTAAGAAA
1 AAAATATTGTAAAAAA
1774741 AAAATATT-TAAAAAA
1 AAAATATTGTAAAAAA
1774756 AAA
1 AAA
1774759 GACACTGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (16 bp):
AAAATATTGTAAAAAA
Found at i:1775718 original size:42 final size:43
Alignment explanation
Indices: 1775670--1775757 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
1775660 TCAATAGCCA
*
1775670 TTCAACGTTCATCTTA-AATTTGAATTTTGAAAAATCAGACCG
1 TTCAACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCG
*
1775712 TTCAACGTTCATCTTATATTTTGAATTTTGAAAAACCAGACCG
1 TTCAACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCG
1775755 TTC
1 TTC
1775758 CTCACCCCGT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
42 16 0.37
43 27 0.63
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.38
Consensus pattern (43 bp):
TTCAACGTTCATCTTATAATTTGAATTTTGAAAAACCAGACCG
Found at i:1776784 original size:12 final size:12
Alignment explanation
Indices: 1776769--1776801 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
1776759 GAAGAAGGTG
1776769 AGAAAGAAACCA
1 AGAAAGAAACCA
*
1776781 AGAAAAAAACCA
1 AGAAAGAAACCA
1776793 AGAAAGAAA
1 AGAAAGAAA
1776802 GGGATCCCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.73, C:0.12, G:0.15, T:0.00
Consensus pattern (12 bp):
AGAAAGAAACCA
Found at i:1780523 original size:9 final size:9
Alignment explanation
Indices: 1780509--1780596 Score: 83
Period size: 9 Copynumber: 9.8 Consensus size: 9
1780499 CTTGCCATGG
1780509 AAAGAAGGA
1 AAAGAAGGA
1780518 AAAGAA-G-
1 AAAGAAGGA
* *
1780525 -ATGAAAGA
1 AAAGAAGGA
*
1780533 CAAGAAGGA
1 AAAGAAGGA
1780542 GAAAGACAAGGA
1 -AAAG--AAGGA
*
1780554 CAAGAAGGA
1 AAAGAAGGA
*
1780563 AAAGAAAGA
1 AAAGAAGGA
1780572 AAAGAAGGA
1 AAAGAAGGA
1780581 AAAGAAGGA
1 AAAGAAGGA
1780590 AAAGAAG
1 AAAGAAG
1780597 ACCGAGAGCA
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
6 4 0.06
7 1 0.02
8 1 0.02
9 48 0.74
10 3 0.05
11 3 0.05
12 5 0.08
ACGTcount: A:0.65, C:0.03, G:0.31, T:0.01
Consensus pattern (9 bp):
AAAGAAGGA
Found at i:1780628 original size:18 final size:18
Alignment explanation
Indices: 1780583--1780630 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1780573 AAGAAGGAAA
*
1780583 AGAAGGAAAAGAAGACCG
1 AGAAGGAGAAGAAGACCG
* *
1780601 AG-AGCAAGAAGAAGCCCG
1 AGAAG-GAGAAGAAGACCG
1780619 AGAAGGAGAAGA
1 AGAAGGAGAAGA
1780631 GTAAGCACAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.52, C:0.12, G:0.35, T:0.00
Consensus pattern (18 bp):
AGAAGGAGAAGAAGACCG
Found at i:1780827 original size:20 final size:20
Alignment explanation
Indices: 1780777--1780816 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1780767 GTGCAATGTA
1780777 AGACTATAAATTATCATATC
1 AGACTATAAATTATCATATC
1780797 AGACTATAAATTATCATATC
1 AGACTATAAATTATCATATC
1780817 TCCTATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (20 bp):
AGACTATAAATTATCATATC
Found at i:1800449 original size:19 final size:19
Alignment explanation
Indices: 1800425--1800461 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1800415 CTAAACCTTT
1800425 TTTAAAATTTATATTTTTA
1 TTTAAAATTTATATTTTTA
* *
1800444 TTTAAATTTTTTATTTTT
1 TTTAAAATTTATATTTTT
1800462 CGAACAAATC
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:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTAAAATTTATATTTTTA
Found at i:1800792 original size:7 final size:7
Alignment explanation
Indices: 1800780--1800811 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
1800770 GGGGAAGGAG
1800780 GGAGAAA
1 GGAGAAA
1800787 GGAGAAA
1 GGAGAAA
1800794 GGAGAAA
1 GGAGAAA
*
1800801 GGGGAAA
1 GGAGAAA
1800808 GGAG
1 GGAG
1800812 GGGCATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (7 bp):
GGAGAAA
Found at i:1802226 original size:6 final size:6
Alignment explanation
Indices: 1802215--1802251 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
1802205 CTTGGTGACG
*
1802215 ATCAGC ATCAGC ATCAGC ATCAGC ATCAGC AGCAGC A
1 ATCAGC ATCAGC ATCAGC ATCAGC ATCAGC ATCAGC A
1802252 CCACCACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.35, C:0.32, G:0.19, T:0.14
Consensus pattern (6 bp):
ATCAGC
Found at i:1812625 original size:24 final size:23
Alignment explanation
Indices: 1812598--1812646 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
1812588 TATTCTATAT
*
1812598 ATAAAGATATTTTTAACAGTAAAA
1 ATAAAGAAATTTTTAACA-TAAAA
* *
1812622 ATAAATAAATTTTTAATATAAAA
1 ATAAAGAAATTTTTAACATAAAA
1812645 AT
1 AT
1812647 TAATTTATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (23 bp):
ATAAAGAAATTTTTAACATAAAA
Found at i:1818165 original size:2 final size:2
Alignment explanation
Indices: 1818158--1818186 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1818148 GCTCATACAC
1818158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1818187 CATAAGACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1821623 original size:186 final size:188
Alignment explanation
Indices: 1821249--1821810 Score: 952
Period size: 186 Copynumber: 3.0 Consensus size: 188
1821239 CATTAGAGAG
* * * *
1821249 ATGTTTAATTCGTGTATACATGCCTTAGCTCATGTCCTTTTCATGTAAACCGTGTA-AATATAAA
1 ATGTTTAATTCGTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTG-AGAGTATAAA
* * * *
1821313 TTCAATACAAATTATTATGTGTCAAAATCCTAAATACGAGTACAATAAATGTA-CTAAATGTGTT
65 TTCAATACAAATTATTATGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTT
*
1821377 GTGTTTATGTCATGTTTTCAGATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
130 GTGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
*
1821436 ATGTTTAATTCGTGTATACATCCCTTAGCTCCTGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
1 ATGTTTAATTCGTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
1821501 TCAATACAAATTA-T-TGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
66 TCAATACAAATTATTATGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
1821564 TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
131 TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
*
1821622 ATGTTTAATTCCTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
1 ATGTTTAATTCGTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
*
1821687 TCAATACAAATTATTATGTGTCATGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
66 TCAATACAAATTATTATGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
***
1821752 TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAGTGCGAGCAAAAAATGA
131 TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
1821810 A
1 A
1821811 GGTACCTGAT
Statistics
Matches: 355, Mismatches: 16, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
185 34 0.10
186 145 0.41
187 72 0.20
188 104 0.29
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (188 bp):
ATGTTTAATTCGTGTATACATCCCTTAGCTCATGTTCTTTTCGTGTAAACCGTGAGAGTATAAAT
TCAATACAAATTATTATGTGTCAAGATCCTAAATATGAGTACAATAAATGTACCAAAATGCGTTG
TGTTTATGTCATGTTTTCATATCGTCAAATCTAGAAAAGAAACCCGAGCAAAAAATGA
Found at i:1838800 original size:116 final size:116
Alignment explanation
Indices: 1838647--1838880 Score: 432
Period size: 116 Copynumber: 2.0 Consensus size: 116
1838637 TAATTACCCA
* *
1838647 CAAAATTTCCGTGACGTAATAATTATGATCCCTAATTAAAGGCGGATTTGAAATCTAATTATTGT
1 CAAAACTTCCGTGACGTAATAATTATGATCCCTAATTAAAGACGGATTTGAAATCTAATTATTGT
1838712 ACAATTGATAGAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
66 ACAATTGATAGAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
1838763 CAAAACTTCCGTGACGTAATAATTATGATCCCTAATTAAAGACGGATTTGAAATCTAATTATTGT
1 CAAAACTTCCGTGACGTAATAATTATGATCCCTAATTAAAGACGGATTTGAAATCTAATTATTGT
* *
1838828 ATAATTGATATAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
66 ACAATTGATAGAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
1838879 CA
1 CA
1838881 GTTTCTTTTC
Statistics
Matches: 114, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
116 114 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.34
Consensus pattern (116 bp):
CAAAACTTCCGTGACGTAATAATTATGATCCCTAATTAAAGACGGATTTGAAATCTAATTATTGT
ACAATTGATAGAAACTTAAAATCCGCCTTTCCCACGGTCTTATATAAGTAT
Found at i:1842175 original size:26 final size:26
Alignment explanation
Indices: 1842145--1842228 Score: 68
Period size: 26 Copynumber: 3.3 Consensus size: 26
1842135 AAAGTTATTT
1842145 ATATTTATAAATTCATATATACTTTA
1 ATATTTATAAATTCATATATACTTTA
***
1842171 ATA-TT-TAAA-TCATGATACTAAAGTA
1 ATATTTATAAATTCAT-ATA-TACTTTA
* *
1842196 A-ATATTAGAAATACATATATACTTTA
1 ATAT-TTATAAATTCATATATACTTTA
1842222 ATATTTA
1 ATATTTA
1842229 AATATTAAAG
Statistics
Matches: 43, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
23 4 0.09
24 8 0.19
25 7 0.16
26 13 0.30
27 8 0.19
28 3 0.07
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (26 bp):
ATATTTATAAATTCATATATACTTTA
Found at i:1842226 original size:25 final size:23
Alignment explanation
Indices: 1842157--1842231 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 23
1842147 ATTTATAAAT
*
1842157 TCATATATACTTTAATATTTAAA
1 TCATATATACTTTAATATTGAAA
** *
1842180 TCATGATACTAAAGTAAATATTAGAAA
1 TCAT-ATA-T-ACTTTAATATT-GAAA
*
1842207 TACATATATACTTTAATATTTAAA
1 T-CATATATACTTTAATATTGAAA
1842231 T
1 T
1842232 ATTAAAGTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
23 4 0.10
24 7 0.18
25 9 0.23
26 9 0.23
27 7 0.18
28 3 0.08
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (23 bp):
TCATATATACTTTAATATTGAAA
Found at i:1842258 original size:12 final size:12
Alignment explanation
Indices: 1842243--1842270 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1842233 TTAAAGTAAA
1842243 TATGCTAATAAC
1 TATGCTAATAAC
1842255 TATGCTAATAAC
1 TATGCTAATAAC
1842267 TATG
1 TATG
1842271 TGTTTAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (12 bp):
TATGCTAATAAC
Found at i:1846382 original size:25 final size:25
Alignment explanation
Indices: 1846335--1846385 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
1846325 TGAGTATACT
* ** *
1846335 TTAAGTACCAAATTGGGATAAAAAA
1 TTAAGTACCAAAATGAAAAAAAAAA
1846360 TTAAGTACCAAAATGAAAAAAAAAA
1 TTAAGTACCAAAATGAAAAAAAAAA
1846385 T
1 T
1846386 ATTTTAGAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.12, T:0.22
Consensus pattern (25 bp):
TTAAGTACCAAAATGAAAAAAAAAA
Found at i:1850546 original size:17 final size:18
Alignment explanation
Indices: 1850518--1850552 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1850508 CTGTAATCTA
*
1850518 AATTTTTAATAATATATT
1 AATTTTTAATAAAATATT
1850536 AATTTTT-ATAAAATATT
1 AATTTTTAATAAAATATT
1850553 TAAAAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
AATTTTTAATAAAATATT
Found at i:1850555 original size:18 final size:18
Alignment explanation
Indices: 1850518--1850555 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
1850508 CTGTAATCTA
*
1850518 AATTTTTAATAATATATT
1 AATTTTTAAAAATATATT
1850536 AATTTTTATAAAATAT-TT
1 AATTTTTA-AAAATATATT
1850554 AA
1 AA
1850556 AAATATGTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
AATTTTTAAAAATATATT
Done.