Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007952.1 Hibiscus syriacus cultivar Beakdansim tig00110377_pilon, whole genome shotgun sequence
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: 3169409
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 16
Found at i:2967905 original size:10 final size:11
Alignment explanation
Indices: 2967886--2967954 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 11
2967876 TTATTGTATT
2967886 TTATCAAATAAA
1 TTAT-AAATAAA
2967898 TTAT-AATAAA
1 TTATAAATAAA
*
2967908 TAATAAATAAA
1 TTATAAATAAA
*
2967919 TTTAAAAGTAATAAAA
1 -TT-ATA--AAT-AAA
2967935 TTATAATATAAA
1 TTATAA-ATAAA
2967947 TTATAAAT
1 TTATAAAT
2967955 CATAAATTTA
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
10 9 0.20
11 8 0.17
12 15 0.33
13 4 0.09
14 2 0.04
15 5 0.11
16 3 0.07
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (11 bp):
TTATAAATAAA
Found at i:2984491 original size:182 final size:182
Alignment explanation
Indices: 2984173--2984626 Score: 748
Period size: 182 Copynumber: 2.5 Consensus size: 182
2984163 ACTTTTTTAC
* * * *
2984173 TACCGGTTTTTTCATTTCGATATCGATTTTGTCATATTTTTATCTGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
2984238 TACATTTTTATAAAGTATCGGCACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
*
2984303 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCTCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTT
* * *
2984355 TACCGGATTTGTCATTTCGAGACCGATTTTATCATATTTTTACCAGTTATATTGTTATGGATCGA
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
2984420 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
2984485 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTT
131 TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTT
* ** * *
2984537 TACCTGTTTTGTCATTTATAGACCGGTTTTGTCAT-TTGTTTACCTGTTTTATTGTTATGGATCG
1 TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATT-TTTACCTGTTATATTGTTATGGATCG
2984601 ATACATTTTTATAAAGTATCGACACT
65 ATACATTTTTATAAAGTATCGACACT
2984627 ATCAACATAT
Statistics
Matches: 252, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
181 2 0.01
182 250 0.99
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
TACCGGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAG
TGTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTT
Found at i:2984585 original size:20 final size:20
Alignment explanation
Indices: 2984535--2984586 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
2984525 CTGGTAGCGC
2984535 TTTACCTGTTTTGTCATTTA
1 TTTACCTGTTTTGTCATTTA
** * *
2984555 TAGACCGGTTTTGTCATTTG
1 TTTACCTGTTTTGTCATTTA
2984575 TTTACCTGTTTT
1 TTTACCTGTTTT
2984587 ATTGTTATGG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.13, C:0.15, G:0.15, T:0.56
Consensus pattern (20 bp):
TTTACCTGTTTTGTCATTTA
Found at i:2984696 original size:112 final size:112
Alignment explanation
Indices: 2984499--2985073 Score: 997
Period size: 112 Copynumber: 5.1 Consensus size: 112
2984489 GATACTTATA
* * *
2984499 ATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2984564 TTTGTCATTTGTTTACCTGTTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
2984611 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
2984676 TTTGTCATTTTATTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
2984723 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
2984788 TTTGTCATTTTTTTACCTGTTATATTGTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
2984835 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGGCCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
2984900 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATAGATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
2984947 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTCATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
2985012 TTTGTCATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
2985059 ATAAAGTAACGACAC
1 ATAAAGTATCGACAC
2985074 AAACCGACAA
Statistics
Matches: 445, Mismatches: 18, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
112 445 1.00
ACGTcount: A:0.25, C:0.16, G:0.15, T:0.44
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:2991034 original size:2 final size:2
Alignment explanation
Indices: 2991027--2991078 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2991017 GAAAATGAAA
2991027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2991069 AT AT AT AT AT
1 AT AT AT AT AT
2991079 GCAAACATAT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2992842 original size:32 final size:32
Alignment explanation
Indices: 2992806--2992872 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
2992796 GGAATTAGTG
2992806 ATACTACTTGTCAAAGTTCTTTGAAGAAAATC
1 ATACTACTTGTCAAAGTTCTTTGAAGAAAATC
2992838 ATACTACTTGTCAAAGTTCTTTGAAGAAAATC
1 ATACTACTTGTCAAAGTTCTTTGAAGAAAATC
2992870 ATA
1 ATA
2992873 AGGTCAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (32 bp):
ATACTACTTGTCAAAGTTCTTTGAAGAAAATC
Found at i:2995360 original size:23 final size:22
Alignment explanation
Indices: 2995218--2995372 Score: 161
Period size: 23 Copynumber: 7.0 Consensus size: 22
2995208 TACTGAAGTG
*
2995218 CCACATAAAATGTCCCGAAGGA
1 CCACATAGAATGTCCCGAAGGA
*
2995240 CCACATAGAATGTCCCAAAGGA
1 CCACATAGAATGTCCCGAAGGA
* *
2995262 CCACATTG-ATGTCCTGAAGGA
1 CCACATAGAATGTCCCGAAGGA
* *
2995283 CCACGTAGAAATGTTCCGAAGGA
1 CCACATAG-AATGTCCCGAAGGA
* *
2995306 CCACGTAGAATTGTTCCGAAGGA
1 CCACATAGAA-TGTCCCGAAGGA
* *
2995329 CCACGTAGAATTGTCCCGAATGA
1 CCACATAGAA-TGTCCCGAAGGA
* *
2995352 CCATATAG-ATGTCCAGAAGGA
1 CCACATAGAATGTCCCGAAGGA
2995373 TTGCGTAGAA
Statistics
Matches: 115, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
21 27 0.23
22 30 0.26
23 58 0.50
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (22 bp):
CCACATAGAATGTCCCGAAGGA
Found at i:2995593 original size:23 final size:23
Alignment explanation
Indices: 2995566--2995609 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2995556 TTATCCCACT
*
2995566 TTTATATTTAATT-ACATAGGTCA
1 TTTATA-TCAATTCACATAGGTCA
2995589 TTTATATCAATTCACATAGGT
1 TTTATATCAATTCACATAGGT
2995610 TACCACACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.45
Consensus pattern (23 bp):
TTTATATCAATTCACATAGGTCA
Found at i:2997874 original size:24 final size:24
Alignment explanation
Indices: 2997847--2997966 Score: 127
Period size: 24 Copynumber: 5.0 Consensus size: 24
2997837 CGGTCGATCA
2997847 TGTATTAGTGCATTCGTGCACTCT
1 TGTATTAGTGCATTCGTGCACTCT
* *
2997871 TGTATTAGTGCCTTTGTGCACTCT
1 TGTATTAGTGCATTCGTGCACTCT
2997895 TGTATTAGTGCATTCGTGCACT-T
1 TGTATTAGTGCATTCGTGCACTCT
** * *
2997918 CCATATTAGTACCATT-GTGTACTCT
1 -TGTATTAGT-GCATTCGTGCACTCT
* *
2997943 TGTATTTAGTACATTCGTGTACTC
1 TGTA-TTAGTGCATTCGTGCACTC
2997967 CTGACTTTAT
Statistics
Matches: 80, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
23 1 0.01
24 61 0.76
25 18 0.22
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (24 bp):
TGTATTAGTGCATTCGTGCACTCT
Found at i:2997925 original size:48 final size:48
Alignment explanation
Indices: 2997847--2997966 Score: 152
Period size: 48 Copynumber: 2.5 Consensus size: 48
2997837 CGGTCGATCA
** * *
2997847 TGTATTAGTGCATTCGTGCACTCTTGTATTAGTGCCTTTGTGCACTCT
1 TGTATTAGTGCATTCGTGCACTCTCATATTAGTACCATTGTGCACTCT
*
2997895 TGTATTAGTGCATTCGTGCACT-TCCATATTAGTACCATTGTGTACTCT
1 TGTATTAGTGCATTCGTGCACTCT-CATATTAGTACCATTGTGCACTCT
* *
2997943 TGTATTTAGTACATTCGTGTACTC
1 TGTA-TTAGTGCATTCGTGCACTC
2997967 CTGACTTTAT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 1 0.02
48 45 0.73
49 16 0.26
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.43
Consensus pattern (48 bp):
TGTATTAGTGCATTCGTGCACTCTCATATTAGTACCATTGTGCACTCT
Found at i:2999098 original size:31 final size:31
Alignment explanation
Indices: 2999060--2999152 Score: 141
Period size: 31 Copynumber: 3.0 Consensus size: 31
2999050 TTGAATCATA
* *
2999060 CTATAAATTAAGAACGTGTTACTATTAAGCT
1 CTATAAATTAAGAATGTATTACTATTAAGCT
*
2999091 CTATAAATTAAGAATGTATTACTATTAAGCA
1 CTATAAATTAAGAATGTATTACTATTAAGCT
* *
2999122 CTATAAACTAAGAATATATTACTATTAAGCT
1 CTATAAATTAAGAATGTATTACTATTAAGCT
2999153 ATAATTATAC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 56 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (31 bp):
CTATAAATTAAGAATGTATTACTATTAAGCT
Found at i:3003688 original size:4 final size:4
Alignment explanation
Indices: 3003681--3003715 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
3003671 CTCCCGTTTT
*
3003681 TTTC TTTC TTTC TTCTC TTTC TTCC TTTC TTTC TT
1 TTTC TTTC TTTC TT-TC TTTC TTTC TTTC TTTC TT
3003716 AGCCTTCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTC
Found at i:3003708 original size:21 final size:23
Alignment explanation
Indices: 3003661--3003715 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 23
3003651 GCCTTGTCTA
* *
3003661 TTTCTTTCTTCTCCCGTTTTTTTC
1 TTTCTTTCTTCT-CCGTTTCTTCC
3003685 TTTCTTTCTTCT-C-TTTCTTCC
1 TTTCTTTCTTCTCCGTTTCTTCC
3003706 TTTCTTTCTT
1 TTTCTTTCTT
3003716 AGCCTTCTCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 16 0.55
22 1 0.03
24 12 0.41
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTCTTTCTTCTCCGTTTCTTCC
Found at i:3003723 original size:21 final size:21
Alignment explanation
Indices: 3003684--3003723 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3003674 CCGTTTTTTT
** *
3003684 CTTTCTTTCTTCTCTTTCTTC
1 CTTTCTTTCTTAGCCTTCTTC
3003705 CTTTCTTTCTTAGCCTTCT
1 CTTTCTTTCTTAGCCTTCT
3003724 CTTCTTCTCT
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:0.03, C:0.33, G:0.03, T:0.62
Consensus pattern (21 bp):
CTTTCTTTCTTAGCCTTCTTC
Found at i:3017616 original size:22 final size:22
Alignment explanation
Indices: 3017588--3017632 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
3017578 TTTCCTTTTC
3017588 GATTTTTTTTTATTAATCTAGG
1 GATTTTTTTTTATTAATCTAGG
3017610 GATTTTTTTTTATTAATCTAGG
1 GATTTTTTTTTATTAATCTAGG
3017632 G
1 G
3017633 TCTTACAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.22, C:0.04, G:0.16, T:0.58
Consensus pattern (22 bp):
GATTTTTTTTTATTAATCTAGG
Found at i:3026710 original size:191 final size:191
Alignment explanation
Indices: 3026379--3026747 Score: 616
Period size: 191 Copynumber: 1.9 Consensus size: 191
3026369 TGACTTCCTA
* *
3026379 TAACTTAGGTAACAATGACATATTGCTAGATGTCACTCATTGTTTGTAATATTAGAATGGTTCTA
1 TAACTTAGGTAACAATGACATATTGCTAGATGTAACTCATTGTTTGTAATATTAGAATGATTCTA
** * **
3026444 ATAATTGCTACTAATGTTATAGGAACCTACAGGGTTGCACCCTAGTGTTGAAAAGAGCAATTTAT
66 ATAATTAATACTAATGTTATAAGAACCTACAGGGTCACACCCTAGTGTTGAAAAGAGCAATTTAT
3026509 AAACGAGTTACACATGTACAATTTTATCATGCATTAATAAAATGTATATATATATATATTG
131 AAACGAGTTACACATGTACAATTTTATCATGCATTAATAAAATGTATATATATATATATTG
*
3026570 TAACTTAGGTGACAATGACATATTGCTAGATGTAACT-ATTTGTTTGTAATATTAGAATGATTCT
1 TAACTTAGGTAACAATGACATATTGCTAGATGTAACTCA-TTGTTTGTAATATTAGAATGATTCT
3026634 AATAATTAATACTAATGTTATAAGAACCTACAGGGTCACACCCTAAG-GTTGAAAAGAGCAATTT
65 AATAATTAATACTAATGTTATAAGAACCTACAGGGTCACACCCT-AGTGTTGAAAAGAGCAATTT
* *
3026698 ATAAATGAGTTACACATGTACAATTTTATTATGCATTAATAAAATGTATA
129 ATAAACGAGTTACACATGTACAATTTTATCATGCATTAATAAAATGTATA
3026748 ATTAATATTA
Statistics
Matches: 166, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
190 1 0.01
191 163 0.98
192 2 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (191 bp):
TAACTTAGGTAACAATGACATATTGCTAGATGTAACTCATTGTTTGTAATATTAGAATGATTCTA
ATAATTAATACTAATGTTATAAGAACCTACAGGGTCACACCCTAGTGTTGAAAAGAGCAATTTAT
AAACGAGTTACACATGTACAATTTTATCATGCATTAATAAAATGTATATATATATATATTG
Found at i:3030337 original size:20 final size:20
Alignment explanation
Indices: 3030308--3030345 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3030298 CCCCTTCAAA
*
3030308 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
3030328 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
3030346 TGCACCAAAA
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:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:3038768 original size:12 final size:12
Alignment explanation
Indices: 3038751--3038782 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
3038741 AAAATAAAAC
3038751 TCAATACGTTTG
1 TCAATACGTTTG
3038763 TCAATACGTTTG
1 TCAATACGTTTG
*
3038775 TGAATACG
1 TCAATACG
3038783 CCTACCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.38
Consensus pattern (12 bp):
TCAATACGTTTG
Found at i:3041035 original size:18 final size:19
Alignment explanation
Indices: 3041012--3041060 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
3041002 CCAATTTTGA
*
3041012 TATCGATACTCATGG-GAG
1 TATCGATACTCAGGGTGAG
*
3041030 TATCGATACTAAGGGTTGAG
1 TATCGATACTCAGGG-TGAG
3041050 TATCGATACTC
1 TATCGATACTC
3041061 TCCATAGGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 13 0.50
20 13 0.50
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (19 bp):
TATCGATACTCAGGGTGAG
Found at i:3053891 original size:3 final size:3
Alignment explanation
Indices: 3053883--3053963 Score: 146
Period size: 3 Copynumber: 27.3 Consensus size: 3
3053873 ATGGATATTT
*
3053883 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
3053931 GAA GAA GAA GAA GAA GAA GAA GAA -AA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
3053964 TCTCGTCTGA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 73 0.97
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:3054033 original size:3 final size:3
Alignment explanation
Indices: 3054025--3054152 Score: 202
Period size: 3 Copynumber: 41.7 Consensus size: 3
3054015 ATGGATATTT
3054025 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
***
3054073 GAA GAA GAA GAA GAA GAA GAA GAA TGGATA TTT GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA --GA-A GAA GAA GAA GAA GAA GAA
3054121 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
3054153 CACACGGGTT
Statistics
Matches: 116, Mismatches: 6, Indels: 6
0.91 0.05 0.05
Matches are distributed among these distances:
3 113 0.97
5 2 0.02
6 1 0.01
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (3 bp):
GAA
Found at i:3054069 original size:142 final size:142
Alignment explanation
Indices: 3053813--3054096 Score: 550
Period size: 142 Copynumber: 2.0 Consensus size: 142
3053803 ATTGTGAGTC
3053813 AAGAACAAGTCTCGTCTGACATTATGTGTCTTTCCGGAAACAAGAATAAGGGAAGTTCAAATGGA
1 AAGAACAAGTCTCGTCTGACATTATGTGTCTTTCCGGAAACAAGAATAAGGGAAGTTCAAATGGA
3053878 TATTTGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAAAGAAGAAGAAGAAGAAGAA
66 TATTTGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAAAGAAGAAGAAGAAGAAGAA
3053943 GAAGAAGAAGAA
131 GAAGAAGAAGAA
*
3053955 AAGAAGAAGTCTCGTCTGACATTATGTGTCTTTCCGGAAACAAGAATAAGGGAAGTTCAAATGGA
1 AAGAACAAGTCTCGTCTGACATTATGTGTCTTTCCGGAAACAAGAATAAGGGAAGTTCAAATGGA
*
3054020 TATTTGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAA
66 TATTTGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAAAGAAGAAGAAGAAGAAGAA
3054085 GAAGAAGAAGAA
131 GAAGAAGAAGAA
3054097 TGGATATTTG
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
142 140 1.00
ACGTcount: A:0.52, C:0.07, G:0.27, T:0.14
Consensus pattern (142 bp):
AAGAACAAGTCTCGTCTGACATTATGTGTCTTTCCGGAAACAAGAATAAGGGAAGTTCAAATGGA
TATTTGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAGAAAAAGAAGAAGAAGAAGAAGAA
GAAGAAGAAGAA
Found at i:3059665 original size:37 final size:35
Alignment explanation
Indices: 3059624--3059748 Score: 89
Period size: 37 Copynumber: 3.5 Consensus size: 35
3059614 ATTATATGAG
3059624 ATAATATATAAGTGACCAAATAGGTATTTTACCCTAA
1 ATAATA-ATAAGTGACCAAATAGGTA-TTTACCCTAA
* * *** *
3059661 ATAATAATCGAGTGACCAAA-A--CA--TAAATTAG
1 ATAATAAT-AAGTGACCAAATAGGTATTTACCCTAA
*
3059692 ATAATATATAAGTGAGCAAATAGGTAGTTTACCCTAA
1 ATAATA-ATAAGTGACCAAATAGGTA-TTTACCCTAA
*
3059729 ATAATAATTGAGTGACCAAA
1 ATAATAA-TAAGTGACCAAA
3059749 ACATAAATTA
Statistics
Matches: 64, Mismatches: 15, Indels: 18
0.66 0.15 0.19
Matches are distributed among these distances:
31 19 0.30
32 3 0.05
34 2 0.03
36 4 0.06
37 36 0.56
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (35 bp):
ATAATAATAAGTGACCAAATAGGTATTTACCCTAA
Found at i:3059712 original size:68 final size:68
Alignment explanation
Indices: 3059528--3059763 Score: 340
Period size: 68 Copynumber: 3.5 Consensus size: 68
3059518 AATTTTAAAA
3059528 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
3059593 CCT
66 CCT
* * * * * * *
3059596 AAATAAAAAT--A-T-A-TATGAA-TTATATGAGATAATATATAAGTGACCAAATAGGTATTTTA
1 AAATAATAATCGAGTGACCA-AAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTA
3059655 CCCT
65 CCCT
*
3059659 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGAGCAAATAGGTAGTTTAC
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
3059724 CCT
66 CCT
*
3059727 AAATAATAATTGAGTGACCAAAACATAAATTAGATAA
1 AAATAATAATCGAGTGACCAAAACATAAATTAGATAA
3059764 GAGAAAATAA
Statistics
Matches: 145, Mismatches: 16, Indels: 14
0.83 0.09 0.08
Matches are distributed among these distances:
63 50 0.34
64 3 0.02
65 2 0.01
66 2 0.01
67 3 0.02
68 85 0.59
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.28
Consensus pattern (68 bp):
AAATAATAATCGAGTGACCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
CCT
Found at i:3059935 original size:21 final size:21
Alignment explanation
Indices: 3059909--3059962 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
3059899 GTTTCCAGAT
*
3059909 TCGCAACGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
3059930 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
3059951 TCGCAATGCGAA
1 TCGCAATGCGAA
3059963 TATGTAAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.26, G:0.24, T:0.20
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:3060051 original size:19 final size:20
Alignment explanation
Indices: 3059995--3060051 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 20
3059985 TCGATTCGCA
* *
3059995 TTGCGATAGGCCAAGTTAGCG
1 TTGCGATAGTCCAAATTA-CG
*
3060016 TTGCGATTTATTCCAAATT-CG
1 TTGCGA--TAGTCCAAATTACG
3060037 TTGCGATAGTCCAAA
1 TTGCGATAGTCCAAA
3060052 AGCGCAACGA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
19 8 0.27
21 14 0.47
23 8 0.27
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCCAAATTACG
Found at i:3060151 original size:6 final size:6
Alignment explanation
Indices: 3060140--3060166 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
3060130 GACACGTTTT
3060140 ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACC
3060167 CGAGACGAGA
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:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:3061230 original size:34 final size:35
Alignment explanation
Indices: 3061183--3061259 Score: 129
Period size: 34 Copynumber: 2.2 Consensus size: 35
3061173 CACCTGTAAA
*
3061183 ATTTAATCTTAATTCGATTCAAATAAGAGAATATC
1 ATTTGATCTTAATTCGATTCAAATAAGAGAATATC
3061218 ATTTGATC-TAATTCGATTCAAATAAGAGAATATC
1 ATTTGATCTTAATTCGATTCAAATAAGAGAATATC
*
3061252 ATTCGATC
1 ATTTGATC
3061260 AAAAGTAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 33 0.82
35 7 0.17
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (35 bp):
ATTTGATCTTAATTCGATTCAAATAAGAGAATATC
Found at i:3065379 original size:25 final size:25
Alignment explanation
Indices: 3065345--3065394 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3065335 AATGCACCGA
*
3065345 AAATTGAAACAATGAAATCAATGTT
1 AAATCGAAACAATGAAATCAATGTT
3065370 AAATCGAAACAATGAAATCAATGTT
1 AAATCGAAACAATGAAATCAATGTT
3065395 GCCGACCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (25 bp):
AAATCGAAACAATGAAATCAATGTT
Found at i:3070020 original size:16 final size:17
Alignment explanation
Indices: 3069999--3070031 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
3069989 TGCAAATGAT
3069999 AAGAAATAAAAA-AAAA
1 AAGAAATAAAAACAAAA
3070015 AAGAAATAAAAACAAAA
1 AAGAAATAAAAACAAAA
3070032 TAAAATAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.85, C:0.03, G:0.06, T:0.06
Consensus pattern (17 bp):
AAGAAATAAAAACAAAA
Found at i:3070746 original size:12 final size:12
Alignment explanation
Indices: 3070726--3070775 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
3070716 TTTTTCACTA
*
3070726 TTCATGGTACTG
1 TTCACGGTACTG
3070738 TTCACGGTACTG
1 TTCACGGTACTG
*
3070750 TTCA--TTACTG
1 TTCACGGTACTG
* *
3070760 TTTACGGTACTA
1 TTCACGGTACTG
3070772 TTCA
1 TTCA
3070776 TAAATACATT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
10 8 0.27
12 22 0.73
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (12 bp):
TTCACGGTACTG
Found at i:3070759 original size:22 final size:22
Alignment explanation
Indices: 3070722--3070776 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 22
3070712 GAAATTTTTC
3070722 ACTATTCATGGTACTGTTCACGGT
1 ACTATTCAT--TACTGTTCACGGT
* *
3070746 ACTGTTCATTACTGTTTACGGT
1 ACTATTCATTACTGTTCACGGT
3070768 ACTATTCAT
1 ACTATTCAT
3070777 AAATACATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 20 0.71
24 8 0.29
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (22 bp):
ACTATTCATTACTGTTCACGGT
Found at i:3072933 original size:2 final size:2
Alignment explanation
Indices: 3072922--3072991 Score: 96
Period size: 2 Copynumber: 37.5 Consensus size: 2
3072912 AATAACATAA
*
3072922 AT AT AT -T AT AT AT -T AT AT AT -T AT A- AA AT A- 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
3072959 AT 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 AT A
3072992 CAATTCGAAA
Statistics
Matches: 62, Mismatches: 1, Indels: 10
0.85 0.01 0.14
Matches are distributed among these distances:
1 5 0.08
2 57 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3074142 original size:21 final size:21
Alignment explanation
Indices: 3074116--3074162 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
3074106 ATATTTAAGT
*
3074116 TTTTTAGTAATTTAATTTTTA
1 TTTTTAGTAATTTAATATTTA
** *
3074137 TTTTTAGTGTTTTTATATTTA
1 TTTTTAGTAATTTAATATTTA
3074158 TTTTT
1 TTTTT
3074163 TGAATATTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.72
Consensus pattern (21 bp):
TTTTTAGTAATTTAATATTTA
Found at i:3086464 original size:82 final size:82
Alignment explanation
Indices: 3086252--3086628 Score: 461
Period size: 82 Copynumber: 4.5 Consensus size: 82
3086242 ATATTATCTC
* * * * *
3086252 AACGGGTGAAGTAATGGTGATGCATTATCATCTTCTGCAACTTTTTATAGGTAATTCAATGCAAA
1 AACGGGTGAAATAAT-G-G-TGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATA
*
3086317 ATTTAAACAA-TTTTCATAA
63 ATTTAAACAACTTTTCAGAA
** * * *
3086336 AATAGGTGAAATAATAGTGGTGCATTATCATATTCTACAACTTTTCAGAGGTCATTCAATGCATT
1 AACGGGTGAAAT-A-A-TGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATA
*
3086401 ATTTAGACAACTTTTCAGAA
63 ATTTAAACAACTTTTCAGAA
* * * *
3086421 AACGGGTGAAATAATGGTGCAATATCATCTTCTGTAACTTTTCAAAGGTCATTCAATTCATAATT
1 AACGGGTGAAATAATGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATT
3086486 TAAACAACTTTTCAGAA
66 TAAACAACTTTTCAGAA
* * * * * *
3086503 AACGTGTGAAATAGTTGTGCATTATCATATTCTGCAACTTTTCAGAGGCCATTCAATGCATTATT
1 AACGGGTGAAATAATGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATT
3086568 TAAACAACTTTTCA-AA
66 TAAACAACTTTTCAGAA
* *
3086584 CAACGGGTGAAATAGTGGTGCATTATCATCTTCTGTAACTTTTCA
1 -AACGGGTGAAATAATGGTGCATTATCATCTTCTGCAACTTTTCA
3086629 ATGATGTATC
Statistics
Matches: 252, Mismatches: 36, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
81 2 0.01
82 169 0.67
83 1 0.00
84 57 0.23
85 20 0.08
86 2 0.01
87 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (82 bp):
AACGGGTGAAATAATGGTGCATTATCATCTTCTGCAACTTTTCAGAGGTCATTCAATGCATAATT
TAAACAACTTTTCAGAA
Found at i:3086558 original size:164 final size:165
Alignment explanation
Indices: 3086251--3086629 Score: 532
Period size: 164 Copynumber: 2.3 Consensus size: 165
3086241 AATATTATCT
* * * *
3086251 CAACGGGTGAAGTAATGGTGATGCATTATCATCTTCTGCAACTTTTTATAGGTAATTCAATGCAA
1 CAACGGGTGAAATAAT-G-G-TGCATTATCATCTTCTGTAACTTTTCAAAGGTAATTCAATGCAA
*
3086316 AATTTAAACAATTTTCATAAAATAGGTGAAATAATAGTGGTGCATTATCATATTCTACAACTTTT
63 AATTTAAACAATTTTCAGAAAATAGGTG-AATAATAGTGGTGCATTATCATATTCTACAACTTTT
* *
3086381 CAGAGGTCATTCAATGCATTATTTAGACAACTTTTCAGAA
127 CAGAGGCCATTCAATGCATTATTTAAACAACTTTTCA-AA
* * * *
3086421 -AACGGGTGAAATAATGGTGCAATATCATCTTCTGTAACTTTTCAAAGGTCATTCAATTCATAAT
1 CAACGGGTGAAATAATGGTGCATTATCATCTTCTGTAACTTTTCAAAGGTAATTCAATGCAAAAT
* * *
3086485 TTAAACAACTTTTCAGAAAA-CGTGTG-A-AATAGTTGTGCATTATCATATTCTGCAACTTTTCA
66 TTAAACAA-TTTTCAGAAAATAG-GTGAATAATAGTGGTGCATTATCATATTCTACAACTTTTCA
3086547 GAGGCCATTCAATGCATTATTTAAACAACTTTTCAAA
129 GAGGCCATTCAATGCATTATTTAAACAACTTTTCAAA
*
3086584 CAACGGGTGAAATAGTGGTGCATTATCATCTTCTGTAACTTTTCAA
1 CAACGGGTGAAATAATGGTGCATTATCATCTTCTGTAACTTTTCAA
3086630 TGATGTATCA
Statistics
Matches: 190, Mismatches: 16, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
163 2 0.01
164 109 0.57
165 1 0.01
166 49 0.26
167 14 0.07
168 1 0.01
169 14 0.07
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (165 bp):
CAACGGGTGAAATAATGGTGCATTATCATCTTCTGTAACTTTTCAAAGGTAATTCAATGCAAAAT
TTAAACAATTTTCAGAAAATAGGTGAATAATAGTGGTGCATTATCATATTCTACAACTTTTCAGA
GGCCATTCAATGCATTATTTAAACAACTTTTCAAA
Found at i:3095893 original size:41 final size:41
Alignment explanation
Indices: 3095872--3095964 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
3095862 ATTTTTGAAG
3095872 GTGTTCATGTTTGGTTCGTGTTCGTTTAAATTTTCAATATC
1 GTGTTCATGTTTGGTTCGTGTTCGTTTAAATTTTCAATATC
3095913 GTGTTCATGTTTGGTTCGTGTTCGTTTAAATTTTCAATATC
1 GTGTTCATGTTTGGTTCGTGTTCGTTTAAATTTTCAATATC
3095954 GTGTTCATGTT
1 GTGTTCATGTT
3095965 CGTTTATTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.52
Consensus pattern (41 bp):
GTGTTCATGTTTGGTTCGTGTTCGTTTAAATTTTCAATATC
Found at i:3096038 original size:24 final size:24
Alignment explanation
Indices: 3095971--3096041 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 24
3095961 TGTTCGTTTA
* *
3095971 TTTATTGTTCATGAACATTTTCA-T
1 TTTA-TGTTCACGAACATGTTCATT
* *
3095995 TTAATGGTCACGAACATGTTCATT
1 TTTATGTTCACGAACATGTTCATT
*
3096019 TTTATGTTCACGAACGTGTTCAT
1 TTTATGTTCACGAACATGTTCAT
3096042 AAACATGTTC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
23 15 0.38
24 24 0.62
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.45
Consensus pattern (24 bp):
TTTATGTTCACGAACATGTTCATT
Found at i:3096072 original size:35 final size:35
Alignment explanation
Indices: 3096007--3096091 Score: 125
Period size: 35 Copynumber: 2.4 Consensus size: 35
3095997 AATGGTCACG
* *
3096007 AACATGTTCATTTTTATGTTCACGAACGTGTTCATA
1 AACATGTTC-GTTTAATGTTCACGAACGTGTTCATA
* *
3096043 AACATGTTCGTTTAATGTTCGCGAGCGTGTTCATA
1 AACATGTTCGTTTAATGTTCACGAACGTGTTCATA
3096078 AACATGTTCGTTTA
1 AACATGTTCGTTTA
3096092 GCGTTCGTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 36 0.80
36 9 0.20
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (35 bp):
AACATGTTCGTTTAATGTTCACGAACGTGTTCATA
Found at i:3096137 original size:24 final size:23
Alignment explanation
Indices: 3096094--3096144 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
3096084 TTCGTTTAGC
*
3096094 GTTCGTTTAATGTTCGCGAATGT
1 GTTCGTTTAATGTTCACGAATGT
*
3096117 GTTCGTTTATCTGTTCACGAATGT
1 GTTCGTTTA-ATGTTCACGAATGT
3096141 GTTC
1 GTTC
3096145 ATGAACAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (23 bp):
GTTCGTTTAATGTTCACGAATGT
Found at i:3096178 original size:70 final size:69
Alignment explanation
Indices: 3096047--3096179 Score: 167
Period size: 70 Copynumber: 1.9 Consensus size: 69
3096037 TTCATAAACA
* * * * **
3096047 TGTTCGTTTAATGTTCGCGAGCGTGTTCATAAACATGTTCGTTTAGCGTTCGTTTAATGTTCGCG
1 TGTTCGTTTAATGTTCACGAACGTGTTCATAAACAAGTTCGTTTAGCATTCAATTAATGTTCGCG
3096112 AATG
66 AATG
* * * *
3096116 TGTTCGTTTATCTGTTCACGAATGTGTTCATGAACAAGTTCGTTTAGCATTCAATTAGTGTTCG
1 TGTTCGTTTA-ATGTTCACGAACGTGTTCATAAACAAGTTCGTTTAGCATTCAATTAATGTTCG
3096180 TTTAGCGTTG
Statistics
Matches: 53, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
69 10 0.19
70 43 0.81
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (69 bp):
TGTTCGTTTAATGTTCACGAACGTGTTCATAAACAAGTTCGTTTAGCATTCAATTAATGTTCGCG
AATG
Found at i:3096195 original size:22 final size:23
Alignment explanation
Indices: 3096153--3096215 Score: 67
Period size: 22 Copynumber: 2.8 Consensus size: 23
3096143 TCATGAACAA
* **
3096153 GTTCGTTTAGCATTC-AATTAGT
1 GTTCGTTTAGCGTTCGTTTTAGT
3096175 GTTCGTTTAGCGTT-GTTTTAGT
1 GTTCGTTTAGCGTTCGTTTTAGT
* *
3096197 GTTTGTTTATCGTTCGTTT
1 GTTCGTTTAGCGTTCGTTT
3096216 ATATATTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
22 30 0.88
23 4 0.12
ACGTcount: A:0.13, C:0.11, G:0.22, T:0.54
Consensus pattern (23 bp):
GTTCGTTTAGCGTTCGTTTTAGT
Found at i:3096434 original size:26 final size:26
Alignment explanation
Indices: 3096395--3096444 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
3096385 GAATTGGGTA
*
3096395 AACGAGTTTGTTCATGAACATAAATG
1 AACGAGTTTATTCATGAACATAAATG
3096421 AACGAGTTTATTCATGAACATAAA
1 AACGAGTTTATTCATGAACATAAA
3096445 CGAATCGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (26 bp):
AACGAGTTTATTCATGAACATAAATG
Found at i:3096506 original size:40 final size:40
Alignment explanation
Indices: 3096462--3096562 Score: 157
Period size: 40 Copynumber: 2.5 Consensus size: 40
3096452 AACACACCTC
* *
3096462 TGTTCGTGTTTGTTTGTTTATTAAATGAACATAAATTTTT
1 TGTTCATGTTCGTTTGTTTATTAAATGAACATAAATTTTT
3096502 TGTTCATGTTCGTTTGTTTATTAAATGAACATAAATTTTTT
1 TGTTCATGTTCGTTTGTTTATTAAATGAACATAAA-TTTTT
* *
3096543 TATTCATGTTCGTTTATTTA
1 TGTTCATGTTCGTTTGTTTA
3096563 GCTTAACAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
40 33 0.59
41 23 0.41
ACGTcount: A:0.25, C:0.07, G:0.13, T:0.55
Consensus pattern (40 bp):
TGTTCATGTTCGTTTGTTTATTAAATGAACATAAATTTTT
Found at i:3098886 original size:10 final size:10
Alignment explanation
Indices: 3098871--3098908 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
3098861 CTTTTACTAA
3098871 ACGCATCGGC
1 ACGCATCGGC
3098881 ACGCATCGGC
1 ACGCATCGGC
*
3098891 CCGCATCGGC
1 ACGCATCGGC
3098901 -CGCATCGG
1 ACGCATCGG
3098909 ATCGCATCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 8 0.30
10 19 0.70
ACGTcount: A:0.16, C:0.42, G:0.32, T:0.11
Consensus pattern (10 bp):
ACGCATCGGC
Found at i:3098914 original size:10 final size:10
Alignment explanation
Indices: 3098872--3098925 Score: 58
Period size: 10 Copynumber: 5.5 Consensus size: 10
3098862 TTTTACTAAA
3098872 CGCATCGG-C
1 CGCATCGGAC
*
3098881 ACGCATCGGCC
1 -CGCATCGGAC
3098892 CGCATCGG-C
1 CGCATCGGAC
*
3098901 CGCATCGGAT
1 CGCATCGGAC
*
3098911 CGCATCAGAC
1 CGCATCGGAC
3098921 CGCAT
1 CGCAT
3098926 TATGTACCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
9 9 0.23
10 29 0.74
11 1 0.03
ACGTcount: A:0.19, C:0.41, G:0.28, T:0.13
Consensus pattern (10 bp):
CGCATCGGAC
Found at i:3098914 original size:19 final size:20
Alignment explanation
Indices: 3098872--3098916 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
3098862 TTTTACTAAA
*
3098872 CGCATCGGCACGCATCGGCC
1 CGCATCGGCACGCATCGGAC
*
3098892 CGCATCGGC-CGCATCGGAT
1 CGCATCGGCACGCATCGGAC
3098911 CGCATC
1 CGCATC
3098917 AGACCGCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.61
20 9 0.39
ACGTcount: A:0.16, C:0.42, G:0.29, T:0.13
Consensus pattern (20 bp):
CGCATCGGCACGCATCGGAC
Found at i:3111019 original size:15 final size:15
Alignment explanation
Indices: 3110999--3111034 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3110989 GTTTTTCATC
3110999 TAAATTTCCTTTCTT
1 TAAATTTCCTTTCTT
*
3111014 TAAATTTCTTTTCTT
1 TAAATTTCCTTTCTT
*
3111029 TCAATT
1 TAAATT
3111035 AATTATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.00, T:0.61
Consensus pattern (15 bp):
TAAATTTCCTTTCTT
Found at i:3121370 original size:55 final size:55
Alignment explanation
Indices: 3121298--3121599 Score: 396
Period size: 55 Copynumber: 5.5 Consensus size: 55
3121288 TGATAAGTCT
* *
3121298 GCTCCCTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAAACGGGTCC
* * *
3121353 GCTCCCTA-TCCGCTCAGGGAGTATAGAACTCGAACAATCTTC-ATAAAATGGGTCC
1 GCTCCCTATTCC-TTCAGAGAGTATAGAACTCGAACAATCTTCAAT-AAACGGGTCC
* * * **
3121408 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATATTCAACAAACGAATCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCC
*
3121463 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAAT-AAACGGGTCC
* * *
3121519 GCTCTCTATTCCTTCAGAGAGTACAGAACTCGGAA-AATCTTCAATAAACAGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCAATAAACGGGTCC
*
3121574 GCTCCATATTCCTTCAGAGAGTATAG
1 GCTCCCTATTCCTTCAGAGAGTATAG
3121600 TTCTCGATAT
Statistics
Matches: 220, Mismatches: 20, Indels: 14
0.87 0.08 0.06
Matches are distributed among these distances:
54 5 0.02
55 159 0.72
56 53 0.24
57 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (55 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGGGTCC
Found at i:3121485 original size:110 final size:110
Alignment explanation
Indices: 3121298--3121599 Score: 407
Period size: 111 Copynumber: 2.7 Consensus size: 110
3121288 TGATAAGTCT
* * * *
3121298 GCTCCCTATTCCTTCAGGGAGTATA-AGACTCGATCAATCTTCAATAAACGGGTCCGCTCCCTA-
1 GCTCTCTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAATAAACGAGTCCGCT-CCTAT
* * *
3121361 TCCGCTCAGGGAGTATAGAACTCGAACAATCTTC-ATAAAATGGGTCC
64 TCC-TTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCC
* * *
3121408 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATATTCAACAAACGAATCCGCTCTCTATT
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGAGTCCGCTC-CTATT
3121473 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCC
65 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCC
*
3121519 GCTCTCTATTCCTTCAGAGAGTACAGAACTCGGAA-AATCTTCAATAAAC-AGGTCCGCTCCATA
1 GCTCTCTATTCCTTCAGAGAGTATAGAACTC-GAACAATCTTCAATAAACGA-GTCCGCTCC-TA
3121582 TTCCTTCAGAGAGTATAG
63 TTCCTTCAGAGAGTATAG
3121600 TTCTCGATAT
Statistics
Matches: 171, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
109 1 0.01
110 82 0.48
111 85 0.50
112 3 0.02
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (110 bp):
GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGAGTCCGCTCCTATTC
CTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAAACGGGTCC
Found at i:3121662 original size:37 final size:36
Alignment explanation
Indices: 3121621--3121692 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
3121611 CATAAAATGA
3121621 GTTTGCTTCACTAATCTTCCATGAAGGCTTACAGATG
1 GTTTGCTTCACTAATCTTCCATGAAGGCTTA-AGATG
* *
3121658 GTTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
1 GTTTGCTTCACTAATCTTCCATGAAGGCTTAAGAT
3121693 TGACCTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.36
Consensus pattern (36 bp):
GTTTGCTTCACTAATCTTCCATGAAGGCTTAAGATG
Found at i:3122983 original size:14 final size:14
Alignment explanation
Indices: 3122960--3122990 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3122950 TTTTCTTTAT
3122960 TTTTTATTTTTCTC
1 TTTTTATTTTTCTC
*
3122974 TTTTTGTTTTTCTC
1 TTTTTATTTTTCTC
3122988 TTT
1 TTT
3122991 CATTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.03, C:0.13, G:0.03, T:0.81
Consensus pattern (14 bp):
TTTTTATTTTTCTC
Found at i:3123024 original size:40 final size:40
Alignment explanation
Indices: 3122974--3123126 Score: 123
Period size: 41 Copynumber: 3.7 Consensus size: 40
3122964 TATTTTTCTC
* *
3122974 TTTTTGTTTTTCTCTTTCATTTTTTCTTCCATTTCCATTT
1 TTTTTCTTTTTCTCTTTCATTTTTTCTTCCATTTTCATTT
* * * *
3123014 TTTTTCTTTTTTTCTTTTCGTTTTTTCCATCAATTTTC-TTT
1 TTTTTCTTTTTCTC-TTTCATTTTTT-CTTCCATTTTCATTT
* * * *
3123055 TTTCTCATTTTTCTTTTCTTCTTTTTCTTCTTCTCATTTTTATTAT
1 TTTTTC-TTTTTC-TCT-TTCATTTT-TTCTTC-CATTTTCATT-T
3123101 TTTTTCTTTTT-T-TTTCATTTTTTCTT
1 TTTTTCTTTTTCTCTTTCATTTTTTCTT
3123127 TTTCTCTTTT
Statistics
Matches: 89, Mismatches: 15, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
40 17 0.19
41 25 0.28
42 15 0.17
43 12 0.13
44 7 0.08
45 7 0.08
46 6 0.07
ACGTcount: A:0.07, C:0.18, G:0.01, T:0.74
Consensus pattern (40 bp):
TTTTTCTTTTTCTCTTTCATTTTTTCTTCCATTTTCATTT
Found at i:3123073 original size:14 final size:14
Alignment explanation
Indices: 3123054--3123095 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
3123044 CAATTTTCTT
3123054 TTTTCTCATTTTTC
1 TTTTCTCATTTTTC
3123068 TTTTCTTC-TTTTTC
1 TTTTC-TCATTTTTC
3123082 TTCTTCTCATTTTT
1 TT-TTCTCATTTTT
3123096 ATTATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 15 0.60
15 10 0.40
ACGTcount: A:0.05, C:0.21, G:0.00, T:0.74
Consensus pattern (14 bp):
TTTTCTCATTTTTC
Found at i:3132880 original size:45 final size:47
Alignment explanation
Indices: 3132808--3132896 Score: 137
Period size: 45 Copynumber: 1.9 Consensus size: 47
3132798 TGCTTTGTTA
*
3132808 TTCACAAAAATAAATCCTAACCACATGATATCTAATTCGCATGCTTG
1 TTCACAAAAATAAATCATAACCACATGATATCTAATTCGCATGCTTG
* *
3132855 TTCA-AAAAATAAA-CATAACCGCATGATATCTAGTTCGCATGC
1 TTCACAAAAATAAATCATAACCACATGATATCTAATTCGCATGC
3132897 ATTTATTTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
45 26 0.67
46 9 0.23
47 4 0.10
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.28
Consensus pattern (47 bp):
TTCACAAAAATAAATCATAACCACATGATATCTAATTCGCATGCTTG
Found at i:3137463 original size:13 final size:13
Alignment explanation
Indices: 3137444--3137476 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3137434 TTTGTTTAAA
3137444 TTCATTTTTTATT
1 TTCATTTTTTATT
*
3137457 TTTATTTTTTATT
1 TTCATTTTTTATT
3137470 TTCATTT
1 TTCATTT
3137477 GACGTTTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (13 bp):
TTCATTTTTTATT
Found at i:3137467 original size:26 final size:27
Alignment explanation
Indices: 3137424--3137476 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
3137414 GCAACTCATA
3137424 TTTAATTTAATTTGTTTAAATTCATTT
1 TTTAATTTAATTTGTTTAAATTCATTT
* * **
3137451 TTTATTTTTATTT-TTTATTTTCATTT
1 TTTAATTTAATTTGTTTAAATTCATTT
3137477 GACGTTTTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.72
Consensus pattern (27 bp):
TTTAATTTAATTTGTTTAAATTCATTT
Found at i:3138608 original size:19 final size:20
Alignment explanation
Indices: 3138586--3138637 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
3138576 TATGATAAAG
3138586 ATAAAAAG-AAAATAGATAA
1 ATAAAAAGTAAAATAGATAA
* *
3138605 ATAAATGAGTAAAATATATAA
1 ATAAA-AAGTAAAATAGATAA
3138626 A-AAAAAGTAAAA
1 ATAAAAAGTAAAA
3138638 GCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (20 bp):
ATAAAAAGTAAAATAGATAA
Found at i:3138720 original size:8 final size:8
Alignment explanation
Indices: 3138707--3138764 Score: 64
Period size: 8 Copynumber: 7.2 Consensus size: 8
3138697 GTAAAATAGG
3138707 AAATATAT
1 AAATATAT
3138715 AAATATAT
1 AAATATAT
*
3138723 ATATATAT
1 AAATATAT
*
3138731 ATATATAT
1 AAATATAT
*
3138739 ATATATAT
1 AAATATAT
*
3138747 ATATATAT
1 AAATATAT
3138755 ATAATA-AT
1 A-AATATAT
3138763 AA
1 AA
3138765 CACTAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
7 1 0.02
8 43 0.91
9 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAATATAT
Found at i:3138722 original size:2 final size:2
Alignment explanation
Indices: 3138709--3138757 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3138699 AAAATAGGAA
*
3138709 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3138751 AT AT AT A
1 AT AT AT A
3138758 ATAATAACAC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3139263 original size:37 final size:37
Alignment explanation
Indices: 3139170--3139271 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
3139160 GTGCTTGTGG
* * * * *
3139170 ATCATATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
3139207 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCATATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* *
3139244 ATCCTATTTTTAGGAGTTTGAATTCTAG
1 ATCATATTTTTAGGAGTTTGAATCCTAG
3139272 TAAGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:3140290 original size:106 final size:106
Alignment explanation
Indices: 3139991--3141028 Score: 1509
Period size: 106 Copynumber: 9.9 Consensus size: 106
3139981 ATCCTCCATC
* ** * ** *
3139991 GTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAACCAGTTGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
* *
3140056 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * * * ***
3140097 ATGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACAATCAGCCACCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
** * *
3140156 GAAGTTGGGCTTGTGTTGTCTTGG-GTCCAAGATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCT
* * *
3140197 GAGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
3140262 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
*
3140303 GTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
3140368 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * * * * * *
3140409 GCGAAGTTGAAACTGGCTCTGAAATTGGGAAATT-ATTGTTGACAACCAACCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
* *
3140473 GAAGTTGAACTTGTGTTGTCTTGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * * * * *
3140514 GTGAAGTTAAAATTGGCTCTGAAATTGAGAAGTTATTTGTTGACAACCAGTGGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
*
3140579 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTTGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
*
3140620 GTGAAGTTGAAATTGGCTCTGAAATT-GGAAAGTTGTTTATTGACAACCAGTGGTCCCTTCGTCG
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAA-TTGTTTATTGACAACCAGCGGTCCCTTCGTCG
*
3140684 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCACT
65 TGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * * *
3140726 GTGAAGTTGAAATTGGCTATGAAATTGGGAAATTATTTATTGACAACCAGTGGTCCCTTCGTCAT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
3140791 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * *
3140832 GTGAAGTTAAAATTGGCTCTGAAATTGGGAAATTGTTTATTTACAACCAGCGGTCCCTTTGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
3140897 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
66 GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
* * *
3140938 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTCGT
1 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
* *
3141003 GAAGTTGAACTTGTGTTGTCTCGAGT
66 GAAGTTGAACTTGCGTTGTCTGGAGT
3141029 GGCACGATAT
Statistics
Matches: 842, Mismatches: 79, Indels: 22
0.89 0.08 0.02
Matches are distributed among these distances:
100 76 0.09
101 5 0.01
102 5 0.01
104 3 0.00
105 102 0.12
106 646 0.77
107 5 0.01
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGT
GAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCT
Found at i:3142636 original size:20 final size:19
Alignment explanation
Indices: 3142599--3142680 Score: 78
Period size: 20 Copynumber: 4.3 Consensus size: 19
3142589 TTTTTGTCCC
*
3142599 TTTTTCTTTTTGAT-TTTTG
1 TTTTTCTTTTT-TTCTTTTG
3142618 TTCTTTCTTTTTTTCTTTTG
1 TT-TTTCTTTTTTTCTTTTG
* *
3142638 TTTCTC-TTTTTTCTTTTT
1 TTTTTCTTTTTTTCTTTTG
* *
3142656 TTTTTCTTTTGCTTCTTTTC
1 TTTTTCTTTT-TTTCTTTTG
3142676 TTTTT
1 TTTTT
3142681 TGTTCTTGAT
Statistics
Matches: 53, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
18 16 0.30
19 9 0.17
20 28 0.53
ACGTcount: A:0.01, C:0.13, G:0.05, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTTTTCTTTTG
Found at i:3142649 original size:18 final size:18
Alignment explanation
Indices: 3142621--3142665 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
3142611 ATTTTTGTTC
3142621 TTTCT-TTTTTTCTTTTG
1 TTTCTCTTTTTTCTTTTG
*
3142638 TTTCTCTTTTTTCTTTTT
1 TTTCTCTTTTTTCTTTTG
*
3142656 TTTTTCTTTT
1 TTTCTCTTTT
3142666 GCTTCTTTTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (18 bp):
TTTCTCTTTTTTCTTTTG
Found at i:3142650 original size:9 final size:8
Alignment explanation
Indices: 3142621--3142681 Score: 70
Period size: 8 Copynumber: 7.2 Consensus size: 8
3142611 ATTTTTGTTC
3142621 TTTCTTTT
1 TTTCTTTT
3142629 TTTCTTTT
1 TTTCTTTT
3142637 GTTTCTCTTT
1 -TTTCT-TTT
3142647 TTTCTTTT
1 TTTCTTTT
3142655 TTT-TTTCT
1 TTTCTTT-T
*
3142663 TTTGCTTCT
1 TTT-CTTTT
3142672 TTTCTTTT
1 TTTCTTTT
3142680 TT
1 TT
3142682 GTTCTTGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
7 3 0.07
8 24 0.52
9 14 0.30
10 5 0.11
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (8 bp):
TTTCTTTT
Found at i:3142658 original size:29 final size:31
Alignment explanation
Indices: 3142613--3142671 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 31
3142603 TCTTTTTGAT
*
3142613 TTTTGTTCTTTCTTTTTTTCTTTTGTTTCTC
1 TTTTGTTCTTTCTTTTTTTCTTTTGCTTCTC
3142644 TTTT-TTCTTT-TTTTTTTCTTTTGCTTCT
1 TTTTGTTCTTTCTTTTTTTCTTTTGCTTCT
3142672 TTTCTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 17 0.63
30 6 0.22
31 4 0.15
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (31 bp):
TTTTGTTCTTTCTTTTTTTCTTTTGCTTCTC
Found at i:3147324 original size:19 final size:20
Alignment explanation
Indices: 3147302--3147353 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
3147292 TAGGATAAAG
3147302 ATAAAAAG-AAAATAGATAA
1 ATAAAAAGTAAAATAGATAA
* *
3147321 ATAAATGAGTAAAATATATAA
1 ATAAA-AAGTAAAATAGATAA
3147342 A-AAAAAGTAAAA
1 ATAAAAAGTAAAA
3147354 GCATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (20 bp):
ATAAAAAGTAAAATAGATAA
Found at i:3147436 original size:2 final size:2
Alignment explanation
Indices: 3147429--3147461 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3147419 AAAATAGGAA
3147429 AT 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 AT A
3147462 ATAACACTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3147964 original size:37 final size:37
Alignment explanation
Indices: 3147871--3147972 Score: 132
Period size: 37 Copynumber: 2.8 Consensus size: 37
3147861 GTGTTTGTGG
* * * * *
3147871 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
*
3147908 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
* *
3147945 ATCCTATTTTTAGAAGTTTGAATTCTAG
1 ATCCTATTTTTAGGAGTTTGAATCCTAG
3147973 TAGGACGAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAACTCT
Found at i:3153862 original size:28 final size:28
Alignment explanation
Indices: 3153826--3153882 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
3153816 ATTGATATTA
*
3153826 GGGTTAGAATATTGATACTCCCAGTAGG
1 GGGTTAGAATATCGATACTCCCAGTAGG
*
3153854 GGGTTAGAATATCGATACTCCTAGTAGG
1 GGGTTAGAATATCGATACTCCCAGTAGG
3153882 G
1 G
3153883 TATCGATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.28
Consensus pattern (28 bp):
GGGTTAGAATATCGATACTCCCAGTAGG
Found at i:3154551 original size:20 final size:20
Alignment explanation
Indices: 3154526--3154564 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
3154516 TTGGACACGA
3154526 GTATCGATATTAGAATAATC
1 GTATCGATATTAGAATAATC
3154546 GTATCGATATTAGAATAAT
1 GTATCGATATTAGAATAAT
3154565 TTCGCTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (20 bp):
GTATCGATATTAGAATAATC
Found at i:3166389 original size:2 final size:2
Alignment explanation
Indices: 3166382--3166420 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3166372 TATCATGCCT
3166382 TA TA TA 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 TA TA TA T
3166421 TTTGCATTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.