Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167949.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_21, 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: 19848060
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Warning! 113000 characters in sequence are not A, C, G, or T
File 8 of 138
Found at i:2153568 original size:16 final size:17
Alignment explanation
Indices: 2153547--2153578 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2153537 TTTTAAATCG
2153547 ATTTTTT-AATTTTTTA
1 ATTTTTTAAATTTTTTA
2153563 ATTTTTTAAATTTTTT
1 ATTTTTTAAATTTTTT
2153579 TCTCACGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTTTAAATTTTTTA
Found at i:2155700 original size:54 final size:54
Alignment explanation
Indices: 2155642--2155744 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
2155632 GACACAGATT
* *
2155642 AATGATG-AGCAAAACCAGTTTCACTCTTCCATACATGATAAGGAGGAAACGAAA
1 AATGATGAAG-AAAACCAGTTTCAATCTTCCATACACGATAAGGAGGAAACGAAA
**
2155696 AATGATGAAGAAAACCAGTTTCAATCTTCTGTACACGATAAGGAGGAAA
1 AATGATGAAGAAAACCAGTTTCAATCTTCCATACACGATAAGGAGGAAA
2155745 ATAGTATCGT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 42 0.95
55 2 0.05
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (54 bp):
AATGATGAAGAAAACCAGTTTCAATCTTCCATACACGATAAGGAGGAAACGAAA
Found at i:2166235 original size:13 final size:12
Alignment explanation
Indices: 2166186--2166252 Score: 59
Period size: 12 Copynumber: 5.6 Consensus size: 12
2166176 ATTAAATATG
2166186 AAAATTTTTTAA-
1 AAAA-TTTTTAAT
2166198 AAAA--TTTAAT
1 AAAATTTTTAAT
* *
2166208 ATATTTTTTAGAT
1 AAAATTTTTA-AT
2166221 AAATATTTTTAAT
1 AAA-ATTTTTAAT
*
2166234 AAAAATTTTAAT
1 AAAATTTTTAAT
2166246 AAAATTT
1 AAAATTT
2166253 GTACAGTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
9 5 0.11
10 2 0.05
12 22 0.50
13 9 0.20
14 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (12 bp):
AAAATTTTTAAT
Found at i:2166582 original size:2 final size:2
Alignment explanation
Indices: 2166575--2166614 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2166565 CAGCTAACGT
2166575 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
2166615 CTTACTTTAG
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):
TA
Found at i:2168497 original size:12 final size:13
Alignment explanation
Indices: 2168480--2168508 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2168470 TAATAAGATC
2168480 TTTTAATTTT-AT
1 TTTTAATTTTAAT
2168492 TTTTAATTTTAAT
1 TTTTAATTTTAAT
2168505 TTTT
1 TTTT
2168509 TTATTTAATC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:2168994 original size:18 final size:16
Alignment explanation
Indices: 2168957--2169032 Score: 50
Period size: 15 Copynumber: 4.8 Consensus size: 16
2168947 CTAATCTAGC
2168957 ATTTATAATATTATAT
1 ATTTATAATATTATAT
*
2168973 -TTTATAATAATTCGTAT
1 ATTTATAAT-ATT-ATAT
*
2168990 ATTTATATTA-TATA-
1 ATTTATAATATTATAT
** * *
2169004 AAATATAAAAATTATGT
1 ATTTAT-AATATTATAT
2169021 ATTTATAATATT
1 ATTTATAATATT
2169033 TTTTAATAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
14 4 0.09
15 12 0.28
16 12 0.28
17 8 0.19
18 7 0.16
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTATAATATTATAT
Found at i:2169104 original size:11 final size:11
Alignment explanation
Indices: 2169084--2169132 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
2169074 AATATAAAAT
*
2169084 ATTTTTTTAAA
1 ATTTTATTAAA
2169095 ATTTTATT-AA
1 ATTTTATTAAA
*
2169105 A-TTTATATATA
1 ATTTTAT-TAAA
2169116 ATTTTATTAAA
1 ATTTTATTAAA
2169127 ATTTTA
1 ATTTTA
2169133 AATCGTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
9 5 0.16
10 4 0.12
11 18 0.56
12 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTATTAAA
Found at i:2169108 original size:21 final size:21
Alignment explanation
Indices: 2169084--2169132 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
2169074 AATATAAAAT
*
2169084 ATTTTTTTAAAATTTTATTAA
1 ATTTTTATAAAATTTTATTAA
* *
2169105 ATTTATATATAATTTTATTAA
1 ATTTTTATAAAATTTTATTAA
*
2169126 AATTTTA
1 ATTTTTA
2169133 AATCGTATTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTTTTATAAAATTTTATTAA
Found at i:2169315 original size:37 final size:37
Alignment explanation
Indices: 2169265--2169339 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
2169255 CATCTCACAT
2169265 TTGTTAGTAAACTACACTAATAATACTACAGGAGATA
1 TTGTTAGTAAACTACACTAATAATACTACAGGAGATA
*
2169302 TTGTTAGTAAACTACACTAATAATACTACAGGATATA
1 TTGTTAGTAAACTACACTAATAATACTACAGGAGATA
2169339 T
1 T
2169340 ATATATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.13, G:0.12, T:0.32
Consensus pattern (37 bp):
TTGTTAGTAAACTACACTAATAATACTACAGGAGATA
Found at i:2169341 original size:2 final size:2
Alignment explanation
Indices: 2169334--2169366 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2169324 ATACTACAGG
*
2169334 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2169367 AAACTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2178337 original size:39 final size:39
Alignment explanation
Indices: 2178263--2178342 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
2178253 AGACCTTCGC
*
2178263 TTTTGAAATCGATTTCAATAACATTAAATTAACAGTTCA
1 TTTTGAAATCGATTTCAATAAAATTAAATTAACAGTTCA
* * *
2178302 TTTTCGAAATTGATTT-GATAAAATTGAATTAACAGTTCA
1 TTTT-GAAATCGATTTCAATAAAATTAAATTAACAGTTCA
2178341 TT
1 TT
2178343 GTCGCATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
39 26 0.72
40 10 0.28
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (39 bp):
TTTTGAAATCGATTTCAATAAAATTAAATTAACAGTTCA
Found at i:2183377 original size:2 final size:2
Alignment explanation
Indices: 2183370--2183401 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2183360 TTATACCTAC
*
2183370 AT AT AT AT AT AT GT 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
2183402 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2186908 original size:22 final size:22
Alignment explanation
Indices: 2186853--2186913 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
2186843 TATAAATATA
* *
2186853 AAATATAAAAATAATATTATTT
1 AAATTTAATAATAATATTATTT
2186875 AAATTTTGAATAATAAT-TATATTT
1 AAA-TTT-AATAATAATAT-TATTT
2186899 AAATTTAATAA-AATA
1 AAATTTAATAATAATA
2186914 AAAAATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
21 3 0.09
22 8 0.24
23 6 0.18
24 16 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AAATTTAATAATAATATTATTT
Found at i:2186914 original size:24 final size:23
Alignment explanation
Indices: 2186860--2186904 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
2186850 ATAAAATATA
2186860 AAAATAATATTATTTAAATTTTG
1 AAAATAATATTATTTAAATTTTG
2186883 AATAATAAT-TATATTTAAATTT
1 AA-AATAATAT-TATTTAAATTT
2186905 AATAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
AAAATAATATTATTTAAATTTTG
Found at i:2187726 original size:10 final size:10
Alignment explanation
Indices: 2187702--2187751 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
2187692 TTATCCATCC
2187702 TTTTATTTA-
1 TTTTATTTAT
2187711 -TTTATTTAT
1 TTTTATTTAT
2187720 TTTTA-TTAT
1 TTTTATTTAT
**
2187729 TGATATTTAT
1 TTTTATTTAT
*
2187739 TTTCATTTAT
1 TTTTATTTAT
2187749 TTT
1 TTT
2187752 CTCCCCATAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
8 8 0.24
9 7 0.21
10 18 0.55
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (10 bp):
TTTTATTTAT
Found at i:2187870 original size:2 final size:2
Alignment explanation
Indices: 2187863--2187894 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2187853 CCTTTCTTTC
2187863 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2187895 TTTAAAGAAC
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2203639 original size:17 final size:15
Alignment explanation
Indices: 2203614--2203655 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
2203604 TTTTTGTTAA
*
2203614 TAAATAATTTATAAGTT
1 TAAAAAATTTATAA--T
2203631 TAAAAAATTTATAAT
1 TAAAAAATTTATAAT
2203646 T-AAAAATTTA
1 TAAAAAATTTA
2203656 ATAAATCTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 9 0.38
15 2 0.08
17 13 0.54
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
TAAAAAATTTATAAT
Found at i:2206620 original size:16 final size:16
Alignment explanation
Indices: 2206599--2206638 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2206589 ATTTTTTATT
*
2206599 ATAAATATAAATTTAA
1 ATAAATATAAATATAA
2206615 ATAAATATAAATATAA
1 ATAAATATAAATATAA
*
2206631 TTAAATAT
1 ATAAATAT
2206639 TTAAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAATATAAATATAA
Found at i:2206638 original size:10 final size:10
Alignment explanation
Indices: 2206600--2206656 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
2206590 TTTTTTATTA
2206600 TAAATATAAATT
1 TAAATAT-AA-T
2206612 TAAATA-AAT
1 TAAATATAAT
2206621 ATAAATATAAT
1 -TAAATATAAT
2206632 TAAATAT--T
1 TAAATATAAT
2206640 TAAA-ATAAT
1 TAAATATAAT
*
2206649 TATATATA
1 TAAATATA
2206657 TCAAATCGAA
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
7 2 0.05
8 5 0.13
9 5 0.13
10 18 0.46
11 3 0.08
12 6 0.15
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TAAATATAAT
Found at i:2206662 original size:17 final size:17
Alignment explanation
Indices: 2206619--2206662 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
2206609 ATTTAAATAA
2206619 ATATAAATATAATTAAAT
1 ATATAAA-ATAATTAAAT
* *
2206637 ATTTAAAATAATTATAT
1 ATATAAAATAATTAAAT
*
2206654 ATATCAAAT
1 ATATAAAAT
2206663 CGAATTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAAAATAATTAAAT
Found at i:2212298 original size:15 final size:15
Alignment explanation
Indices: 2212278--2212308 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2212268 AAGTTACTGG
2212278 TTTATGGCTCTCAAA
1 TTTATGGCTCTCAAA
2212293 TTTATGGCTCTCAAA
1 TTTATGGCTCTCAAA
2212308 T
1 T
2212309 CCTTGGTTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.13, T:0.42
Consensus pattern (15 bp):
TTTATGGCTCTCAAA
Found at i:2213545 original size:5 final size:5
Alignment explanation
Indices: 2213535--2213559 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2213525 TCAACGTCGA
2213535 TAGTT TAGTT TAGTT TAGTT TAGTT
1 TAGTT TAGTT TAGTT TAGTT TAGTT
2213560 GAGAGGTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TAGTT
Found at i:2232102 original size:4 final size:4
Alignment explanation
Indices: 2232093--2232130 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
2232083 GTCTAATTCT
2232093 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT- TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT
2232131 ACCGTTTGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.09
4 30 0.91
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTTC
Found at i:2238105 original size:27 final size:26
Alignment explanation
Indices: 2238052--2238114 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
2238042 CATTGTTAAT
* *
2238052 TATAATTTATTATAAAAAAATAGTTA
1 TATAATTAATTATAAAAAAATAATTA
*
2238078 TCATAATTAATTA-ATAAAAGATAATTA
1 T-ATAATTAATTATA-AAAAAATAATTA
2238105 T-TAATTAATT
1 TATAATTAATT
2238115 TTTTATCTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 9 0.28
26 2 0.06
27 21 0.66
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (26 bp):
TATAATTAATTATAAAAAAATAATTA
Found at i:2238178 original size:25 final size:25
Alignment explanation
Indices: 2238150--2238203 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
2238140 ATTAATTAAT
*
2238150 AAAATTTAATCATAATCAATTAAGA
1 AAAAATTAATCATAATCAATTAAGA
* * * *
2238175 AAAAATTAATCCTACTTAATTAATA
1 AAAAATTAATCATAATCAATTAAGA
2238200 AAAA
1 AAAA
2238204 CAAAATTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.31
Consensus pattern (25 bp):
AAAAATTAATCATAATCAATTAAGA
Found at i:2238219 original size:25 final size:25
Alignment explanation
Indices: 2238150--2238224 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 25
2238140 ATTAATTAAT
* *
2238150 AAAATTTAATCATAATCAATTAAGA
1 AAAAATTAATCATAATCAATTAAAA
*
2238175 AAAAATTAATCCTACTTAATTAA-TAAAA
1 AAAAATTAAT-C-A--TAATCAATTAAAA
*
2238203 ACAAAATTAATCATAATAAATT
1 A-AAAATTAATCATAATCAATT
2238225 GATAACAATA
Statistics
Matches: 40, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
25 15 0.38
26 2 0.05
27 2 0.05
28 6 0.15
29 15 0.38
ACGTcount: A:0.57, C:0.09, G:0.01, T:0.32
Consensus pattern (25 bp):
AAAAATTAATCATAATCAATTAAAA
Found at i:2238237 original size:29 final size:28
Alignment explanation
Indices: 2238147--2238237 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
2238137 TTAATTAATT
* *
2238147 AATAAAATTTAATCATAATCAA-T-TAAG
1 AATAAAA-TTAATCATAATAAATTATAAA
* * *
2238174 AA-AAAATTAATCCTACTTAATTAATAAA
1 AATAAAATTAATCATAATAAATT-ATAAA
* *
2238202 AACAAAATTAATCATAATAAATTGATAAC
1 AATAAAATTAATCATAATAAATT-ATAAA
2238231 AATAAAA
1 AATAAAA
2238238 ATGCCCAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
25 11 0.22
26 5 0.10
27 2 0.04
28 5 0.10
29 27 0.54
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (28 bp):
AATAAAATTAATCATAATAAATTATAAA
Found at i:2246265 original size:2 final size:2
Alignment explanation
Indices: 2246258--2246285 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2246248 CTTAATTACC
2246258 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
2246286 TTATGAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2250858 original size:21 final size:22
Alignment explanation
Indices: 2250834--2250878 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2250824 TATTTAATAC
*
2250834 ATAAGATTATAATA-AAATAAG
1 ATAAGATGATAATATAAATAAG
*
2250855 ATAAGATGATATTATAAATAAG
1 ATAAGATGATAATATAAATAAG
2250877 AT
1 AT
2250879 TATATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.58, C:0.00, G:0.11, T:0.31
Consensus pattern (22 bp):
ATAAGATGATAATATAAATAAG
Found at i:2250877 original size:17 final size:18
Alignment explanation
Indices: 2250850--2250885 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2250840 TTATAATAAA
2250850 ATAAGATAAGATGATATT
1 ATAAGATAAGATGATATT
*
2250868 ATAA-ATAAGATTATATT
1 ATAAGATAAGATGATATT
2250885 A
1 A
2250886 AATAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (18 bp):
ATAAGATAAGATGATATT
Found at i:2254713 original size:18 final size:19
Alignment explanation
Indices: 2254681--2254719 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2254671 ATAAATTATG
**
2254681 ATATAATTTTTATATA-AA
1 ATATAATTTAAATATATAA
2254699 ATATAATTTAAATATATAA
1 ATATAATTTAAATATATAA
2254718 AT
1 AT
2254720 TTTAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAATTTAAATATATAA
Found at i:2254713 original size:29 final size:29
Alignment explanation
Indices: 2254609--2254714 Score: 76
Period size: 30 Copynumber: 3.7 Consensus size: 29
2254599 TTTAAAATTT
* *
2254609 TAAATA-ATAATTAT-ATATAAATTTAATA
1 TAAATATA-AATTATAATATAATTTTTATA
* * * *
2254637 -AAATAAAAAATATATTTTATATTTTTATA
1 TAAATATAAATTATAATATA-ATTTTTATA
* *
2254666 TTAATATAAATTATGATATAATTTTTATA
1 TAAATATAAATTATAATATAATTTTTATA
*
2254695 TAAAATATAATTTA-AATATA
1 T-AAATATAAATTATAATATA
2254715 TAAATTTTAA
Statistics
Matches: 59, Mismatches: 14, Indels: 9
0.72 0.17 0.11
Matches are distributed among these distances:
27 10 0.17
28 4 0.07
29 22 0.37
30 23 0.39
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (29 bp):
TAAATATAAATTATAATATAATTTTTATA
Found at i:2254843 original size:18 final size:18
Alignment explanation
Indices: 2254820--2254854 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2254810 AAATAAATTT
2254820 TAAAAAATAAAAAGGAAA
1 TAAAAAATAAAAAGGAAA
*
2254838 TAAAAAATAAAGAGGAA
1 TAAAAAATAAAAAGGAA
2254855 GACAGAAGAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (18 bp):
TAAAAAATAAAAAGGAAA
Found at i:2255762 original size:2 final size:2
Alignment explanation
Indices: 2255755--2255782 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2255745 GAGACTTCCC
2255755 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
2255783 GCAATTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2264257 original size:3 final size:3
Alignment explanation
Indices: 2264180--2264241 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
2264170 GTGACGACAT
* * *
2264180 TTC TCC TTC TTTC TTC TTC TTC TTC TTC TTC TTC TAC TTC TTC CTC
1 TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
**
2264226 TTC GCC TTC TTC TTC T
1 TTC TTC TTC TTC TTC T
2264242 CCGCATTACT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
3 45 0.94
4 3 0.06
ACGTcount: A:0.02, C:0.37, G:0.02, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:2268441 original size:12 final size:12
Alignment explanation
Indices: 2268403--2268450 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
2268393 AATTTTCATC
*
2268403 TAATTGAAATTAA
1 TAATT-AAATAAA
*
2268416 -AATT-AATCAA
1 TAATTAAATAAA
2268426 TAATTAAATAAA
1 TAATTAAATAAA
2268438 TAATTAAATAAA
1 TAATTAAATAAA
2268450 T
1 T
2268451 TTTAAATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 5 0.16
11 4 0.13
12 22 0.71
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (12 bp):
TAATTAAATAAA
Found at i:2275201 original size:39 final size:39
Alignment explanation
Indices: 2275147--2275224 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
2275137 AAATAATATG
2275147 AATTGTGTTAAGATTGGAAAGTGCCTTATCTACAGTTAA
1 AATTGTGTTAAGATTGGAAAGTGCCTTATCTACAGTTAA
2275186 AATTGTGTTAAGATTGGAAAGTGCCTTATCTACAGTTAA
1 AATTGTGTTAAGATTGGAAAGTGCCTTATCTACAGTTAA
2275225 CAGACTCAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.33, C:0.10, G:0.21, T:0.36
Consensus pattern (39 bp):
AATTGTGTTAAGATTGGAAAGTGCCTTATCTACAGTTAA
Found at i:2282921 original size:19 final size:19
Alignment explanation
Indices: 2282897--2282950 Score: 56
Period size: 22 Copynumber: 2.7 Consensus size: 19
2282887 ATAAAAATGA
*
2282897 AATAATTTAAAATTTTAAT
1 AATAATTTAAAAATTTAAT
2282916 AATAATTATATATAAATTTAAT
1 AATAATT-TA-A-AAATTTAAT
2282938 AA-AATTTTAAAAA
1 AATAA-TTTAAAAA
2282951 AAAATTTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 10 0.33
20 3 0.10
21 5 0.17
22 12 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATAATTTAAAAATTTAAT
Found at i:2287347 original size:13 final size:13
Alignment explanation
Indices: 2287329--2287365 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2287319 TTCAGTTTAG
2287329 ATTAAATTTAGAT
1 ATTAAATTTAGAT
* *
2287342 ATTAAATGTATAT
1 ATTAAATTTAGAT
2287355 ATTAAATTTAG
1 ATTAAATTTAG
2287366 GTGATATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTAAATTTAGAT
Found at i:2287445 original size:19 final size:18
Alignment explanation
Indices: 2287421--2287463 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
2287411 CTAAACAAAA
2287421 TTATAT-ATTTTACTAGTTT
1 TTATATAATTTTA-TA-TTT
2287440 TTATATACATTTTATATTT
1 TTATATA-ATTTTATATTT
2287459 TTATA
1 TTATA
2287464 AAATAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 14 0.64
20 2 0.09
21 6 0.27
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTATATAATTTTATATTT
Found at i:2287451 original size:21 final size:19
Alignment explanation
Indices: 2287422--2287463 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
2287412 TAAACAAAAT
*
2287422 TATATATTTTACTAGTTTTTA
1 TATACATTTTA-TA-TTTTTA
2287443 TATACATTTTATATTTTTA
1 TATACATTTTATATTTTTA
2287462 TA
1 TA
2287464 AAATAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 2 0.10
21 10 0.50
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (19 bp):
TATACATTTTATATTTTTA
Found at i:2287500 original size:9 final size:9
Alignment explanation
Indices: 2287481--2287543 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 9
2287471 ATAATTATTT
2287481 TATATTTAAA
1 TATA-TTAAA
2287491 TATATTAAA
1 TATATTAAA
2287500 TATATTAAAAA
1 TATATT--AAA
2287511 TTATATTAAA
1 -TATATTAAA
2287521 TAATATATAAAA
1 T-ATAT-T-AAA
2287533 TATAATTAAA
1 TAT-ATTAAA
2287543 T
1 T
2287544 TTTAAAAATA
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
9 12 0.26
10 15 0.33
11 7 0.15
12 12 0.26
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
TATATTAAA
Found at i:2287517 original size:12 final size:11
Alignment explanation
Indices: 2287488--2287542 Score: 55
Period size: 12 Copynumber: 5.1 Consensus size: 11
2287478 TTTTATATTT
2287488 AAATATATT--
1 AAATATATTAA
2287497 AAATATATTAA
1 AAATATATTAA
2287508 AAATTATATTAA
1 AAA-TATATTAA
2287520 ATAATATA-T-A
1 A-AATATATTAA
2287530 AAATATAATTAA
1 AAATAT-ATTAA
2287542 A
1 A
2287543 TTTTAAAAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 14 0.36
10 3 0.08
11 5 0.13
12 15 0.38
13 2 0.05
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAATATATTAA
Found at i:2287517 original size:21 final size:21
Alignment explanation
Indices: 2287491--2287552 Score: 69
Period size: 21 Copynumber: 3.0 Consensus size: 21
2287481 TATATTTAAA
2287491 TATATTAAATATATTAAAAAT
1 TATATTAAATATATTAAAAAT
2287512 TATATTAAATA-ATATATAAAA-
1 TATATTAAATATAT-TA-AAAAT
2287533 TATAATTAAAT-T-TTAAAAAT
1 TAT-ATTAAATATATTAAAAAT
2287553 AAATAAACTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
19 4 0.11
20 4 0.11
21 17 0.47
22 11 0.31
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TATATTAAATATATTAAAAAT
Found at i:2287683 original size:180 final size:181
Alignment explanation
Indices: 2287490--2287847 Score: 664
Period size: 180 Copynumber: 2.0 Consensus size: 181
2287480 TTATATTTAA
2287490 ATATATTAAATATATTAAAAATTATATTAAATAATATATAAAATATAATTAAATTTTAAAAATAA
1 ATATATTAAATATATTAAAAATTATATTAAATAATATATAAAATATAATTAAATTTTAAAAATAA
* *
2287555 ATAAACTAAACAGATAAAATTTAATTTGAATTGAATAATATGAAAATTCGATTCAGATTCAAATT
66 ATAAACTAAACAGATAAAATTTAATTTGAATTGAATAATATGAAAATTCGATTAAGATTCAAACT
2287620 AAATTATTAAATTTCATAATTTTATATATTATTCAAAAAAATTACATATTT
131 AAATTATTAAATTTCATAATTTTATATATTATTCAAAAAAATTACATATTT
* *
2287671 ATAT-TTAAATATATTAAAAATTATATTAAATAATATATATAATATAATTAAATTTTAAAAATCA
1 ATATATTAAATATATTAAAAATTATATTAAATAATATATAAAATATAATTAAATTTTAAAAATAA
*
2287735 ATAAACTAAATAGATAAAATTTAATTTGAATTGAATAATATGAAAATTCGATTAAGATTCAAACT
66 ATAAACTAAACAGATAAAATTTAATTTGAATTGAATAATATGAAAATTCGATTAAGATTCAAACT
2287800 AAATTATTAAATTTCATAATTTTATATATTATTCAAAAAAATTACATA
131 AAATTATTAAATTTCATAATTTTATATATTATTCAAAAAAATTACATA
2287848 AAATCCAATT
Statistics
Matches: 172, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
180 168 0.98
181 4 0.02
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (181 bp):
ATATATTAAATATATTAAAAATTATATTAAATAATATATAAAATATAATTAAATTTTAAAAATAA
ATAAACTAAACAGATAAAATTTAATTTGAATTGAATAATATGAAAATTCGATTAAGATTCAAACT
AAATTATTAAATTTCATAATTTTATATATTATTCAAAAAAATTACATATTT
Found at i:2287697 original size:12 final size:14
Alignment explanation
Indices: 2287679--2287710 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
2287669 TTATATTTAA
2287679 ATATATTAAA-AAT
1 ATATATTAAATAAT
2287692 -TATATTAAATAAT
1 ATATATTAAATAAT
2287705 ATATAT
1 ATATAT
2287711 AATATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 9 0.53
13 3 0.18
14 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATATATTAAATAAT
Found at i:2294375 original size:27 final size:27
Alignment explanation
Indices: 2294345--2294452 Score: 75
Period size: 27 Copynumber: 4.0 Consensus size: 27
2294335 AACATTTTAT
2294345 TAATTTTAAATTAAATCAAATCAAATA
1 TAATTTTAAATTAAATCAAATCAAATA
* *
2294372 TAATTTTATA-TAATATCAAATTAAAT-
1 TAATTTTAAATTAA-ATCAAATCAAATA
*
2294398 T-ATATTTAAATATAAA-AATAAT-AAA-A
1 TAAT-TTTAAAT-TAAATCA-AATCAAATA
*
2294424 TAATTTATCAAATCAAATCAAATTCAAAT
1 TAATTT-T-AAATTAAATCAAA-TCAAAT
2294453 TTTATATATT
Statistics
Matches: 62, Mismatches: 6, Indels: 23
0.68 0.07 0.25
Matches are distributed among these distances:
25 2 0.03
26 16 0.26
27 32 0.52
28 9 0.15
29 3 0.05
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (27 bp):
TAATTTTAAATTAAATCAAATCAAATA
Found at i:2297453 original size:32 final size:33
Alignment explanation
Indices: 2297409--2297486 Score: 104
Period size: 32 Copynumber: 2.4 Consensus size: 33
2297399 GATCACTTAT
* *
2297409 AATTCTTATGAAGGAAAACTTCCTGATAACTTG
1 AATTCTTCTGAAGCAAAACTTCCTGATAACTTG
* * *
2297442 -ATTCTTCTGAAGCATAGCTTCTTGATAACTTG
1 AATTCTTCTGAAGCAAAACTTCCTGATAACTTG
2297474 AATTCTTCTGAAG
1 AATTCTTCTGAAG
2297487 TAAGAGTGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 27 0.69
33 12 0.31
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (33 bp):
AATTCTTCTGAAGCAAAACTTCCTGATAACTTG
Found at i:2302843 original size:18 final size:17
Alignment explanation
Indices: 2302812--2302879 Score: 77
Period size: 18 Copynumber: 4.0 Consensus size: 17
2302802 ATTTTTAAAT
2302812 TATTTAT-TTAATTTTA
1 TATTTATATTAATTTTA
2302828 TATTTATATATAATTTTA
1 TATTTATAT-TAATTTTA
** *
2302846 TATTTATATTAAAAATAA
1 TATTTATATT-AATTTTA
2302864 TATTT-TATTAATTTTA
1 TATTTATATTAATTTTA
2302880 AATAAGATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
16 11 0.26
17 6 0.14
18 26 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTATATTAATTTTA
Found at i:2302863 original size:23 final size:23
Alignment explanation
Indices: 2302837--2302881 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2302827 ATATTTATAT
*
2302837 ATAAT-TTTATATTTATATTAAAA
1 ATAATATTT-TATTAATATTAAAA
*
2302860 ATAATATTTTATTAATTTTAAA
1 ATAATATTTTATTAATATTAAA
2302882 TAAGATTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATAATATTTTATTAATATTAAAA
Found at i:2306399 original size:16 final size:16
Alignment explanation
Indices: 2306378--2306410 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2306368 TGATAAACGA
*
2306378 ATGATAATGATGATTT
1 ATGATAATGATAATTT
2306394 ATGATAATGATAATTT
1 ATGATAATGATAATTT
2306410 A
1 A
2306411 CGATGACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (16 bp):
ATGATAATGATAATTT
Found at i:2309318 original size:18 final size:18
Alignment explanation
Indices: 2309278--2309318 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
2309268 ATCTCTTGAG
2309278 TCAACATCGGTAGTTGCT
1 TCAACATCGGTAGTTGCT
*
2309296 GCAACATCGGT-GTTGGCT
1 TCAACATCGGTAGTT-GCT
2309314 TCAAC
1 TCAAC
2309319 CTCTTCTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.29
Consensus pattern (18 bp):
TCAACATCGGTAGTTGCT
Found at i:2315208 original size:19 final size:20
Alignment explanation
Indices: 2315184--2315224 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2315174 CTAAATATTC
*
2315184 ATATTTT-TGTATTTTTTAA
1 ATATTTTATATATTTTTTAA
2315203 ATATTTTAATATATTTTTTAA
1 ATATTTT-ATATATTTTTTAA
2315224 A
1 A
2315225 AATCAAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
ATATTTTATATATTTTTTAA
Found at i:2327208 original size:43 final size:43
Alignment explanation
Indices: 2327147--2327235 Score: 160
Period size: 43 Copynumber: 2.1 Consensus size: 43
2327137 AACAAGAACT
*
2327147 TGAAAAAAAATAATACTGAAAGCAAGAGAAGGAGATATATTAA
1 TGAAAAAAAATAATACTGAAAGCAAGAGAAGGAGACATATTAA
*
2327190 TGAAAAAAAATAATACTGAAAGCAGGAGAAGGAGACATATTAA
1 TGAAAAAAAATAATACTGAAAGCAAGAGAAGGAGACATATTAA
2327233 TGA
1 TGA
2327236 CAAAGTGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (43 bp):
TGAAAAAAAATAATACTGAAAGCAAGAGAAGGAGACATATTAA
Found at i:2327437 original size:5 final size:5
Alignment explanation
Indices: 2327427--2327493 Score: 54
Period size: 5 Copynumber: 14.0 Consensus size: 5
2327417 GATAATCTAA
* *
2327427 AATAT AATAT -A-AT AATAT GATAT AAATAT TATAT AA-AT AATA- AATA-
1 AATAT AATAT AATAT AATAT AATAT -AATAT AATAT AATAT AATAT AATAT
*
2327473 AATAAT AATAT AATTT AATAT
1 AAT-AT AATAT AATAT AATAT
2327494 TTTAATAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
3 2 0.04
4 13 0.26
5 28 0.56
6 7 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:2327449 original size:13 final size:13
Alignment explanation
Indices: 2327418--2327492 Score: 68
Period size: 13 Copynumber: 5.8 Consensus size: 13
2327408 GATAGATGTG
*
2327418 ATAATCTAA-AAT
1 ATAATATAATAAT
2327430 ATAATATAATAAT
1 ATAATATAATAAT
*
2327443 ATGATATAAATATTAT
1 ATAATAT-AATA--AT
2327459 ATAA-ATAATAA-
1 ATAATATAATAAT
2327470 ATAA-ATAATAAT
1 ATAATATAATAAT
*
2327482 ATAATTTAATA
1 ATAATATAATA
2327493 TTTTAATAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
11 11 0.21
12 13 0.25
13 14 0.26
14 8 0.15
15 2 0.04
16 5 0.09
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (13 bp):
ATAATATAATAAT
Found at i:2327473 original size:22 final size:24
Alignment explanation
Indices: 2327426--2327485 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
2327416 TGATAATCTA
2327426 AAATATAATAT-AATAATATGATAT
1 AAATATAATATAAATAATA-GATAT
*
2327450 AAATATTATATAAATAATA-A-AT
1 AAATATAATATAAATAATAGATAT
2327472 AAATAATAATATAA
1 AAAT-ATAATATAA
2327486 TTTAATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
22 6 0.19
23 9 0.28
24 10 0.31
25 7 0.22
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATATAATATAAATAATAGATAT
Found at i:2327521 original size:19 final size:20
Alignment explanation
Indices: 2327499--2327538 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
2327489 AATATTTTAA
2327499 TAATT-ATTATATATAAATT
1 TAATTAATTATATATAAATT
2327518 TAATTAAATTATATATAAATT
1 TAATT-AATTATATATAAATT
2327539 ATAACATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
21 14 0.74
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TAATTAATTATATATAAATT
Found at i:2327538 original size:11 final size:11
Alignment explanation
Indices: 2327504--2327590 Score: 65
Period size: 11 Copynumber: 7.8 Consensus size: 11
2327494 TTTAATAATT
2327504 ATTATATATAA
1 ATTATATATAA
2327515 ATT-TA-ATTAA
1 ATTATATA-TAA
2327525 ATTATATATAA
1 ATTATATATAA
2327536 ATTATAACATATAA
1 ATTAT---ATATAA
* *
2327550 TTTTTATATAA
1 ATTATATATAA
*
2327561 AATATAATATAA
1 ATTAT-ATATAA
*
2327573 A-TATATAAAA
1 ATTATATATAA
2327583 ATTA-ATAT
1 ATTATATAT
2327591 TTTATATAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
9 1 0.02
10 17 0.28
11 26 0.43
12 8 0.13
14 9 0.15
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTATATATAA
Found at i:2327571 original size:37 final size:36
Alignment explanation
Indices: 2327500--2327609 Score: 100
Period size: 35 Copynumber: 3.0 Consensus size: 36
2327490 ATATTTTAAT
* * * *
2327500 AATTATTATATATAAATTTAAT-TAAATTAT-ATATA
1 AATTA-TAAATATAATTTTTATATAAAATATAATATA
2327535 AATTATAACATATAATTTTTATATAAAATATAATATA
1 AATTATAA-ATATAATTTTTATATAAAATATAATATA
* *
2327572 AATATATAAAAATTAATATTTTATATAATATA-AATATA
1 AAT-TATAAATA-TAAT-TTTTATATAAAATATAATATA
2327610 CAAATTATTA
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
34 2 0.03
35 16 0.25
36 7 0.11
37 10 0.16
38 15 0.24
39 13 0.21
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.45
Consensus pattern (36 bp):
AATTATAAATATAATTTTTATATAAAATATAATATA
Found at i:2332343 original size:2 final size:2
Alignment explanation
Indices: 2332336--2332380 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
2332326 CGAATGACAC
* * *
2332336 TA TA TA TA TA CA TA CA TA CA 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
2332378 TA T
1 TA T
2332381 CTGATTTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:2335387 original size:52 final size:52
Alignment explanation
Indices: 2335301--2335425 Score: 160
Period size: 52 Copynumber: 2.4 Consensus size: 52
2335291 TATAACCATA
* * *
2335301 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGCAAAT
* * * * *
2335353 CAAACTTGCCTATTAAGAATCCCTTTTCTTTTAGAATTTTTTTCTTGCAAAT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGCAAAT
* *
2335405 CAAACATACCTATTAAGAATC
1 CAAACTTGCCTATTAAGAATC
2335426 ATCTTTCTCT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGCAAAT
Found at i:2335500 original size:11 final size:11
Alignment explanation
Indices: 2335484--2335513 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2335474 AATATCTGAT
2335484 AAATCTCTAAC
1 AAATCTCTAAC
*
2335495 AAATCTCAAAC
1 AAATCTCTAAC
2335506 AAATCTCT
1 AAATCTCT
2335514 TATGGGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATCTCTAAC
Found at i:2335862 original size:31 final size:31
Alignment explanation
Indices: 2335824--2335908 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
2335814 TTCGAACCTT
2335824 CAGCTTTGATACCACTTGTTGGGGAACACCA
1 CAGCTTTGATACCACTTGTTGGGGAACACCA
* **
2335855 CAGCTTTGATACCACTTGTTGGAGATTACCA
1 CAGCTTTGATACCACTTGTTGGGGAACACCA
* *
2335886 CAGCTCTGATACCATTTGTTGGG
1 CAGCTTTGATACCACTTGTTGGG
2335909 CTAAAAGCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (31 bp):
CAGCTTTGATACCACTTGTTGGGGAACACCA
Found at i:2336484 original size:52 final size:52
Alignment explanation
Indices: 2336398--2336522 Score: 160
Period size: 52 Copynumber: 2.4 Consensus size: 52
2336388 TATAACCATA
* * *
2336398 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGCAAAT
* * * * *
2336450 CAAACTTGCCTATTAAGAATCCCTTTTCTTTTAGAATTTTTTTCTTGCAAAT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGCAAAT
* *
2336502 CAAACATACCTATTAAGAATC
1 CAAACTTGCCTATTAAGAATC
2336523 ATCTTTCTCT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGCAAAT
Found at i:2336597 original size:11 final size:11
Alignment explanation
Indices: 2336581--2336610 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2336571 AATATCTGAT
2336581 AAATCTCTAAC
1 AAATCTCTAAC
*
2336592 AAATCTCAAAC
1 AAATCTCTAAC
2336603 AAATCTCT
1 AAATCTCT
2336611 TATGGGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.47, C:0.27, G:0.00, T:0.27
Consensus pattern (11 bp):
AAATCTCTAAC
Found at i:2341544 original size:14 final size:15
Alignment explanation
Indices: 2341515--2341553 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
2341505 AAATTTCATT
*
2341515 AATATTTTTATTAAA
1 AATATTTATATTAAA
2341530 AATATTTAT-TTAAA
1 AATATTTATATTAAA
*
2341544 AATATATATA
1 AATATTTATA
2341554 AAAATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
AATATTTATATTAAA
Found at i:2344397 original size:2 final size:2
Alignment explanation
Indices: 2344386--2344428 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
2344376 TAAGCTAAGT
2344386 TA TA -A 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
2344427 TA
1 TA
2344429 AGAGATGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2345459 original size:16 final size:16
Alignment explanation
Indices: 2345438--2345469 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2345428 TAAAACCAGT
2345438 TTGATTTTATAATTAA
1 TTGATTTTATAATTAA
2345454 TTGATTTTATAATTAA
1 TTGATTTTATAATTAA
2345470 ACTACTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTGATTTTATAATTAA
Found at i:2345838 original size:18 final size:16
Alignment explanation
Indices: 2345815--2345867 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
2345805 TTGATACCAT
2345815 AATTAAAAATAATTATAA
1 AATTAAAAAT-A-TATAA
*
2345833 AATTAATAATATATAA
1 AATTAAAAATATATAA
*
2345849 AATTAATAAA-AAATAA
1 AATTAA-AAATATATAA
2345865 AAT
1 AAT
2345868 GTTAATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 19 0.61
17 3 0.10
18 9 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AATTAAAAATATATAA
Found at i:2345847 original size:16 final size:16
Alignment explanation
Indices: 2345822--2345867 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
2345812 CATAATTAAA
2345822 AATAAT-TATAAAATT
1 AATAATATATAAAATT
2345837 AATAATATATAAAATT
1 AATAATATATAAAATT
* *
2345853 AATAAAAAATAAAAT
1 AATAATATATAAAAT
2345868 GTTAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
15 6 0.21
16 22 0.79
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAATATATAAAATT
Found at i:2346041 original size:34 final size:31
Alignment explanation
Indices: 2345983--2346060 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 31
2345973 TTTGATTTTA
*
2345983 ATTTT-TTTTTACTAATTTTCATATAAATATAAAT
1 ATTTTCTTTTTATTAA-TTTC-TAT--ATATAAAT
2346017 ATTTTCTTTTTATTAATTT-TATATATAAAT
1 ATTTTCTTTTTATTAATTTCTATATATAAAT
2346047 A-TTTCTTTTTATTA
1 ATTTTCTTTTTATTA
2346061 CATAAAGATT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
29 13 0.31
30 9 0.21
32 3 0.07
34 8 0.19
35 9 0.21
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (31 bp):
ATTTTCTTTTTATTAATTTCTATATATAAAT
Found at i:2354282 original size:2 final size:2
Alignment explanation
Indices: 2354275--2354299 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2354265 ACATCTTCAA
2354275 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2354300 AAAGGAAGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2378252 original size:12 final size:12
Alignment explanation
Indices: 2378235--2378260 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2378225 ATTCATTCAA
2378235 TATAAATTTTTT
1 TATAAATTTTTT
2378247 TATAAATTTTTT
1 TATAAATTTTTT
2378259 TA
1 TA
2378261 ATTACAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATAAATTTTTT
Found at i:2378302 original size:23 final size:24
Alignment explanation
Indices: 2378251--2378304 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
2378241 TTTTTTTATA
* * *
2378251 AATTTTTTTAATTACAGTTATAAT
1 AATTTTTTTAATCACAGATACAAT
*
2378275 AATTTTTTTAATCATAGATACAAT
1 AATTTTTTTAATCACAGATACAAT
2378299 -ATTTTT
1 AATTTTT
2378305 ATTATTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.54
Consensus pattern (24 bp):
AATTTTTTTAATCACAGATACAAT
Found at i:2378453 original size:15 final size:17
Alignment explanation
Indices: 2378433--2378465 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
2378423 AGTGAATTTT
2378433 TTGTTATA-A-AGAAGA
1 TTGTTATATATAGAAGA
2378448 TTGTTATATATAGAAGA
1 TTGTTATATATAGAAGA
2378465 T
1 T
2378466 AAAGGGGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
16 1 0.06
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (17 bp):
TTGTTATATATAGAAGA
Found at i:2402156 original size:218 final size:220
Alignment explanation
Indices: 2401776--2402203 Score: 770
Period size: 218 Copynumber: 1.9 Consensus size: 220
2401766 ATGGGCTCAA
* *
2401776 TAAGGCTGGGCTAATCTAGGTAGCTTTTTGAGTGGCTTTAGTAACATATACTAGTTAGGTTGCTC
1 TAAGGCTGGGCTAATCTAGGTAGCCTTTTGAGTGGCTTTAGTAACACATACTAGTTAGGTTGCTC
* *
2401841 TTGTCACACTGACCCGTCTAAAAAATACCCATTTGACTAACACCACACAAATTCGGTTGCTCAAG
66 -TGTCACACTCACCCGTCTAAAAAATACCCATTTGACTAACACCACACAAATTAGGTTGCTCAAG
2401906 CTTTTCCTGCTCTTAGAAATTTGACTAACACCCC-AATCTTTTCAGCTTGAATGGGTGTCCTTTG
130 CTTTTCCTGCTCTTAGAAATTTGACTAACACCCCAAATCTTTTCAGCTTGAATGGGTGTCCTTTG
2401970 GTCTCAGTTGAATCAGCAGCCTTTGT
195 GTCTCAGTTGAATCAGCAGCCTTTGT
2401996 TAAGGCTGGGCTAATCTAGGTAGCCTTTTGAGTGGCTTTAGTAACACATACTAGTTAGGTTGCTC
1 TAAGGCTGGGCTAATCTAGGTAGCCTTTTGAGTGGCTTTAGTAACACATACTAGTTAGGTTGCTC
* * *
2402061 -GTCTCACTCACCTGTCTAAAAAATACCCATTTGACTAACACCATACAAATTAGGTTGCTCAAGC
66 TGTCACACTCACCCGTCTAAAAAATACCCATTTGACTAACACCACACAAATTAGGTTGCTCAAGC
2402125 TTTTCCTGCTCTTAGAAATTTGACTAACACCCCAAATCTTTTCAGCTTGAATGGGTGTCCTTTGG
131 TTTTCCTGCTCTTAGAAATTTGACTAACACCCCAAATCTTTTCAGCTTGAATGGGTGTCCTTTGG
2402190 TCTCAGTTGAATCA
196 TCTCAGTTGAATCA
2402204 TCTTTGTGTG
Statistics
Matches: 200, Mismatches: 7, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
218 92 0.46
219 45 0.22
220 63 0.31
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.33
Consensus pattern (220 bp):
TAAGGCTGGGCTAATCTAGGTAGCCTTTTGAGTGGCTTTAGTAACACATACTAGTTAGGTTGCTC
TGTCACACTCACCCGTCTAAAAAATACCCATTTGACTAACACCACACAAATTAGGTTGCTCAAGC
TTTTCCTGCTCTTAGAAATTTGACTAACACCCCAAATCTTTTCAGCTTGAATGGGTGTCCTTTGG
TCTCAGTTGAATCAGCAGCCTTTGT
Found at i:2402636 original size:12 final size:12
Alignment explanation
Indices: 2402621--2402681 Score: 70
Period size: 12 Copynumber: 4.8 Consensus size: 12
2402611 TTTAATTAAT
2402621 TATTTAATTTTA
1 TATTTAATTTTA
2402633 TATTTAATTTTA
1 TATTTAATTTTA
*
2402645 TATATT-TTTATATA
1 TAT-TTAATT-T-TA
2402659 TATTTAATTTTA
1 TATTTAATTTTA
2402671 TATTTATATTT
1 TATTTA-ATTT
2402682 AAAATAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
12 25 0.60
13 10 0.24
14 7 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTTAATTTTA
Found at i:2415596 original size:37 final size:37
Alignment explanation
Indices: 2415544--2415622 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
2415534 GAATTTAAAA
2415544 AAAAAAAATTGCTTGAAATCATAACATGTGATTATAC
1 AAAAAAAATTGCTTGAAATCATAACATGTGATTATAC
* * * *
2415581 AAAAAAAGTTTCTTGAAATCCTAACATGTGATTATAT
1 AAAAAAAATTGCTTGAAATCATAACATGTGATTATAC
2415618 AAAAA
1 AAAAA
2415623 TCATGTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.49, C:0.10, G:0.10, T:0.30
Consensus pattern (37 bp):
AAAAAAAATTGCTTGAAATCATAACATGTGATTATAC
Found at i:2431794 original size:22 final size:23
Alignment explanation
Indices: 2431746--2431807 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
2431736 TATTATTTTT
**
2431746 TAAATATAAATATAAAAATTTTA
1 TAAATATAAATATAAAAATTAAA
*
2431769 -AAATATAAATAT-AATATTAAA
1 TAAATATAAATATAAAAATTAAA
2431790 TAAATAATAAA-A-AAAAAT
1 TAAAT-ATAAATATAAAAAT
2431808 ATTGAATCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 6 0.19
22 21 0.66
23 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
TAAATATAAATATAAAAATTAAA
Found at i:2439582 original size:27 final size:27
Alignment explanation
Indices: 2439540--2439591 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2439530 TCGCACCATC
* *
2439540 ACCATCACCATTATCA-TCTAGACTTAA
1 ACCACCACCATCATCACTCT-GACTTAA
2439567 ACCACCACCATCATCACTCTGACTT
1 ACCACCACCATCATCACTCTGACTT
2439592 GGTGTTGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.33, C:0.37, G:0.04, T:0.27
Consensus pattern (27 bp):
ACCACCACCATCATCACTCTGACTTAA
Found at i:2442965 original size:26 final size:26
Alignment explanation
Indices: 2442916--2442964 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
2442906 TTTCAAAAAT
*
2442916 TAAAAATTTTCAAACTTATATTTTAA
1 TAAAAATTTTCAAACCTATATTTTAA
*
2442942 TAAAAA-TTTCGAACCTATATTTT
1 TAAAAATTTTCAAACCTATATTTT
2442965 TTATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.45
Consensus pattern (26 bp):
TAAAAATTTTCAAACCTATATTTTAA
Found at i:2443520 original size:20 final size:20
Alignment explanation
Indices: 2443455--2443522 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
2443445 CCCCCCGACA
* *
2443455 CCCCACCACACCCAATCCCT
1 CCCCACCCCACCCAATCCTT
* * * *
2443475 CCCTACCCCCCCCAACGCCTCA
1 CCCCACCCCACCCAA-TCCT-T
2443497 CCCCACCCCACCCAATCCTT
1 CCCCACCCCACCCAATCCTT
2443517 CCCCAC
1 CCCCAC
2443523 GTGCAAAATG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
20 18 0.50
21 5 0.14
22 13 0.36
ACGTcount: A:0.21, C:0.68, G:0.01, T:0.10
Consensus pattern (20 bp):
CCCCACCCCACCCAATCCTT
Found at i:2449880 original size:56 final size:56
Alignment explanation
Indices: 2449774--2449883 Score: 175
Period size: 56 Copynumber: 2.0 Consensus size: 56
2449764 GATGATTTTG
* * *
2449774 TTGGAGTGCTACTTCCTAAACTAAATAAACTTCAATTATATATAATACAAACTCAC
1 TTGGAGTGCTACTTCCTAAACTAAAAAAACTTCAATTATATACAACACAAACTCAC
* *
2449830 TTGGAGTGCTACTTCCTAAACTAAAAAAATTTCAATTATATACGACACAAACTC
1 TTGGAGTGCTACTTCCTAAACTAAAAAAACTTCAATTATATACAACACAAACTC
2449884 TTTGATTAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (56 bp):
TTGGAGTGCTACTTCCTAAACTAAAAAAACTTCAATTATATACAACACAAACTCAC
Found at i:2452486 original size:16 final size:16
Alignment explanation
Indices: 2452465--2452496 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2452455 CCGCTAGACA
*
2452465 TGAGCCCGCCCTTAGG
1 TGAGCCCGCCCGTAGG
2452481 TGAGCCCGCCCGTAGG
1 TGAGCCCGCCCGTAGG
2452497 CCATCAGAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.38, G:0.34, T:0.16
Consensus pattern (16 bp):
TGAGCCCGCCCGTAGG
Found at i:2453023 original size:19 final size:20
Alignment explanation
Indices: 2452974--2453024 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
2452964 TATGTTGATC
2452974 TTTATTTAT-TTATTGATTA
1 TTTATTTATATTATTGATTA
2452993 TTTA-TTATTATTATT-ATTA
1 TTTATTTA-TATTATTGATTA
2453012 TTTATTTATATTA
1 TTTATTTATATTA
2453025 ATGTGCATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.10
19 18 0.62
20 8 0.28
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTATTTATATTATTGATTA
Found at i:2454091 original size:26 final size:25
Alignment explanation
Indices: 2454061--2454116 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
2454051 ATATTAATAA
*
2454061 AAATG-TGAGAATAATTAATAATTAT
1 AAATGATGA-AATAATTAAAAATTAT
**
2454086 CAAATGATGAAATTTTTAAAAATTAT
1 -AAATGATGAAATAATTAAAAATTAT
2454112 AAATG
1 AAATG
2454117 GCTAATTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
25 5 0.19
26 18 0.69
27 3 0.12
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (25 bp):
AAATGATGAAATAATTAAAAATTAT
Found at i:2454250 original size:10 final size:10
Alignment explanation
Indices: 2454235--2454270 Score: 72
Period size: 10 Copynumber: 3.6 Consensus size: 10
2454225 ATTCAAATAA
2454235 AAAATTTAAT
1 AAAATTTAAT
2454245 AAAATTTAAT
1 AAAATTTAAT
2454255 AAAATTTAAT
1 AAAATTTAAT
2454265 AAAATT
1 AAAATT
2454271 CTTGGAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
AAAATTTAAT
Found at i:2454864 original size:15 final size:16
Alignment explanation
Indices: 2454840--2454873 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
2454830 AATTAAATAT
*
2454840 ATTTTCAATAAAGCAA
1 ATTTTCAATAAAACAA
2454856 ATTTT-AATAAAACAA
1 ATTTTCAATAAAACAA
2454871 ATT
1 ATT
2454874 GATTAAATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.53, C:0.09, G:0.03, T:0.35
Consensus pattern (16 bp):
ATTTTCAATAAAACAA
Found at i:2455948 original size:23 final size:24
Alignment explanation
Indices: 2455917--2455964 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 24
2455907 ATATTGTTTG
2455917 CATTATCA-TTTAACTTTGTGCAT
1 CATTATCAGTTTAACTTTGTGCAT
*
2455940 CATTTTCATGTTTAACTTTGTGCAT
1 CATTATCA-GTTTAACTTTGTGCAT
2455965 TTACATCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
25 15 0.68
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (24 bp):
CATTATCAGTTTAACTTTGTGCAT
Found at i:2461093 original size:17 final size:16
Alignment explanation
Indices: 2461061--2461096 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
2461051 AGAAAGGAAA
*
2461061 AGAAAAAAATAAAAAT
1 AGAAAAAAAAAAAAAT
2461077 AGAAAACAAAAAAAAAT
1 AGAAAA-AAAAAAAAAT
2461094 AGA
1 AGA
2461097 GATTAATGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.81, C:0.03, G:0.08, T:0.08
Consensus pattern (16 bp):
AGAAAAAAAAAAAAAT
Found at i:2461402 original size:7 final size:8
Alignment explanation
Indices: 2461390--2461447 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 8
2461380 GTGTTTAAGT
2461390 AAAAAAGA
1 AAAAAAGA
2461398 AAAAAAGAA
1 AAAAAAG-A
2461407 AAAAAAGGA
1 AAAAAA-GA
2461416 ACAAAGAAGA
1 A-AAA-AAGA
2461426 AAAAAATGA
1 AAAAAA-GA
2461435 AGAAAAACGA
1 A-AAAAA-GA
2461445 AAA
1 AAA
2461448 TGAATAATTA
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
8 9 0.21
9 17 0.40
10 15 0.35
11 2 0.05
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (8 bp):
AAAAAAGA
Found at i:2461410 original size:17 final size:18
Alignment explanation
Indices: 2461390--2461447 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 18
2461380 GTGTTTAAGT
2461390 AAAAAAGAA-AAAAAGAA
1 AAAAAAGAACAAAAAGAA
2461407 AAAAAAGGAACAAAGAAGAA
1 AAAAAA-GAACAAA-AAGAA
* *
2461427 AAAAATGAAGAAAAACGAA
1 AAAAAAGAACAAAAA-GAA
2461446 AA
1 AA
2461448 TGAATAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
17 6 0.17
18 5 0.14
19 14 0.40
20 10 0.29
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAAAGAACAAAAAGAA
Found at i:2462576 original size:38 final size:39
Alignment explanation
Indices: 2462522--2462612 Score: 121
Period size: 38 Copynumber: 2.4 Consensus size: 39
2462512 TTGGTTATTA
* * *
2462522 CCCTTATTTTTAAAGTTATGTACCTCTGTTTATGAGGA-
1 CCCTTATTTTAAAAGTTATGTACCTCTATTTATAAGGAG
* * *
2462560 CCTTTATTTTAAAAGTTGTGTGCCTCTATTTATAAGGAG
1 CCCTTATTTTAAAAGTTATGTACCTCTATTTATAAGGAG
2462599 CCCTTATTTTAAAA
1 CCCTTATTTTAAAA
2462613 ATGTGTTCCT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
38 32 0.71
39 13 0.29
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.44
Consensus pattern (39 bp):
CCCTTATTTTAAAAGTTATGTACCTCTATTTATAAGGAG
Found at i:2462618 original size:38 final size:39
Alignment explanation
Indices: 2462522--2462637 Score: 119
Period size: 38 Copynumber: 3.0 Consensus size: 39
2462512 TTGGTTATTA
* * * * *
2462522 CCCTTATTTTTAAAGTTATGTACCTCTGTTTATGAGGA-
1 CCCTTATTTTAAAAGATGTGTGCCTCTATTTATGAGGAG
* * *
2462560 CCTTTATTTTAAAAGTTGTGTGCCTCTATTTATAAGGAG
1 CCCTTATTTTAAAAGATGTGTGCCTCTATTTATGAGGAG
* * *
2462599 CCCTTATTTTAAAA-ATGTGTTCCTTTATTTTTGAGGAG
1 CCCTTATTTTAAAAGATGTGTGCCTCTATTTATGAGGAG
2462637 C
1 C
2462638 TTGTCAAAAG
Statistics
Matches: 65, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 52 0.80
39 13 0.20
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (39 bp):
CCCTTATTTTAAAAGATGTGTGCCTCTATTTATGAGGAG
Found at i:2463848 original size:17 final size:18
Alignment explanation
Indices: 2463826--2463872 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 18
2463816 GAGCTGATTC
2463826 TTTTATTT-TGGTATTTA
1 TTTTATTTATGGTATTTA
2463843 TTTTATCTTTTATGGTATTTA
1 TTTTA---TTTATGGTATTTA
2463864 -TTTATTTAT
1 TTTTATTTAT
2463873 TTTGTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 10 0.38
20 7 0.27
21 9 0.35
ACGTcount: A:0.19, C:0.02, G:0.09, T:0.70
Consensus pattern (18 bp):
TTTTATTTATGGTATTTA
Found at i:2464610 original size:22 final size:22
Alignment explanation
Indices: 2464582--2464629 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
2464572 AAAAGTTTAG
*
2464582 ATTTTAGGAAAGATATTTCTAA
1 ATTTTAGAAAAGATATTTCTAA
* *
2464604 ATTTTAGAAAATATTTTTCTAA
1 ATTTTAGAAAAGATATTTCTAA
2464626 ATTT
1 ATTT
2464630 AGTCCAAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (22 bp):
ATTTTAGAAAAGATATTTCTAA
Found at i:2466716 original size:29 final size:28
Alignment explanation
Indices: 2466670--2466753 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 28
2466660 TTTTCGTTTG
* *
2466670 AAATAATAACTTACTTG-ATACAAATTAAA
1 AAATAATAATTTATTTGAATAC-AA-TAAA
*
2466699 AAATAATATTTTATTTGAATACAATAAA
1 AAATAATAATTTATTTGAATACAATAAA
* * *
2466727 AATATAAAAATTTATTTAAATAAAATA
1 AA-ATAATAATTTATTTGAATACAATA
2466754 TTGAAATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
28 6 0.13
29 36 0.78
30 4 0.09
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATAATAATTTATTTGAATACAATAAA
Found at i:2479735 original size:19 final size:20
Alignment explanation
Indices: 2479711--2479755 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
2479701 TTTAATTCAT
2479711 TTTTCAAAG-AAAATTGATA
1 TTTTCAAAGAAAAATTGATA
2479730 TTTTC-AAGAAAAATTGATA
1 TTTTCAAAGAAAAATTGATA
2479749 TTTTCAA
1 TTTTCAA
2479756 CTTTTCCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.12
19 20 0.83
20 1 0.04
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (20 bp):
TTTTCAAAGAAAAATTGATA
Found at i:2479746 original size:74 final size:75
Alignment explanation
Indices: 2479657--2479812 Score: 203
Period size: 76 Copynumber: 2.1 Consensus size: 75
2479647 AAAATTTTAT
* *
2479657 TTTTAAAGAAAATTGATACTTTCAACTTTTCCTTAAA-A-TATTTTTTTAATTCAT-TTTTC-AA
1 TTTTCAAGAAAATTGATACTTTCAACTTTTCCTCAAAGATTATTTTTTTAATT-ATGTTTTCGAA
2479718 AGAAAATTGATA
65 A-AAAATTGATA
* * *
2479730 TTTTCAAGAAAAATTGATATTTTCAACTTTTCCTCAAAGATTTTTTTTTTAATTTTGTTTTCGAA
1 TTTTCAAG-AAAATTGATACTTTCAACTTTTCCTCAAAGATTATTTTTTTAATTATGTTTTCGAA
2479795 AAAAATTGATA
65 AAAAATTGATA
*
2479806 CTTTCAA
1 TTTTCAA
2479813 CTTTCCCTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
73 7 0.10
74 27 0.38
75 2 0.03
76 33 0.46
77 3 0.04
ACGTcount: A:0.36, C:0.10, G:0.06, T:0.47
Consensus pattern (75 bp):
TTTTCAAGAAAATTGATACTTTCAACTTTTCCTCAAAGATTATTTTTTTAATTATGTTTTCGAAA
AAAATTGATA
Found at i:2479996 original size:16 final size:14
Alignment explanation
Indices: 2479961--2480002 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 14
2479951 TATTTCAATT
2479961 TAATCAATAAAAAAA
1 TAAT-AATAAAAAAA
2479976 TAATAATAAATAAAA
1 TAATAATAAA-AAAA
2479991 TAAATAATAAAA
1 T-AATAATAAAA
2480003 CTAAAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.24
15 10 0.40
16 9 0.36
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
TAATAATAAAAAAA
Found at i:2479997 original size:19 final size:18
Alignment explanation
Indices: 2479961--2480014 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
2479951 TATTTCAATT
*
2479961 TAATCAATAAAAAAATAA
1 TAATAAATAAAAAAATAA
2479979 TAATAAATAAAATAAATAA
1 TAATAAATAAAA-AAATAA
* *
2479998 TAA-AACTAAAAGAATAA
1 TAATAAATAAAAAAATAA
2480015 AAAACCTTTG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.16
18 18 0.56
19 9 0.28
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (18 bp):
TAATAAATAAAAAAATAA
Found at i:2480388 original size:20 final size:19
Alignment explanation
Indices: 2480360--2480398 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
2480350 TCATCGATTT
*
2480360 CTGGGTTTTATAGCCGAAAA
1 CTGGATTTTATA-CCGAAAA
*
2480380 CTGGATTTTTTACCGAAAA
1 CTGGATTTTATACCGAAAA
2480399 AATGTCAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (19 bp):
CTGGATTTTATACCGAAAA
Found at i:2481658 original size:86 final size:86
Alignment explanation
Indices: 2481210--2481690 Score: 361
Period size: 86 Copynumber: 5.7 Consensus size: 86
2481200 TTGACATAAG
* * * * * * * * * *
2481210 TCAAAATCTCAAAACAAAATGACCTGGATGGAACCAAAGTTTGAAATGAATACCTTAGACTAGGC
1 TCAAAATCTAAAAATAGAATGACCTGGATTGAATCGAAGTCTGAAATGAATAACTTGGACTAAGC
* *
2481275 TAAAGAAAGATCTGGCATATG-
66 TAAAAAAAGATCTAGCATA-GA
* * * * * * * *
2481296 TCGAGATCTAAAAACAGAATTACCTGGATTGAACCTAAGT-TAAACATGAATAACTTAGACTAAG
1 TCAAAATCTAAAAATAGAATGACCTGGATTGAATCGAAGTCTGAA-ATGAATAACTTGGACTAAG
* *
2481360 ------AAAGAT-TTGACA-AAA
65 CTAAAAAAAGATCTAG-CATAGA
* * * * * * * *
2481375 GTCAAAATC-CAAAATTGAAAGACCTGGACTAAATCGAAGCCT--AA--AATAACTTAGACTGAG
1 -TCAAAATCTAAAAATAGAATGACCTGGATTGAATCGAAGTCTGAAATGAATAACTTGGACTAAG
* *
2481435 CTAAAAAAAGATCTAGTATAGG
65 CTAAAAAAAGATCTAGCATAGA
*
2481457 TCAAAATCTAAAAATAGAATGACCTGGATTGAATCGAAGTCTGAAATGAATAACTTGGGCTAAGC
1 TCAAAATCTAAAAATAGAATGACCTGGATTGAATCGAAGTCTGAAATGAATAACTTGGACTAAGC
* *
2481522 TAGAGAAAGATCT-GACATAGA
66 TAAAAAAAGATCTAG-CATAGA
* * *
2481543 TCGAAAT-TCAAAAATA-AGATGACCTGGATTGAACCGAAGTCTGAAATGAATGACTTGGACTAA
1 TCAAAATCT-AAAAATAGA-ATGACCTGGATTGAATCGAAGTCTGAAATGAATAACTTGGACTAA
* *
2481606 GTTAAAAAAAGATCTAGCATATA
64 GCTAAAAAAAGATCTAGCATAGA
* * * *
2481629 CCAAAATCTGAAAATAGAATGACCTGGATTAAATCGAAG-CTCGAAATGAATAATTTGGACTA
1 TCAAAATCTAAAAATAGAATGACCTGGATTGAATCGAAGTCT-GAAATGAATAACTTGGACTA
2481691 TCAATGCAAG
Statistics
Matches: 313, Mismatches: 57, Indels: 50
0.75 0.14 0.12
Matches are distributed among these distances:
75 15 0.05
77 1 0.00
78 1 0.00
79 24 0.08
80 15 0.05
81 15 0.05
82 30 0.10
84 2 0.01
85 8 0.03
86 199 0.64
87 3 0.01
ACGTcount: A:0.44, C:0.14, G:0.18, T:0.23
Consensus pattern (86 bp):
TCAAAATCTAAAAATAGAATGACCTGGATTGAATCGAAGTCTGAAATGAATAACTTGGACTAAGC
TAAAAAAAGATCTAGCATAGA
Found at i:2493243 original size:55 final size:55
Alignment explanation
Indices: 2493123--2493319 Score: 168
Period size: 57 Copynumber: 3.5 Consensus size: 55
2493113 TCACATAAAA
* * ** * * *
2493123 TTTCAACTTTTTCTTAAAATGCTTATTGAAATTTTCATTTTTAAAGAAACTTGATACT
1 TTTCAACTTTTTCTTAAAATGTTTTTTTTAA--TTCATTTTCAAGGAAAATTGATA-T
2493181 TTT-AACTTTTTCTTAAAATGTTTTTTTTAATTCATTTTCAAGGAAAATTGATAT
1 TTTCAACTTTTTCTTAAAATGTTTTTTTTAATTCATTTTCAAGGAAAATTGATAT
** * *
2493235 TTTCAAC-TTTTCTTCAAAGAT-TTTTTTTTAAATTTGTTTTC-AGAAAAAATTGATAC
1 TTTCAACTTTTTCTT-AAA-ATGTTTTTTTT-AATTCATTTTCAAG-GAAAATTGATAT
* * *
2493291 TTTCAACTTTTCCTCAAAAATATTTTTTT
1 TTTCAACTTTTTCT-TAAAATGTTTTTTT
2493320 AAAAATTTTT
Statistics
Matches: 118, Mismatches: 13, Indels: 17
0.80 0.09 0.11
Matches are distributed among these distances:
54 11 0.09
55 36 0.31
56 30 0.25
57 38 0.32
58 3 0.03
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.51
Consensus pattern (55 bp):
TTTCAACTTTTTCTTAAAATGTTTTTTTTAATTCATTTTCAAGGAAAATTGATAT
Found at i:2493287 original size:56 final size:55
Alignment explanation
Indices: 2493156--2493322 Score: 164
Period size: 56 Copynumber: 3.0 Consensus size: 55
2493146 TATTGAAATT
* *
2493156 TTCATTTTTAA-AGAAACTTGATACTTTT-AACTTTTTCTT-AAAATGTTTTTTTT-AA
1 TTCATTTTCAAGA-AAAATTGATA-TTTTCAAC-TTTTCTTCAAAAT-TTTTTTTTAAA
*
2493211 TTCATTTTCAAGGAAAATTGATATTTTCAACTTTTCTTCAAAGATTTTTTTTTAAA
1 TTCATTTTCAAGAAAAATTGATATTTTCAACTTTTCTTCAAA-ATTTTTTTTTAAA
** * * *
2493267 TTTGTTTTC-AGAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAAA
1 TTCATTTTCAAG-AAAAATTGATATTTTCAACTTTTCTTC-AAAATTTTTTTTTAAA
2493323 AATTTTTTTA
Statistics
Matches: 96, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
54 11 0.11
55 35 0.36
56 47 0.49
57 3 0.03
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (55 bp):
TTCATTTTCAAGAAAAATTGATATTTTCAACTTTTCTTCAAAATTTTTTTTTAAA
Found at i:2493344 original size:68 final size:68
Alignment explanation
Indices: 2493257--2493452 Score: 247
Period size: 66 Copynumber: 2.9 Consensus size: 68
2493247 TTCAAAGATT
**
2493257 TTTTTTTAAATTTGTTTTCAGAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAA
1 TTTTTTTATTTTTGTTTTCAGAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAA
2493322 AAA
66 AAA
* * * * *
2493325 TTTTTTTATTTTTATTTTCA-AGGAAAATTGATACTTTCAACTTTTCTTCAAATAT-TTTTTTTT
1 TTTTTTTATTTTTGTTTTCAGA-AAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTA
*
2493388 GAAA
65 AAAA
* * * *
2493392 -TTTTTTATTCTTGTTTTCAGAAAAAATTGATACTTTCAATTTTTTCTCAAAAA-ATGTTTTT
1 TTTTTTTATTTTTGTTTTCAGAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTT
2493453 GTGAAGATTT
Statistics
Matches: 109, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
66 50 0.46
67 12 0.11
68 47 0.43
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.53
Consensus pattern (68 bp):
TTTTTTTATTTTTGTTTTCAGAAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAA
AAA
Found at i:2493662 original size:19 final size:19
Alignment explanation
Indices: 2493638--2493676 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
2493628 TTATTTCAAT
*
2493638 TTAATAAGTAAAGAAATAA
1 TTAATAAATAAAGAAATAA
*
2493657 TTAATAAATAAATAAATAA
1 TTAATAAATAAAGAAATAA
2493676 T
1 T
2493677 AAAACTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (19 bp):
TTAATAAATAAAGAAATAA
Found at i:2493664 original size:15 final size:15
Alignment explanation
Indices: 2493640--2493679 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
2493630 ATTTCAATTT
2493640 AATAAGTAAAGAAATA
1 AATAA-TAAAGAAATA
* *
2493656 ATTAATAAATAAATA
1 AATAATAAAGAAATA
2493671 AATAATAAA
1 AATAATAAA
2493680 ACTAAAAGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (15 bp):
AATAATAAAGAAATA
Found at i:2494606 original size:21 final size:21
Alignment explanation
Indices: 2494580--2494629 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2494570 ATTTTTATTA
2494580 AATAATAGATATTAAT-AAGAT
1 AATAATA-ATATTAATAAAGAT
* *
2494601 AATAATAATATTATTAAATAT
1 AATAATAATATTAATAAAGAT
2494622 AATAATAA
1 AATAATAA
2494630 AAATTAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (21 bp):
AATAATAATATTAATAAAGAT
Found at i:2494620 original size:24 final size:24
Alignment explanation
Indices: 2494580--2494629 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
2494570 ATTTTTATTA
2494580 AATAATAGATATTAATA-AGATAAT
1 AATAATAGATATTAATATA-ATAAT
*
2494604 AATAATA-TTATTAAATATAATAAT
1 AATAATAGATATT-AATATAATAAT
2494628 AA
1 AA
2494630 AAATTAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 4 0.17
24 18 0.78
25 1 0.04
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (24 bp):
AATAATAGATATTAATATAATAAT
Found at i:2494658 original size:8 final size:7
Alignment explanation
Indices: 2494647--2494703 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 7
2494637 ACAAAATACA
2494647 AAAAAAT
1 AAAAAAT
2494654 GAAAAAAGT
1 -AAAAAA-T
2494663 AAAAAAAT
1 -AAAAAAT
2494671 AAAAAAAT
1 -AAAAAAT
2494679 AAAAAAT
1 AAAAAAT
2494686 -AAAAA-
1 AAAAAAT
*
2494691 AACAAAT
1 AAAAAAT
2494698 AAAAAA
1 AAAAAA
2494704 ATACAAGAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
6 9 0.21
7 12 0.28
8 15 0.35
9 7 0.16
ACGTcount: A:0.84, C:0.02, G:0.04, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:2494678 original size:35 final size:36
Alignment explanation
Indices: 2494622--2494721 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 36
2494612 TATTAAATAT
*
2494622 AATAATAAAAATTAAACAAAATACAAAAA-AATGAAAA-A
1 AATAA-AAAAA-TAAACAAAATA-AAAAATAA-AAAAACA
*
2494660 AGTAAAAAAATAAA-AAAATAAAAAATAAAAAAACA
1 AATAAAAAAATAAACAAAATAAAAAATAAAAAAACA
* *
2494695 AATAAAAAAATACAAGAGAATAAAAAA
1 AATAAAAAAATA-AACAAAATAAAAAA
2494722 ATACATGGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
34 9 0.17
35 20 0.37
36 6 0.11
37 15 0.28
38 4 0.07
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (36 bp):
AATAAAAAAATAAACAAAATAAAAAATAAAAAAACA
Found at i:2494705 original size:8 final size:8
Alignment explanation
Indices: 2494622--2494724 Score: 80
Period size: 9 Copynumber: 11.5 Consensus size: 8
2494612 TATTAAATAT
2494622 AATAATAAA
1 AATAA-AAA
2494631 AATTAAACAA
1 AA-TAAA-AA
2494641 AATACAAAAA
1 AAT--AAAAA
2494651 AATGAAAAA
1 AAT-AAAAA
*
2494660 AGTAAAAA
1 AATAAAAA
2494668 AATAAAAA
1 AATAAAAA
2494676 AATAAAAAA
1 AAT-AAAAA
*
2494685 TAAAAAAACA
1 -AATAAAA-A
2494695 AATAAAAA
1 AATAAAAA
*
2494703 AATACAAGAG
1 AATA-AA-AA
2494713 AATAAAAA
1 AATAAAAA
2494721 AATA
1 AATA
2494725 CATGGCACCA
Statistics
Matches: 78, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
8 25 0.32
9 30 0.38
10 20 0.26
11 3 0.04
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.14
Consensus pattern (8 bp):
AATAAAAA
Found at i:2497046 original size:20 final size:20
Alignment explanation
Indices: 2497008--2497046 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2496998 GAAAAAGCCA
*
2497008 AAAAAAAAAAACAACAAATC
1 AAAAAAAAAAACAAAAAATC
* *
2497028 AAAAAGAAAAAGAAAAAAT
1 AAAAAAAAAAACAAAAAAT
2497047 TAACACATGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.82, C:0.08, G:0.05, T:0.05
Consensus pattern (20 bp):
AAAAAAAAAAACAAAAAATC
Found at i:2501875 original size:21 final size:22
Alignment explanation
Indices: 2501851--2501891 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2501841 AAGAAAAGTC
* *
2501851 AAAAAATCCAAATTG-TGAAGA
1 AAAAAAGCAAAATTGATGAAGA
2501872 AAAAAAGCAAAATTGATGAA
1 AAAAAAGCAAAATTGATGAA
2501892 AATGAATAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.61, C:0.07, G:0.15, T:0.17
Consensus pattern (22 bp):
AAAAAAGCAAAATTGATGAAGA
Found at i:2502139 original size:35 final size:34
Alignment explanation
Indices: 2502100--2502218 Score: 125
Period size: 35 Copynumber: 3.5 Consensus size: 34
2502090 GTATTTTTTT
*
2502100 GAAAAGATATTTGCATTTCATGCGTATCATTTTAA
1 GAAAAGACATTTGCATTTCATGCG-ATCATTTTAA
* * * *
2502135 GAAAAGGCATTTGTATTTCATGTGCATCATTTTAG
1 GAAAAGACATTTGCATTTCATGCG-ATCATTTTAA
* *
2502170 GAAAAGACATTTGTATTTACAT-C-CTCATTTTAA
1 GAAAAGACATTTGCATTT-CATGCGATCATTTTAA
*
2502203 GAGAAGACATTTGCAT
1 GAAAAGACATTTGCAT
2502219 CATAATGGTA
Statistics
Matches: 71, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
33 22 0.31
35 46 0.65
36 3 0.04
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (34 bp):
GAAAAGACATTTGCATTTCATGCGATCATTTTAA
Found at i:2502519 original size:75 final size:75
Alignment explanation
Indices: 2502396--2502666 Score: 274
Period size: 75 Copynumber: 3.5 Consensus size: 75
2502386 GTGATAAATT
* * * *
2502396 ATTTTCAAAGTTCTCGGTGGTGATATCTGAGTATTAAAATATGAATTTCATTTTTTTGGTGGTGA
1 ATTTTCAAAGTTATCAGTGGTGATATCCGAGTATTAAAGTATGAATTTCATTTTTTTGGTGGTGA
*
2502461 TATCTAAGAC
66 TATCCAAGAC
* * * *
2502471 ATTTTCAAAGTTTTCAGTGGTGATATCCGAGTATTAAAGTATGAATTTCATTTTCTTGATGATGA
1 ATTTTCAAAGTTATCAGTGGTGATATCCGAGTATTAAAGTATGAATTTCATTTTTTTGGTGGTGA
2502536 TATCCAAGAC
66 TATCCAAGAC
* * * * *
2502546 ATTTTCAAAATCAATCAATGGTGATATCCGAGT-TTAAAGTTTAAATTTGCATTTGTATTTTCTT
1 ATTTTCAAAGT-TATCAGTGGTGATATCCGAGTATTAAAGTATGAATTT-CA----T-TTTT-TT
*
2502610 GGTGGTGAAATCCAAGAC
58 GGTGGTGATATCCAAGAC
* * * **
2502628 ATTTTCAAAATCACTCGGTGGTGATATATGAGTATTAAA
1 ATTTTCAAAGTTA-TCAGTGGTGATATCCGAGTATTAAA
2502667 AAAAAGGTCA
Statistics
Matches: 163, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
75 90 0.55
76 20 0.12
80 1 0.01
81 4 0.02
82 43 0.26
83 5 0.03
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (75 bp):
ATTTTCAAAGTTATCAGTGGTGATATCCGAGTATTAAAGTATGAATTTCATTTTTTTGGTGGTGA
TATCCAAGAC
Found at i:2502763 original size:42 final size:42
Alignment explanation
Indices: 2502704--2502846 Score: 152
Period size: 42 Copynumber: 3.4 Consensus size: 42
2502694 GTGATGTCCT
* * *
2502704 AGTGTTAAGATTTGAATTACGTTTTTTTGCG-T-TTGATATCTG
1 AGTGTTAAGATTTGAATTAC-ATTTTCT-CGATGATGATATCTG
**
2502746 AGTGTTAAGGCTTGAATTACATTTTCTCGATGATGATATCTG
1 AGTGTTAAGATTTGAATTACATTTTCTCGATGATGATATCTG
* *
2502788 AGTGTTAAGATTTGAATTGCATCTTT-TCGATGGTGATATCTG
1 AGTGTTAAGATTTGAATTACAT-TTTCTCGATGATGATATCTG
2502830 AGT-TTAA-AGTTTGAATT
1 AGTGTTAAGA-TTTGAATT
2502847 TGCATTTGCA
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
40 3 0.03
41 18 0.20
42 64 0.73
43 3 0.03
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.45
Consensus pattern (42 bp):
AGTGTTAAGATTTGAATTACATTTTCTCGATGATGATATCTG
Found at i:2502850 original size:42 final size:42
Alignment explanation
Indices: 2502737--2502916 Score: 168
Period size: 42 Copynumber: 4.1 Consensus size: 42
2502727 TTTTTGCGTT
* * *
2502737 TGATATCTGAGTGTTAAGGCTTGAATTACATTTTCTCGATGA
1 TGATATCTGAGTGTTAAAGTTTGAATTGCATTTTCTCGATGA
*
2502779 TGATATCTGAGTGTT-AAGATTTGAATTGCATCTTT-TCGATGG
1 TGATATCTGAGTGTTAAAG-TTTGAATTGCAT-TTTCTCGATGA
*
2502821 TGATATCTGAGT-TTAAAGTTTGAATTTGCATTTGCATTCTCTTGACGA
1 TGATATCTGAGTGTTAAAGTTTGAA-TTGCA-TT---TTCTC--GATGA
** * * *
2502869 TGATATCCAAGTATTAAAGCTTGAATTGCATTTTCTCGATGG
1 TGATATCTGAGTGTTAAAGTTTGAATTGCATTTTCTCGATGA
2502911 TGATAT
1 TGATAT
2502917 TCAAGTTGTC
Statistics
Matches: 115, Mismatches: 11, Indels: 24
0.77 0.07 0.16
Matches are distributed among these distances:
41 10 0.09
42 61 0.53
43 4 0.03
44 5 0.04
45 2 0.02
46 2 0.02
47 2 0.02
48 18 0.16
49 11 0.10
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (42 bp):
TGATATCTGAGTGTTAAAGTTTGAATTGCATTTTCTCGATGA
Done.