Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr4
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: 31929104
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1434590 characters in sequence are not A, C, G, or T
File 9 of 82
Found at i:2928562 original size:23 final size:23
Alignment explanation
Indices: 2928513--2928611 Score: 76
Period size: 23 Copynumber: 4.3 Consensus size: 23
2928503 CACACCTCTC
* * * * *
2928513 TCACATATTCTCACCGTGCTGTC
1 TCACACATTATCACCCTGCCGTG
2928536 TCACACATTATCACCCTGCCGTG
1 TCACACATTATCACCCTGCCGTG
* * *
2928559 TCACAGATT-TCCACCATGGCGTG
1 TCACACATTAT-CACCCTGCCGTG
*
2928582 TCACACACTCTA-AACCCTGCCGTG
1 TCACACA-T-TATCACCCTGCCGTG
2928606 TCACAC
1 TCACAC
2928612 CCTTGTCAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
22 1 0.02
23 42 0.70
24 16 0.27
25 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.14, T:0.26
Consensus pattern (23 bp):
TCACACATTATCACCCTGCCGTG
Found at i:2928583 original size:104 final size:104
Alignment explanation
Indices: 2928262--2929287 Score: 838
Period size: 104 Copynumber: 9.9 Consensus size: 104
2928252 CACACGTTCT
* * * * * * *
2928262 GACCATGGCATGTCCCACACTTTAAACACTGTCGTGTCACACCCGCT-CCACATATTCTCATCGT
1 GACCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCG-TGTCACATATTATCACCGT
* * * *
2928326 GCCGTCT--CACATTATCACCCTGTCATGTCATAGATTCC
65 GCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTC
** * * * *
2928364 CTCCATGGCATGTCACACACTCTAAACCCTG-CTGTGTCACACCCGTGTCAAACATTATTACC--
1 GACCATGGCGTGTCACACACTCTAAACCCTGTC-GTGTCACACCCGTGTCACATATTATCACCGT
* * * * * *
2928426 -ACGATGTCACATATTA-AACCCATGGCGTGTCACACG-TTTT
65 GCCG-TCTCACACATTATCACCC-TGCCGTGTCACA-GATTTC
* * * * *
2928466 GACCATGGTGTGTCACACACTCTAAACGCTATCGTGTCACACCTC-TCTCACATATTCTCACCGT
1 GACCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACC-CGTGTCACATATTATCACCGT
*
2928530 GCTGTCTCACACATTATCACCCTGCCGTGTCACAGATTTC
65 GCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTC
* * * * *
2928570 CACCATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACACCCTTGTCAAATATTATCACTGTG
1 GACCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACATATTATCACCGTG
* * * **
2928635 CCGTTTCACACATTATGACCTTATCGTGTCACACG--TTC
66 CCGTCTCACACATTATCACCCTGCCGTGTCACA-GATTTC
* * * * * * * *
2928673 TGACCATGGCCTGTCAGACACTGTAAACGCTGCCGTGTCACACCCGTCTCACATATTCTCACCAT
1 -GACCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACATATTATCACCGT
* * *
2928738 GCCGTCTCACACATTATCACCCTGTCGTGGCACAGATTCC
65 GCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTC
** * * * * * **
2928778 CTCCATGACGTGTCACACACTCTAAACCTTGTCGTGTCACACCCCTGTCAAACATTATCACTATG
1 GACCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACATATTATCACCGTG
* * * * *
2928843 CTGTTTCACACATTATGACCCTGTCATGTCACACG--TTC
66 CCGTCTCACACATTATCACCCTGCCGTGTCACA-GATTTC
* * * * * **
2928881 TGACCATGGCGTGTCACACATTCTAAACGCTGCCGTGTCACACCCGTCTCACATATTCTCACTAT
1 -GACCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACATATTATCACCGT
*
2928946 GCCGTCTCACACATTATCACCCTGCCGTGTCGCAGATTTC
65 GCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTC
* * * * * *
2928986 -ATCCATGGCGTGTCACACACTCTAAACCCTATAGTGTCACACCTGTGTCAAACATTATCACTGT
1 GA-CCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACATATTATCACCGT
* * * * *
2929050 GCCGTTTCACACATTATGA-CCTTCTCATGTCACACG-TCT-
65 GCCGTCTCACACATTATCACCCTGC-CGTGTCACA-GATTTC
* * ** * *
2929089 GACCATGGCGTGTCACACACTCTAAACCCT-ACTGTGTGACACTTGTGTCACACATTATCACTGT
1 GACCATGGCGTGTCACACACTCTAAACCCTGTC-GTGTCACACCCGTGTCACATATTATCACCGT
* * * * * * *
2929153 GTCATTTCACACATTGTAACCCT-CTCGTGTCACACATCT-
65 GCCGTCTCACACATTATCACCCTGC-CGTGTCACAGATTTC
* * * *
2929192 GACCATGGCGTGTCACACACTTTAAACCCTGTCGTGTCATACCCTTGTCAC--ATTCTCACCGTG
1 GACCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACATATTATCACCGTG
* *
2929255 CCGTCTCACACATTAGCACCCTGACGTGTCACA
66 CCGTCTCACACATTATCACCCTGCCGTGTCACA
2929288 CACTCTAAAC
Statistics
Matches: 739, Mismatches: 153, Indels: 65
0.77 0.16 0.07
Matches are distributed among these distances:
99 2 0.00
100 2 0.00
101 41 0.06
102 111 0.15
103 143 0.19
104 427 0.58
105 13 0.02
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.28
Consensus pattern (104 bp):
GACCATGGCGTGTCACACACTCTAAACCCTGTCGTGTCACACCCGTGTCACATATTATCACCGTG
CCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTC
Found at i:2928747 original size:208 final size:208
Alignment explanation
Indices: 2928247--2929269 Score: 1182
Period size: 208 Copynumber: 5.0 Consensus size: 208
2928237 AAACCCATGG
* * * * *
2928247 CGTGTCACACGTTCTGACCATGGCATGTCCCACACTTTAAACACTGTCGTGTCACACCCG-CTCC
1 CGTGTCACACGTTCTGACCATGGCGTGTCACACACTCTAAACGCTGCCGTGTCACACCCGTCT-C
* * * * * * *
2928311 ACATATTCTCATCGTGCCGTCT--CACATTATCACCCTGTCATGTCATAGATTCCCTCCATGGCA
65 ACATATTCTCACCGTGCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTCCACCATGGCG
* * *
2928374 TGTCACACACTCTAAACCCTG-CTGTGTCACACCCGTGTCAAACATTATTAC----CACGATGTC
130 TGTCACACACTCTAAACCCTGTC-GTGTCACACCCTTGTCAAACATTATCACTGTGC-CG-TTTC
* * *
2928434 ACATATTA-AACC-CAT
192 ACACATTATGACCTTAT
* * **
2928449 GGCGTGTCACACGTTTTGACCATGGTGTGTCACACACTCTAAACGCTATCGTGTCACACCTC-TC
1 --CGTGTCACACGTTCTGACCATGGCGTGTCACACACTCTAAACGCTGCCGTGTCACACC-CGTC
*
2928513 TCACATATTCTCACCGTGCTGTCTCACACATTATCACCCTGCCGTGTCACAGATTTCCACCATGG
63 TCACATATTCTCACCGTGCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTCCACCATGG
* *
2928578 CGTGTCACACACTCTAAACCCTGCCGTGTCACACCCTTGTCAAATATTATCACTGTGCCGTTTCA
128 CGTGTCACACACTCTAAACCCTGTCGTGTCACACCCTTGTCAAACATTATCACTGTGCCGTTTCA
2928643 CACATTATGACCTTAT
193 CACATTATGACCTTAT
* * *
2928659 CGTGTCACACGTTCTGACCATGGCCTGTCAGACACTGTAAACGCTGCCGTGTCACACCCGTCTCA
1 CGTGTCACACGTTCTGACCATGGCGTGTCACACACTCTAAACGCTGCCGTGTCACACCCGTCTCA
* * * * * *
2928724 CATATTCTCACCATGCCGTCTCACACATTATCACCCTGTCGTGGCACAGATTCCCTCCATGACGT
66 CATATTCTCACCGTGCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTCCACCATGGCGT
* * * *
2928789 GTCACACACTCTAAACCTTGTCGTGTCACACCCCTGTCAAACATTATCACTATGCTGTTTCACAC
131 GTCACACACTCTAAACCCTGTCGTGTCACACCCTTGTCAAACATTATCACTGTGCCGTTTCACAC
* *
2928854 ATTATGACCCTGT
196 ATTATGACCTTAT
* *
2928867 CATGTCACACGTTCTGACCATGGCGTGTCACACATTCTAAACGCTGCCGTGTCACACCCGTCTCA
1 CGTGTCACACGTTCTGACCATGGCGTGTCACACACTCTAAACGCTGCCGTGTCACACCCGTCTCA
** *
2928932 CATATTCTCACTATGCCGTCTCACACATTATCACCCTGCCGTGTCGCAGATTT-CATCCATGGCG
66 CATATTCTCACCGTGCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTCCA-CCATGGCG
* *
2928996 TGTCACACACTCTAAACCCTATAGTGTCACA-CCTGTGTCAAACATTATCACTGTGCCGTTTCAC
130 TGTCACACACTCTAAACCCTGTCGTGTCACACCCT-TGTCAAACATTATCACTGTGCCGTTTCAC
*
2929060 ACATTATGACCTTCT
194 ACATTATGACCTTAT
* * * * * ** *
2929075 CATGTCACACG-TCTGACCATGGCGTGTCACACACTCTAAACCCTACTGTGTGACACTTGTGTCA
1 CGTGTCACACGTTCTGACCATGGCGTGTCACACACTCTAAACGCTGCCGTGTCACACCCGTCTCA
* * * * * * * * * * *
2929139 CACATTATCACTGTGTCATTTCACACATTGTAACCCT-CTCGTGTCACACATCT-GACCATGGCG
66 CATATTCTCACCGTGCCGTCTCACACATTATCACCCTGC-CGTGTCACAGATTTCCACCATGGCG
* * * * *
2929202 TGTCACACACTTTAAACCCTGTCGTGTCATACCCTTGTC--ACATTCTCACCGTGCCGTCTCACA
130 TGTCACACACTCTAAACCCTGTCGTGTCACACCCTTGTCAAACATTATCACTGTGCCGTTTCACA
2929265 CATTA
195 CATTA
2929270 GCACCCTGAC
Statistics
Matches: 712, Mismatches: 91, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
204 98 0.14
205 3 0.00
206 121 0.17
207 94 0.13
208 388 0.54
209 5 0.01
210 3 0.00
ACGTcount: A:0.23, C:0.34, G:0.15, T:0.29
Consensus pattern (208 bp):
CGTGTCACACGTTCTGACCATGGCGTGTCACACACTCTAAACGCTGCCGTGTCACACCCGTCTCA
CATATTCTCACCGTGCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTTCCACCATGGCGT
GTCACACACTCTAAACCCTGTCGTGTCACACCCTTGTCAAACATTATCACTGTGCCGTTTCACAC
ATTATGACCTTAT
Found at i:2928904 original size:23 final size:23
Alignment explanation
Indices: 2928848--2928904 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
2928838 CTATGCTGTT
* * *
2928848 TCACACATTATGACCCTGTCATG
1 TCACACATTCTGACCATGGCATG
* *
2928871 TCACACGTTCTGACCATGGCGTG
1 TCACACATTCTGACCATGGCATG
2928894 TCACACATTCT
1 TCACACATTCT
2928905 AAACGCTGCC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.30
Consensus pattern (23 bp):
TCACACATTCTGACCATGGCATG
Found at i:2928971 original size:23 final size:23
Alignment explanation
Indices: 2928924--2929004 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 23
2928914 CGTGTCACAC
* * *
2928924 CCGTCTCACATATTCTCACTATG
1 CCGTCTCACACATTATCACCATG
*
2928947 CCGTCTCACACATTATCACCCTG
1 CCGTCTCACACATTATCACCATG
* * *
2928970 CCGTGTCGCAGATT-TCATCCATG
1 CCGTCTCACACATTATCA-CCATG
* *
2928993 GCGTGTCACACA
1 CCGTCTCACACA
2929005 CTCTAAACCC
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
22 3 0.07
23 43 0.93
ACGTcount: A:0.21, C:0.36, G:0.15, T:0.28
Consensus pattern (23 bp):
CCGTCTCACACATTATCACCATG
Found at i:2929227 original size:24 final size:22
Alignment explanation
Indices: 2929159--2929230 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
2929149 CTGTGTCATT
* *
2929159 TCACACATTGTAACCCTCTCGTG
1 TCACACA-TCTAACCCTGTCGTG
* * *
2929182 TCACACATCTGACCATGGCGTG
1 TCACACATCTAACCCTGTCGTG
*
2929204 TCACACACTTTAAACCCTGTCGTG
1 TCACACA-TCT-AACCCTGTCGTG
2929228 TCA
1 TCA
2929231 TACCCTTGTC
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
22 17 0.45
23 9 0.24
24 12 0.32
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.28
Consensus pattern (22 bp):
TCACACATCTAACCCTGTCGTG
Found at i:2930040 original size:22 final size:22
Alignment explanation
Indices: 2930022--2930063 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2930012 TCTTGACTAC
*
2930022 TTTTTAGGCATTGCGTGACTGA
1 TTTTTAGGCATTGCATGACTGA
* *
2930044 TTTTTATGTATTGCATGACT
1 TTTTTAGGCATTGCATGACT
2930064 TGTTGTTATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.19, C:0.12, G:0.21, T:0.48
Consensus pattern (22 bp):
TTTTTAGGCATTGCATGACTGA
Found at i:2931503 original size:68 final size:68
Alignment explanation
Indices: 2931394--2931529 Score: 245
Period size: 68 Copynumber: 2.0 Consensus size: 68
2931384 GCAACTGAGG
2931394 AATCCAAATCAATGGACGACCACTTACATCACTGAAAAGTGTTTCCATCGAAGGTCAAATTGAAA
1 AATCCAAATCAATGGACGACCACTTACATCACTGAAAAGTGTTTCCATCGAAGGTCAAATTGAAA
2931459 CGA
66 CGA
* * *
2931462 AATCCAGATCAATGGATGACCACTTATATCACTGAAAAGTGTTTCCATCGAAGGTCAAATTGAAA
1 AATCCAAATCAATGGACGACCACTTACATCACTGAAAAGTGTTTCCATCGAAGGTCAAATTGAAA
2931527 CGA
66 CGA
2931530 GCTTTGATCA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 65 1.00
ACGTcount: A:0.39, C:0.21, G:0.17, T:0.24
Consensus pattern (68 bp):
AATCCAAATCAATGGACGACCACTTACATCACTGAAAAGTGTTTCCATCGAAGGTCAAATTGAAA
CGA
Found at i:2934074 original size:19 final size:20
Alignment explanation
Indices: 2934052--2934092 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
2934042 TGTAGGGGTC
*
2934052 AAAATATCAA-AGGTTCAAA
1 AAAATATAAATAGGTTCAAA
*
2934071 AAAATATAAATATGTTCAAA
1 AAAATATAAATAGGTTCAAA
2934091 AA
1 AA
2934093 CTTTAAAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (20 bp):
AAAATATAAATAGGTTCAAA
Found at i:2935207 original size:20 final size:19
Alignment explanation
Indices: 2935173--2935210 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
2935163 AATAAAAATA
*
2935173 TTAATTAAAATAATATATT
1 TTAATTAAAACAATATATT
2935192 TTAATGTAAAACAATATAT
1 TTAAT-TAAAACAATATAT
2935211 ATATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (19 bp):
TTAATTAAAACAATATATT
Found at i:2936131 original size:13 final size:13
Alignment explanation
Indices: 2936113--2936137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2936103 ATTTTCAAAA
2936113 ATTTTATAAAATT
1 ATTTTATAAAATT
2936126 ATTTTATAAAAT
1 ATTTTATAAAAT
2936138 CCCATTTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:2937353 original size:28 final size:30
Alignment explanation
Indices: 2937291--2937357 Score: 95
Period size: 28 Copynumber: 2.3 Consensus size: 30
2937281 GTAAATTTTT
2937291 AAAAATTACACTTTTATCCCCATAAAAGTG
1 AAAAATTACACTTTTATCCCCATAAAAGTG
*
2937321 AAAAATTACA-TTTT-TGCCCCA-AAAATTG
1 AAAAATTACACTTTTAT-CCCCATAAAAGTG
2937349 AAAAATTAC
1 AAAAATTAC
2937358 CAAAATGCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
28 16 0.46
29 9 0.26
30 10 0.29
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (30 bp):
AAAAATTACACTTTTATCCCCATAAAAGTG
Found at i:2938987 original size:23 final size:23
Alignment explanation
Indices: 2938936--2939136 Score: 132
Period size: 23 Copynumber: 8.7 Consensus size: 23
2938926 ACAATAAGTG
* * * **
2938936 AGTCACGCAATCCCATATCAAAA
1 AGTCACGCGATTCCATATTAACT
* *
2938959 AGTCACACGATTCCATATTTACT
1 AGTCACGCGATTCCATATTAACT
* *
2938982 ACTCACGCGATTCAATATTAACT
1 AGTCACGCGATTCCATATTAACT
* * * * *
2939005 AGTAACGTGATTCCAAATTGAGT
1 AGTCACGCGATTCCATATTAACT
* *
2939028 AGTCACCCGATTTCATATTAACT
1 AGTCACGCGATTCCATATTAACT
* * * *
2939051 AGTCACGCAATTCCAAATTTAGT
1 AGTCACGCGATTCCATATTAACT
* * * *
2939074 AGTCGCACGATTCCATATCAAAT
1 AGTCACGCGATTCCATATTAACT
* ** * *
2939097 ACTCGGGCGATTCAATATCAACT
1 AGTCACGCGATTCCATATTAACT
*
2939120 GGTCACGCGATTCCATA
1 AGTCACGCGATTCCATA
2939137 CACACCATTC
Statistics
Matches: 130, Mismatches: 48, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 130 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.28
Consensus pattern (23 bp):
AGTCACGCGATTCCATATTAACT
Found at i:2939464 original size:26 final size:26
Alignment explanation
Indices: 2939427--2939497 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
2939417 TGCCCTTTTC
2939427 TTTGTTAAATGATACAAAAAAGAAAAA
1 TTTG-TAAATGATACAAAAAAGAAAAA
* *
2939454 TTTGTAAATGATACAACAAAGAATAA
1 TTTGTAAATGATACAAAAAAGAAAAA
* *
2939480 TTTGGAGATGATACAAAA
1 TTTGTAAATGATACAAAA
2939498 CAATGTTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
26 35 0.90
27 4 0.10
ACGTcount: A:0.54, C:0.06, G:0.14, T:0.27
Consensus pattern (26 bp):
TTTGTAAATGATACAAAAAAGAAAAA
Found at i:2940820 original size:132 final size:132
Alignment explanation
Indices: 2940583--2940840 Score: 311
Period size: 132 Copynumber: 2.0 Consensus size: 132
2940573 CACACATGCA
* * * * * * *
2940583 TCTTCGACCTGAGGTGGAGGTGAAACCTTAAGAGAAAGTGTGATCTCACCATGCTAGGGGGCCTT
1 TCTTCAACCTGAGATGGAGGTGAAACCTCAAGAAAAAGTGTGATCTCACAATGCTAAGGGGCCTC
* *
2940648 TGGTGGAGTTAGGATAAGAGCAGGACGCAGGGAAGTTGTAGTTGGACTACTCGCAAGATGAGGTG
66 TAGTGGAGATAGGATAAGAGCAGGACGCAGGGAAGTTGTAGTTGGACTACTCGCAAGATGAGGTG
2940713 CC
131 CC
* * * *
2940715 TCTTCAACCTGAGATGGTGGTGAAGCCTCAGGAAAAAGTGTGCAT-TGACAATGCTAAGGGGCCT
1 TCTTCAACCTGAGATGGAGGTGAAACCTCAAGAAAAAGTGTG-ATCTCACAATGCTAAGGGGCCT
* * * * ** * *
2940779 CTAGTGGAGATGGGATAGGAGTAGGATGTGGGGAAGTTGTAGTTGGACTACTGGCAGGATGA
65 CTAGTGGAGATAGGATAAGAGCAGGACGCAGGGAAGTTGTAGTTGGACTACTCGCAAGATGA
2940841 TCTTCAATCG
Statistics
Matches: 104, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
132 102 0.98
133 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.36, T:0.23
Consensus pattern (132 bp):
TCTTCAACCTGAGATGGAGGTGAAACCTCAAGAAAAAGTGTGATCTCACAATGCTAAGGGGCCTC
TAGTGGAGATAGGATAAGAGCAGGACGCAGGGAAGTTGTAGTTGGACTACTCGCAAGATGAGGTG
CC
Found at i:2941982 original size:86 final size:86
Alignment explanation
Indices: 2941878--2942565 Score: 990
Period size: 86 Copynumber: 8.0 Consensus size: 86
2941868 TGATATGTTA
* * *
2941878 TTAAGTTTACATCATAGTTCAAATAATATTAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
*
2941943 TAATACAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* * *
2941964 TTAAGTTTGCATTATAGTTCAAGTAATANAATATAAAATTAATTTTACATTTTTTTAGTTTATAA
1 TTAAGTTTGCATCATAGTTCAAG---T--AATAT-AAATTAATTTTACA-TTTGTTAGTTTACAA
* *
2942029 GTTCAACTAATGTTAAAATTTTATATAT
59 GTTCAACTAATATAAAAATTTTATATAT
* * *
2942057 TTAAGTTTTCATCATAGTTCAAGTAATATATATTAATTTTACATTTTTTTAGTTTACAAGTTCAA
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACA-TTTGTTAGTTTACAAGTTCAA
* *
2942122 CTAATATAAAAATATTATCTAT
65 CTAATATAAAAATTTTATATAT
* *
2942144 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTATTAGTTTACAAATTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
*
2942209 TAATATAAAAATTTTATATTT
66 TAATATAAAAATTTTATATAT
* * *
2942230 TTAAGATTGCATCATAGTTGAAGTAGTATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
*
2942295 TAATATAAATATTTTATATAT
66 TAATATAAAAATTTTATATAT
* * *
2942316 TTAAGTTGGCATCATAATTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTAAAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
2942381 TAATATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* * *
2942402 TTAAGTTTACATTATAGTTCAAGTAATATTAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
*
2942467 GAATATAAAAATTTTATATAT
66 TAATATAAAAATTTTATATAT
* *
2942488 TTAAGTTTGCATC--A--T-AAGTAATATAAATTAATTTTACATTTATTAGTTTACAAATTCAAC
1 TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
*
2942548 TAATATAAAGATTTTATA
66 TAATATAAAAATTTTATA
2942566 AAAATTTTAT
Statistics
Matches: 543, Mismatches: 52, Indels: 19
0.88 0.08 0.03
Matches are distributed among these distances:
81 58 0.11
82 1 0.00
84 1 0.00
86 306 0.56
87 93 0.17
88 5 0.01
89 1 0.00
90 1 0.00
91 5 0.01
92 13 0.02
93 59 0.11
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (86 bp):
TTAAGTTTGCATCATAGTTCAAGTAATATAAATTAATTTTACATTTGTTAGTTTACAAGTTCAAC
TAATATAAAAATTTTATATAT
Found at i:2948906 original size:13 final size:13
Alignment explanation
Indices: 2948888--2948912 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2948878 GGAGCAATTG
2948888 TGATTTTATAAAA
1 TGATTTTATAAAA
2948901 TGATTTTATAAA
1 TGATTTTATAAA
2948913 TTTTTTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:2959257 original size:67 final size:67
Alignment explanation
Indices: 2959175--2959310 Score: 220
Period size: 67 Copynumber: 2.0 Consensus size: 67
2959165 GAAAAGTTAG
* *
2959175 TTTTGGGTTTTGGTTGATCCCGAT-AAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGTGAAAAG
1 TTTTGGGTTTTGGTTGATCCCG-TGAAAAACCATTGTTAAAGGTTGTGGCTGAGCCTATGAAAAG
*
2959239 GCA
65 CCA
*
2959242 TTTTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTAAAGGTTGTGGCTGCGCCTATGAAAAGC
1 TTTTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTAAAGGTTGTGGCTGAGCCTATGAAAAGC
2959307 CA
66 CA
2959309 TT
1 TT
2959311 GTAAAAGCTT
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 1 0.02
67 63 0.98
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (67 bp):
TTTTGGGTTTTGGTTGATCCCGTGAAAAACCATTGTTAAAGGTTGTGGCTGAGCCTATGAAAAGC
CA
Found at i:2959310 original size:35 final size:35
Alignment explanation
Indices: 2959199--2959317 Score: 109
Period size: 35 Copynumber: 3.5 Consensus size: 35
2959189 TGATCCCGAT
*
2959199 AAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGTG
1 AAAAACCATTGTTAAAGGTTGTGGCTGAGCCTGTG
** * * * * *
2959234 AAAAGGCATT-TT--GGGTTTTGGTTGATCCCGTG
1 AAAAACCATTGTTAAAGGTTGTGGCTGAGCCTGTG
* *
2959266 AAAAACCATTGTTAAAGGTTGTGGCTGCGCCTATG
1 AAAAACCATTGTTAAAGGTTGTGGCTGAGCCTGTG
* *
2959301 AAAAGCCATTGTAAAAG
1 AAAAACCATTGTTAAAG
2959318 CTTGGTGGAA
Statistics
Matches: 62, Mismatches: 19, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
32 22 0.35
33 2 0.03
34 2 0.03
35 36 0.58
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.30
Consensus pattern (35 bp):
AAAAACCATTGTTAAAGGTTGTGGCTGAGCCTGTG
Found at i:2965566 original size:228 final size:227
Alignment explanation
Indices: 2965169--2965623 Score: 892
Period size: 228 Copynumber: 2.0 Consensus size: 227
2965159 CAAATCTTCT
2965169 CTCTCTAAATTCAGTCAGCCATGAATCCTTCATGGCATCTTGTGATTCAACCATGAAAAATGTAA
1 CTCTCTAAATTCAGTCAGCCATGAATCCTTCATGGCATCTTGTGATTCAACCATGAAAAATGTAA
2965234 AATAATGCATGGGAAAGGTAGATCACAAGTCAAAATCAAGAAATTTTACCTTTGATTGCTTGATT
66 AATAATGCATGGGAAAGGTAGATCACAAGTCAAAATCAAGAAATTTTACCTTTGATTGCTTGATT
2965299 ACTTGAATTTTCACACTTTTCCCTTCAATTTTTCCACCTAGGGTTTGTTTTCTTGTTTTCTTCTT
131 ACTTGAATTTTCACACTTTTCCCTTCAATTTTTCCACCTAGGGTTTGTTTTCTTGTTTTCTTCTT
2965364 TTCTTCCTTTGTTCTTGCTTTGGCCGGCCATA
196 TTCTTCCTTTGTTCTTGCTTTGGCCGGCCATA
2965396 NCTCTCTAAATTCAGTCAGCCATGAATCCTTCATGGCATCTTGTGATTCAACCATGAAAAATGTA
1 -CTCTCTAAATTCAGTCAGCCATGAATCCTTCATGGCATCTTGTGATTCAACCATGAAAAATGTA
2965461 AAATAATGCATGGGAAAGGTAGATCACAAGTCAAAATCAAGAAATTTTACCTTTGATTGCTTGAT
65 AAATAATGCATGGGAAAGGTAGATCACAAGTCAAAATCAAGAAATTTTACCTTTGATTGCTTGAT
*
2965526 TACTTGAATTTTCACACTTTTCCCTTGAATTTTTCCACCTAGGGTTTGTTTTCTTGTTTTCTTCT
130 TACTTGAATTTTCACACTTTTCCCTTCAATTTTTCCACCTAGGGTTTGTTTTCTTGTTTTCTTCT
2965591 TTTCTTCCTTTGTTCTTGCTTTGGCCGGCCATA
195 TTTCTTCCTTTGTTCTTGCTTTGGCCGGCCATA
2965624 TGAAGAGAAA
Statistics
Matches: 226, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
228 226 1.00
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.40
Consensus pattern (227 bp):
CTCTCTAAATTCAGTCAGCCATGAATCCTTCATGGCATCTTGTGATTCAACCATGAAAAATGTAA
AATAATGCATGGGAAAGGTAGATCACAAGTCAAAATCAAGAAATTTTACCTTTGATTGCTTGATT
ACTTGAATTTTCACACTTTTCCCTTCAATTTTTCCACCTAGGGTTTGTTTTCTTGTTTTCTTCTT
TTCTTCCTTTGTTCTTGCTTTGGCCGGCCATA
Found at i:2970944 original size:73 final size:73
Alignment explanation
Indices: 2970797--2970933 Score: 213
Period size: 72 Copynumber: 1.9 Consensus size: 73
2970787 GAGTAAAGCA
* * *
2970797 GATTGCAAGATAGAAAAGACTTAATAGACTAAGAAGTATGGTTAGCCAGCTAAAAGCTCACTGTC
1 GATTGCAAGATAGAAAAGACTTAATAGACTAAGAAGAATGATTAGCCAACTAAAAGCTCACTGTC
2970862 AAAAATTT
66 AAAAATTT
* * *
2970870 GATTGCGAGCTAGAAAAGACTTAAT-GACTAAGAAGAATGATTAGCCAATTAAAAGCTCACTGTC
1 GATTGCAAGATAGAAAAGACTTAATAGACTAAGAAGAATGATTAGCCAACTAAAAGCTCACTGTC
2970934 TAAGGATTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
72 35 0.60
73 23 0.40
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.24
Consensus pattern (73 bp):
GATTGCAAGATAGAAAAGACTTAATAGACTAAGAAGAATGATTAGCCAACTAAAAGCTCACTGTC
AAAAATTT
Found at i:2972248 original size:13 final size:13
Alignment explanation
Indices: 2972230--2972254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2972220 ATTTTCAAAA
2972230 ATTTTATAAAATT
1 ATTTTATAAAATT
2972243 ATTTTATAAAAT
1 ATTTTATAAAAT
2972255 CTCATTTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:2974117 original size:35 final size:35
Alignment explanation
Indices: 2974078--2974183 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 35
2974068 TTAATCTCAA
2974078 GAAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGT
1 GAAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGT
* * * ** * **
2974113 GAAAAGCCATT-TT-GA-GTTTTGATTGATCCCGT
1 GAAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGT
*
2974145 GAAAAATCATTGTTAAAGGTTGTGGCTGAGCTTGT
1 GAAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGT
2974180 GAAA
1 GAAA
2974184 GGTCATTGTA
Statistics
Matches: 51, Mismatches: 17, Indels: 6
0.69 0.23 0.08
Matches are distributed among these distances:
32 20 0.39
33 3 0.06
34 3 0.06
35 25 0.49
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.33
Consensus pattern (35 bp):
GAAAAACCATTGTTAAAGGTTGTGGCTGAGCTTGT
Found at i:2974190 original size:35 final size:35
Alignment explanation
Indices: 2974085--2974197 Score: 106
Period size: 35 Copynumber: 3.3 Consensus size: 35
2974075 CAAGAAAAAC
*
2974085 CATTGTTAAAGGTTGTGGCTGAGCTTGTGAAAAGC
1 CATTGTTAAAGGTTGTGGCTGAGCTTGTGAAAAGT
* * ** * ** *
2974120 CATT-TT-GA-GTTTTGATTGATCCCGTGAAAAAT
1 CATTGTTAAAGGTTGTGGCTGAGCTTGTGAAAAGT
*
2974152 CATTGTTAAAGGTTGTGGCTGAGCTTGTGAAAGGT
1 CATTGTTAAAGGTTGTGGCTGAGCTTGTGAAAAGT
*
2974187 CATTGTAAAAG
1 CATTGTTAAAG
2974198 CTTGGGAATT
Statistics
Matches: 56, Mismatches: 19, Indels: 6
0.69 0.23 0.07
Matches are distributed among these distances:
32 20 0.36
33 3 0.05
34 3 0.05
35 30 0.54
ACGTcount: A:0.27, C:0.11, G:0.27, T:0.35
Consensus pattern (35 bp):
CATTGTTAAAGGTTGTGGCTGAGCTTGTGAAAAGT
Found at i:2974895 original size:21 final size:23
Alignment explanation
Indices: 2974871--2974921 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
2974861 CAATAAAAAA
2974871 TAAATATTATTT-A-AA-TTTTCT
1 TAAATATTATTTAAGAACTTTT-T
2974892 TAAATA--ATTTAAGAACTTTTT
1 TAAATATTATTTAAGAACTTTTT
2974913 TAAATATTA
1 TAAATATTA
2974922 AGTCAATCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
19 4 0.16
20 1 0.04
21 15 0.60
22 4 0.16
23 1 0.04
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TAAATATTATTTAAGAACTTTTT
Found at i:2980187 original size:20 final size:21
Alignment explanation
Indices: 2980158--2980212 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
2980148 ATCACATGAT
2980158 TTAAAATAAAAAT-ATAAAAA
1 TTAAAATAAAAATAATAAAAA
* *
2980178 TTAAATTAAATATAATAAAAA
1 TTAAAATAAAAATAATAAAAA
*
2980199 ATAAAA-AAAAATAA
1 TTAAAATAAAAATAA
2980213 ATTATAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 18 0.62
21 11 0.38
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (21 bp):
TTAAAATAAAAATAATAAAAA
Found at i:2989733 original size:29 final size:30
Alignment explanation
Indices: 2989679--2989752 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
2989669 AATATTACTA
*
2989679 AAATTCTTTAA-TTATTTTAACTATT-ATTT
1 AAATT-TTTAATTTATTTTAACAATTAATTT
*
2989708 TAATTTTTAATTTATTTTTAA-AATTAATTT
1 AAATTTTTAATTTA-TTTTAACAATTAATTT
2989738 AAATTTATTAATTTA
1 AAATTT-TTAATTTA
2989753 AATTTTATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
28 5 0.13
29 10 0.26
30 15 0.39
31 8 0.21
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (30 bp):
AAATTTTTAATTTATTTTAACAATTAATTT
Found at i:2989763 original size:14 final size:14
Alignment explanation
Indices: 2989730--2989757 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2989720 TATTTTTAAA
2989730 ATTAATTTAAATTT
1 ATTAATTTAAATTT
2989744 ATTAATTTAAATTT
1 ATTAATTTAAATTT
2989758 TATAATAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTAATTTAAATTT
Found at i:3000981 original size:37 final size:37
Alignment explanation
Indices: 3000940--3001012 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
3000930 GATAGGATAG
3000940 TTATTTAGATATTTAAAAATTATTAATACTCAAATCC
1 TTATTTAGATATTTAAAAATTATTAATACTCAAATCC
* *
3000977 TTATTTGGATATTTAAAAATTATTAGTACTCAAATC
1 TTATTTAGATATTTAAAAATTATTAATACTCAAATC
3001013 TAAATAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (37 bp):
TTATTTAGATATTTAAAAATTATTAATACTCAAATCC
Found at i:3000998 original size:125 final size:116
Alignment explanation
Indices: 3000852--3001132 Score: 377
Period size: 116 Copynumber: 2.3 Consensus size: 116
3000842 AGTAGGAGAG
*
3000852 TTATTTAGATATTTAAAAATTATTAGTACTCGAATTCAAATAAAGACAAGAATTAGTTTAATTCT
1 TTATTTGGATATTTAAAAATTATTAGTACTCGAATTCAAATAAAGACAAG-A--A---T--TTC-
* *
3000917 AAATTTTAACAAAGATAGGATAGTTATTTAGATATTTAAAAATTATTAATACTCAAATCC
57 AAATTCTAACAAAGATAGGAGAGTTATTTAGATATTTAAAAATTATTAATACTCAAATCC
* *
3000977 TTATTTGGATATTTAAAAATTATTAGTACTC-AAATCTAAATAAAGACATGAATTTCAAATTCTA
1 TTATTTGGATATTTAAAAATTATTAGTACTCGAATTC-AAATAAAGACAAGAATTTCAAATTCTA
* *
3001041 ATAAAGATAGGAGAGTTATTTAGATATTTAAAAATTATTAATACTCAAATTC
65 ACAAAGATAGGAGAGTTATTTAGATATTTAAAAATTATTAATACTCAAATCC
*
3001093 TTATTTGGATACTTT-AAAATTATTAGTACTCGAATCCAAA
1 TTATTTGGATA-TTTAAAAATTATTAGTACTCGAATTCAAA
3001133 AAAAAAAAAA
Statistics
Matches: 144, Mismatches: 9, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
116 86 0.60
117 9 0.06
119 1 0.01
122 1 0.01
124 5 0.03
125 42 0.29
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (116 bp):
TTATTTGGATATTTAAAAATTATTAGTACTCGAATTCAAATAAAGACAAGAATTTCAAATTCTAA
CAAAGATAGGAGAGTTATTTAGATATTTAAAAATTATTAATACTCAAATCC
Found at i:3003000 original size:16 final size:15
Alignment explanation
Indices: 3002975--3003004 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
3002965 TCTAAACCAC
3002975 ATGAGACATATATAG
1 ATGAGACATATATAG
3002990 ATGAGGACATATATA
1 ATGA-GACATATATA
3003005 TAGCTTCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.27
Consensus pattern (15 bp):
ATGAGACATATATAG
Found at i:3004757 original size:18 final size:18
Alignment explanation
Indices: 3004734--3004773 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3004724 TATACACGTT
3004734 TTAAACACAATAACACGA
1 TTAAACACAATAACACGA
* *
3004752 TTAAACACGATAACATGA
1 TTAAACACAATAACACGA
3004770 TTAA
1 TTAA
3004774 GTAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.17, G:0.07, T:0.23
Consensus pattern (18 bp):
TTAAACACAATAACACGA
Found at i:3005733 original size:6 final size:6
Alignment explanation
Indices: 3005706--3005749 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
3005696 TTCATTGTTG
* * * *
3005706 TCTTCC TCTTCT TCATCG TCTTCC TCTTCC TCTGCC TCTTCC TC
1 TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TCTTCC TC
3005750 CTCGTCTTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.02, C:0.45, G:0.05, T:0.48
Consensus pattern (6 bp):
TCTTCC
Found at i:3006568 original size:41 final size:39
Alignment explanation
Indices: 3006490--3006570 Score: 92
Period size: 39 Copynumber: 2.0 Consensus size: 39
3006480 TAGCTTGTTT
* **
3006490 AAAATATTTAGAAAAAGATTATAATTAATCATTAATAAA
1 AAAATATATAGAAAAAGATTATAATTAATCAAAAATAAA
*
3006529 AAAATATATAGAGAAAGATGTACTATATT-ATCAAAAATAAA
1 AAAATATATAGAAAAAGAT-TA-TA-ATTAATCAAAAATAAA
3006570 A
1 A
3006571 GAAGTAACGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
39 17 0.49
40 2 0.06
41 13 0.37
42 3 0.09
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (39 bp):
AAAATATATAGAAAAAGATTATAATTAATCAAAAATAAA
Found at i:3014103 original size:33 final size:33
Alignment explanation
Indices: 3014065--3014132 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
3014055 CTTGGCTTAA
3014065 AGCCTTACAAGAAATACTAAACGACATTGTATG
1 AGCCTTACAAGAAATACTAAACGACATTGTATG
*
3014098 AGCCTTACAAGAAATACTAAACGACATTGTTTG
1 AGCCTTACAAGAAATACTAAACGACATTGTATG
3014131 AG
1 AG
3014133 TAACAACATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.25
Consensus pattern (33 bp):
AGCCTTACAAGAAATACTAAACGACATTGTATG
Found at i:3014412 original size:27 final size:26
Alignment explanation
Indices: 3014381--3014437 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
3014371 GTCATTCTCT
*
3014381 CTGTCCCAACCCTCCGTTTCCTCTCCC
1 CTGTCCCAACCCTCC-CTTCCTCTCCC
* * *
3014408 CTGTCCCGACCTTCCCTTGCTCTCCC
1 CTGTCCCAACCCTCCCTTCCTCTCCC
3014434 CTGT
1 CTGT
3014438 GAGGCTATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 13 0.50
27 13 0.50
ACGTcount: A:0.05, C:0.53, G:0.11, T:0.32
Consensus pattern (26 bp):
CTGTCCCAACCCTCCCTTCCTCTCCC
Found at i:3015086 original size:33 final size:33
Alignment explanation
Indices: 3015024--3015086 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
3015014 ATTTTGAATC
* *
3015024 AGAAAATATTTTCAATAATGTCTTTCAAACGGT
1 AGAAAATATTTTCAACAATGTCTTACAAACGGT
*
3015057 AGAAAATATTTTCTACAATGT-TATACAAAC
1 AGAAAATATTTTCAACAATGTCT-TACAAAC
3015087 AAGAGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 1 0.04
33 25 0.96
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.35
Consensus pattern (33 bp):
AGAAAATATTTTCAACAATGTCTTACAAACGGT
Found at i:3019860 original size:63 final size:64
Alignment explanation
Indices: 3019787--3019913 Score: 213
Period size: 63 Copynumber: 2.0 Consensus size: 64
3019777 CAATTCAACG
* *
3019787 CAGCATTGGCTGCCTCATCACTTCCCAAGATTGTTGCTTGCGGTTCTC-TCTGCAA-TTTTCCAC
1 CAGCATTGGCTGCCTCATCACTTCCCAAGATTGTTGCTTGCAGTTCCCTTC-GCAATTTTTCCAC
3019850 CAGCATTGGCTGCCTCATCACTTCCCAAGATTGTTGCTTGCAGTTCCCTTCGCAATTTTTCCAC
1 CAGCATTGGCTGCCTCATCACTTCCCAAGATTGTTGCTTGCAGTTCCCTTCGCAATTTTTCCAC
3019914 TTTTCGTTCA
Statistics
Matches: 60, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
63 50 0.83
64 10 0.17
ACGTcount: A:0.17, C:0.32, G:0.17, T:0.35
Consensus pattern (64 bp):
CAGCATTGGCTGCCTCATCACTTCCCAAGATTGTTGCTTGCAGTTCCCTTCGCAATTTTTCCAC
Found at i:3026741 original size:3 final size:3
Alignment explanation
Indices: 3026733--3026757 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
3026723 CCCATCAAAC
3026733 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
3026758 ATTTCTTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:3028733 original size:2 final size:2
Alignment explanation
Indices: 3028721--3028768 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
3028711 CATTTTCCAC
*
3028721 TA TA TA CA 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
3028763 T- TA TA T
1 TA TA TA T
3028769 TCATGTGAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3040663 original size:33 final size:32
Alignment explanation
Indices: 3040596--3040669 Score: 94
Period size: 32 Copynumber: 2.3 Consensus size: 32
3040586 AATAAAATTT
* * *
3040596 AATATTTTTTGTTGTTTGGATAAATTGTGGAA
1 AATATTTTTTATTGTTTGGATAAATTATGAAA
**
3040628 AATATTTTTTATTGTTTGGATTATTTTATGAAA
1 AATATTTTTTATTGTTTGGA-TAAATTATGAAA
3040661 AATATTTTT
1 AATATTTTT
3040670 CATCATGACG
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 19 0.53
33 17 0.47
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (32 bp):
AATATTTTTTATTGTTTGGATAAATTATGAAA
Found at i:3041077 original size:74 final size:74
Alignment explanation
Indices: 3040922--3041063 Score: 223
Period size: 74 Copynumber: 1.9 Consensus size: 74
3040912 AAACCTATAC
*
3040922 TTATAAATATGTATTCAGTAAATGACAATCATTGAAATATTTTGTATTATAATTATTGGTAAGAT
1 TTATAAATATGTATTCAGTAAATGACAATCATTGAAATATTTTGTATTATAATTATTAGTAAGAT
3040987 TTACACCTA
66 TTACACCTA
* ** *
3040996 TTATAAATGTGTATTCA-TCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGTAAGA
1 TTATAAATATGTATTCAGT-AAATGACAATCATTGAAATATTTTGTATTATAATTATTAGTAAGA
3041060 TTTA
65 TTTA
3041064 TTCTATTTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
73 1 0.02
74 61 0.98
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (74 bp):
TTATAAATATGTATTCAGTAAATGACAATCATTGAAATATTTTGTATTATAATTATTAGTAAGAT
TTACACCTA
Found at i:3041184 original size:35 final size:35
Alignment explanation
Indices: 3041145--3041225 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
3041135 AATGTATAAT
*
3041145 TTAAATATTAATATTTTAAATTAAT-TTTTTTAAAG
1 TTAAATATTAATATTTTAAATTAATATATTTT-AAG
* * * *
3041180 TTAAATAGTAATATTTTTATTTTATATATTTTAAG
1 TTAAATATTAATATTTTAAATTAATATATTTTAAG
3041215 TTAAATATTAA
1 TTAAATATTAA
3041226 CATTCATCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 34 0.87
36 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (35 bp):
TTAAATATTAATATTTTAAATTAATATATTTTAAG
Found at i:3041819 original size:14 final size:17
Alignment explanation
Indices: 3041784--3041821 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
3041774 GGATGATAGA
3041784 AAGAAAAGCACAAAAAG
1 AAGAAAAGCACAAAAAG
3041801 AAGAAAA-CA-AAAAAG
1 AAGAAAAGCACAAAAAG
3041816 -AGAAAA
1 AAGAAAA
3041822 AACACGATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 2 0.10
17 7 0.33
ACGTcount: A:0.76, C:0.08, G:0.16, T:0.00
Consensus pattern (17 bp):
AAGAAAAGCACAAAAAG
Found at i:3042230 original size:25 final size:25
Alignment explanation
Indices: 3042184--3042232 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
3042174 ATAAGCTCTT
*
3042184 TTAATTAATAATTTATTAATTATTA
1 TTAATTAATAATTCATTAATTATTA
*
3042209 TTAATTAA-AATATCATTTATTATT
1 TTAATTAATAAT-TCATTAATTATT
3042233 TTATATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (25 bp):
TTAATTAATAATTCATTAATTATTA
Found at i:3042723 original size:12 final size:12
Alignment explanation
Indices: 3042706--3042733 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3042696 CGATAAATAC
3042706 ATATCGATATAT
1 ATATCGATATAT
3042718 ATATCGATATAT
1 ATATCGATATAT
3042730 ATAT
1 ATAT
3042734 ATACACATCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (12 bp):
ATATCGATATAT
Found at i:3042729 original size:14 final size:14
Alignment explanation
Indices: 3042695--3042735 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
3042685 TAATGTAATC
* *
3042695 TCGATAAATACATA
1 TCGATATATATATA
3042709 TCG--ATATATATA
1 TCGATATATATATA
3042721 TCGATATATATATA
1 TCGATATATATATA
3042735 T
1 T
3042736 ACACATCGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.44, C:0.10, G:0.07, T:0.39
Consensus pattern (14 bp):
TCGATATATATATA
Found at i:3052178 original size:14 final size:14
Alignment explanation
Indices: 3052159--3052197 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
3052149 TTATATTAGA
*
3052159 TGTTATTATTATTT
1 TGTTATAATTATTT
3052173 TGTTATAATTA-TT
1 TGTTATAATTATTT
3052186 T-TTATAATTATT
1 TGTTATAATTATT
3052198 AATTTTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 9 0.39
13 4 0.17
14 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
TGTTATAATTATTT
Found at i:3060187 original size:44 final size:43
Alignment explanation
Indices: 3060117--3060205 Score: 99
Period size: 44 Copynumber: 2.0 Consensus size: 43
3060107 TTTCTTTTTT
* * * * *
3060117 AAATTACAAATTTATTTTTCATAATTTTCT-ATTTTCATATAAA
1 AAATTAAAAATTTATATTACAAAATTTT-TAATTTTAATATAAA
3060160 AAATTAAAATATTTATATTACAAAATTTTTAAATTTTAATATAAA
1 AAATTAAAA-ATTTATATTACAAAATTTTT-AATTTTAATATAAA
3060205 A
1 A
3060206 TATATCAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
43 9 0.24
44 16 0.42
45 13 0.34
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (43 bp):
AAATTAAAAATTTATATTACAAAATTTTTAATTTTAATATAAA
Found at i:3063342 original size:27 final size:26
Alignment explanation
Indices: 3063307--3063360 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 26
3063297 AAAATTTTAA
**
3063307 ATTATTTAAATTATTTTTTATTTTTT
1 ATTATTTAAATTAGATTTTATTTTTT
3063333 ATTATATTAAATTAGATTTTATTTTTT
1 ATTAT-TTAAATTAGATTTTATTTTTT
3063360 A
1 A
3063361 AAATTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (26 bp):
ATTATTTAAATTAGATTTTATTTTTT
Found at i:3063393 original size:18 final size:19
Alignment explanation
Indices: 3063353--3063394 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
3063343 ATTAGATTTT
3063353 ATTTTT-TAAAATTAAATA
1 ATTTTTATAAAATTAAATA
*
3063371 A-TTTTATATAATT-AATA
1 ATTTTTATAAAATTAAATA
3063388 ATTTTTA
1 ATTTTTA
3063395 ATTAAAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTATAAAATTAAATA
Found at i:3063548 original size:26 final size:25
Alignment explanation
Indices: 3063499--3063548 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 25
3063489 AAAATAATCT
3063499 ATTTGATTAAAAATAAAATTACAAGG
1 ATTTGATTAAAAATAAAA-TACAAGG
3063525 ATTTGATTGAAGAAATAAAA-ACAA
1 ATTTGATT-AA-AAATAAAATACAA
3063549 AACTATTCGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 12 0.55
27 2 0.09
28 8 0.36
ACGTcount: A:0.56, C:0.04, G:0.12, T:0.28
Consensus pattern (25 bp):
ATTTGATTAAAAATAAAATACAAGG
Found at i:3068299 original size:2 final size:2
Alignment explanation
Indices: 3068292--3068333 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
3068282 CTAATAAAAT
3068292 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA -A GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
3068333 G
1 G
3068334 CAGGAACAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:3084845 original size:2 final size:2
Alignment explanation
Indices: 3084838--3084862 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3084828 CTAGTATGTA
3084838 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
3084863 ATATACATAC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3091195 original size:37 final size:35
Alignment explanation
Indices: 3091137--3091212 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 35
3091127 GTTCCATTTT
* * * *
3091137 AAAATATAAAAAATTAAATTAATCAAATTTTTATA
1 AAAAAATAAAAAATCAAATTAATCAAATTATAATA
*
3091172 AAAAAATAAATAAATCAATATTAATTAAATTATAATA
1 AAAAAATAAA-AAATCAA-ATTAATCAAATTATAATA
3091209 AAAA
1 AAAA
3091213 TTTAAAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 9 0.26
36 6 0.18
37 19 0.56
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (35 bp):
AAAAAATAAAAAATCAAATTAATCAAATTATAATA
Found at i:3091200 original size:27 final size:27
Alignment explanation
Indices: 3091139--3091200 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
3091129 TCCATTTTAA
* *
3091139 AATATAAAAAATTAAATTAATCAAATT
1 AATATAAAAAAATAAATAAATCAAATT
**
3091166 TTTATAAAAAAATAAATAAATCAATATT
1 AATATAAAAAAATAAATAAATCAA-ATT
3091194 AAT-TAAA
1 AATATAAA
3091201 TTATAATAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (27 bp):
AATATAAAAAAATAAATAAATCAAATT
Found at i:3093887 original size:43 final size:43
Alignment explanation
Indices: 3093826--3093907 Score: 137
Period size: 43 Copynumber: 1.9 Consensus size: 43
3093816 GATCTGGAAG
* * *
3093826 AACATCCACTAGAGCAGAATGTTTCCTGTTGTGGCACAAGAAC
1 AACATCCACCAGAACAGAACGTTTCCTGTTGTGGCACAAGAAC
3093869 AACATCCACCAGAACAGAACGTTTCCTGTTGTGGCACAA
1 AACATCCACCAGAACAGAACGTTTCCTGTTGTGGCACAA
3093908 TCAGCTTATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 36 1.00
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (43 bp):
AACATCCACCAGAACAGAACGTTTCCTGTTGTGGCACAAGAAC
Found at i:3103026 original size:30 final size:30
Alignment explanation
Indices: 3102990--3103048 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
3102980 ATTAACCTAG
3102990 TTTTATATTTTTATTTT-AATCTAAATAAAC
1 TTTTATATTTTTATTTTAAAT-TAAATAAAC
3103020 TTTTATATTTTTATTTTAAATTAAATAAA
1 TTTTATATTTTTATTTTAAATTAAATAAA
3103049 TTCTTATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTTATATTTTTATTTTAAATTAAATAAAC
Found at i:3103333 original size:22 final size:21
Alignment explanation
Indices: 3103287--3103363 Score: 64
Period size: 22 Copynumber: 3.6 Consensus size: 21
3103277 ATTTTTATTT
* * *
3103287 TTAAAATATTAAAAAATTATAA
1 TTAAAAT-TTTAAAATTTAAAA
3103309 TTAAAATTTTAAAATTTAAATA
1 TTAAAATTTTAAAATTTAAA-A
** * *
3103331 TTAATTTTTTATAATTTATAA
1 TTAAAATTTTAAAATTTAAAA
*
3103352 TTAAAGTTTTAA
1 TTAAAATTTTAA
3103364 TTTAATTTTA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
21 20 0.45
22 24 0.55
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (21 bp):
TTAAAATTTTAAAATTTAAAA
Found at i:3106954 original size:20 final size:20
Alignment explanation
Indices: 3106931--3106971 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
3106921 ATCAAATCTC
*
3106931 ATTTCATTTCATATAAATCA
1 ATTTCATTTCATAAAAATCA
*
3106951 ATTTCATTTCGTAAAAATCA
1 ATTTCATTTCATAAAAATCA
3106971 A
1 A
3106972 CAAGGCTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTCATTTCATAAAAATCA
Found at i:3112897 original size:28 final size:27
Alignment explanation
Indices: 3112861--3112913 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
3112851 ATATCCTGGT
*
3112861 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
3112888 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
3112914 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:3114034 original size:6 final size:6
Alignment explanation
Indices: 3114023--3114047 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3114013 ATTCCATTAC
3114023 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
3114048 CATACCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:3115637 original size:15 final size:13
Alignment explanation
Indices: 3115624--3115675 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
3115614 GTGAAATATG
3115624 TAAAATAAAAATA
1 TAAAATAAAAATA
*
3115637 TAAGATAAAAATA
1 TAAAATAAAAATA
* *
3115650 AAAAATTAAAATTTA
1 TAAAA-TAAAA-ATA
3115665 TATAAATAAAA
1 TA-AAATAAAA
3115676 TTGGTGTCTA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
13 15 0.48
14 5 0.16
15 8 0.26
16 3 0.10
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (13 bp):
TAAAATAAAAATA
Found at i:3117251 original size:19 final size:19
Alignment explanation
Indices: 3117229--3117266 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3117219 ATGATGGTTG
3117229 GATAAAAAA-ATGATATGGA
1 GATAAAAAAGA-GATATGGA
3117248 GATAAAAAAGAGATATGGA
1 GATAAAAAAGAGATATGGA
3117267 AATAGTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.58, C:0.00, G:0.24, T:0.18
Consensus pattern (19 bp):
GATAAAAAAGAGATATGGA
Found at i:3118637 original size:21 final size:21
Alignment explanation
Indices: 3118613--3118652 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3118603 AATTTCTATT
*
3118613 ATATATATATATATACTTTTA
1 ATATAAATATATATACTTTTA
*
3118634 ATATAAATATATTTACTTT
1 ATATAAATATATATACTTT
3118653 ATATTTTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATAAATATATATACTTTTA
Found at i:3119572 original size:22 final size:22
Alignment explanation
Indices: 3119547--3119619 Score: 65
Period size: 22 Copynumber: 3.1 Consensus size: 22
3119537 GAGCATTGCA
3119547 TGACTTGTTTATAGGCATTACG
1 TGACTTGTTTATAGGCATTACG
* * * * *
3119569 TGACTGAATATTTGTTGAGCGTTGCG
1 TGACT---TGTTTATAG-GCATTACG
3119595 TGACTTGTTTATAGGCATTACG
1 TGACTTGTTTATAGGCATTACG
3119617 TGA
1 TGA
3119620 TTGAATATTA
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
22 14 0.38
23 6 0.16
25 6 0.16
26 11 0.30
ACGTcount: A:0.22, C:0.12, G:0.26, T:0.40
Consensus pattern (22 bp):
TGACTTGTTTATAGGCATTACG
Found at i:3119586 original size:48 final size:48
Alignment explanation
Indices: 3119515--3119628 Score: 201
Period size: 48 Copynumber: 2.4 Consensus size: 48
3119505 GTGCCTGAAT
3119515 ATTACGTGATTGAATATTTGTTGAGCATTGCATGACTTGTTTATAGGC
1 ATTACGTGATTGAATATTTGTTGAGCATTGCATGACTTGTTTATAGGC
* * *
3119563 ATTACGTGACTGAATATTTGTTGAGCGTTGCGTGACTTGTTTATAGGC
1 ATTACGTGATTGAATATTTGTTGAGCATTGCATGACTTGTTTATAGGC
3119611 ATTACGTGATTGAATATT
1 ATTACGTGATTGAATATT
3119629 ACGTGACTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.41
Consensus pattern (48 bp):
ATTACGTGATTGAATATTTGTTGAGCATTGCATGACTTGTTTATAGGC
Found at i:3119631 original size:15 final size:15
Alignment explanation
Indices: 3119611--3119643 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3119601 GTTTATAGGC
*
3119611 ATTACGTGATTGAAT
1 ATTACGTGACTGAAT
3119626 ATTACGTGACTGAAT
1 ATTACGTGACTGAAT
3119641 ATT
1 ATT
3119644 TGTTGAGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.39
Consensus pattern (15 bp):
ATTACGTGACTGAAT
Found at i:3119632 original size:63 final size:63
Alignment explanation
Indices: 3119563--3119682 Score: 195
Period size: 63 Copynumber: 1.9 Consensus size: 63
3119553 GTTTATAGGC
* *
3119563 ATTACGTGACTGAATATTTGTTGAGCGTTGCGTGACTTGTTTATAGGCATTACGTGATTGAAT
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTGTTTATAGGCATTACGTGATTGAAT
* * *
3119626 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTGTTTGTGGGCATTGCGTGA
1 ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTGTTTATAGGCATTACGTGA
3119683 CTTTATCTAC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (63 bp):
ATTACGTGACTGAATATTTGTTGAGCATTGCGTGACCTGTTTATAGGCATTACGTGATTGAAT
Found at i:3124358 original size:22 final size:22
Alignment explanation
Indices: 3124333--3124382 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
3124323 TTTTTTAGGC
*
3124333 ATTGCGTGA-CTGGTTTTTATAT
1 ATTGCGTGACCT-GTTGTTATAT
*
3124355 ATTGCGTGACCTGTTGTTATGT
1 ATTGCGTGACCTGTTGTTATAT
3124377 ATTGCG
1 ATTGCG
3124383 AGAGTGGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.92
23 2 0.08
ACGTcount: A:0.16, C:0.12, G:0.26, T:0.46
Consensus pattern (22 bp):
ATTGCGTGACCTGTTGTTATAT
Found at i:3124372 original size:119 final size:119
Alignment explanation
Indices: 3124159--3124455 Score: 429
Period size: 119 Copynumber: 2.5 Consensus size: 119
3124149 GGTGCGTGAC
* * * *
3124159 TGACTTGTGTAATTCATGTGTTGTTTTGAAGCTTTTGTTCAGTAGTTTTTTAGGCATTGTGTGAT
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCATTGCGTGAC
* *
3124224 TGGTTTTTATATATTGCGTTACCTATTGTTATGTATTGCGAGAGTGGTGGCGCG
66 TGGTTTTTATATATTGCGTGACCTATTGTTATGTATTGCGAGAGTGGTGGCGCA
3124278 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCATTGCGTGAC
1 TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCATTGCGTGAC
* *
3124343 TGGTTTTTATATATTGCGTGACCTGTTGTTATGTATTGCGAGAGTGGTGGTGCA
66 TGGTTTTTATATATTGCGTGACCTATTGTTATGTATTGCGAGAGTGGTGGCGCA
* * * * * *
3124397 TGACTTGTTCAATT--TGCCTATTGTTTTGAGACGTTTGTTCACTAG-TTATTAGGCATTGC
1 TGACTTGTGCAATTCATG--TGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCATTGC
3124456 ATGAATGTGT
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
117 2 0.01
118 13 0.08
119 147 0.91
ACGTcount: A:0.17, C:0.11, G:0.26, T:0.46
Consensus pattern (119 bp):
TGACTTGTGCAATTCATGTGTTGTTTTGAGGCTTTTGTTCAGTAGTTTTTTAGGCATTGCGTGAC
TGGTTTTTATATATTGCGTGACCTATTGTTATGTATTGCGAGAGTGGTGGCGCA
Found at i:3128926 original size:2 final size:2
Alignment explanation
Indices: 3128919--3128957 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
3128909 ATGTCTTTTA
*
3128919 AT AT AT AT ACT TT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3128958 TCGATTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3148065 original size:21 final size:20
Alignment explanation
Indices: 3148026--3148070 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
3148016 GTTTTTACAT
* *
3148026 TTTTTATGTTTCTGTTTATG
1 TTTTTATGTTTATGATTATG
3148046 ATTTTTATGTTTATGATTATG
1 -TTTTTATGTTTATGATTATG
3148067 TTTT
1 TTTT
3148071 GAAGCTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.16, C:0.02, G:0.13, T:0.69
Consensus pattern (20 bp):
TTTTTATGTTTATGATTATG
Found at i:3152067 original size:26 final size:26
Alignment explanation
Indices: 3152038--3152130 Score: 114
Period size: 26 Copynumber: 3.6 Consensus size: 26
3152028 TTTTACAATC
3152038 AGAAGTGGATGGATAATTTTGCCACA
1 AGAAGTGGATGGATAATTTTGCCACA
* *
3152064 AGAAGTGGACGGATAATTTTGCCACC
1 AGAAGTGGATGGATAATTTTGCCACA
* * ** *
3152090 AGAAGTGGATGAACAATTTTATCACT
1 AGAAGTGGATGGATAATTTTGCCACA
*
3152116 AGAAGTTGATGGATA
1 AGAAGTGGATGGATA
3152131 CCTTAACCCA
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (26 bp):
AGAAGTGGATGGATAATTTTGCCACA
Found at i:3157595 original size:15 final size:16
Alignment explanation
Indices: 3157575--3157610 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
3157565 TTTTTTCCAT
*
3157575 AAAAAC-AATTTTGTC
1 AAAAACAAATTTTATC
3157590 AAAAACAAATTTTATC
1 AAAAACAAATTTTATC
3157606 AAAAA
1 AAAAA
3157611 TTCACCGAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.58, C:0.11, G:0.03, T:0.28
Consensus pattern (16 bp):
AAAAACAAATTTTATC
Found at i:3158680 original size:2 final size:2
Alignment explanation
Indices: 3158667--3158697 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3158657 GATCAACTAG
*
3158667 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3158698 ACACGATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3158790 original size:2 final size:2
Alignment explanation
Indices: 3158785--3158814 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3158775 CTCCCATGGA
3158785 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
3158815 TGATTTGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3160908 original size:2 final size:2
Alignment explanation
Indices: 3160901--3160938 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3160891 TTGGTAATTA
3160901 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
3160939 TTCTCAATCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3162487 original size:21 final size:22
Alignment explanation
Indices: 3162461--3162510 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
3162451 GACTAAATAT
* *
3162461 AAAAAATATTCAA-GATTTAAG
1 AAAAAATATTAAATGATTTAAC
*
3162482 AAAAAA-ATTAAATTATTTAAC
1 AAAAAATATTAAATGATTTAAC
3162503 AAAAAATA
1 AAAAAATA
3162511 AAAGTTTATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 5 0.21
21 18 0.75
22 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (22 bp):
AAAAAATATTAAATGATTTAAC
Found at i:3163451 original size:40 final size:40
Alignment explanation
Indices: 3163406--3163481 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
3163396 AGTCTTGCCT
* * * *
3163406 TAAAAAAGTTTGAAGTTGAAAATTAAAAATAAATCAAAAA
1 TAAAAAAATTGGAAATTAAAAATTAAAAATAAATCAAAAA
3163446 TAAAAAAATTGGAAATTAAAAATTAAAAATAAATCA
1 TAAAAAAATTGGAAATTAAAAATTAAAAATAAATCA
3163482 TTATAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (40 bp):
TAAAAAAATTGGAAATTAAAAATTAAAAATAAATCAAAAA
Found at i:3163723 original size:150 final size:148
Alignment explanation
Indices: 3163354--3163935 Score: 538
Period size: 150 Copynumber: 3.8 Consensus size: 148
3163344 ATAAATCAGC
* * * * * *
3163354 AAAAAAGTATGAAAG-TGGAAATTAAAAATAAATCATAATAAAAGTCTTGCCTTAAAAAAGTTTG
1 AAAAAAGTATG-AAGTTGGAAACTAAAAATAAATCATAATAAAAATCTCGCCGTAAAAAAGTCTA
* *
3163418 AAGTTGAAAATTAAAAATAAATCAAAAATAAAAAAATTGGAAATTAAAAATTAAA--AATAAATC
65 AAGTTGAAAATTAAAAATAAATCAAAAAT-AAAAAATTGGAAACTAAAAA-TAAATCATTAAA--
* * * **
3163481 ATTATAAATAACTGAATATATCAGC
126 A-AATAAATAACT-AATAAATAAAT
* * *
3163506 AAAAAAGTCTGAAGTTGGAAACT-AAAATCAAATCGTAATAAAAATCTCACCGTAAAAAAGTGC-
1 AAAAAAGTATGAAGTTGGAAACTAAAAAT-AAATCATAATAAAAATCTCGCCGTAAAAAAGT-CT
* *
3163569 AAAGTTGAAAGTTAAAAATAAATCAAAAATAAAAAATTGGAAAATAAAAATAAATCATTAAAAAA
64 AAAGTTGAAAATTAAAAATAAATCAAAAATAAAAAATTGGAAACTAAAAATAAATCATTAAAAAA
*
3163634 CTAACTAACTAACTAAATAAAT
129 -TAAATAACTAA-TAAATAAAT
* * * * * * * *
3163656 AAATAAGTATGAAGTTGGAAAATAAAAATAGATCATAACAAAAGTCTCGTCATAAAAATGTCTAA
1 AAAAAAGTATGAAGTTGGAAACTAAAAATAAATCATAATAAAAATCTCGCCGTAAAAAAGTCTAA
* *
3163721 AGTTGAAAATTAAAAATAAATC---AA-AAGAAATTGGAAACTAAAAATAAATGAAAAATTAAAA
66 AGTTGAAAATTAAAAATAAATCAAAAATAAAAAATTGGAAACTAAAAATAAAT----CATT-AAA
**
3163782 ATGAATAATTATAAAAAATAAATAAAT
126 A--AATAA--ATAACTAATAAATAAAT
*
3163809 CAGCAAAAAAGTCTGAAGTTGGAAACTAAAAATAAATCATAATAAAAATCTC-CCTGTAAAAAAG
1 ----AAAAAAGTATGAAGTTGGAAACTAAAAATAAATCATAATAAAAATCTCGCC-GTAAAAAAG
** *
3163873 AATAAAGTTGAAATTTAAAAATAAAT-AACAAATAAAAAATTGGAAACTAAAAATAAATCATTA
61 TCTAAAGTTGAAAATTAAAAATAAATCAA-AAATAAAAAATTGGAAACTAAAAATAAATCATTA
3163936 TACAAAATTA
Statistics
Matches: 352, Mismatches: 50, Indels: 52
0.78 0.11 0.11
Matches are distributed among these distances:
146 23 0.07
147 2 0.01
149 4 0.01
150 88 0.25
151 36 0.10
152 80 0.23
153 11 0.03
154 5 0.01
156 2 0.01
157 75 0.21
160 2 0.01
161 24 0.07
ACGTcount: A:0.59, C:0.08, G:0.10, T:0.24
Consensus pattern (148 bp):
AAAAAAGTATGAAGTTGGAAACTAAAAATAAATCATAATAAAAATCTCGCCGTAAAAAAGTCTAA
AGTTGAAAATTAAAAATAAATCAAAAATAAAAAATTGGAAACTAAAAATAAATCATTAAAAAATA
AATAACTAATAAATAAAT
Found at i:3163882 original size:307 final size:301
Alignment explanation
Indices: 3163358--3163935 Score: 799
Period size: 307 Copynumber: 1.9 Consensus size: 301
3163348 ATCAGCAAAA
* * * * * *
3163358 AAGTATGAAAGTGGAAATTAAAAATAAATCATAATAAAAGTCTTGCCTTAAAAAAGTTTGAAGTT
1 AAGTATGAAAGTGGAAAATAAAAATAAATCATAACAAAAGTCTCGCCATAAAAAAGTCTAAAGTT
* * *
3163423 GAAAATTAAAAATAAATCAAAAATAAAAAAATTGGAAATTAAAAATTAAAAATAAATCATTATAA
66 GAAAATTAAAAATAAATCAAAAATAAAAAAAAT-GAAATGAAAAATTAAAAATAAATAATTATAA
* * * *
3163488 ATAACTGAATATATCAGCAAAAAAGTCTGAAGTTGGAAACTAAAATCAAATCGTAATAAAAATCT
130 ATAAATAAATAAATCAGCAAAAAAGTCTGAAGTTGGAAACTAAAATCAAATCATAATAAAAATCT
**
3163553 CACCGTAAAAAAGTGCAAAGTTGAAAGTTAAAAATAAATCAA-AAATAAAAAATTGGAAAATAAA
195 CACCGTAAAAAAGAACAAAGTTGAAAGTTAAAAATAAAT-AACAAATAAAAAATTGGAAAATAAA
3163617 AATAAATCATTAAAAAACTAACTAACTAACTAAATAAATAAAT
259 AATAAATCATTAAAAAACTAACTAACTAACTAAATAAATAAAT
* * *
3163660 AAGTATG-AAGTTGGAAAATAAAAATAGATCATAACAAAAGTCTCGTCATAAAAATGTCTAAAGT
1 AAGTATGAAAG-TGGAAAATAAAAATAAATCATAACAAAAGTCTCGCCATAAAAAAGTCTAAAGT
*
3163724 TGAAAATTAAAAATAAATCAAAAGAAATTGGAAACTAAAAAT-AAATGAAAAATTAAAAATGAAT
65 TGAAAATTAAAAATAAATC--AA-AAA-T--AAA--AAAAATGAAATGAAAAATTAAAAATAAAT
3163788 AATTATAAA-AAATAAATAAATCAGCAAAAAAGTCTGAAGTTGGAAACTAAAAAT-AAATCATAA
122 AATTATAAATAAATAAATAAATCAGCAAAAAAGTCTGAAGTTGGAAACT-AAAATCAAATCATAA
* *
3163851 TAAAAATCTC-CCTGTAAAAAAGAATAAAGTTGAAATTTAAAAATAAATAACAAATAAAAAATTG
186 TAAAAATCTCACC-GTAAAAAAGAACAAAGTTGAAAGTTAAAAATAAATAACAAATAAAAAATTG
*
3163915 GAAACTAAAAATAAATCATTA
250 GAAAATAAAAATAAATCATTA
3163936 TACAAAATTA
Statistics
Matches: 242, Mismatches: 22, Indels: 19
0.86 0.08 0.07
Matches are distributed among these distances:
301 3 0.01
302 70 0.29
304 2 0.01
305 3 0.01
306 5 0.02
307 118 0.49
308 36 0.15
310 5 0.02
ACGTcount: A:0.58, C:0.08, G:0.10, T:0.24
Consensus pattern (301 bp):
AAGTATGAAAGTGGAAAATAAAAATAAATCATAACAAAAGTCTCGCCATAAAAAAGTCTAAAGTT
GAAAATTAAAAATAAATCAAAAATAAAAAAAATGAAATGAAAAATTAAAAATAAATAATTATAAA
TAAATAAATAAATCAGCAAAAAAGTCTGAAGTTGGAAACTAAAATCAAATCATAATAAAAATCTC
ACCGTAAAAAAGAACAAAGTTGAAAGTTAAAAATAAATAACAAATAAAAAATTGGAAAATAAAAA
TAAATCATTAAAAAACTAACTAACTAACTAAATAAATAAAT
Found at i:3164026 original size:22 final size:22
Alignment explanation
Indices: 3163998--3164122 Score: 87
Period size: 22 Copynumber: 5.5 Consensus size: 22
3163988 GTTGGAAACT
3163998 AAAATAAATCATTATAAAATAA
1 AAAATAAATCATTATAAAATAA
* *
3164020 AAAAT-AAT-AGGTTAGAAACT-A
1 AAAATAAATCA--TTATAAAATAA
* *
3164041 AAAATAAATCATTACAAAAAATA
1 AAAATAAATCATTATAAAATA-A
*
3164064 AAAATAAATCATTACAAAAAACTAA
1 AAAATAAATCATT--ATAAAA-TAA
*
3164089 ATAAATCAATCATTATAAAA-AA
1 A-AAATAAATCATTATAAAATAA
*
3164111 CTAAATAAATCA
1 -AAAATAAATCA
3164123 GTAAAAAAGT
Statistics
Matches: 81, Mismatches: 11, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
20 1 0.01
21 15 0.19
22 26 0.32
23 15 0.19
24 5 0.06
25 7 0.09
26 12 0.15
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.24
Consensus pattern (22 bp):
AAAATAAATCATTATAAAATAA
Found at i:3164065 original size:23 final size:24
Alignment explanation
Indices: 3164058--3164130 Score: 73
Period size: 26 Copynumber: 3.1 Consensus size: 24
3164048 ATCATTACAA
3164058 AAAA-TAAAAATAAATCATTACAA
1 AAAACTAAAAATAAATCATTACAA
* *
3164081 AAAACTAAATAAATCAATCATTATAA
1 AAAACT-AA-AAATAAATCATTACAA
*
3164107 AAAACT--AAATAAATCAGTA-AA
1 AAAACTAAAAATAAATCATTACAA
3164128 AAA
1 AAA
3164131 GTTTGAAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
21 5 0.12
22 11 0.26
23 4 0.09
24 1 0.02
25 2 0.05
26 20 0.47
ACGTcount: A:0.67, C:0.10, G:0.01, T:0.22
Consensus pattern (24 bp):
AAAACTAAAAATAAATCATTACAA
Found at i:3164101 original size:26 final size:24
Alignment explanation
Indices: 3164035--3164130 Score: 119
Period size: 23 Copynumber: 4.1 Consensus size: 24
3164025 AATAGGTTAG
3164035 AAACTAAAAATAAATCATTACAAA
1 AAACTAAAAATAAATCATTACAAA
3164059 AAA-TAAAAATAAATCATTACAAA
1 AAACTAAAAATAAATCATTACAAA
* *
3164082 AAACTAAATAAATCAATCATTATAAA
1 AAACT-AA-AAATAAATCATTACAAA
*
3164108 AAACT--AAATAAATCAGTA-AAA
1 AAACTAAAAATAAATCATTACAAA
3164129 AA
1 AA
3164131 GTTTGAAGTT
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
21 5 0.08
22 11 0.17
23 23 0.35
24 4 0.06
25 2 0.03
26 20 0.31
ACGTcount: A:0.67, C:0.10, G:0.01, T:0.22
Consensus pattern (24 bp):
AAACTAAAAATAAATCATTACAAA
Found at i:3164198 original size:21 final size:21
Alignment explanation
Indices: 3164154--3164212 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
3164144 GATTAAAAAT
* *
3164154 AAATCAAAAATAAAAAATTGTA
1 AAAT-AAAAATAAATAATTATA
* *
3164176 AACTAAAAATAAATCATTATA
1 AAATAAAAATAAATAATTATA
*
3164197 AAATAATAATAAATAA
1 AAATAAAAATAAATAA
3164213 AAAATAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 27 0.90
22 3 0.10
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (21 bp):
AAATAAAAATAAATAATTATA
Found at i:3165491 original size:37 final size:36
Alignment explanation
Indices: 3165379--3165493 Score: 101
Period size: 36 Copynumber: 3.2 Consensus size: 36
3165369 GATCGCGTGG
* * * *
3165379 AAAAGCT-GTTGTAAGGGTTATTGCCTAATCTTGTTA
1 AAAAGCTAG-TGTAAGAGTTATCGCTTGATCTTGTTA
*
3165415 AAAAGCTAGTGTAAGAGTTATCGCTTGATCTTGTGA
1 AAAAGCTAGTGTAAGAGTTATCGCTTGATCTTGTTA
* * *
3165451 AAAAGCTATTGTGAGGATTTAAT-GCTTGA-CTTCGTTA
1 AAAAGCTAGTGT-AAGAGTT-ATCGCTTGATCTT-GTTA
3165488 AAAAGC
1 AAAAGC
3165494 ATGTTTCCTT
Statistics
Matches: 66, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
36 43 0.65
37 21 0.32
38 2 0.03
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.35
Consensus pattern (36 bp):
AAAAGCTAGTGTAAGAGTTATCGCTTGATCTTGTTA
Found at i:3166477 original size:21 final size:21
Alignment explanation
Indices: 3166439--3166478 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3166429 TAGAAATAAA
** *
3166439 AAATAAATCATTACAAAAAAT
1 AAATAAATCAGAAAAAAAAAT
3166460 AAATAAATCAGAAAAAAAA
1 AAATAAATCAGAAAAAAAA
3166479 GTCTGAAGTT
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:0.72, C:0.07, G:0.03, T:0.17
Consensus pattern (21 bp):
AAATAAATCAGAAAAAAAAAT
Found at i:3166530 original size:18 final size:16
Alignment explanation
Indices: 3166491--3166541 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
3166481 CTGAAGTTGC
3166491 AAATTAAAAATATAAA
1 AAATTAAAAATATAAA
**
3166507 TCATTATAAAATTATAAA
1 AAATTA-AAAA-TATAAA
*
3166525 AAATTAAAAAAATAAA
1 AAATTAAAAATATAAA
3166541 A
1 A
3166542 TAAACATTTC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 10 0.36
17 8 0.29
18 10 0.36
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATTAAAAATATAAA
Found at i:3168130 original size:41 final size:41
Alignment explanation
Indices: 3168068--3168151 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
3168058 AGATAAAATT
3168068 TTATAAATCTCATACTAATAAGAGATGAAGTAGGTATTGAA
1 TTATAAATCTCATACTAATAAGAGATGAAGTAGGTATTGAA
*
3168109 TTATGAATCTCATACTAATAAGAGATGAAGTAGGTATTGAA
1 TTATAAATCTCATACTAATAAGAGATGAAGTAGGTATTGAA
3168150 TT
1 TT
3168152 TATATCTAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.33
Consensus pattern (41 bp):
TTATAAATCTCATACTAATAAGAGATGAAGTAGGTATTGAA
Found at i:3168791 original size:6 final size:7
Alignment explanation
Indices: 3168776--3168800 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3168766 AATTTACTGG
3168776 AAAAGAA
1 AAAAGAA
3168783 AAAAGAA
1 AAAAGAA
3168790 AAAAGAA
1 AAAAGAA
3168797 AAAA
1 AAAA
3168801 AATTGTGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAGAA
Found at i:3173078 original size:29 final size:27
Alignment explanation
Indices: 3173037--3173093 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 27
3173027 GAATTATGTC
* *
3173037 TATTTATTTAATTAAGTTTTCTATTTTT
1 TATTTATCTAATTAAGTCTT-TATTTTT
3173065 TATTATATCTAATTAAGTCTTTATTTTT
1 TATT-TATCTAATTAAGTCTTTATTTTT
3173093 T
1 T
3173094 GATTCGTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 12 0.46
29 14 0.54
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (27 bp):
TATTTATCTAATTAAGTCTTTATTTTT
Found at i:3173668 original size:55 final size:54
Alignment explanation
Indices: 3173582--3173815 Score: 200
Period size: 55 Copynumber: 4.3 Consensus size: 54
3173572 AATCGCATTG
* * * * * * * *
3173582 AAAATGTAGTTTTTATATATCACGTTAAAAATTTAGTTGTTATATATTATGTTAA
1 AAAATGTAGTTGTTATATGTCATGTTGAAAATGTAGTTGTTACACATCATGTT-A
* *
3173637 AAAATGTAGTTGTTATACGTCATGTTGAAAATGTAGTTGTTACACGTCATGTTA
1 AAAATGTAGTTGTTATATGTCATGTTGAAAATGTAGTTGTTACACATCATGTTA
* * * ** *
3173691 CAAATTTAGTTGTTACATGTCATGTTGAAAAATGTAGTTGTTACATGTCATGTTG
1 AAAATGTAGTTGTTATATGTCATGTTG-AAAATGTAGTTGTTACACATCATGTTA
* * * * * * *
3173746 AAAAT-TCAGTTATGACATGCCATGTTGAAAAATGTAATTGTTATACATCATGTTG
1 AAAATGT-AGTTGTTATATGTCATGTTG-AAAATGTAGTTGTTACACATCATGTTA
* *
3173801 AAAATTTAGTGGTTA
1 AAAATGTAGTTGTTA
3173816 CACATCATGT
Statistics
Matches: 149, Mismatches: 27, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
54 25 0.17
55 123 0.83
56 1 0.01
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (54 bp):
AAAATGTAGTTGTTATATGTCATGTTGAAAATGTAGTTGTTACACATCATGTTA
Found at i:3173668 original size:82 final size:82
Alignment explanation
Indices: 3173579--3173750 Score: 236
Period size: 82 Copynumber: 2.1 Consensus size: 82
3173569 AAAAATCGCA
* * * * *
3173579 TTGAAAATGTAGTTTTTATATATCACGTTAAAAATTTAGTTGTTATATATTATGTTAAAAAATGT
1 TTGAAAATGTAGTTGTTACACATCACGTTAAAAATTTAGTTGTTACATATCATGTTAAAAAATGT
*
3173644 AGTTGTTATACGTCATG
66 AGTTGTTACACGTCATG
* * * * *
3173661 TTGAAAATGTAGTTGTTACACGTCATGTTACAAATTTAGTTGTTACATGTCATGTTGAAAAATGT
1 TTGAAAATGTAGTTGTTACACATCACGTTAAAAATTTAGTTGTTACATATCATGTTAAAAAATGT
*
3173726 AGTTGTTACATGTCATG
66 AGTTGTTACACGTCATG
3173743 TTGAAAAT
1 TTGAAAAT
3173751 TCAGTTATGA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.34, C:0.07, G:0.17, T:0.42
Consensus pattern (82 bp):
TTGAAAATGTAGTTGTTACACATCACGTTAAAAATTTAGTTGTTACATATCATGTTAAAAAATGT
AGTTGTTACACGTCATG
Found at i:3173717 original size:15 final size:15
Alignment explanation
Indices: 3173699--3173745 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
3173689 TACAAATTTA
3173699 GTTGTTACATGTCAT
1 GTTGTTACATGTCAT
** *
3173714 GTTGAAAAATGT-A-
1 GTTGTTACATGTCAT
3173727 GTTGTTACATGTCAT
1 GTTGTTACATGTCAT
3173742 GTTG
1 GTTG
3173746 AAAATTCAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
13 9 0.38
14 2 0.08
15 13 0.54
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.43
Consensus pattern (15 bp):
GTTGTTACATGTCAT
Found at i:3173763 original size:27 final size:27
Alignment explanation
Indices: 3173579--3173831 Score: 213
Period size: 27 Copynumber: 9.3 Consensus size: 27
3173569 AAAAATCGCA
* * * *
3173579 TTGAAAATGTAGTTTTTATATATCACG
1 TTGAAAATGTAGTTGTTACATGTCATG
* * * * *
3173606 TTAAAAATTTAGTTGTTATATATTATG
1 TTGAAAATGTAGTTGTTACATGTCATG
* * *
3173633 TTAAAAAATGTAGTTGTTATACGTCATG
1 TT-GAAAATGTAGTTGTTACATGTCATG
*
3173661 TTGAAAATGTAGTTGTTACACGTCATG
1 TTGAAAATGTAGTTGTTACATGTCATG
*
3173688 TT-ACAAATTTAGTTGTTACATGTCATG
1 TTGA-AAATGTAGTTGTTACATGTCATG
3173715 TTGAAAAATGTAGTTGTTACATGTCATG
1 TTG-AAAATGTAGTTGTTACATGTCATG
* * *
3173743 TTGAAAAT-TCAGTTATGACATGCCATG
1 TTGAAAATGT-AGTTGTTACATGTCATG
* * **
3173770 TTGAAAAATGTAATTGTTATACATCATG
1 TTG-AAAATGTAGTTGTTACATGTCATG
* * **
3173798 TTGAAAATTTAGTGGTTACACATCATG
1 TTGAAAATGTAGTTGTTACATGTCATG
*
3173825 TTAAAAA
1 TTGAAAA
3173832 ATTTAAACCC
Statistics
Matches: 190, Mismatches: 29, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
26 2 0.01
27 120 0.63
28 66 0.35
29 2 0.01
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (27 bp):
TTGAAAATGTAGTTGTTACATGTCATG
Found at i:3173770 original size:82 final size:82
Alignment explanation
Indices: 3173605--3173831 Score: 260
Period size: 82 Copynumber: 2.8 Consensus size: 82
3173595 TATATATCAC
* * *
3173605 GTTAAAAATTTAGTTGTTATATATTATGTTAAAAAATGTAGTTGTTATACGTCATGTTGAAAATG
1 GTTAAAAATTTAGTTGTTATATATCATGTTGAAAAATGTAGTTGTTACACGTCATGTTGAAAATG
* * *
3173670 TAGTTGTTACACGTCAT
66 TAGTTATGACACGCCAT
* * * *
3173687 GTTACAAATTTAGTTGTTACATGTCATGTTGAAAAATGTAGTTGTTACATGTCATGTTGAAAAT-
1 GTTAAAAATTTAGTTGTTATATATCATGTTGAAAAATGTAGTTGTTACACGTCATGTTGAAAATG
*
3173751 TCAGTTATGACATGCCAT
66 T-AGTTATGACACGCCAT
* * * * * * *
3173769 GTTGAAAAATGTAATTGTTATACATCATGTTG-AAAATTTAGTGGTTACACATCATGTTAAAAA
1 GTT-AAAAATTTAGTTGTTATATATCATGTTGAAAAATGTAGTTGTTACACGTCATGTTGAAAA
3173832 ATTTAAACCC
Statistics
Matches: 121, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
81 1 0.01
82 98 0.81
83 22 0.18
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (82 bp):
GTTAAAAATTTAGTTGTTATATATCATGTTGAAAAATGTAGTTGTTACACGTCATGTTGAAAATG
TAGTTATGACACGCCAT
Found at i:3173825 original size:55 final size:55
Alignment explanation
Indices: 3173608--3173833 Score: 231
Period size: 55 Copynumber: 4.1 Consensus size: 55
3173598 ATATCACGTT
* * * * * * *
3173608 AAAAATTTAGTTGTTATATATTATGTTAAAAAATGTAGTTGTTATACGTCATGTTG
1 AAAAATGTAGTTGTTACACATCATGTT-GAAAATTTAGTTGTTACACGTCATGTTG
* *
3173664 -AAAATGTAGTTGTTACACGTCATGTT-ACAAATTTAGTTGTTACATGTCATGTTG
1 AAAAATGTAGTTGTTACACATCATGTTGA-AAATTTAGTTGTTACACGTCATGTTG
** * * * * *
3173718 AAAAATGTAGTTGTTACATGTCATGTTGAAAATTCAGTTATGACATGCCATGTTG
1 AAAAATGTAGTTGTTACACATCATGTTGAAAATTTAGTTGTTACACGTCATGTTG
* * * * *
3173773 AAAAATGTAATTGTTATACATCATGTTGAAAATTTAGTGGTTACACATCATGTTA
1 AAAAATGTAGTTGTTACACATCATGTTGAAAATTTAGTTGTTACACGTCATGTTG
3173828 AAAAAT
1 AAAAAT
3173834 TTAAACCCCA
Statistics
Matches: 142, Mismatches: 25, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
53 1 0.01
54 23 0.16
55 117 0.82
56 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.39
Consensus pattern (55 bp):
AAAAATGTAGTTGTTACACATCATGTTGAAAATTTAGTTGTTACACGTCATGTTG
Found at i:3175646 original size:33 final size:33
Alignment explanation
Indices: 3175582--3175646 Score: 76
Period size: 33 Copynumber: 2.0 Consensus size: 33
3175572 ATGTCATGTA
* *
3175582 ATCATAAATTATAATATGTCAGTATATTACATC
1 ATCATAAATTATAATATATCAGTATACTACATC
* * * *
3175615 ATCATCAATTATGATATATTAGTATGCTACAT
1 ATCATAAATTATAATATATCAGTATACTACAT
3175647 TAACGTCATG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (33 bp):
ATCATAAATTATAATATATCAGTATACTACATC
Found at i:3175997 original size:17 final size:17
Alignment explanation
Indices: 3175947--3176004 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
3175937 ATACTAAATC
*
3175947 TTCCTTCTTCTTCTTTT
1 TTCCTTTTTCTTCTTTT
3175964 TT-CTTTTT-TTCCCTTTT
1 TTCCTTTTTCTT--CTTTT
*
3175981 TTCCTTTTTCTTTTTTT
1 TTCCTTTTTCTTCTTTT
3175998 TTCCTTT
1 TTCCTTT
3176005 ATATTTATAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
15 2 0.06
16 5 0.14
17 20 0.57
18 6 0.17
19 2 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCCTTTTTCTTCTTTT
Found at i:3176278 original size:51 final size:51
Alignment explanation
Indices: 3176218--3176326 Score: 182
Period size: 51 Copynumber: 2.1 Consensus size: 51
3176208 CTTTTATTTA
* * * *
3176218 AATTATTAATGAAATTTTATGTTGTAATTTAATTTTATTTCAAAATTGATT
1 AATTTTTAATGAAATTTTATATTATAATTTAATTTTATTTCAAAAGTGATT
3176269 AATTTTTAATGAAATTTTATATTATAATTTAATTTTATTTCAAAAGTGATT
1 AATTTTTAATGAAATTTTATATTATAATTTAATTTTATTTCAAAAGTGATT
3176320 AATTTTT
1 AATTTTT
3176327 TTACTTTGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (51 bp):
AATTTTTAATGAAATTTTATATTATAATTTAATTTTATTTCAAAAGTGATT
Found at i:3178955 original size:17 final size:16
Alignment explanation
Indices: 3178922--3178964 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
3178912 TATAACTTTT
3178922 ATAAATTAAT-ACTTA
1 ATAAATTAATAACTTA
3178937 ATAAATTAATAATCTTA
1 ATAAATTAATAA-CTTA
3178954 ATTAAA-TAATA
1 A-TAAATTAATA
3178965 TTTTTGATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 10 0.40
16 1 0.04
17 10 0.40
18 4 0.16
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAATTAATAACTTA
Found at i:3179986 original size:2 final size:2
Alignment explanation
Indices: 3179981--3180043 Score: 65
Period size: 2 Copynumber: 32.0 Consensus size: 2
3179971 CTCCCCCCCC
* * * * * *
3179981 CT CT CT CT CT CT CT CT CT CT CT CT CN CC CC CC CT CC CC CT C-
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
3180022 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
3180044 TCCCTTGTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.40
Consensus pattern (2 bp):
CT
Found at i:3188098 original size:15 final size:15
Alignment explanation
Indices: 3188078--3188110 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3188068 AATTTGTGGC
3188078 ATTTTACCCTACTCA
1 ATTTTACCCTACTCA
*
3188093 ATTTTACCCTATTCA
1 ATTTTACCCTACTCA
3188108 ATT
1 ATT
3188111 GTGCAACGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (15 bp):
ATTTTACCCTACTCA
Found at i:3188239 original size:31 final size:31
Alignment explanation
Indices: 3188198--3188262 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
3188188 TATAGGAGAG
*
3188198 GGACTCTTACACTAAACTTAAGCCCAATAAA
1 GGACTATTACACTAAACTTAAGCCCAATAAA
*
3188229 GGACTATTACATTAAACTTAAGCCCAATAAA
1 GGACTATTACACTAAACTTAAGCCCAATAAA
3188260 GGA
1 GGA
3188263 GAGAGACTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.12, T:0.23
Consensus pattern (31 bp):
GGACTATTACACTAAACTTAAGCCCAATAAA
Found at i:3188838 original size:24 final size:24
Alignment explanation
Indices: 3188808--3188877 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
3188798 CTTGTTATTT
*
3188808 TAATATTTTTTACA-TAATATTTTA
1 TAATATTTTTTA-ATTAATATTATA
* *
3188832 TAATATTTTTGAATTAATATTATG
1 TAATATTTTTTAATTAATATTATA
3188856 TGAATATTTTTTTCAATTAATA
1 T-AATA-TTTTTT-AATTAATA
3188878 GTTCGTGAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 1 0.03
24 20 0.53
25 4 0.11
26 5 0.13
27 8 0.21
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (24 bp):
TAATATTTTTTAATTAATATTATA
Found at i:3188885 original size:27 final size:27
Alignment explanation
Indices: 3188831--3188893 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3188821 ATAATATTTT
* *
3188831 ATAATATTTTTGAATTAATATTATGTGA
1 ATAAT-TTTTTCAATTAATATTACGTGA
*
3188859 ATATTTTTTTCAATTAATAGTT-CGTGA
1 ATAATTTTTTCAATTAATA-TTACGTGA
3188886 ATAATTTT
1 ATAATTTT
3188894 ATTTTCATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 24 0.80
28 6 0.20
ACGTcount: A:0.35, C:0.03, G:0.10, T:0.52
Consensus pattern (27 bp):
ATAATTTTTTCAATTAATATTACGTGA
Found at i:3189870 original size:15 final size:16
Alignment explanation
Indices: 3189843--3189875 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
3189833 GTTTGGTACC
3189843 TTACAATGTAATGTGA
1 TTACAATGTAATGTGA
3189859 TTACAA-GTAATGTGA
1 TTACAATGTAATGTGA
3189874 TT
1 TT
3189876 GTAGGGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TTACAATGTAATGTGA
Found at i:3191337 original size:17 final size:17
Alignment explanation
Indices: 3191315--3191356 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
3191305 TCTCAATTTT
3191315 ATTTGATTATTTTATTA
1 ATTTGATTATTTTATTA
3191332 ATTTGATTATTTTATTA
1 ATTTGATTATTTTATTA
3191349 ATTT-ATTA
1 ATTTGATTA
3191357 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (17 bp):
ATTTGATTATTTTATTA
Found at i:3191353 original size:8 final size:8
Alignment explanation
Indices: 3191315--3191357 Score: 50
Period size: 8 Copynumber: 5.1 Consensus size: 8
3191305 TCTCAATTTT
3191315 ATTTGATTA
1 ATTT-ATTA
*
3191324 TTTTATTA
1 ATTTATTA
3191332 ATTTGATTA
1 ATTT-ATTA
*
3191341 TTTTATTA
1 ATTTATTA
3191349 ATTTATTA
1 ATTTATTA
3191357 A
1 A
3191358 AAAAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 19 0.66
9 10 0.34
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.63
Consensus pattern (8 bp):
ATTTATTA
Found at i:3197019 original size:35 final size:35
Alignment explanation
Indices: 3196973--3197050 Score: 147
Period size: 35 Copynumber: 2.2 Consensus size: 35
3196963 TGAGAGCTTG
*
3196973 TGTCATGGATTTTGGAGGTTTTTAGGATCGACGTT
1 TGTCATGGATTTTGGAGGTTCTTAGGATCGACGTT
3197008 TGTCATGGATTTTGGAGGTTCTTAGGATCGACGTT
1 TGTCATGGATTTTGGAGGTTCTTAGGATCGACGTT
3197043 TGTCATGG
1 TGTCATGG
3197051 GCAAAATTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.17, C:0.10, G:0.32, T:0.41
Consensus pattern (35 bp):
TGTCATGGATTTTGGAGGTTCTTAGGATCGACGTT
Found at i:3197869 original size:36 final size:37
Alignment explanation
Indices: 3197781--3197869 Score: 99
Period size: 37 Copynumber: 2.4 Consensus size: 37
3197771 TCTGATATAC
** *
3197781 TTCTGACCCATACCACTAGGGTTAATTGTGGTTCTAA
1 TTCTGACCCACGCCACTAGGGTTAATTGGGGTTCTAA
* * *
3197818 TTCTGACCCATGCCACTTGGGTTAATTGGGGTT-TTA
1 TTCTGACCCACGCCACTAGGGTTAATTGGGGTTCTAA
* *
3197854 TTTTGACCTACGCCAC
1 TTCTGACCCACGCCAC
3197870 AGGAGTAAAG
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
36 15 0.33
37 30 0.67
ACGTcount: A:0.20, C:0.24, G:0.20, T:0.36
Consensus pattern (37 bp):
TTCTGACCCACGCCACTAGGGTTAATTGGGGTTCTAA
Found at i:3198698 original size:33 final size:33
Alignment explanation
Indices: 3198661--3198726 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3198651 TTTTAATATC
* * *
3198661 ATATATTTTATTTTCATTTCTTATTATAGTTTT
1 ATATATTTTACTTTCATTTCTTAATATAATTTT
3198694 ATATATTTTACTTTCATTTCTTAATATAATTTT
1 ATATATTTTACTTTCATTTCTTAATATAATTTT
3198727 TTACATTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.27, C:0.08, G:0.02, T:0.64
Consensus pattern (33 bp):
ATATATTTTACTTTCATTTCTTAATATAATTTT
Found at i:3209345 original size:3 final size:3
Alignment explanation
Indices: 3209337--3209362 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3209327 TAAGTGTCTG
3209337 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
3209363 AAGCAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:3218199 original size:2 final size:2
Alignment explanation
Indices: 3218192--3218232 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
3218182 ATAAAACTTA
3218192 AT AT AT AT AT AT GAT AT AT AT AT -T 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 AT AT AT AT A
3218233 AAATATGGAN
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 34 0.92
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3218210 original size:13 final size:12
Alignment explanation
Indices: 3218192--3218232 Score: 66
Period size: 11 Copynumber: 3.4 Consensus size: 12
3218182 ATAAAACTTA
3218192 ATATATATATAT
1 ATATATATATAT
3218204 GATATATATAT-T
1 -ATATATATATAT
3218216 ATATATATATAT
1 ATATATATATAT
3218228 ATATA
1 ATATA
3218233 AAATATGGAN
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 10 0.37
12 7 0.26
13 10 0.37
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
ATATATATATAT
Found at i:3230511 original size:6 final size:6
Alignment explanation
Indices: 3230496--3230532 Score: 56
Period size: 6 Copynumber: 6.2 Consensus size: 6
3230486 CTGTAACACC
* *
3230496 CCCCCN CCCCCC CCCCCA CCCCCA CCCCCA CCCCCA C
1 CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA CCCCCA C
3230533 GCACTCACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.11, C:0.86, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCCA
Found at i:3241278 original size:20 final size:19
Alignment explanation
Indices: 3241255--3241308 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
3241245 TAAATATAAA
3241255 TAACATAAAACT-AACATTAT
1 TAACATAAAA-TAAACATT-T
*
3241275 TAACTTAAAATAAACATTT
1 TAACATAAAATAAACATTT
* *
3241294 AAACATAAATTAAAC
1 TAACATAAAATAAAC
3241309 TAAACTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (19 bp):
TAACATAAAATAAACATTT
Found at i:3243800 original size:33 final size:32
Alignment explanation
Indices: 3243763--3243836 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 32
3243753 GTTGATAGTG
* *
3243763 AAAAATATTTATTACGAGATGATCCAAAAAATA
1 AAAAATATTT-TCACAAGATGATCCAAAAAATA
* *
3243796 AAAAATACTTTTCATAAGATGATCCAAATAATA
1 AAAAATA-TTTTCACAAGATGATCCAAAAAATA
*
3243829 GAAAATAT
1 AAAAATAT
3243837 AAAATTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
32 1 0.03
33 31 0.89
34 3 0.09
ACGTcount: A:0.54, C:0.09, G:0.08, T:0.28
Consensus pattern (32 bp):
AAAAATATTTTCACAAGATGATCCAAAAAATA
Found at i:3244408 original size:22 final size:21
Alignment explanation
Indices: 3244382--3244446 Score: 58
Period size: 22 Copynumber: 3.0 Consensus size: 21
3244372 AGAGTCTAAT
3244382 TTGATGTTTAATTTAAAATTAA
1 TTGAT-TTTAATTTAAAATTAA
* **
3244404 TTGATATTAAATAAAAAATTAA
1 TTGAT-TTTAATTTAAAATTAA
* *
3244426 TTAATTTTAAATTAAATATTA
1 TTGATTTTAATTTAAA-ATTA
3244447 CATTACAAAA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
21 7 0.21
22 26 0.79
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (21 bp):
TTGATTTTAATTTAAAATTAA
Done.