Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 143 of 208
Found at i:43743581 original size:25 final size:25
Alignment explanation
Indices: 43743526--43743587 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 25
43743516 TTTTAAGTGT
* *
43743526 TTTCAGTATAGT-CTATCTATAATAG
1 TTTCAGTATA-TACTACCTATAACAG
* *
43743551 TCTCAGTATATACTACCTATAGCAG
1 TTTCAGTATATACTACCTATAACAG
*
43743576 TTTCAGGATATA
1 TTTCAGTATATA
43743588 ATATCAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (25 bp):
TTTCAGTATATACTACCTATAACAG
Found at i:43743953 original size:18 final size:18
Alignment explanation
Indices: 43743922--43743970 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
43743912 GTATCGTTCG
*
43743922 TTTCTAAATTATTATTC-A
1 TTTC-AAATCATTATTCAA
43743940 TTTACAAATCATTATTCAA
1 TTT-CAAATCATTATTCAA
*
43743959 TTTCAAAACATT
1 TTTCAAATCATT
43743971 TTTTTTCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 22 0.81
19 5 0.19
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (18 bp):
TTTCAAATCATTATTCAA
Found at i:43755342 original size:25 final size:25
Alignment explanation
Indices: 43755308--43755367 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
43755298 CAGTGGTGCA
*
43755308 GTGGCAAGGTGGT-G-A-CACAGGT
1 GTGGCAAGGAGGTGGCATCACAGGT
43755330 GTGGCAAGGAGGTGGCATCACAGGT
1 GTGGCAAGGAGGTGGCATCACAGGT
*
43755355 GTGGTAAGGAGGT
1 GTGGCAAGGAGGT
43755368 CAAAGGTTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
22 12 0.36
23 1 0.03
24 1 0.03
25 19 0.58
ACGTcount: A:0.23, C:0.12, G:0.47, T:0.18
Consensus pattern (25 bp):
GTGGCAAGGAGGTGGCATCACAGGT
Found at i:43758731 original size:40 final size:40
Alignment explanation
Indices: 43758615--43758749 Score: 216
Period size: 41 Copynumber: 3.3 Consensus size: 40
43758605 GCTCTGTACT
43758615 TAGCAGGCTTAATGCTAGTGAAATAATTCAGACTTTACGTC
1 TAGCAGGCTTAATGC-AGTGAAATAATTCAGACTTTACGTC
*
43758656 TAGCAGGCTTAATGCCAGTGAAATAATTCAAACTTTACGTC
1 TAGCAGGCTTAATG-CAGTGAAATAATTCAGACTTTACGTC
* *
43758697 TAGCAGGCTTAATGCAGTGAAATATTTCAGACTTTACATC
1 TAGCAGGCTTAATGCAGTGAAATAATTCAGACTTTACGTC
*
43758737 TAGTAGGCTTAAT
1 TAGCAGGCTTAAT
43758750 ACCGGTGTTC
Statistics
Matches: 88, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
40 35 0.40
41 52 0.59
42 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.32
Consensus pattern (40 bp):
TAGCAGGCTTAATGCAGTGAAATAATTCAGACTTTACGTC
Found at i:43761678 original size:11 final size:11
Alignment explanation
Indices: 43761664--43761688 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43761654 TATATATAAG
43761664 TAATTTAATGA
1 TAATTTAATGA
43761675 TAATTTAATGA
1 TAATTTAATGA
43761686 TAA
1 TAA
43761689 AAGTGGATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (11 bp):
TAATTTAATGA
Found at i:43765354 original size:64 final size:64
Alignment explanation
Indices: 43765253--43765383 Score: 226
Period size: 64 Copynumber: 2.0 Consensus size: 64
43765243 TAAAATTGTC
*
43765253 TTAACAATAAAATTTAGGAGAAACATAGAAATATTAATATAAAATGAAGTTTTAATCATTTAAT
1 TTAACAATAAAATTTAGGAGAAACATAGAAATATTAATATAAAATAAAGTTTTAATCATTTAAT
* * *
43765317 TTAACAATAAAATTTAGGAGAAATATAGAAATATTAATATAAAATAAATTTTTAGTCATTTAAT
1 TTAACAATAAAATTTAGGAGAAACATAGAAATATTAATATAAAATAAAGTTTTAATCATTTAAT
43765381 TTA
1 TTA
43765384 GAATAGGAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (64 bp):
TTAACAATAAAATTTAGGAGAAACATAGAAATATTAATATAAAATAAAGTTTTAATCATTTAAT
Found at i:43765359 original size:32 final size:32
Alignment explanation
Indices: 43765259--43765361 Score: 84
Period size: 32 Copynumber: 3.2 Consensus size: 32
43765249 TGTCTTAACA
*
43765259 ATAAAATTTAGGAGAAACATAGAAATATTAAT
1 ATAAAATTTAGGAGAAATATAGAAATATTAAT
** **** ** *
43765291 ATAAAATGAAGTTTTAATCAT-TTAAT-TTAACA
1 ATAAAATTTAGGAGAAAT-ATAGAAATATTAA-T
43765323 ATAAAATTTAGGAGAAATATAGAAATATTAAT
1 ATAAAATTTAGGAGAAATATAGAAATATTAAT
43765355 ATAAAAT
1 ATAAAAT
43765362 AAATTTTTAG
Statistics
Matches: 48, Mismatches: 19, Indels: 8
0.64 0.25 0.11
Matches are distributed among these distances:
31 6 0.12
32 36 0.75
33 6 0.12
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (32 bp):
ATAAAATTTAGGAGAAATATAGAAATATTAAT
Found at i:43765534 original size:46 final size:46
Alignment explanation
Indices: 43765467--43765573 Score: 160
Period size: 46 Copynumber: 2.3 Consensus size: 46
43765457 ACTTTATTTC
* * *
43765467 AAAATTTCAAAAGTTTCTTAATATATAAATAATTTACCCTGATAGT
1 AAAATTTTAAAATTTTCTTAATATATAAATAATTTACCCTAATAGT
* *
43765513 AAAATTTTATAATTTTCTTAATATATAAATAATTTATCCTAATAGT
1 AAAATTTTAAAATTTTCTTAATATATAAATAATTTACCCTAATAGT
*
43765559 AAACTTTTAAAATTT
1 AAAATTTTAAAATTT
43765574 ATACAAATGA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (46 bp):
AAAATTTTAAAATTTTCTTAATATATAAATAATTTACCCTAATAGT
Found at i:43767407 original size:3 final size:3
Alignment explanation
Indices: 43767393--43767432 Score: 71
Period size: 3 Copynumber: 13.0 Consensus size: 3
43767383 TGTTTAACAC
43767393 ATT ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
43767433 TAACACAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:43767793 original size:9 final size:9
Alignment explanation
Indices: 43767779--43767815 Score: 74
Period size: 9 Copynumber: 4.1 Consensus size: 9
43767769 TGAGTTTTCG
43767779 AATTCGAAT
1 AATTCGAAT
43767788 AATTCGAAT
1 AATTCGAAT
43767797 AATTCGAAT
1 AATTCGAAT
43767806 AATTCGAAT
1 AATTCGAAT
43767815 A
1 A
43767816 TCAAACTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43769920 original size:5 final size:5
Alignment explanation
Indices: 43769910--43769935 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
43769900 CTCGAAAATT
43769910 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
43769936 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:43780258 original size:7 final size:7
Alignment explanation
Indices: 43780247--43780314 Score: 84
Period size: 7 Copynumber: 9.7 Consensus size: 7
43780237 CTTCAATCTC
*
43780247 CAATTTC
1 CAATTTT
43780254 CAATTTT
1 CAATTTT
*
43780261 CTATTTT
1 CAATTTT
*
43780268 CAATATT
1 CAATTTT
43780275 CAATTTT
1 CAATTTT
43780282 CAA-TTT
1 CAATTTT
43780288 CGAATTTT
1 C-AATTTT
43780296 CAATTTT
1 CAATTTT
*
43780303 CTATTTT
1 CAATTTT
43780310 CAATT
1 CAATT
43780315 CTAAATCCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
6 4 0.08
7 44 0.85
8 4 0.08
ACGTcount: A:0.28, C:0.16, G:0.01, T:0.54
Consensus pattern (7 bp):
CAATTTT
Found at i:43800228 original size:3 final size:3
Alignment explanation
Indices: 43800220--43800260 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
43800210 TGATAAGGTT
43800220 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
43800261 TACACAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:43805883 original size:21 final size:22
Alignment explanation
Indices: 43805859--43805904 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
43805849 CTGTTGAAAA
43805859 TAATA-AAAAATAATCAAAATT
1 TAATATAAAAATAATCAAAATT
* * *
43805880 TAATATAAAATTAATTAAGATT
1 TAATATAAAAATAATCAAAATT
43805902 TAA
1 TAA
43805905 CATGTTAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TAATATAAAAATAATCAAAATT
Found at i:43807986 original size:7 final size:7
Alignment explanation
Indices: 43807973--43808003 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
43807963 TTTGGTTGTA
43807973 ATTGGAC
1 ATTGGAC
*
43807980 TTTGGAC
1 ATTGGAC
43807987 ATTGGAC
1 ATTGGAC
43807994 ATTGGAC
1 ATTGGAC
43808001 ATT
1 ATT
43808004 TTATTTTGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (7 bp):
ATTGGAC
Found at i:43810701 original size:45 final size:46
Alignment explanation
Indices: 43810636--43810762 Score: 150
Period size: 45 Copynumber: 2.8 Consensus size: 46
43810626 TTGATTCAAA
** * *
43810636 TGAGTAAGACCATAATTGAAAGACATTATGGCATCATGACAGA-AG
1 TGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGACAAATAG
* * * **
43810681 TGAGTAAGACCATGGCTGAAAGATGCTATGGCATCATGGTAAATAG
1 TGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGACAAATAG
*
43810727 -GACTAAGACCATAGCTGAAAGACGTTATGGCATCAT
1 TGAGTAAGACCATAGCTGAAAGACGTTATGGCATCAT
43810763 TTCATAGTTA
Statistics
Matches: 68, Mismatches: 13, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
45 66 0.97
46 2 0.03
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (46 bp):
TGAGTAAGACCATAGCTGAAAGACGTTATGGCATCATGACAAATAG
Found at i:43813558 original size:5 final size:5
Alignment explanation
Indices: 43813548--43813575 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
43813538 AAAAGAAGGA
43813548 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAA
43813576 TAGGATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:43819415 original size:23 final size:23
Alignment explanation
Indices: 43819342--43819415 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
43819332 CTGGGTCTCA
* *
43819342 CACACGACCATACCTTTGACAGT
1 CACACGACCACACCCTTGACAGT
*
43819365 CACACGACCACACCCTCGACAGT
1 CACACGACCACACCCTTGACAGT
* *
43819388 CACACGACTACACCCTTGATAGT
1 CACACGACCACACCCTTGACAGT
*
43819411 TACAC
1 CACAC
43819416 AGTCAGCCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.31, C:0.39, G:0.12, T:0.18
Consensus pattern (23 bp):
CACACGACCACACCCTTGACAGT
Found at i:43820586 original size:17 final size:17
Alignment explanation
Indices: 43820555--43820587 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
43820545 GTATTGATTT
43820555 TGACATTCTTATGTCAA
1 TGACATTCTTATGTCAA
43820572 TGACAATTCTT-TGTCA
1 TGAC-ATTCTTATGTCA
43820588 TCAATCAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.42
Consensus pattern (17 bp):
TGACATTCTTATGTCAA
Found at i:43820804 original size:17 final size:17
Alignment explanation
Indices: 43820782--43820837 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
43820772 AACAAGTATG
43820782 TGATTACAATAATCTCA
1 TGATTACAATAATCTCA
* * * *
43820799 TGATTAAAACAAGTAT-G
1 TGATTACAATAA-TCTCA
43820816 TGATTACAATAATCTCA
1 TGATTACAATAATCTCA
43820833 TGATT
1 TGATT
43820838 GGCCTTTGGG
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
16 2 0.07
17 25 0.86
18 2 0.07
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (17 bp):
TGATTACAATAATCTCA
Found at i:43820807 original size:34 final size:34
Alignment explanation
Indices: 43820769--43820837 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
43820759 ATAAACAAGG
43820769 TAAAACAAGTATGTGATTACAATAATCTCATGAT
1 TAAAACAAGTATGTGATTACAATAATCTCATGAT
43820803 TAAAACAAGTATGTGATTACAATAATCTCATGAT
1 TAAAACAAGTATGTGATTACAATAATCTCATGAT
43820837 T
1 T
43820838 GGCCTTTGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (34 bp):
TAAAACAAGTATGTGATTACAATAATCTCATGAT
Found at i:43821301 original size:20 final size:20
Alignment explanation
Indices: 43821276--43821317 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
43821266 CATCATAGTT
43821276 AATACCATGAACTTAGCGAA
1 AATACCATGAACTTAGCGAA
43821296 AATACCATGAACTTAGCGAA
1 AATACCATGAACTTAGCGAA
43821316 AA
1 AA
43821318 CCTTTAGTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.19, G:0.14, T:0.19
Consensus pattern (20 bp):
AATACCATGAACTTAGCGAA
Found at i:43823261 original size:29 final size:30
Alignment explanation
Indices: 43823214--43823271 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
43823204 TTGGCTTTGA
43823214 CATTGTCCTTAGGCTTTGCCTTAGACTTAG
1 CATTGTCCTTAGGCTTTGCCTTAGACTTAG
43823244 CATT-TCCTTAGGCTTTGCCTTAGACTTA
1 CATTGTCCTTAGGCTTTGCCTTAGACTTA
43823272 ACAATTCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.17, C:0.24, G:0.17, T:0.41
Consensus pattern (30 bp):
CATTGTCCTTAGGCTTTGCCTTAGACTTAG
Found at i:43824833 original size:16 final size:17
Alignment explanation
Indices: 43824800--43824833 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
43824790 TCGGGCTATA
*
43824800 ACCATGCATTTCCAAAC
1 ACCATGCATATCCAAAC
43824817 ACCATGCATAT-CAAAC
1 ACCATGCATATCCAAAC
43824833 A
1 A
43824834 TAGTATACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.41, C:0.32, G:0.06, T:0.21
Consensus pattern (17 bp):
ACCATGCATATCCAAAC
Found at i:43826281 original size:11 final size:11
Alignment explanation
Indices: 43826265--43826289 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
43826255 TCCATTTGAG
43826265 TTTTTCTTTGC
1 TTTTTCTTTGC
43826276 TTTTTCTTTGC
1 TTTTTCTTTGC
43826287 TTT
1 TTT
43826290 ATTAGTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.08, T:0.76
Consensus pattern (11 bp):
TTTTTCTTTGC
Found at i:43829175 original size:18 final size:17
Alignment explanation
Indices: 43829153--43829192 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
43829143 AAAAATTAGA
*
43829153 TAAATGATATACTTTAT
1 TAAATGATACACTTTAT
*
43829170 TCAAATTATACACTTTAT
1 T-AAATGATACACTTTAT
43829188 TAAAT
1 TAAAT
43829193 ATAATACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.45
Consensus pattern (17 bp):
TAAATGATACACTTTAT
Found at i:43829312 original size:22 final size:24
Alignment explanation
Indices: 43829257--43829312 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 24
43829247 ACGATGAGAG
*
43829257 AAATTTTAATATGAAAAAAAATGT
1 AAATTTAAATATGAAAAAAAATGT
*
43829281 AAATTAAAATA-GAAAAAAAA-G-
1 AAATTTAAATATGAAAAAAAATGT
43829302 ATAATTTAAAT
1 A-AATTTAAAT
43829313 GACAAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
21 1 0.04
22 9 0.32
23 9 0.32
24 9 0.32
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (24 bp):
AAATTTAAATATGAAAAAAAATGT
Found at i:43829324 original size:26 final size:27
Alignment explanation
Indices: 43829287--43829359 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
43829277 ATGTAAATTA
**
43829287 AAAT-AGAAAAAAAAGATAATTTAAATG
1 AAATGAGAAAAAAATTA-AATTTAAATG
*
43829314 ACAA-GAGAAAAAAATTAAATTTAAGTG
1 A-AATGAGAAAAAAATTAAATTTAAATG
43829341 AAATGAGAAAAAAATTAAA
1 AAATGAGAAAAAAATTAAA
43829360 ATGGAAAGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 26 0.65
28 12 0.30
ACGTcount: A:0.66, C:0.01, G:0.12, T:0.21
Consensus pattern (27 bp):
AAATGAGAAAAAAATTAAATTTAAATG
Found at i:43829324 original size:27 final size:27
Alignment explanation
Indices: 43829270--43829359 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 27
43829260 TTTTAATATG
* *
43829270 AAAAA-AAATGTAAATTAAAAT-AGAAA
1 AAAAATAAATTTAAA-TGAAATGAGAAA
*
43829296 AAAAAGATAATTTAAATGACAA-GAGAAA
1 AAAAATA-AATTTAAATGA-AATGAGAAA
* *
43829324 AAAATTAAATTTAAGTGAAATGAGAAA
1 AAAAATAAATTTAAATGAAATGAGAAA
*
43829351 AAAATTAAA
1 AAAAATAAA
43829360 ATGGAAAGAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
26 7 0.13
27 28 0.52
28 19 0.35
ACGTcount: A:0.67, C:0.01, G:0.11, T:0.21
Consensus pattern (27 bp):
AAAAATAAATTTAAATGAAATGAGAAA
Found at i:43829370 original size:27 final size:27
Alignment explanation
Indices: 43829318--43829371 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
43829308 TAAATGACAA
** *
43829318 GAGAAAAAAATTAAATTTAAGTGAAAT
1 GAGAAAAAAATTAAATGGAAGAGAAAT
43829345 GAGAAAAAAATTAAAATGGAA-AGAAAT
1 GAGAAAAAAATT-AAATGGAAGAGAAAT
43829372 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 17 0.74
28 6 0.26
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (27 bp):
GAGAAAAAAATTAAATGGAAGAGAAAT
Found at i:43829386 original size:43 final size:45
Alignment explanation
Indices: 43829322--43829449 Score: 125
Period size: 51 Copynumber: 2.7 Consensus size: 45
43829312 TGACAAGAGA
*
43829322 AAAAAATTAAATTTAAGTGAAATGAGAAAAAAATTAAAATGGAAA-G
1 AAAAAA-T-AATTTAAATGAAATGAGAAAAAAATTAAAATGGAAATG
* * **
43829368 -AAATATAATTTAAATGAAATGAGGAAGAAATTAAATTTAAATTTAAATG
1 AAAAAATAATTTAAATGAAATGA-G-A-AAA--AAATTAAAATGGAAATG
43829417 AAAAAAATAATTTAAATGAAATGAGAAAAAAAT
1 -AAAAAATAATTTAAATGAAATGAGAAAAAAAT
43829450 AAATTTAAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
43 15 0.22
44 2 0.03
45 5 0.07
46 7 0.10
48 15 0.22
49 2 0.03
50 1 0.01
51 21 0.31
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.26
Consensus pattern (45 bp):
AAAAAATAATTTAAATGAAATGAGAAAAAAATTAAAATGGAAATG
Found at i:43829399 original size:70 final size:71
Alignment explanation
Indices: 43829281--43829437 Score: 192
Period size: 70 Copynumber: 2.2 Consensus size: 71
43829271 AAAAAAATGT
43829281 AAATTAAAATAGAAAAAAAAGATAATTTAAATGACAAGAGAAAAAAATTAAATTT-AAGTGAAAT
1 AAATTAAAAT-GAAAAAAAAGATAATTTAAATGACAAGAGAAAAAAATTAAATTTAAAGTGAAAT
*
43829345 GAGAAAA
65 GAAAAAA
* * * * * * *
43829352 AAATTAAAATGGAAAGAAATATAATTTAAATGA-AATGAGGAAGAAATTAAATTTAAATTTAAAT
1 AAATTAAAATGAAAAAAAAGATAATTTAAATGACAA-GAGAAAAAAATTAAATTTAAAGTGAAAT
43829416 GAAAAAA
65 GAAAAAA
*
43829423 ATAATTTAAATGAAA
1 A-AATTAAAATGAAA
43829438 TGAGAAAAAA
Statistics
Matches: 73, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
69 2 0.03
70 36 0.49
71 24 0.33
72 11 0.15
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (71 bp):
AAATTAAAATGAAAAAAAAGATAATTTAAATGACAAGAGAAAAAAATTAAATTTAAAGTGAAATG
AAAAAA
Found at i:43829437 original size:51 final size:53
Alignment explanation
Indices: 43829352--43829459 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 53
43829342 AATGAGAAAA
* *
43829352 AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGAGGAAGAAATTAAATTT
1 AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGA-GAAAAAAATAAATTT
*
43829406 AAATTTAAAT-GAAA-AAA-ATAATTTAAATGAAATGAGAAAAAAATAAATTT
1 AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGAGAAAAAAATAAATTT
43829456 AAAT
1 AAAT
43829460 AGAAAAAATG
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
50 17 0.33
51 18 0.35
52 3 0.06
53 4 0.08
54 9 0.18
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (53 bp):
AAATTAAAATGGAAAGAAATATAATTTAAATGAAATGAGAAAAAAATAAATTT
Found at i:43829893 original size:19 final size:18
Alignment explanation
Indices: 43829871--43829909 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
43829861 GTATATTAGG
*
43829871 AAAAAATAAATTTAAATGA
1 AAAAAATAAA-TGAAATGA
*
43829890 AAAAAATTAATGAAATGA
1 AAAAAATAAATGAAATGA
43829908 AA
1 AA
43829910 TGTTAAATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (18 bp):
AAAAAATAAATGAAATGA
Found at i:43829908 original size:5 final size:5
Alignment explanation
Indices: 43829898--43829998 Score: 58
Period size: 5 Copynumber: 18.0 Consensus size: 5
43829888 GAAAAAAATT
* *
43829898 AATGA AATGA AATGTTA AATGAA ATATGA ATATGA AATGA AATGTA ATTTGT
1 AATGA AATGA AATG--A AATG-A A-ATGA A-ATGA AATGA AATG-A A-ATGA
** *
43829950 AATGA ATATGA AATGA AATGA GGTGTTA AATGA ATATAA AATGA AATGA
1 AATGA A-ATGA AATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA
43829999 TGATTATGAA
Statistics
Matches: 76, Mismatches: 11, Indels: 18
0.72 0.10 0.17
Matches are distributed among these distances:
5 41 0.54
6 22 0.29
7 13 0.17
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:43829916 original size:30 final size:30
Alignment explanation
Indices: 43829874--43829998 Score: 86
Period size: 30 Copynumber: 4.2 Consensus size: 30
43829864 TATTAGGAAA
43829874 AAAT-AAAT-TTAAATGAAA-A-AAATTAATG
1 AAATGAAATGTTAAATGAAATATAAA-T-ATG
*
43829902 AAATGAAATGTTAAATGAAATATGAATATG
1 AAATGAAATGTTAAATGAAATATAAATATG
* *
43829932 AAATGAAATG-TAATTTGTAATGAATATGAA-ATG
1 AAATGAAATGTTAA-ATG--A--AATATAAATATG
**
43829965 AAATGAGGTGTTAAATG-AATATAAA-ATG
1 AAATGAAATGTTAAATGAAATATAAATATG
43829993 AAATGA
1 AAATGA
43829999 TGATTATGAA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
28 20 0.25
29 7 0.09
30 25 0.31
31 2 0.02
32 3 0.04
33 13 0.16
34 11 0.14
ACGTcount: A:0.54, C:0.00, G:0.16, T:0.30
Consensus pattern (30 bp):
AAATGAAATGTTAAATGAAATATAAATATG
Found at i:43829919 original size:12 final size:12
Alignment explanation
Indices: 43829900--43829969 Score: 56
Period size: 12 Copynumber: 6.0 Consensus size: 12
43829890 AAAAAATTAA
43829900 TGAAATGAAATG
1 TGAAATGAAATG
* *
43829912 TTAAATGAAATA
1 TGAAATGAAATG
43829924 TGAATATGAAA--
1 TGAA-ATGAAATG
* *
43829935 TGAAATGTAATT
1 TGAAATGAAATG
* *
43829947 TGTAATG-AATA
1 TGAAATGAAATG
43829958 TGAAATGAAATG
1 TGAAATGAAATG
43829970 AGGTGTTAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
10 5 0.11
11 13 0.28
12 22 0.48
13 6 0.13
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
TGAAATGAAATG
Found at i:43829937 original size:35 final size:33
Alignment explanation
Indices: 43829900--43829970 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 33
43829890 AAAAAATTAA
*
43829900 TGAAATGAAATGTT-AAATGAAATATGAATATGAAA
1 TGAAATGAAAT-TTGAAAT-GAATATGAA-ATGAAA
* *
43829935 TGAAATGTAATTTGTAATGAATATGAAATGAAA
1 TGAAATGAAATTTGAAATGAATATGAAATGAAA
43829968 TGA
1 TGA
43829971 GGTGTTAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 9 0.28
34 10 0.31
35 13 0.41
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (33 bp):
TGAAATGAAATTTGAAATGAATATGAAATGAAA
Found at i:43829981 original size:28 final size:27
Alignment explanation
Indices: 43829923--43829998 Score: 91
Period size: 28 Copynumber: 2.7 Consensus size: 27
43829913 TAAATGAAAT
*
43829923 ATGAATATGAAATGAAATGTAATTTGTA
1 ATGAATATGAAATGAAATG-AATTTGAA
*
43829951 ATGAATATGAAATGAAATGAGGTGTT-AA
1 ATGAATATGAAATGAAATGA-AT-TTGAA
*
43829979 ATGAATATAAAATGAAATGA
1 ATGAATATGAAATGAAATGA
43829999 TGATTATGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
27 1 0.02
28 40 0.93
29 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (27 bp):
ATGAATATGAAATGAAATGAATTTGAA
Found at i:43830087 original size:20 final size:20
Alignment explanation
Indices: 43830033--43830132 Score: 79
Period size: 20 Copynumber: 5.1 Consensus size: 20
43830023 AAATGAAAAT
*
43830033 AAATTATAAATTT-AAATG-
1 AAATAATAAATTTGAAATGA
*
43830051 AAATCAA-AAA-CTGAAATGA
1 AAAT-AATAAATTTGAAATGA
43830070 AAATAA-AAATTTTGAAATGA
1 AAATAATAAA-TTTGAAATGA
43830090 GAAATAATTAAATTT-AAATGGA
1 -AAATAA-TAAATTTGAAAT-GA
*
43830112 AAATAATTAATTT-AAATGA
1 AAATAATAAATTTGAAATGA
43830131 AA
1 AA
43830133 TTATAAATGG
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
17 1 0.01
18 17 0.25
19 9 0.13
20 18 0.26
21 16 0.23
22 5 0.07
23 3 0.04
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.30
Consensus pattern (20 bp):
AAATAATAAATTTGAAATGA
Found at i:43830108 original size:21 final size:21
Alignment explanation
Indices: 43830064--43830130 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
43830054 TCAAAAACTG
43830064 AAATGA-AAATAA--AAATTTT
1 AAATGAGAAATAATTAAA-TTT
43830083 GAAATGAGAAATAATTAAATTT
1 -AAATGAGAAATAATTAAATTT
43830105 AAATG-GAAAATAATT-AATTT
1 AAATGAG-AAATAATTAAATTT
43830125 AAATGA
1 AAATGA
43830131 AATTATAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
20 17 0.40
21 19 0.45
22 3 0.07
23 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATGAGAAATAATTAAATTT
Found at i:43830147 original size:19 final size:17
Alignment explanation
Indices: 43830098--43830160 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
43830088 GAGAAATAAT
43830098 TAAATTTAAATGGAAAA
1 TAAATTTAAATGGAAAA
**
43830115 T-AA-TT-AAT-TTAAA
1 TAAATTTAAATGGAAAA
43830128 TGAAATTATAAATGGAAAA
1 T-AAATT-TAAATGGAAAA
*
43830147 TTAATTTAAATGGA
1 TAAATTTAAATGGA
43830161 GAAAAATTCA
Statistics
Matches: 35, Mismatches: 5, Indels: 12
0.67 0.10 0.23
Matches are distributed among these distances:
13 4 0.11
14 3 0.09
15 4 0.11
16 3 0.09
17 10 0.29
18 7 0.20
19 4 0.11
ACGTcount: A:0.54, C:0.00, G:0.11, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATGGAAAA
Found at i:43830156 original size:29 final size:30
Alignment explanation
Indices: 43830099--43830158 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
43830089 AGAAATAATT
43830099 AAATTTAAATGGAAAATAATTAATTTAAATG
1 AAATTTAAATGG-AAATAATTAATTTAAATG
43830130 AAATTATAAATGG-AA-AATTAATTTAAATG
1 AAATT-TAAATGGAAATAATTAATTTAAATG
43830159 GAGAAAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 14 0.50
30 2 0.07
31 5 0.18
32 7 0.25
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.35
Consensus pattern (30 bp):
AAATTTAAATGGAAATAATTAATTTAAATG
Found at i:43830196 original size:5 final size:5
Alignment explanation
Indices: 43830186--43830247 Score: 61
Period size: 5 Copynumber: 11.6 Consensus size: 5
43830176 ATGTAGATGT
* * *
43830186 AAATG AAATG AAATG AAAATAT AAATG AAATG AAATG CAAAGG AAATAC
1 AAATG AAATG AAATG -AAAT-G AAATG AAATG AAATG -AAATG AAAT-G
43830235 AAATG AAATG AAA
1 AAATG AAATG AAA
43830248 AAAAAAAGGT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
5 31 0.66
6 16 0.34
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:43830199 original size:22 final size:22
Alignment explanation
Indices: 43830185--43830248 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
43830175 AATGTAGATG
43830185 TAAATGAAATGAAATGAAAATA
1 TAAATGAAATGAAATGAAAATA
* *
43830207 TAAATGAAATGAAATGCAAA-G
1 TAAATGAAATGAAATGAAAATA
* *
43830228 GAAATACAAATGAAATGAAAA
1 TAAAT-GAAATGAAATGAAAA
43830249 AAAAAAGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 4 0.11
22 32 0.89
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (22 bp):
TAAATGAAATGAAATGAAAATA
Found at i:43830216 original size:27 final size:27
Alignment explanation
Indices: 43830186--43830247 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
43830176 ATGTAGATGT
*
43830186 AAATGAAATG-AAATGAAAATATAAATG
1 AAATGAAATGCAAA-GAAAATACAAATG
*
43830213 AAATGAAATGCAAAGGAAATACAAATG
1 AAATGAAATGCAAAGAAAATACAAATG
43830240 AAATGAAA
1 AAATGAAA
43830248 AAAAAAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.63, C:0.03, G:0.16, T:0.18
Consensus pattern (27 bp):
AAATGAAATGCAAAGAAAATACAAATG
Found at i:43830231 original size:11 final size:11
Alignment explanation
Indices: 43830186--43830244 Score: 59
Period size: 11 Copynumber: 5.5 Consensus size: 11
43830176 ATGTAGATGT
43830186 AAATG-AAATG
1 AAATGCAAATG
* *
43830196 AAATGAAAATAT
1 AAATGCAAAT-G
43830208 AAATG-AAATG
1 AAATGCAAATG
*
43830218 AAATGCAAAGG
1 AAATGCAAATG
*
43830229 AAATACAAATG
1 AAATGCAAATG
43830240 AAATG
1 AAATG
43830245 AAAAAAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
10 10 0.25
11 25 0.62
12 5 0.12
ACGTcount: A:0.61, C:0.03, G:0.17, T:0.19
Consensus pattern (11 bp):
AAATGCAAATG
Found at i:43830665 original size:23 final size:23
Alignment explanation
Indices: 43830622--43830665 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
43830612 GTATATTAGG
*
43830622 AAAAAAGTAATAAATTTAAATGA
1 AAAAAAGTAATAAATTCAAATGA
*
43830645 AAAAAATTAATGAAA-TCAAAT
1 AAAAAAGTAAT-AAATTCAAAT
43830666 ATTAAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.66, C:0.02, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAAAAGTAATAAATTCAAATGA
Found at i:43830696 original size:23 final size:23
Alignment explanation
Indices: 43830663--43830723 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
43830653 AATGAAATCA
*
43830663 AATATTAAATGAAATATG-AATAAG
1 AATATGAAATGAAATATGTAAT--G
* *
43830687 AA-ATGAAATGTAATTTGTAATG
1 AATATGAAATGAAATATGTAATG
43830709 AATATGAAATGAAAT
1 AATATGAAATGAAAT
43830724 GAAATAAAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
22 3 0.10
23 23 0.74
24 5 0.16
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (23 bp):
AATATGAAATGAAATATGTAATG
Found at i:43830783 original size:18 final size:18
Alignment explanation
Indices: 43830760--43830800 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
43830750 TTATAAATGA
* *
43830760 AAATGAAAAGAAGAACTG
1 AAATGAAAAAAAAAACTG
*
43830778 AAATGAAAAAAAAAATTG
1 AAATGAAAAAAAAAACTG
43830796 AAATG
1 AAATG
43830801 GTAAATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.66, C:0.02, G:0.17, T:0.15
Consensus pattern (18 bp):
AAATGAAAAAAAAAACTG
Found at i:43836355 original size:12 final size:11
Alignment explanation
Indices: 43836324--43836362 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
43836314 TTGTTTTAAG
43836324 TTTTATTATTA
1 TTTTATTATTA
43836335 TTATTATTATTA
1 TT-TTATTATTA
*
43836347 TTTTAATTAATA
1 TTTT-ATTATTA
43836359 TTTT
1 TTTT
43836363 TAATATATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 4 0.16
12 21 0.84
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:43841265 original size:8 final size:8
Alignment explanation
Indices: 43841254--43841297 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
43841244 TTTATTCAAT
43841254 TATTTTAC
1 TATTTTAC
*
43841262 TATTTTAT
1 TATTTTAC
43841270 TATTTTAC
1 TATTTTAC
43841278 TATTTT-C
1 TATTTTAC
*
43841285 -ATTTTAT
1 TATTTTAC
43841292 TATTTT
1 TATTTT
43841298 CATCTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
6 5 0.16
7 1 0.03
8 25 0.81
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (8 bp):
TATTTTAC
Found at i:43841271 original size:16 final size:16
Alignment explanation
Indices: 43841252--43841283 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
43841242 AATTTATTCA
43841252 ATTATTTTACTATTTT
1 ATTATTTTACTATTTT
43841268 ATTATTTTACTATTTT
1 ATTATTTTACTATTTT
43841284 CATTTTATTA
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:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (16 bp):
ATTATTTTACTATTTT
Found at i:43844878 original size:28 final size:28
Alignment explanation
Indices: 43844842--43844896 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
43844832 CCACATGCTA
* *
43844842 GTGTAGCCCTATGGCCTAACACACGCCC
1 GTGTAGCCCCACGGCCTAACACACGCCC
*
43844870 GTGTGGCCCCACGGCCTAACACACGCC
1 GTGTAGCCCCACGGCCTAACACACGCC
43844897 AACCCGTATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.20, C:0.42, G:0.24, T:0.15
Consensus pattern (28 bp):
GTGTAGCCCCACGGCCTAACACACGCCC
Found at i:43851425 original size:21 final size:21
Alignment explanation
Indices: 43851400--43851440 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
43851390 ATATGACCAC
43851400 AAAAATCACTTTTTCACTTTA
1 AAAAATCACTTTTTCACTTTA
*
43851421 AAAAATCAGTTTTTCACTTT
1 AAAAATCACTTTTTCACTTT
43851441 GGCATGCGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.44
Consensus pattern (21 bp):
AAAAATCACTTTTTCACTTTA
Found at i:43851529 original size:2 final size:2
Alignment explanation
Indices: 43851522--43851558 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43851512 ATATTTACAC
43851522 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
43851559 CAATATTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43856852 original size:38 final size:38
Alignment explanation
Indices: 43856810--43856891 Score: 112
Period size: 38 Copynumber: 2.2 Consensus size: 38
43856800 TCTTTTAATA
* * *
43856810 TTTTTGTTTCAAC-CAATTGTCATTGGGGTTAATTGTGG
1 TTTTTGTTTCAACTC-ATTGCCACTGGGGTTAATTATGG
*
43856848 TTTTTGTTTCGACTCATTGCCACTGGGGTTAATTATGG
1 TTTTTGTTTCAACTCATTGCCACTGGGGTTAATTATGG
43856886 TTTTTG
1 TTTTTG
43856892 ATATTTATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
38 38 0.97
39 1 0.03
ACGTcount: A:0.16, C:0.12, G:0.23, T:0.49
Consensus pattern (38 bp):
TTTTTGTTTCAACTCATTGCCACTGGGGTTAATTATGG
Found at i:43857010 original size:341 final size:342
Alignment explanation
Indices: 43856469--43857499 Score: 1638
Period size: 342 Copynumber: 3.0 Consensus size: 342
43856459 TGAATTGTGG
* * * * *
43856469 TTTTTATTCCAACCAATTATCATTGGGGTTAATTGCGGTTTATGTTTCGACCCATTGTCACTGGG
1 TTTTTGTTCCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGCCACTGGG
* * *
43856534 GTTAATTGTGG-TTTTGACATTTGTCATCGGGGTTAAGGGATAAAAAAAAGGAGTTGTTATTTTT
66 GTTAATTATGGTTTTTGACATTTATCATCGGGGTTAAGGGATAAAAAAGA-GAGTTGTTATTTTT
* * * * *
43856598 TTTATCTATCAATATTTTAGAAATTATTGATTTGTCTTTATCATAGTTTTGACACAGAATATGAT
130 TTTATCTATCAGTATTTAAGAAATTATTGATTTGTCTTTATCACAGTTTTGACACGGAATATGCT
43856663 TTGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGC
195 TTGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGC
* * *
43856728 CT-ATGCTTTTGTGCTTGCTTAACTAAACCAAGGGAAATTCTAGTTACTTACTGTGTAGTAAAAC
260 CTAATGCTTTTGTGCTTGCTTAACTCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAAC
*
43856792 TAACTCCATCTTTTAATA
325 TCACTCCATCTTTTAATA
* *
43856810 TTTTTGTTTCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACTCATTGCCACTGGG
1 TTTTTGTTCCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGCCACTGGG
* *
43856875 GTTAATTATGGTTTTTGATATTTATCATCGGGGTTAAAGGATAAAAAAGAGAGTTGTTATTTTTT
66 GTTAATTATGGTTTTTGACATTTATCATCGGGGTTAAGGGATAAAAAAGAGAGTTGTTATTTTTT
* *
43856940 TTATCTATCAGTATTTAAGAAATTATTGAATTATCTTTATCACAGTTTTGACACGGAATATGCTT
131 TTATCTATCAGTATTTAAGAAATTATTGATTTGTCTTTATCACAGTTTTGACACGGAATATGCTT
*
43857005 TGAATTATTTATTGTGGTATAATCATAAATTTTACAACTATGGATTTTTTACTAAATATTTAGCC
196 TGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGCC
* *
43857070 TAAATGCTTTTGTGCTTGCTTAACTCAACTAAGGGAAATGCTAGTTACTTACTTTGTAGTTAAAC
261 T-AATGCTTTTGTGCTTGCTTAACTCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAAC
*
43857135 TCACTCTATCTTTTAATA
325 TCACTCCATCTTTTAATA
* * *
43857153 ATTTTGTTCCAACCAATTGCCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGGCACTGGG
1 TTTTTGTTCCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGCCACTGGG
* * * *
43857218 GTTAATTATGATTTTTGACATTTTTCATCGAGGTTAAGGGAGAAAAAATG-GAGTTGTTA-TTTT
66 GTTAATTATGGTTTTTGACATTTATCATCGGGGTTAAGGGATAAAAAA-GAGAGTTGTTATTTTT
* *
43857281 TTTATCTATCAGTATTTCAGAAATTATTGATTTGTCTTTACCACAGTTTTGACACGGAATATGCT
130 TTTATCTATCAGTATTTAAGAAATTATTGATTTGTCTTTATCACAGTTTTGACACGGAATATGCT
* * *
43857346 TTGAATTATTTATTGTGGTATAATCATAAATTTTAAAATTATGGGTTTTTTACTAGATATTTAGC
195 TTGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGC
*
43857411 CTAAATGCTTTTGTGCTTGCTTAACCCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAA
260 CT-AATGCTTTTGTGCTTGCTTAACTCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAA
43857476 CTCACTCCATCTTTTAATA
324 CTCACTCCATCTTTTAATA
43857495 TTTTT
1 TTTTT
43857500 ACAGGTTTTG
Statistics
Matches: 635, Mismatches: 51, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
341 206 0.32
342 244 0.38
343 184 0.29
344 1 0.00
ACGTcount: A:0.28, C:0.12, G:0.16, T:0.43
Consensus pattern (342 bp):
TTTTTGTTCCAACCAATTGTCATTGGGGTTAATTGTGGTTTTTGTTTCGACCCATTGCCACTGGG
GTTAATTATGGTTTTTGACATTTATCATCGGGGTTAAGGGATAAAAAAGAGAGTTGTTATTTTTT
TTATCTATCAGTATTTAAGAAATTATTGATTTGTCTTTATCACAGTTTTGACACGGAATATGCTT
TGAATTATTTATTGTGGTATAATCATAAATTTTACAATTATGGATTTTTTACTAAATATTTAGCC
TAATGCTTTTGTGCTTGCTTAACTCAACCAAGGGAAATGCTAGTTACTTACTGTGTAGTTAAACT
CACTCCATCTTTTAATA
Found at i:43857196 original size:38 final size:38
Alignment explanation
Indices: 43857154--43857234 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
43857144 CTTTTAATAA
* * *
43857154 TTTTGTTCCAACCAATTGCCATTGGGGTTAATTGTGGT
1 TTTTGTTCCAACCAATTGCCACTGGGGTTAATTATGAT
* * * *
43857192 TTTTGTTTCGACCCATTGGCACTGGGGTTAATTATGAT
1 TTTTGTTCCAACCAATTGCCACTGGGGTTAATTATGAT
43857230 TTTTG
1 TTTTG
43857235 ACATTTTTCA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.44
Consensus pattern (38 bp):
TTTTGTTCCAACCAATTGCCACTGGGGTTAATTATGAT
Found at i:43863172 original size:16 final size:16
Alignment explanation
Indices: 43863148--43863183 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
43863138 AATGGATACA
*
43863148 TTATCTAATTAAATTT
1 TTATCTAATTAAATAT
*
43863164 TTATTTAATTAAATAT
1 TTATCTAATTAAATAT
43863180 TTAT
1 TTAT
43863184 ATAGATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (16 bp):
TTATCTAATTAAATAT
Found at i:43864100 original size:20 final size:21
Alignment explanation
Indices: 43864067--43864105 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
43864057 TTAATTTCAA
*
43864067 TTTTTTAATATTATTTAATAT
1 TTTTTTAATATTATGTAATAT
*
43864088 TTTTTTCAT-TTATGTAAT
1 TTTTTTAATATTATGTAAT
43864106 TTTAATTAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTTTTAATATTATGTAATAT
Found at i:43871164 original size:126 final size:126
Alignment explanation
Indices: 43870914--43871308 Score: 551
Period size: 126 Copynumber: 3.1 Consensus size: 126
43870904 GGCCAAGCAG
* * * * * * * * *
43870914 GAACTACTATAGAAAAGGAGCATCCAAGTGGGAGATTTTTTCAGTAATGTTGCTGATAGTGCCTC
1 GAACTACTGTAAAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
*
43870979 CTGCTTGAAGCG-TTTTGACACTAGTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* *
43871039 GAACTACTGTAAAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAATGTATC
1 GAACTACTGTAAAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
*
43871104 CTGCTTGAAGCGTTTTTAACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
* * * *
43871165 GAATTAATGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTACATC
1 GAACTACTGTAAAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
* * * * * *
43871230 CTGTTTGAAGCGTTTTTGACATTATCTTTTCATAACCATCTTCTCAAAATTAATTTTTC-A
66 CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
43871290 GAAACTACTGTAGAAAAAA
1 G-AACTACTGTA-AAAAAA
43871309 ATAAAATCCT
Statistics
Matches: 238, Mismatches: 29, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
125 68 0.29
126 165 0.69
127 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (126 bp):
GAACTACTGTAAAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGACAGTGCATC
CTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTTCAA
Found at i:43871454 original size:34 final size:34
Alignment explanation
Indices: 43871406--43871506 Score: 154
Period size: 34 Copynumber: 3.1 Consensus size: 34
43871396 TATTATTTTT
43871406 AAAAC-CTAAACCCTAATTTAATTAATTTTCTTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
*
43871439 AAAACTCTAAACCCTAATTTAATTAATTTACTTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
* *
43871473 AAACCTCTAAAACCTAATTTAATT-ATTTT-TTA
1 AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
43871505 AA
1 AA
43871507 TTCTAAACCT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
32 5 0.08
33 9 0.14
34 49 0.78
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAACTCTAAACCCTAATTTAATTAATTTTCTTA
Found at i:43874357 original size:20 final size:20
Alignment explanation
Indices: 43874332--43874372 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
43874322 CACATGGTAG
*
43874332 TGTGTTTGAAAACCATAACT
1 TGTGTTGGAAAACCATAACT
*
43874352 TGTGTTGGAAAACCGTAACT
1 TGTGTTGGAAAACCATAACT
43874372 T
1 T
43874373 TGCTAAATAC
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:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (20 bp):
TGTGTTGGAAAACCATAACT
Found at i:43876728 original size:86 final size:85
Alignment explanation
Indices: 43876631--43876802 Score: 226
Period size: 86 Copynumber: 2.0 Consensus size: 85
43876621 TTAATACAAT
* *
43876631 TAACAATTAATAATTTGATGTAATTTG-ATAATTTTACTAATAATTAAT-ACAATT-A-ACAATT
1 TAACAATTAATAA-TT-A-ATAATTTGAATAATTTGA-TAAT-ATTAATAACAATTAATACAATT
43876692 AATAATTTTACTAACAAAATGTTAG
61 AATAATTTTACTAACAAAATGTTAG
* *
43876717 TAACAATTAATAATTAATAATTTGATATAATTTGATAATTTTAGTAACAATTAATACAATTAATA
1 TAACAATTAATAATTAATAATTTGA-ATAATTTGATAATATTAATAACAATTAATACAATTAATA
43876782 ATTTTACTAACAAAATGTTAG
65 ATTTTACTAACAAAATGTTAG
43876803 ATTTTACAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 10
0.85 0.04 0.11
Matches are distributed among these distances:
83 11 0.14
84 11 0.14
85 11 0.14
86 44 0.57
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (85 bp):
TAACAATTAATAATTAATAATTTGAATAATTTGATAATATTAATAACAATTAATACAATTAATAA
TTTTACTAACAAAATGTTAG
Found at i:43876827 original size:17 final size:17
Alignment explanation
Indices: 43876791--43876830 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
43876781 AATTTTACTA
*
43876791 ACAAAATGTTAGATTTT
1 ACAAAATGTTAGATTGT
43876808 ACAAAATGTT-GATTGGT
1 ACAAAATGTTAGATT-GT
43876825 ACAAAA
1 ACAAAA
43876831 AATATATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.45, C:0.07, G:0.15, T:0.33
Consensus pattern (17 bp):
ACAAAATGTTAGATTGT
Found at i:43876867 original size:16 final size:16
Alignment explanation
Indices: 43876848--43876904 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
43876838 AATTTGATAC
*
43876848 AATTTTAATAATAATT
1 AATTTTAATAACAATT
*
43876864 AATTTTGATAACAATT
1 AATTTTAATAACAATT
43876880 AATTTTAATAACAATT
1 AATTTTAATAACAATT
*
43876896 AGTTTTAAT
1 AATTTTAAT
43876905 TTTAATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (16 bp):
AATTTTAATAACAATT
Found at i:43876888 original size:22 final size:23
Alignment explanation
Indices: 43876878--43876939 Score: 90
Period size: 22 Copynumber: 2.7 Consensus size: 23
43876868 TTGATAACAA
* *
43876878 TTAATTTTAATAACAAT-TAGTT
1 TTAATTTTAATAAAAATATAATT
43876900 TTAATTTTAATAAAAATATAATT
1 TTAATTTTAATAAAAATATAATT
43876923 TTAATTTTAATTAAAAA
1 TTAATTTTAA-TAAAAA
43876940 ACGGGCCGGG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 14 0.39
24 6 0.17
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
TTAATTTTAATAAAAATATAATT
Found at i:43878702 original size:32 final size:32
Alignment explanation
Indices: 43878607--43878705 Score: 82
Period size: 32 Copynumber: 3.2 Consensus size: 32
43878597 AGCCTTTAAT
*
43878607 AATTTTTAAAAT--TTTTAATTAGAC-CCCCA
1 AATTTTTAAAATAATTTTAATTAGACTCTCCA
* * * * * * *
43878636 ATTTTTTTAGA-AATTCTCATTAGGCT-TCTAA
1 AATTTTTAAAATAATTTTAATTAGACTCTC-CA
43878667 AATTTTTAAAATAATTTTAATTAGACTCTCCA
1 AATTTTTAAAATAATTTTAATTAGACTCTCCA
43878699 AATTTTT
1 AATTTTT
43878706 TGGAGATCCT
Statistics
Matches: 49, Mismatches: 15, Indels: 9
0.67 0.21 0.12
Matches are distributed among these distances:
29 8 0.16
30 10 0.20
31 9 0.18
32 20 0.41
33 2 0.04
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.46
Consensus pattern (32 bp):
AATTTTTAAAATAATTTTAATTAGACTCTCCA
Found at i:43878730 original size:63 final size:60
Alignment explanation
Indices: 43878591--43878731 Score: 147
Period size: 63 Copynumber: 2.3 Consensus size: 60
43878581 TGAAAAGTTA
** * *
43878591 TCATTAAGCCTTTAATAATTTTTAAAATTTTTAATTAGACCCCCAATTTTTTTAGAAATTC
1 TCATTAAGCCCCTAA-AATTTTTAAAATTTTTAATTAGACCCCCAAATTTTTTAGAAATCC
* ** * * *
43878652 TCATTAGGCTTCTAAAATTTTTAAAATAATTTTAATTAGACTCTCCAAATTTTTTGGAGATCC
1 TCATTAAGCCCCTAAAATTTTTAAAAT--TTTTAATTAGAC-CCCCAAATTTTTTAGAAATCC
*
43878715 TCATTAATCCCCTAAAA
1 TCATTAAGCCCCTAAAA
43878732 GTTCTAAGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
60 12 0.18
61 12 0.18
62 12 0.18
63 29 0.45
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (60 bp):
TCATTAAGCCCCTAAAATTTTTAAAATTTTTAATTAGACCCCCAAATTTTTTAGAAATCC
Found at i:43879476 original size:15 final size:16
Alignment explanation
Indices: 43879450--43879479 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
43879440 ACATATATAT
43879450 ATATATTATTTTTAAG
1 ATATATTATTTTTAAG
43879466 ATATA-TATTTTTAA
1 ATATATTATTTTTAA
43879480 TTTATGGGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
ATATATTATTTTTAAG
Found at i:43880232 original size:27 final size:27
Alignment explanation
Indices: 43880202--43880339 Score: 100
Period size: 27 Copynumber: 5.1 Consensus size: 27
43880192 AACATGTCAA
** *
43880202 GAAAGGAAATTCTTTGTGGTGAAATAT
1 GAAAGGAAAGCCTTTGTGGCGAAATAT
* *
43880229 GAAAGGAAAGCCTTTGTGACAAAATA-
1 GAAAGGAAAGCCTTTGTGGCGAAATAT
* * *
43880255 CAAGAGAAAAGCCTTTGTAGCGAAATAT
1 GAA-AGGAAAGCCTTTGTGGCGAAATAT
* * *
43880283 GAAAAGAAAGTCTTTGTGGTG-AATCAT
1 GAAAGGAAAGCCTTTGTGGCGAAAT-AT
* * * * *
43880310 GAAAGAAAAGCTTTTATGGTGAATTAT
1 GAAAGGAAAGCCTTTGTGGCGAAATAT
43880337 GAA
1 GAA
43880340 TGGATAGTCT
Statistics
Matches: 85, Mismatches: 22, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
26 5 0.06
27 76 0.89
28 4 0.05
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (27 bp):
GAAAGGAAAGCCTTTGTGGCGAAATAT
Found at i:43882921 original size:48 final size:49
Alignment explanation
Indices: 43882857--43882949 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
43882847 ATTAGTGTGG
* *
43882857 TCACATATAGAGTTAACACT-AAAAGTAATCCATTGAAAGTTGGTACCT
1 TCACATATAGAATTAACACTAAAAAATAATCCATTGAAAGTTGGTACCT
* *
43882905 TCACATCTAGAATTAACACTAAAAAATAATTCATTGAAAGTTGGT
1 TCACATATAGAATTAACACTAAAAAATAATCCATTGAAAGTTGGT
43882950 GCCTCCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 18 0.45
49 22 0.55
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (49 bp):
TCACATATAGAATTAACACTAAAAAATAATCCATTGAAAGTTGGTACCT
Found at i:43887827 original size:24 final size:26
Alignment explanation
Indices: 43887780--43887832 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
43887770 GAAAAAAAGT
43887780 ATAATATTATTTATATGTTTATA-TAA
1 ATAATATTA-TTATATGTTTATATTAA
*
43887806 ATAATATTA-TATGTGTTTATATTAA
1 ATAATATTATTATATGTTTATATTAA
43887831 AT
1 AT
43887833 TATAATTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 11 0.44
25 5 0.20
26 9 0.36
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (26 bp):
ATAATATTATTATATGTTTATATTAA
Found at i:43890154 original size:27 final size:27
Alignment explanation
Indices: 43890115--43890237 Score: 192
Period size: 27 Copynumber: 4.6 Consensus size: 27
43890105 ACATAATCAT
*
43890115 ACAGCCATTTTATAACATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
* *
43890142 ACTGTCATTTTATAACATAGGGGTATA
1 ACAGTCATTTTATAACATAGGGGCATA
*
43890169 ACAGTCATTTTATAACATAGGGGCTTA
1 ACAGTCATTTTATAACATAGGGGCATA
*
43890196 ACAGTCATTTTATAGCATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGCATA
*
43890223 ATAGTCATTTTATAA
1 ACAGTCATTTTATAA
43890238 TAGTTTAGGG
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 86 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAGGGGCATA
Found at i:43897712 original size:27 final size:27
Alignment explanation
Indices: 43897676--43897741 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
43897666 CATAAATCAT
43897676 ACAGTCATTTTATAACATAGGGGAATA
1 ACAGTCATTTTATAACATAGGGGAATA
* * *
43897703 ATAGTCATTTTATAGCATAGGGGCATA
1 ACAGTCATTTTATAACATAGGGGAATA
43897730 ACAGTCATTTTA
1 ACAGTCATTTTA
43897742 CCACGTGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (27 bp):
ACAGTCATTTTATAACATAGGGGAATA
Found at i:43905955 original size:19 final size:19
Alignment explanation
Indices: 43905931--43905971 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
43905921 AACTAACTAA
43905931 AAAAAGAAAAATTAAAAA-G
1 AAAAAG-AAAATTAAAAATG
43905950 AAAAAGAAAATTAAAAATG
1 AAAAAGAAAATTAAAAATG
43905969 AAA
1 AAA
43905972 CTGAAACTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.78, C:0.00, G:0.10, T:0.12
Consensus pattern (19 bp):
AAAAAGAAAATTAAAAATG
Found at i:43909406 original size:20 final size:20
Alignment explanation
Indices: 43909373--43909411 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
43909363 CGGCACCGAT
43909373 TCTGTAAGTGTTTTAAAAAC
1 TCTGTAAGTGTTTTAAAAAC
43909393 TCTGATAAGT-TTTTAAAAA
1 TCTG-TAAGTGTTTTAAAAA
43909412 TATGAGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.41
Consensus pattern (20 bp):
TCTGTAAGTGTTTTAAAAAC
Found at i:43918103 original size:21 final size:19
Alignment explanation
Indices: 43918078--43918117 Score: 62
Period size: 21 Copynumber: 2.0 Consensus size: 19
43918068 TTCGTTTGAT
43918078 AAGGGAAGAAGAAGGAAAGGA
1 AAGGGAAGAAG-A-GAAAGGA
43918099 AAGGGAAGAAGAGAAAGGA
1 AAGGGAAGAAGAGAAAGGA
43918118 GGAAAGGGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 1 0.05
21 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.42, T:0.00
Consensus pattern (19 bp):
AAGGGAAGAAGAGAAAGGA
Found at i:43924624 original size:24 final size:24
Alignment explanation
Indices: 43924579--43924624 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
43924569 TTCACTTTGC
** * *
43924579 GCCACCCCTGCGCCGTTGTCGAAT
1 GCCACCCCCACGCCGCTATCGAAT
43924603 GCCACCCCCACGCCGCTATCGA
1 GCCACCCCCACGCCGCTATCGA
43924625 CACCAATACA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.15, C:0.48, G:0.22, T:0.15
Consensus pattern (24 bp):
GCCACCCCCACGCCGCTATCGAAT
Found at i:43927628 original size:14 final size:14
Alignment explanation
Indices: 43927609--43927639 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
43927599 TTGAATGCTT
43927609 TGAGTGAACCTTAG
1 TGAGTGAACCTTAG
43927623 TGAGTGAACCTTAG
1 TGAGTGAACCTTAG
43927637 TGA
1 TGA
43927640 CTGCTTATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (14 bp):
TGAGTGAACCTTAG
Found at i:43933316 original size:43 final size:43
Alignment explanation
Indices: 43933241--43933384 Score: 211
Period size: 43 Copynumber: 3.3 Consensus size: 43
43933231 GCGTCGCAAA
* *
43933241 CTTTAGCGGCG-TTTCCACAAAAAAACGCCGCTAAAGATCAAGAC
1 CTTTAGCGGCGCTTTCCAC--ACAAACGCCGCTAAAGACCAAGAC
43933285 CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
* *
43933328 CTTTAGCTGCGCTTCTCC-CACAAATGCCGCTAAAGACCAAGAC
1 CTTTAGCGGCGCTT-TCCACACAAACGCCGCTAAAGACCAAGAC
43933371 CTTTAGCGGCGCTT
1 CTTTAGCGGCGCTT
43933385 CTTTTACAAA
Statistics
Matches: 93, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
43 72 0.77
44 14 0.15
45 7 0.08
ACGTcount: A:0.29, C:0.32, G:0.19, T:0.20
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTCCACACAAACGCCGCTAAAGACCAAGAC
Found at i:43933385 original size:43 final size:43
Alignment explanation
Indices: 43933263--43933405 Score: 216
Period size: 43 Copynumber: 3.3 Consensus size: 43
43933253 TTCCACAAAA
*
43933263 AAACGCCGCTAAAGATCAAGACCTTTAGCGGCGCTT-TCCACAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCC-CAC
*
43933306 AAACGCCGCTAAAGACCAAGACCTTTAGCTGCGCTTCTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
* ***
43933349 AAATGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTTTTAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
43933392 AAACGCCGCTAAAG
1 AAACGCCGCTAAAG
43933406 GTTCTTCTCC
Statistics
Matches: 91, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
43 88 0.97
44 3 0.03
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTCTCCCAC
Found at i:43936309 original size:25 final size:25
Alignment explanation
Indices: 43936281--43936690 Score: 220
Period size: 25 Copynumber: 16.3 Consensus size: 25
43936271 TATATATTTC
* **
43936281 TGTATTAAGTAAATTATGTAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* *
43936306 TGTATTATATAAGTTATGTAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* *
43936331 CGTATTATGTGAGCTATGTAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* *
43936356 CGTATTATGTGAGCTATGTAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* * *
43936381 TTTAGTATGTAAGCTATGTAAGTTG
1 TGTATTATGTAAGCTATGTAAGTTA
43936406 TGTATTATGTAAGCTATGT-A-TTA
1 TGTATTATGTAAGCTATGTAAGTTA
** * *
43936429 TGTTAGTTATGTCGGTTATAT-A-TTA
1 TG-TA-TTATGTAAGCTATGTAAGTTA
*
43936454 TGTATGTTATGTAAG-T-TGTTCAGTTA
1 TGTA--TTATGTAAGCTATG-TAAGTTA
* * * *
43936480 T-AAGCTATGTAAGTTATGTGAGTTA
1 TGTA-TTATGTAAGCTATGTAAGTTA
*
43936505 --TA-TATGTAAGTTATGTATAAGTTTAA
1 TGTATTATGTAAGCTATG--TAAG-TT-A
*
43936531 T-T-TGTAT-TAAGCTATGTAAGTTG
1 TGTAT-TATGTAAGCTATGTAAGTTA
* * * *
43936554 TGAATAATGTAAGTTATGAAAGTTA
1 TGTATTATGTAAGCTATGTAAGTTA
* *
43936579 TGTATTATGTTAAGTTATGAAAGTTA
1 TGTATTATG-TAAGCTATGTAAGTTA
* * *
43936605 TGTATTAAGTTGTGTA-TTATGTAAGTTG
1 TGTATT-A--TGT-AAGCTATGTAAGTTA
* * *
43936633 TGAATAATGTAAGTTATG-AACGTTA
1 TGTATTATGTAAGCTATGTAA-GTTA
* *
43936658 TGTATTATGTTAAGTTATGAAAGTTA
1 TGTATTATG-TAAGCTATGTAAGTTA
43936684 TGTATTA
1 TGTATTA
43936691 AGTTGTGTAT
Statistics
Matches: 313, Mismatches: 45, Indels: 53
0.76 0.11 0.13
Matches are distributed among these distances:
22 13 0.04
23 6 0.02
24 27 0.09
25 184 0.59
26 49 0.16
27 13 0.04
28 18 0.06
29 3 0.01
ACGTcount: A:0.32, C:0.03, G:0.20, T:0.45
Consensus pattern (25 bp):
TGTATTATGTAAGCTATGTAAGTTA
Found at i:43936312 original size:16 final size:17
Alignment explanation
Indices: 43936292--43936687 Score: 109
Period size: 16 Copynumber: 24.1 Consensus size: 17
43936282 GTATTAAGTA
43936292 AATTATGTAAGTTATGT
1 AATTATGTAAGTTATGT
*
43936309 -ATTATATAAGTTATGT
1 AATTATGTAAGTTATGT
*
43936325 AAGTTACGT-A-TTATGT
1 AA-TTATGTAAGTTATGT
** *
43936341 GAGCTATGTAAGTTACGT
1 -AATTATGTAAGTTATGT
* *
43936359 -ATTATGTGAGCTATGT
1 AATTATGTAAGTTATGT
*
43936375 AAGTTAT-TTAG-TATGT
1 AA-TTATGTAAGTTATGT
* *
43936391 AAGCTATGTAAGTTGTGT
1 AA-TTATGTAAGTTATGT
*
43936409 -ATTATGTAAGCTATGT
1 AATTATGTAAGTTATGT
*
43936425 -ATTATGTTAGTTATGT
1 AATTATGTAAGTTATGT
** *
43936441 CGGTTATAT-A-TTATGT
1 -AATTATGTAAGTTATGT
* *
43936457 ATGTTATGTAAGTTGT-T
1 A-ATTATGTAAGTTATGT
* *
43936474 CAGTTA--TAAGCTATGT
1 -AATTATGTAAGTTATGT
*
43936490 AAGTTATGTGAGTTA--T
1 AA-TTATGTAAGTTATGT
43936506 -A-TATGTAAGTTATGT
1 AATTATGTAAGTTATGT
* * *
43936521 -ATAAGTTTAATTTGTAT-T
1 AATTA-TGTAA-GT-TATGT
* *
43936539 AAGCTATGTAAGTTGTG-
1 AA-TTATGTAAGTTATGT
* *
43936556 AATAATGTAAGTTATGA
1 AATTATGTAAGTTATGT
43936573 AAGTTATGT-A-TTATGTT
1 AA-TTATGTAAGTTATG-T
*
43936590 AAGTTATGAAAGTTATG-
1 AA-TTATGTAAGTTATGT
*
43936607 ---TAT-TAAGTTGTGT
1 AATTATGTAAGTTATGT
*
43936620 -ATTATGTAAGTTGTG-
1 AATTATGTAAGTTATGT
*
43936635 AATAATGTAAGTTATG-
1 AATTATGTAAGTTATGT
43936651 AACGTTATGT-A-TTATGTT
1 AA--TTATGTAAGTTATG-T
*
43936669 AAGTTATGAAAGTTATGT
1 AA-TTATGTAAGTTATGT
43936687 A
1 A
43936688 TTAAGTTGTG
Statistics
Matches: 283, Mismatches: 52, Indels: 87
0.67 0.12 0.21
Matches are distributed among these distances:
12 7 0.02
13 13 0.05
15 13 0.05
16 136 0.48
17 45 0.16
18 50 0.18
19 18 0.06
20 1 0.00
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (17 bp):
AATTATGTAAGTTATGT
Found at i:43936327 original size:9 final size:9
Alignment explanation
Indices: 43936289--43936687 Score: 170
Period size: 9 Copynumber: 47.3 Consensus size: 9
43936279 TCTGTATTAA
*
43936289 GTAAATTAT
1 GTAAGTTAT
43936298 GTAAGTTAT
1 GTAAGTTAT
43936307 GT-A-TTAT
1 GTAAGTTAT
*
43936314 ATAAGTTAT
1 GTAAGTTAT
*
43936323 GTAAGTTAC
1 GTAAGTTAT
43936332 GT-A-TTAT
1 GTAAGTTAT
* *
43936339 GTGAGCTAT
1 GTAAGTTAT
*
43936348 GTAAGTTAC
1 GTAAGTTAT
43936357 GT-A-TTAT
1 GTAAGTTAT
* *
43936364 GTGAGCTAT
1 GTAAGTTAT
43936373 GTAAGTTAT
1 GTAAGTTAT
*
43936382 -TTAG-TAT
1 GTAAGTTAT
*
43936389 GTAAGCTAT
1 GTAAGTTAT
*
43936398 GTAAGTTGT
1 GTAAGTTAT
43936407 GT-A-TTAT
1 GTAAGTTAT
*
43936414 GTAAGCTAT
1 GTAAGTTAT
43936423 GT-A-TTAT
1 GTAAGTTAT
*
43936430 GTTAGTTAT
1 GTAAGTTAT
**
43936439 GTCGGTTAT
1 GTAAGTTAT
*
43936448 AT-A-TTAT
1 GTAAGTTAT
*
43936455 GTATGTTAT
1 GTAAGTTAT
*
43936464 GTAAGTTGT
1 GTAAGTTAT
*
43936473 -TCAGTTA-
1 GTAAGTTAT
*
43936480 -TAAGCTAT
1 GTAAGTTAT
43936488 GTAAGTTAT
1 GTAAGTTAT
*
43936497 GTGAGTTA-
1 GTAAGTTAT
43936505 -T-A--TAT
1 GTAAGTTAT
43936510 GTAAGTTAT
1 GTAAGTTAT
43936519 GTATAAG-T-T
1 G--TAAGTTAT
*
43936528 -TAATTTGTAT
1 GTAA-GT-TAT
*
43936538 -TAAGCTAT
1 GTAAGTTAT
*
43936546 GTAAGTTGT
1 GTAAGTTAT
*
43936555 G-AA-TAAT
1 GTAAGTTAT
43936562 GTAAGTTAT
1 GTAAGTTAT
*
43936571 GAAAGTTAT
1 GTAAGTTAT
43936580 GT-A-TTAT
1 GTAAGTTAT
43936587 GTTAAGTTAT
1 G-TAAGTTAT
*
43936597 GAAAGTTAT
1 GTAAGTTAT
*
43936606 GTATTAAGTTGT
1 G---TAAGTTAT
43936618 GT-A-TTAT
1 GTAAGTTAT
*
43936625 GTAAGTTGT
1 GTAAGTTAT
*
43936634 G-AA-TAAT
1 GTAAGTTAT
43936641 GTAAGTTAT
1 GTAAGTTAT
43936650 G-AACGTTAT
1 GTAA-GTTAT
43936659 GT-A-TTAT
1 GTAAGTTAT
43936666 GTTAAGTTAT
1 G-TAAGTTAT
*
43936676 GAAAGTTAT
1 GTAAGTTAT
43936685 GTA
1 GTA
43936688 TTAAGTTGTG
Statistics
Matches: 291, Mismatches: 54, Indels: 90
0.67 0.12 0.21
Matches are distributed among these distances:
4 2 0.01
6 5 0.02
7 61 0.21
8 39 0.13
9 158 0.54
10 15 0.05
11 4 0.01
12 7 0.02
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.45
Consensus pattern (9 bp):
GTAAGTTAT
Found at i:43936415 original size:41 final size:41
Alignment explanation
Indices: 43936370--43936466 Score: 104
Period size: 41 Copynumber: 2.4 Consensus size: 41
43936360 TTATGTGAGC
* * *
43936370 TATGTAAGTTATTTAGTATGTAAGCTATGTAAGTTGTGTAT
1 TATGTAAGTTATGTAGTATGTAAGCTATGTAAGTTATATAT
* * * * **
43936411 TATGTAAGCTATGTATTATGTTAGTTATGTCGGTTATATAT
1 TATGTAAGTTATGTAGTATGTAAGCTATGTAAGTTATATAT
*
43936452 TATGTATGTTATGTA
1 TATGTAAGTTATGTA
43936467 AGTTGTTCAG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (41 bp):
TATGTAAGTTATGTAGTATGTAAGCTATGTAAGTTATATAT
Found at i:43936599 original size:26 final size:26
Alignment explanation
Indices: 43936537--43936690 Score: 159
Period size: 26 Copynumber: 5.9 Consensus size: 26
43936527 TTAATTTGTA
* * * * *
43936537 TTAAGCTATGTAAGTTGTGAATAATG
1 TTAAGTTATGAAAGTTATGTATTATG
43936563 -TAAGTTATGAAAGTTATGTATTATG
1 TTAAGTTATGAAAGTTATGTATTATG
*
43936588 TTAAGTTATGAAAGTTATGTATTAAG
1 TTAAGTTATGAAAGTTATGTATTATG
** * * * *
43936614 TTGTGTATTATGTAAGTTGTGAATAATG
1 TTAAG--TTATGAAAGTTATGTATTATG
*
43936642 -TAAGTTATGAACGTTATGTATTATG
1 TTAAGTTATGAAAGTTATGTATTATG
43936667 TTAAGTTATGAAAGTTATGTATTA
1 TTAAGTTATGAAAGTTATGTATTA
43936691 AGTTGTGTAT
Statistics
Matches: 103, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
25 36 0.35
26 49 0.48
27 2 0.02
28 16 0.16
ACGTcount: A:0.34, C:0.01, G:0.21, T:0.44
Consensus pattern (26 bp):
TTAAGTTATGAAAGTTATGTATTATG
Found at i:43936620 original size:12 final size:12
Alignment explanation
Indices: 43936573--43936727 Score: 53
Period size: 12 Copynumber: 12.1 Consensus size: 12
43936563 TAAGTTATGA
43936573 AAGTTATGTATT
1 AAGTTATGTATT
* * *
43936585 ATGTTAAGTTATGA
1 AAGTTATG-TAT-T
43936599 AAGTTATGTATT
1 AAGTTATGTATT
*
43936611 AAGTTGTGTATT
1 AAGTTATGTATT
* * *
43936623 ATGTAAGTTGTGAAT
1 AAGTTA--TGT-ATT
* *
43936638 AA-TGTAAGTTATG
1 AAGT-TATG-TATT
43936651 AACGTTATGTATT
1 AA-GTTATGTATT
* * *
43936664 ATGTTAAGTTATGA
1 AAGTTATG-TAT-T
43936678 AAGTTATGTATT
1 AAGTTATGTATT
*
43936690 AAGTTGTGTATT
1 AAGTTATGTATT
*
43936702 ATGTTA-GTTATTT
1 AAGTTATG-TA-TT
*
43936715 AAGCTATGTATT
1 AAGTTATGTATT
43936727 A
1 A
43936728 TGAAATTTTA
Statistics
Matches: 100, Mismatches: 29, Indels: 28
0.64 0.18 0.18
Matches are distributed among these distances:
11 1 0.01
12 45 0.45
13 28 0.28
14 21 0.21
15 5 0.05
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (12 bp):
AAGTTATGTATT
Found at i:43936731 original size:79 final size:79
Alignment explanation
Indices: 43936543--43936710 Score: 318
Period size: 79 Copynumber: 2.1 Consensus size: 79
43936533 TGTATTAAGC
43936543 TATGTAAGTTGTGAATAATGTAAGTTATGAAAGTTATGTATTATGTTAAGTTATGAAAGTTATGT
1 TATGTAAGTTGTGAATAATGTAAGTTATGAAAGTTATGTATTATGTTAAGTTATGAAAGTTATGT
43936608 ATTAAGTTGTGTAT
66 ATTAAGTTGTGTAT
*
43936622 TATGTAAGTTGTGAATAATGTAAGTTATGAACGTTATGTATTATGTTAAGTTATGAAAGTTATGT
1 TATGTAAGTTGTGAATAATGTAAGTTATGAAAGTTATGTATTATGTTAAGTTATGAAAGTTATGT
43936687 ATTAAGTTGTGTAT
66 ATTAAGTTGTGTAT
*
43936701 TATGTTAGTT
1 TATGTAAGTT
43936711 ATTTAAGCTA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
79 87 1.00
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (79 bp):
TATGTAAGTTGTGAATAATGTAAGTTATGAAAGTTATGTATTATGTTAAGTTATGAAAGTTATGT
ATTAAGTTGTGTAT
Found at i:43936817 original size:37 final size:36
Alignment explanation
Indices: 43936776--43936882 Score: 127
Period size: 37 Copynumber: 3.1 Consensus size: 36
43936766 TAGAAACTGA
43936776 TATGTAATTAGAAATTGTATCTTAATATTATATAAGT
1 TATGTAATTAGAAATT-TATCTTAATATTATATAAGT
*
43936813 TATGTAATGAG-AA---A--TTAATATTATATAAGT
1 TATGTAATTAGAAATTTATCTTAATATTATATAAGT
* *
43936843 TATGTAATTCGAAATTTTATCTTAATATTGTATAAGT
1 TATGTAATTAGAAA-TTTATCTTAATATTATATAAGT
43936880 TAT
1 TAT
43936883 CTAAATATAT
Statistics
Matches: 59, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
30 25 0.42
31 2 0.03
32 1 0.02
35 1 0.02
36 2 0.03
37 28 0.47
ACGTcount: A:0.40, C:0.03, G:0.11, T:0.46
Consensus pattern (36 bp):
TATGTAATTAGAAATTTATCTTAATATTATATAAGT
Found at i:43936952 original size:94 final size:97
Alignment explanation
Indices: 43936826--43937098 Score: 304
Period size: 94 Copynumber: 2.8 Consensus size: 97
43936816 GTAATGAGAA
* *
43936826 ATTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTGTATAAGTTATCTAAATAT
1 ATTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTTATCTTAATAT
* *
43936891 ATA-AATTTAAGTGTACTTAGAAA-TTA-C-AAT
66 ATAGAAGTT-A-TGTAATTAGAAATTTATCTAAT
* * * * *
43936921 -TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATCTTAATAT
1 ATTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTTATCTTAATA-
43936985 TATAGAAGTTATGTAATTAGAAATTTTATCTTAAT
65 TATAGAAGTTATGTAATTAGAAA-TTTATC-TAAT
* * * * *
43937020 ATTATATAAGTATATAAGTTATGTAATTAGAAATTTTGTCTTAATACTATATAAGTAATCTTAAT
1 ATTA-AT-ATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTTATCTTAAT
*
43937085 ATTATATAAGTTAT
64 A-TATAGAAGTTAT
43937099 CTTAATTTTA
Statistics
Matches: 148, Mismatches: 20, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
94 67 0.45
95 5 0.03
96 7 0.05
97 1 0.01
99 3 0.02
100 3 0.02
101 2 0.01
102 60 0.41
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (97 bp):
ATTAATATTATATAAGTTATGTAATTCGAAATTTTATCTTAATATTATATAAGTTATCTTAATAT
ATAGAAGTTATGTAATTAGAAATTTATCTAAT
Found at i:43936982 original size:57 final size:57
Alignment explanation
Indices: 43936921--43937028 Score: 162
Period size: 57 Copynumber: 1.9 Consensus size: 57
43936911 AAATTACAAT
* *
43936921 TTAATATTATATAAGTTATGTAATTCCAAATTTAATCTTAAAATAATATAACTTATC
1 TTAATATTATAGAAGTTATGTAATTACAAATTTAATCTTAAAATAATATAACTTATC
* * * *
43936978 TTAATATTATAGAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAA
1 TTAATATTATAGAAGTTATGTAATTACAAATTTAATCTTAAAATAATATAA
43937029 GTATATAAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.45
Consensus pattern (57 bp):
TTAATATTATAGAAGTTATGTAATTACAAATTTAATCTTAAAATAATATAACTTATC
Found at i:43937023 original size:37 final size:37
Alignment explanation
Indices: 43936973--43937075 Score: 107
Period size: 45 Copynumber: 2.6 Consensus size: 37
43936963 ATAATATAAC
43936973 TTATCTTAATATTATAGAAGTTATGTAATTAGAAATT
1 TTATCTTAATATTATAGAAGTTATGTAATTAGAAATT
43937010 TTATCTTAATATTATATAAGTATATAAGTTATGTAATTAGAAATT
1 TTATCTTAATA-T-TAT-AG-----AAGTTATGTAATTAGAAATT
* * *
43937055 TTGTCTTAATACTATATAAGT
1 TTATCTTAATATTATAGAAGT
43937076 AATCTTAATA
Statistics
Matches: 55, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
37 15 0.27
38 1 0.02
39 3 0.05
40 2 0.04
42 1 0.02
43 3 0.05
45 30 0.55
ACGTcount: A:0.40, C:0.04, G:0.10, T:0.47
Consensus pattern (37 bp):
TTATCTTAATATTATAGAAGTTATGTAATTAGAAATT
Found at i:43937054 original size:45 final size:45
Alignment explanation
Indices: 43936985--43937076 Score: 157
Period size: 45 Copynumber: 2.0 Consensus size: 45
43936975 ATCTTAATAT
*
43936985 TATAGAAGTTATGTAATTAGAAATTTTATCTTAATATTATATAAG
1 TATAGAAGTTATGTAATTAGAAATTTTATCTTAATACTATATAAG
* *
43937030 TATATAAGTTATGTAATTAGAAATTTTGTCTTAATACTATATAAG
1 TATAGAAGTTATGTAATTAGAAATTTTATCTTAATACTATATAAG
43937075 TA
1 TA
43937077 ATCTTAATAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (45 bp):
TATAGAAGTTATGTAATTAGAAATTTTATCTTAATACTATATAAG
Found at i:43937109 original size:20 final size:20
Alignment explanation
Indices: 43937058--43937109 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
43937048 AGAAATTTTG
*
43937058 TCTTAATACTATATAAGTAA
1 TCTTAATATTATATAAGTAA
*
43937078 TCTTAATATTATATAAGTTA
1 TCTTAATATTATATAAGTAA
*
43937098 TCTTAATTTTAT
1 TCTTAATATTAT
43937110 GTTATTTCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (20 bp):
TCTTAATATTATATAAGTAA
Found at i:43940625 original size:7 final size:7
Alignment explanation
Indices: 43940592--43940668 Score: 57
Period size: 7 Copynumber: 11.0 Consensus size: 7
43940582 TAATTAATCA
*
43940592 TAAATCC
1 TAAACCC
43940599 TAAACCC
1 TAAACCC
* **
43940606 CAAACTA
1 TAAACCC
43940613 TAAACCC
1 TAAACCC
*
43940620 TTAACCC
1 TAAACCC
43940627 TAAACCC
1 TAAACCC
43940634 TAAATCCC
1 TAAA-CCC
* *
43940642 -AAATCG
1 TAAACCC
* *
43940648 TAAAACT
1 TAAACCC
43940655 TAAACCC
1 TAAACCC
43940662 TAAACCC
1 TAAACCC
43940669 ATCAATTAAC
Statistics
Matches: 53, Mismatches: 15, Indels: 4
0.74 0.21 0.06
Matches are distributed among these distances:
6 1 0.02
7 49 0.92
8 3 0.06
ACGTcount: A:0.44, C:0.35, G:0.01, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:43940643 original size:35 final size:35
Alignment explanation
Indices: 43940592--43940668 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
43940582 TAATTAATCA
*
43940592 TAAATCCTAAACCCCAAA-C-TATAAACCCTT-AACCC
1 TAAACCCTAAACCCCAAATCGTA-AAA--CTTAAACCC
*
43940627 TAAACCCTAAATCCCAAATCGTAAAACTTAAACCC
1 TAAACCCTAAACCCCAAATCGTAAAACTTAAACCC
43940662 TAAACCC
1 TAAACCC
43940669 ATCAATTAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
34 3 0.08
35 28 0.76
36 4 0.11
37 2 0.05
ACGTcount: A:0.44, C:0.35, G:0.01, T:0.19
Consensus pattern (35 bp):
TAAACCCTAAACCCCAAATCGTAAAACTTAAACCC
Found at i:43941602 original size:114 final size:112
Alignment explanation
Indices: 43941230--43941611 Score: 258
Period size: 114 Copynumber: 3.3 Consensus size: 112
43941220 CGCTAATGAA
* * * * *
43941230 TCTATACGTGAAGCCGAAACGATGCATTTTGGTCAAAATTTTTGCGGCGCTTAAGCAGAAGCGCC
1 TCTATACGTCAAGACGAAACGATGCATTTTGTTCAAAATATTTGCGGCGATTAAGCA-AAGCGCC
* * * *
43941295 ACTAAAAGCTGATATATAGCGGCGTTTACGGGTACGCGTCACTAAAGGC
65 ACTAAAAGCTGATATATAGCGGCATTTTC-GGTAAGCGCCACTAAAGGC
* * * * * *** * *
43941344 GCTATA-GCTCAAGACGAAACGTTGCATTTCGGTTTAAAA-ATTTTCAGTGTTTTTTAGTTAAA-
1 TCTATACG-TCAAGACGAAACGATGCATTT-TGTTCAAAATATTTGC-G-GCGATTAAG-CAAAG
** ** * * *
43941406 CGCCACTATTTA--TGGGATATAGCGGCATTTTCAGGTAAGCACCACTAATGCC
61 CGCCACTA-AAAGCTGATATATAGCGGCATTTTC-GGTAAGCGCCACTAAAGGC
* ** * *
43941458 TTTATACGTCAA-ACCCG-AACGATGTGTTTTGTTCAAAATATTTGCGGCGATTCAGGAATAGCG
1 TCTATACGTCAAGA--CGAAACGATGCATTTTGTTCAAAATATTTGCGGCGATTAAGCAA-AGCG
*
43941521 CCACTAAAAGCTGATATATAGCGGCATTTTCGGCTAAGCGCCGCTAAAGGC
63 CCACTAAAAGCTGATATATAGCGGCATTTTCGG-TAAGCGCCACTAAAGGC
* *
43941572 TCTATA-GCTCAAGACGAAACGTTGCGTTTTGGTTTCAAAA
1 TCTATACG-TCAAGACGAAACGATGCATTTT-G-TTCAAAA
43941612 GTTCCGGCAT
Statistics
Matches: 198, Mismatches: 50, Indels: 38
0.69 0.17 0.13
Matches are distributed among these distances:
111 2 0.01
112 7 0.04
113 23 0.12
114 130 0.66
115 20 0.10
116 15 0.08
117 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (112 bp):
TCTATACGTCAAGACGAAACGATGCATTTTGTTCAAAATATTTGCGGCGATTAAGCAAAGCGCCA
CTAAAAGCTGATATATAGCGGCATTTTCGGTAAGCGCCACTAAAGGC
Found at i:43941657 original size:228 final size:228
Alignment explanation
Indices: 43941247--43941665 Score: 536
Period size: 228 Copynumber: 1.8 Consensus size: 228
43941237 GTGAAGCCGA
* *
43941247 AACGATGCATTTTGGTCAAAATTTTTGCGGCGCTTAAGCAGAAGCGCCACTAAAAGCTGATATAT
1 AACGATGCATTTTGGTCAAAATATTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTGATATAT
* * * *
43941312 AGCGGCGTTTACGGGTACGCGTCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGGT
66 AGCGGCATTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGGT
* * ** * * *
43941377 TTAAAAATTTTCAGTGTTTTTTAGTTAAACGCCACTATTTATGGGATATAGCGGCATTTTCAGGT
131 TTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATACGGGATATAGCGGCATTTTCAGGT
43941442 AAGCACCACTAATGCCTTTATACGTCAAACCCG
196 AAGCACCACTAATGCCTTTATACGTCAAACCCG
** * * *
43941475 AACGATGTGTTTTGTTCAAAATATTTGCGGCGATTCAGGA-ATAGCGCCACTAAAAGCTGATATA
1 AACGATGCATTTTGGTCAAAATATTTGCGGCGATTAAGCAGA-AGCGCCACTAAAAGCTGATATA
* * * * *
43941539 TAGCGGCATTTTCGGCTAAGCGCCGCTAAAGGCTCTATAGCTCAAGACGAAACGTTGCGTTTTGG
65 TAGCGGCATTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGG
* * * ** * *
43941604 TTTCAAAAGTTCCGGCATTTTTCGGTTACGCGCCGCTA-ATAGCGGGCTATAGCGGCATTTTC
130 TTTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATA-CGGGATATAGCGGCATTTTC
43941666 CACAAGCGCC
Statistics
Matches: 159, Mismatches: 30, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
227 3 0.02
228 156 0.98
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (228 bp):
AACGATGCATTTTGGTCAAAATATTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTGATATAT
AGCGGCATTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGGT
TTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATACGGGATATAGCGGCATTTTCAGGT
AAGCACCACTAATGCCTTTATACGTCAAACCCG
Found at i:43941732 original size:228 final size:227
Alignment explanation
Indices: 43941246--43941734 Score: 522
Period size: 228 Copynumber: 2.1 Consensus size: 227
43941236 CGTGAAGCCG
*
43941246 AAACGATGCATTTTGG-TCAAAATTTTTGCGGCGCTTAAGCAGAAGCGCCACTAAAAGCTGATAT
1 AAACGATGCATTTTGGTTCAAAA-TTTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTGATAT
* * * *
43941310 ATAGCGGCGTTTACGGGTACGCGTCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCG
65 ATAGCGGCATTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCG
* * ** * * *
43941375 GTTTAAAAATTTTCAGTGTTTTTTAGTTAAACGCCACTATTTATGGGATATAGCGGCATTTTCAG
130 GTTTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATACGGGATATAGCGGCATTTTCA-
* * *
43941440 GTAAGCACCACTAATGCCTTTATACGTCAAACCC
194 GCAAGCACCACTAATGCCTCTATACCTCAAACCC
* ** * *
43941474 GAACGATGTGTTTT-GTTCAAAATATTTGCGGCGATTCAGGA-ATAGCGCCACTAAAAGCTGATA
1 AAACGATGCATTTTGGTTCAAAAT-TTTGCGGCGATTAAGCAGA-AGCGCCACTAAAAGCTGATA
* * * * *
43941537 TATAGCGGCATTTTCGGCTAAGCGCCGCTAAAGGCTCTATAGCTCAAGACGAAACGTTGCGTTTT
64 TATAGCGGCATTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTC
* * * ** * *
43941602 GGTTTCAAAAGTTCCGGCATTTTTCGGTTACGCGCCGCTA-ATAGCGGGCTATAGCGGCATTTTC
129 GGTTTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATA-CGGGATATAGCGGCATTTT-
* * * *
43941666 CA-CAAGCGCCACTATTGGCTCTATGCCTCAATA-CC
192 CAGCAAGCACCACTAATGCCTCTATACCTCAA-ACCC
* *
43941701 AAACGTTGCATTTTGGTTCAGATATTTTGCGGCG
1 AAACGATGCATTTTGGTTCA-AAATTTTGCGGCG
43941735 CTTGTACTAT
Statistics
Matches: 212, Mismatches: 41, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
227 39 0.18
228 168 0.79
229 5 0.02
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (227 bp):
AAACGATGCATTTTGGTTCAAAATTTTGCGGCGATTAAGCAGAAGCGCCACTAAAAGCTGATATA
TAGCGGCATTTACGGCTAAGCGCCACTAAAGGCGCTATAGCTCAAGACGAAACGTTGCATTTCGG
TTTAAAAAGTTCCAGCATTTTTCAGTTAAACGCCACTATATACGGGATATAGCGGCATTTTCAGC
AAGCACCACTAATGCCTCTATACCTCAAACCC
Found at i:43943814 original size:38 final size:38
Alignment explanation
Indices: 43943747--43943852 Score: 139
Period size: 38 Copynumber: 2.8 Consensus size: 38
43943737 CAAGTGTTTC
*
43943747 AAAATATTT--AATAAA-TTAGAAATGTGATTAAAAAT
1 AAAATATTTACAATAAATTTAGAAATGAGATTAAAAAT
*
43943782 AAAATATTTACAATAAATTTAGAAACGAGATTAAAAAT
1 AAAATATTTACAATAAATTTAGAAATGAGATTAAAAAT
*
43943820 AAAATA-TCAGCAAATAAATTTAGAAATGAGATT
1 AAAATATTTA-C-AATAAATTTAGAAATGAGATT
43943853 TTTTACCCAT
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
35 9 0.15
37 8 0.13
38 25 0.40
39 20 0.32
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (38 bp):
AAAATATTTACAATAAATTTAGAAATGAGATTAAAAAT
Found at i:43946613 original size:15 final size:15
Alignment explanation
Indices: 43946593--43946622 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43946583 ATGTAGGAGG
*
43946593 GATAAATCATATCCT
1 GATAAATCAAATCCT
43946608 GATAAATCAAATCCT
1 GATAAATCAAATCCT
43946623 ACTACATGGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (15 bp):
GATAAATCAAATCCT
Found at i:43949700 original size:14 final size:14
Alignment explanation
Indices: 43949681--43949709 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
43949671 GTAATAAGAG
43949681 TATCTTGTATATGT
1 TATCTTGTATATGT
43949695 TATCTTGTATATGT
1 TATCTTGTATATGT
43949709 T
1 T
43949710 TTAAGTACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.14, T:0.59
Consensus pattern (14 bp):
TATCTTGTATATGT
Found at i:43951536 original size:18 final size:18
Alignment explanation
Indices: 43951515--43951550 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
43951505 CAACCTGGAT
43951515 TATTTTTGTAAA-TATTTA
1 TATTTTT-TAAATTATTTA
43951533 TATTTTTTAAATTATTTA
1 TATTTTTTAAATTATTTA
43951551 AGTAAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TATTTTTTAAATTATTTA
Found at i:43958802 original size:20 final size:20
Alignment explanation
Indices: 43958749--43958806 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
43958739 ATTTTAGTAT
* *
43958749 AAAATATTATAGTATTATTT
1 AAAATATTATAGTAATATTA
*
43958769 TAAA-ATT-T--TAATATTA
1 AAAATATTATAGTAATATTA
43958785 AAAATATTATAGTAATATTA
1 AAAATATTATAGTAATATTA
43958805 AA
1 AA
43958807 TAGTTCCCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
16 9 0.30
17 3 0.10
18 2 0.07
19 3 0.10
20 13 0.43
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
AAAATATTATAGTAATATTA
Found at i:43964262 original size:17 final size:16
Alignment explanation
Indices: 43964233--43964273 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
43964223 AGCAATTAAA
*
43964233 ATTTTTTTT--CTTTT
1 ATTTTTTTTAACTTTC
43964247 ATTTTCTTTTAACTTTC
1 ATTTT-TTTTAACTTTC
43964264 ATTTTTTTTA
1 ATTTTTTTTA
43964274 TTTATTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 5 0.22
15 4 0.17
16 5 0.22
17 9 0.39
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.76
Consensus pattern (16 bp):
ATTTTTTTTAACTTTC
Found at i:43967106 original size:9 final size:9
Alignment explanation
Indices: 43967084--43967168 Score: 102
Period size: 9 Copynumber: 9.4 Consensus size: 9
43967074 TTTAGTGAAA
*
43967084 AATTACCCG
1 AATTAACCG
43967093 AATTAACCG
1 AATTAACCG
* *
43967102 GATTACCCG
1 AATTAACCG
43967111 AATTAACCG
1 AATTAACCG
*
43967120 GATT-ACCTG
1 AATTAACC-G
43967129 AATTAACCG
1 AATTAACCG
43967138 AATT-ACCTG
1 AATTAACC-G
43967147 AATTAACCG
1 AATTAACCG
43967156 AATTAACCG
1 AATTAACCG
43967165 AATT
1 AATT
43967169 GAATCACTAC
Statistics
Matches: 65, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
8 6 0.09
9 53 0.82
10 6 0.09
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:43967108 original size:18 final size:18
Alignment explanation
Indices: 43967084--43967168 Score: 125
Period size: 18 Copynumber: 4.7 Consensus size: 18
43967074 TTTAGTGAAA
43967084 AATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
*
43967102 GATTACCCGAATTAACCG
1 AATTACCCGAATTAACCG
* *
43967120 GATTACCTGAATTAACCG
1 AATTACCCGAATTAACCG
*
43967138 AATTACCTGAATTAACCG
1 AATTACCCGAATTAACCG
*
43967156 AATTAACCGAATT
1 AATTACCCGAATT
43967169 GAATCACTAC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.38, C:0.24, G:0.13, T:0.26
Consensus pattern (18 bp):
AATTACCCGAATTAACCG
Found at i:43967219 original size:6 final size:6
Alignment explanation
Indices: 43967208--43967236 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
43967198 ACTTTTAGAC
43967208 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
43967237 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:43967260 original size:20 final size:20
Alignment explanation
Indices: 43967192--43967249 Score: 66
Period size: 18 Copynumber: 3.0 Consensus size: 20
43967182 ATTAAATTAT
* *
43967192 TTTTAGACTTTTAGACTTTAG
1 TTTTAGAATTTTAG-TTTTAG
43967213 TTTTAG--TTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
43967231 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
43967250 TTTATTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
18 11 0.33
19 6 0.18
20 10 0.30
21 6 0.18
ACGTcount: A:0.22, C:0.03, G:0.12, T:0.62
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:43967331 original size:29 final size:28
Alignment explanation
Indices: 43967278--43967333 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
43967268 ATTTTTATGA
* *
43967278 TTGGGTTGGGTTGGGTTGGGTTGAATAC
1 TTGGGTTGGATTGGGTTAGGTTGAATAC
43967306 TTGGGTTTGGATTGGGTTTAGG-TGAATA
1 TTGGG-TTGGATTGGG-TTAGGTTGAATA
43967334 GTGGGCCTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 15 0.62
30 4 0.17
ACGTcount: A:0.14, C:0.02, G:0.43, T:0.41
Consensus pattern (28 bp):
TTGGGTTGGATTGGGTTAGGTTGAATAC
Found at i:43970400 original size:19 final size:20
Alignment explanation
Indices: 43970376--43970444 Score: 67
Period size: 19 Copynumber: 3.7 Consensus size: 20
43970366 TAAATAAAAT
*
43970376 AACTAAAAAC-AAAAACTAA
1 AACTAAAAACTAAAAAATAA
43970395 AACT-AAAACTAAAAAATAA
1 AACTAAAAACTAAAAAATAA
* *
43970414 AAATAAAAA-TAAATAA-AA
1 AACTAAAAACTAAAAAATAA
*
43970432 TA-TAAAAACTAAA
1 AACTAAAAACTAAA
43970445 TGAAATCACT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
17 6 0.14
18 12 0.28
19 21 0.49
20 4 0.09
ACGTcount: A:0.75, C:0.09, G:0.00, T:0.16
Consensus pattern (20 bp):
AACTAAAAACTAAAAAATAA
Found at i:43970415 original size:6 final size:6
Alignment explanation
Indices: 43970379--43970444 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
43970369 ATAAAATAAC
* * *
43970379 TAAAAA CAAAAA CTAAAAC TAAAAC TAAAAAA TAAAAA TAAAAA T--AAA
1 TAAAAA TAAAAA -TAAAAA TAAAAA T-AAAAA TAAAAA TAAAAA TAAAAA
43970427 TAAAATA TAAAAA CTAAA
1 TAAAA-A TAAAAA -TAAA
43970445 TGAAATCACT
Statistics
Matches: 50, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
4 4 0.08
6 27 0.54
7 19 0.38
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:43970421 original size:12 final size:12
Alignment explanation
Indices: 43970379--43970444 Score: 55
Period size: 13 Copynumber: 5.3 Consensus size: 12
43970369 ATAAAATAAC
*
43970379 TAAAAACAAAAA
1 TAAAAATAAAAA
* *
43970391 CTAAAACTAAAAC
1 -TAAAAATAAAAA
43970404 TAAAAAATAAAAA
1 T-AAAAATAAAAA
43970417 TAAAAAT--AAA
1 TAAAAATAAAAA
43970427 TAAAATATAAAAA
1 TAAAA-ATAAAAA
43970440 CTAAA
1 -TAAA
43970445 TGAAATCACT
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
10 8 0.19
11 2 0.05
12 7 0.16
13 22 0.51
14 4 0.09
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.17
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:43973006 original size:15 final size:15
Alignment explanation
Indices: 43972982--43973013 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43972972 TATGCATGCA
*
43972982 AAATATAAAAGACAT
1 AAATACAAAAGACAT
43972997 AAATACAAAAGACAT
1 AAATACAAAAGACAT
43973012 AA
1 AA
43973014 TAGTGAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:43975152 original size:16 final size:17
Alignment explanation
Indices: 43975125--43975156 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
43975115 AGTATATATC
43975125 TATAATTATTATTTTAT
1 TATAATTATTATTTTAT
43975142 TATAA-TATTATTTTA
1 TATAATTATTATTTTA
43975157 AGGGTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TATAATTATTATTTTAT
Found at i:43977130 original size:33 final size:34
Alignment explanation
Indices: 43977064--43977131 Score: 86
Period size: 33 Copynumber: 2.0 Consensus size: 34
43977054 TGTTATGTTA
* * *
43977064 TGCTTGAAATTTTTGTTAAGTGATTACTTATATT
1 TGCTTGAAATATTTGTTAAGTGACTACTGATATT
43977098 TGCTTGAAA-ATTTGTTAAG-GAACTACTGATATT
1 TGCTTGAAATATTTGTTAAGTG-ACTACTGATATT
43977131 T
1 T
43977132 ATATTAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 1 0.03
33 20 0.67
34 9 0.30
ACGTcount: A:0.29, C:0.07, G:0.16, T:0.47
Consensus pattern (34 bp):
TGCTTGAAATATTTGTTAAGTGACTACTGATATT
Found at i:43979628 original size:3 final size:3
Alignment explanation
Indices: 43979622--43979682 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
43979612 GTACATGGTT
43979622 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
43979670 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
43979683 GAGTATTAAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:43981116 original size:44 final size:43
Alignment explanation
Indices: 43981061--43981377 Score: 192
Period size: 44 Copynumber: 7.4 Consensus size: 43
43981051 GATCTACTCT
* * *
43981061 CTGCAAATTCAGAGAGATAAGATCTATGGCTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCT-TGGCTTTAATCTGCTCCA
* *
43981105 CTGCAACTTCAGGGAGATAGGA--TTGGTTTCTTCT-GTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTTGG---CTT-TAATCTGCTCCA
* * *** *
43981149 CTACAACTTCAGGGAGATAAGA-C-TGGATGCGATCTGCTCTA
1 CTGCAACTTCAGGGAGATAAGATCTTGGCTTTAATCTGCTCCA
* ** * *
43981190 CTGCAACTTTAGCAAGATAAGATCTGTGGTTTTAATCCGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCT-TGGCTTTAATCTGCTCCA
* *
43981234 CTGCAACTTCAGGGAGATAGGA--TTGGTTTCTTCT-GTCTGCTCCA
1 CTGCAACTTCAGGGAGATAAGATCTTGG---CTT-TAATCTGCTCCA
* *** *
43981278 CTGCAACTTCAGGGAGATAAGA-C-TGGATACGATCTGCTCTA
1 CTGCAACTTCAGGGAGATAAGATCTTGGCTTTAATCTGCTCCA
* * **
43981319 CTGCAACTTTAGAGAGATAAGATC-T-G-TTTAATCCACTCCA
1 CTGCAACTTCAGGGAGATAAGATCTTGGCTTTAATCTGCTCCA
* *
43981359 TTGCAACTTTAGGGAGATA
1 CTGCAACTTCAGGGAGATA
43981378 GGATTGGTNN
Statistics
Matches: 212, Mismatches: 45, Indels: 36
0.72 0.15 0.12
Matches are distributed among these distances:
40 25 0.12
41 63 0.30
42 5 0.02
44 117 0.55
45 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (43 bp):
CTGCAACTTCAGGGAGATAAGATCTTGGCTTTAATCTGCTCCA
Done.