Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 154 of 160
Found at i:31006879 original size:17 final size:17
Alignment explanation
Indices: 31006857--31006894 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
31006847 TTTATGATTA
**
31006857 AAAAAAATTAATTAATT
1 AAAAAAATTAAAAAATT
31006874 AAAAAAATTAAAAAATT
1 AAAAAAATTAAAAAATT
31006891 AAAA
1 AAAA
31006895 TTAAAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAAAAATTAAAAAATT
Found at i:31006894 original size:6 final size:6
Alignment explanation
Indices: 31006885--31006918 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
31006875 AAAAAATTAA
*
31006885 AAAATT AAAATT AAAATT AAAATT AAAAAT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
31006919 AGAAAAGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (6 bp):
AAAATT
Found at i:31006924 original size:18 final size:18
Alignment explanation
Indices: 31006885--31006924 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
31006875 AAAAAATTAA
* **
31006885 AAAATTAAAATTAAAATT
1 AAAATTAAAAATAAAAAG
31006903 AAAATTAAAAATAAAAAG
1 AAAATTAAAAATAAAAAG
31006921 AAAA
1 AAAA
31006925 GAAAGAAGAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATTAAAAATAAAAAG
Found at i:31008751 original size:12 final size:12
Alignment explanation
Indices: 31008734--31008761 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
31008724 CTACTTGGTG
31008734 ATAAAATATTTT
1 ATAAAATATTTT
31008746 ATAAAATATTTT
1 ATAAAATATTTT
31008758 ATAA
1 ATAA
31008762 TAAAAAAGAA
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:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATAAAATATTTT
Found at i:31013913 original size:205 final size:205
Alignment explanation
Indices: 31013579--31013967 Score: 495
Period size: 205 Copynumber: 1.9 Consensus size: 205
31013569 AATTTAATTA
* * * *
31013579 TATTGAAGATTTTCTATAAATATTCTAATACGCTGGTAGTATTTTACAAAAAATCTTCTCACCTA
1 TATTGAAAATTTTCTATAAATACTCCAATACACTGGTAGTATTTTACAAAAAATCTTCTCACCTA
* * * *
31013644 CAGATTTCTTAAAGCATATCTACTCGAAATACTTTTAGAATCTCATCATTGGATTAAATTTCTTT
66 CAGATTTCGTAAAGCATATCTACTCGAAATACCTTTAGAATCTCATCATCGGATAAAATTTCTTT
* *
31013709 TCTT-CCTATTTTTATTACTTATATTTTTAATTTATT-AATCAATTTTTAT-TTATTACTTAAAA
131 TCTTACAT-TTTTTATTA-TTATATTATTAA-TTATTAAATCAATTTTTATATTATTACTTAAAA
31013771 ATTTTTTTTGCTG
193 ATTTTTTTTGCTG
*
31013784 TATTGAAAATTTTTTTATAAATACTCCAATACACTGGTAGTATTTTA-AAAAAATCTTCTCACCT
1 TATTGAAAA-TTTTCTATAAATACTCCAATACACTGGTAGTATTTTACAAAAAATCTTCTCACCT
* * * * *
31013848 AGAGATTTCGT-AGGCATCA-CTACTTGGAATACCTTT-GAATCTCATTATCGGATAAAAATTTT
65 ACAGATTTCGTAAAGCAT-ATCTACTCGAAATACCTTTAGAATCTCATCATCGGAT-AAAA-TTT
* **
31013910 CTTTTCTTACATTTTTTATTATTTTATTATTAATTATTAAATTTATTTTTATATTATT
127 CTTTTCTTACATTTTTTATTATTATATTATTAATTATTAAATCAATTTTTATATTATT
31013968 GTTTTTAAAG
Statistics
Matches: 158, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
203 20 0.13
204 43 0.27
205 60 0.38
206 35 0.22
ACGTcount: A:0.32, C:0.13, G:0.07, T:0.48
Consensus pattern (205 bp):
TATTGAAAATTTTCTATAAATACTCCAATACACTGGTAGTATTTTACAAAAAATCTTCTCACCTA
CAGATTTCGTAAAGCATATCTACTCGAAATACCTTTAGAATCTCATCATCGGATAAAATTTCTTT
TCTTACATTTTTTATTATTATATTATTAATTATTAAATCAATTTTTATATTATTACTTAAAAATT
TTTTTTGCTG
Found at i:31013981 original size:27 final size:26
Alignment explanation
Indices: 31013924--31013985 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
31013914 TCTTACATTT
31013924 TTTATTATTTTATTATTAATTATTAAA
1 TTTATT-TTTTATTATTAATTATTAAA
* *
31013951 TTTATTTTTATATTATT-GTTTTTAAA
1 TTTATTTTT-TATTATTAATTATTAAA
31013977 GTTTATTTT
1 -TTTATTTT
31013986 AAAAATTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 10 0.32
27 21 0.68
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (26 bp):
TTTATTTTTTATTATTAATTATTAAA
Found at i:31014995 original size:17 final size:17
Alignment explanation
Indices: 31014969--31015019 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
31014959 CCAGATAAGG
*
31014969 ATGAAAAAGAAAGAAAA
1 ATGAAGAAGAAAGAAAA
31014986 ATGAAGAAGAGAA-AAAA
1 ATGAAGAAGA-AAGAAAA
31015003 A--AAGAAGAAAGAGAAA
1 ATGAAGAAGAAAGA-AAA
31015019 A
1 A
31015020 AGACAAACGT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 2 0.07
15 8 0.27
16 4 0.13
17 14 0.47
18 2 0.07
ACGTcount: A:0.75, C:0.00, G:0.22, T:0.04
Consensus pattern (17 bp):
ATGAAGAAGAAAGAAAA
Found at i:31015007 original size:15 final size:15
Alignment explanation
Indices: 31014972--31015010 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
31014962 GATAAGGATG
31014972 AAAAAGAA-AGAAAA
1 AAAAAGAAGAGAAAA
**
31014986 ATGAAGAAGAGAAAA
1 AAAAAGAAGAGAAAA
31015001 AAAAAGAAGA
1 AAAAAGAAGA
31015011 AAGAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
AAAAAGAAGAGAAAA
Found at i:31015009 original size:18 final size:19
Alignment explanation
Indices: 31014971--31015020 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
31014961 AGATAAGGAT
* *
31014971 GAAAAAGAAAGAAAAATGAA
1 GAAAGAGAAA-AAAAAAGAA
31014991 G-AAGAGAAAAAAAAAGAA
1 GAAAGAGAAAAAAAAAGAA
31015009 GAAAGAGAAAAA
1 GAAAGAGAAAAA
31015021 GACAAACGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
18 9 0.33
19 17 0.63
20 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (19 bp):
GAAAGAGAAAAAAAAAGAA
Found at i:31015389 original size:48 final size:48
Alignment explanation
Indices: 31015274--31015698 Score: 528
Period size: 48 Copynumber: 9.0 Consensus size: 48
31015264 TTGAAAGTTT
* *
31015274 AAAAGGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAA-TTC-TCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTG
* *
31015320 AAAAAAGCTCCTCTCAGCAGAGGTTCAACAATTTTAAAATTTCATCTTG
1 -AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTG
* * * *
31015369 GAAAAGCTCCTCTCAACAGAGGCTTAACAACTTTAAAATCTCATCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTG
** *
31015417 AAAAAGCTCCTCTCAATAGAGGCTCAACAACTTTAAAA-TTC-TCTTA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTG
* * *
31015463 AAAAAGCTGCTCTCAACAGAAGCTCAACAACTTTAAAATTTCATCTT-
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTG
** * *
31015510 AGAAAAGCTCCTCTCAATAGAGGCTCAACAACTTTAAAATCTCAT-TTT
1 A-AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTG
*
31015558 AGAAAAGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTT--TCTTG
1 A-AAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTG
*
31015605 AAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAA-TTC-TCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTG
* * *
31015651 AAAAAAGCTCCTTTCAGCAGAGGTTCAACAACTTTAAAAATTCCATCT
1 -AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTTCATCT
31015699 GTTTTTAAAT
Statistics
Matches: 333, Mismatches: 33, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
45 2 0.01
46 80 0.24
47 76 0.23
48 165 0.50
49 7 0.02
50 3 0.01
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (48 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTCATCTTG
Found at i:31015507 original size:94 final size:95
Alignment explanation
Indices: 31015274--31015698 Score: 549
Period size: 94 Copynumber: 4.5 Consensus size: 95
31015264 TTGAAAGTTT
* * * *
31015274 AAAAGGCTCCTTTCAGCAGAGGCTCAACAACTTTAAAA-TTC-TCTTGAAAAAAGCTCCTCTCAG
1 AAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTTCATCTTG-AAAAAGCTCCTCTCAA
* * * *
31015337 CAGAGGTTCAACAATTTTAAAATTTCATCTTG
65 TAGAGGCTCAACAACTTTAAAA-TTCATCTTA
* * *
31015369 GAAAAGCTCCTCTCAACAGAGGCTTAACAACTTTAAAATCTCATCTTGAAAAAGCTCCTCTCAAT
1 AAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAAT
31015434 AGAGGCTCAACAACTTTAAAATTC-TCTTA
66 AGAGGCTCAACAACTTTAAAATTCATCTTA
* *
31015463 AAAAAGCTGCTCTCAACAGAAGCTCAACAACTTTAAAATTTCATCTT-AGAAAAGCTCCTCTCAA
1 AAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTTCATCTTGA-AAAAGCTCCTCTCAA
*
31015527 TAGAGGCTCAACAACTTTAAAATCTCATTTTA
65 TAGAGGCTCAACAACTTTAAAAT-TCATCTTA
* * * *
31015559 GAAAAGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTT--TCTTGAAAAAGCTCCTCTCAGT
1 AAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAAT
31015622 AGAGGCTCAACAACTTTAAAATTC-TCTTGA
66 AGAGGCTCAACAACTTTAAAATTCATCTT-A
* * * *
31015652 AAAAAGCTCCTTTCAGCAGAGGTTCAACAACTTTAAAAATTCCATCT
1 AAAAAGCTCCTCTCAACAGAGGCTCAACAACTTT-AAAATTTCATCT
31015699 GTTTTTAAAT
Statistics
Matches: 291, Mismatches: 29, Indels: 19
0.86 0.09 0.06
Matches are distributed among these distances:
92 3 0.01
93 34 0.12
94 131 0.45
95 39 0.13
96 79 0.27
97 5 0.02
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (95 bp):
AAAAAGCTCCTCTCAACAGAGGCTCAACAACTTTAAAATTTCATCTTGAAAAAGCTCCTCTCAAT
AGAGGCTCAACAACTTTAAAATTCATCTTA
Found at i:31015691 original size:142 final size:143
Alignment explanation
Indices: 31015274--31015689 Score: 585
Period size: 142 Copynumber: 2.9 Consensus size: 143
31015264 TTGAAAGTTT
*
31015274 AAAAGGCTCCT-TTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAAGCTCCTCTCAGC
1 AAAAAGCTCCTCTT-AGCAGAGGCTCAACAACTTTAAAATTCTCTTG-AAAAAGCTCCTCTCAGC
* *
31015338 AGAGGTTCAACAATTTTAAAATTTCATCTTG-GAAAAGCTCCTCTCAACAGAGGCTT-AACAACT
64 AGAGGCTCAACAACTTTAAAATTTCATCTTGAGAAAAGCTCCTCTCAACAGAGG-TTCAACAACT
31015401 TTAAAATCTCATCTTG
128 TTAAAATCTCATCTTG
* ** * * *
31015417 AAAAAGCTCCTCTCAATAGAGGCTCAACAACTTTAAAATTCTCTTAAAAAAGCTGCTCTCAACAG
1 AAAAAGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAGCAG
* * *
31015482 AAGCTCAACAACTTTAAAATTTCATCTT-AGAAAAGCTCCTCTCAATAGAGGCTCAACAACTTTA
66 AGGCTCAACAACTTTAAAATTTCATCTTGAGAAAAGCTCCTCTCAACAGAGGTTCAACAACTTTA
*
31015546 AAATCTCAT-TTT
131 AAATCTCATCTTG
* *
31015558 AGAAAAGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTTTCTTGAAAAAGCTCCTCTCAGTA
1 A-AAAAGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAGCA
* * *
31015623 GAGGCTCAACAACTTTAAAA-TTC-TCTTGAAAAAAGCTCCTTTCAGCAGAGGTTCAACAACTTT
65 GAGGCTCAACAACTTTAAAATTTCATCTTGAGAAAAGCTCCTCTCAACAGAGGTTCAACAACTTT
31015686 AAAA
130 AAAA
31015690 ATTCCATCTG
Statistics
Matches: 241, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
140 4 0.02
141 41 0.17
142 156 0.65
143 39 0.16
144 1 0.00
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (143 bp):
AAAAAGCTCCTCTTAGCAGAGGCTCAACAACTTTAAAATTCTCTTGAAAAAGCTCCTCTCAGCAG
AGGCTCAACAACTTTAAAATTTCATCTTGAGAAAAGCTCCTCTCAACAGAGGTTCAACAACTTTA
AAATCTCATCTTG
Found at i:31025100 original size:28 final size:28
Alignment explanation
Indices: 31025049--31025113 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 28
31025039 TGTGTGTGAG
* *
31025049 TTTCTTTTTGTTTTTTTTC-TTTTTTCTT
1 TTTCTTTTTGTTTGTTTTCGTTTTGT-TT
31025077 TTTCTTTTTGATTTGTTTT-GTTTTGTTT
1 TTTCTTTTTG-TTTGTTTTCGTTTTGTTT
*
31025105 TTTTTTTTT
1 TTTCTTTTT
31025114 ACTAAAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 20 0.62
29 12 0.38
ACGTcount: A:0.02, C:0.06, G:0.08, T:0.85
Consensus pattern (28 bp):
TTTCTTTTTGTTTGTTTTCGTTTTGTTT
Found at i:31025831 original size:12 final size:12
Alignment explanation
Indices: 31025814--31025842 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
31025804 TTTTTCAAAA
31025814 ATTTTATTAATT
1 ATTTTATTAATT
31025826 ATTTTATTAATT
1 ATTTTATTAATT
31025838 -TTTTA
1 ATTTTA
31025843 ATTTTAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 5 0.29
12 12 0.71
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
ATTTTATTAATT
Found at i:31026252 original size:27 final size:27
Alignment explanation
Indices: 31026226--31026283 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 27
31026216 ACATTTTTTA
*
31026226 TTATTTTTTTATTA--ATTATTAAA-T
1 TTATTTTTATATTATTATTATTAAAGT
*
31026250 TTATTTTTATATTATTATTTTTAAAGT
1 TTATTTTTATATTATTATTATTAAAGT
31026277 TTATTTT
1 TTATTTT
31026284 AAAAATTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 13 0.45
26 8 0.28
27 8 0.28
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (27 bp):
TTATTTTTATATTATTATTATTAAAGT
Found at i:31026272 original size:20 final size:19
Alignment explanation
Indices: 31026223--31026272 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
31026213 CTTACATTTT
31026223 TTATTATTTTT-TTATTAA
1 TTATTATTTTTATTATTAA
** *
31026241 TTATTAAATTTATTTTTATA
1 TTATTATTTTTATTATTA-A
31026261 TTATTATTTTTA
1 TTATTATTTTTA
31026273 AAGTTTATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 9 0.36
19 5 0.20
20 11 0.44
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTATTTTTATTATTAA
Found at i:31027387 original size:15 final size:15
Alignment explanation
Indices: 31027349--31027400 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
31027339 AGATAAGGAT
31027349 GAAA-AAGAAGAAAA
1 GAAATAAGAAGAAAA
**
31027363 -AAGGAAGAAGAAAA
1 GAAATAAGAAGAAAA
31027377 GAAATAAGAAG-AAA
1 GAAATAAGAAGAAAA
31027391 GAGAATAAGA
1 GA-AATAAGA
31027401 CAAACGCAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 2 0.06
14 15 0.47
15 15 0.47
ACGTcount: A:0.71, C:0.00, G:0.25, T:0.04
Consensus pattern (15 bp):
GAAATAAGAAGAAAA
Found at i:31035520 original size:68 final size:68
Alignment explanation
Indices: 31035439--31035667 Score: 214
Period size: 68 Copynumber: 3.4 Consensus size: 68
31035429 AATATTTGGC
* * * * *
31035439 TCATGGTTTAATCCCAATCATTTTATTTTTTGACTCACAGTTTAATCCCAATCTCTTTATCCTCT
1 TCATGATTCAATCCCGATCATTTTATTTTTTGACTCACAGTTTAATCTCGATCTCTTTATCCTCT
*
31035504 TAT
66 AAT
* ** * *
31035507 TCATGATTCAATCCCGATC-TCTTTA-ATTTAAAATCACAGTTTAATCTCGAT-TGTTGTTATCC
1 TCATGATTCAATCCCGATCAT-TTTATTTTTTGACTCACAGTTTAATCTCGATCT-CT-TTATCC
*
31035569 TCTAAC
63 TCTAAT
* * * *
31035575 TCATGATTTAGTCCCGATCATTTCATTTTTTGACTCA-TGATTTAATCTCGATCTCTTTATCCTC
1 TCATGATTCAATCCCGATCATTTTATTTTTTGACTCACAG-TTTAATCTCGATCTCTTTATCCTC
*
31035639 TGAT
65 TAAT
* * *
31035643 TCACGATTCAATCCTGATCTTTTTA
1 TCATGATTCAATCCCGATCATTTTA
31035668 ATTTAAAATC
Statistics
Matches: 125, Mismatches: 29, Indels: 14
0.74 0.17 0.08
Matches are distributed among these distances:
66 1 0.01
67 22 0.18
68 80 0.64
69 21 0.17
70 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.45
Consensus pattern (68 bp):
TCATGATTCAATCCCGATCATTTTATTTTTTGACTCACAGTTTAATCTCGATCTCTTTATCCTCT
AAT
Found at i:31035605 original size:136 final size:132
Alignment explanation
Indices: 31035438--31036229 Score: 785
Period size: 136 Copynumber: 6.1 Consensus size: 132
31035428 CAATATTTGG
* * * *
31035438 CTCATGGTTTAATCCCAATCATTTTATTTTTTGACTCACAGTTTAATCCCAATCTCTTTATCCTC
1 CTCATGGTTTAGTCCCGATCATTTCATTTTTTGACTCAC-GTTTAATCTCAATCTCTTTATCCTC
*
31035503 TTATTCATGATTCAATCCCGATCTCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTATC
65 -TATTC-T-ATTCAATCCCGATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATC
*
31035568 CTCTAA
127 CTCTGA
* * *
31035574 CTCATGATTTAGTCCCGATCATTTCATTTTTTGACTCATGATTTAATCTCGATCTCTTTATCCTC
1 CTCATGGTTTAGTCCCGATCATTTCATTTTTTGACTCACG-TTTAATCTCAATCTCTTTATCCTC
* * * * *
31035639 TGATTCACGATTCAATCCTGATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTGTTGTTATC
65 T-ATT--CTATTCAATCCCGATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATC
31035704 CTCTGA
127 CTCTGA
** * * *
31035710 CTTGTTGTTTAGTCCCGATCATTTCATTTTTTGACTCGCG----AT-TTAATC-C--TAGT-CTC
1 CTCATGGTTTAGTCCCGATCATTTCATTTTTTGACTCACGTTTAATCTCAATCTCTTTA-TCCTC
* *
31035766 --TT-TA-TCTATCCCAATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATCCTC
65 TATTCTATTCAATCCCGATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATCCTC
31035827 TGA
130 TGA
* * * * *
31035830 CTCGTGGTTTAGTCCCGGTCA-TTCATTTTTTAACTCACGGTTTAATTTCGATCTCTTTATCCTC
1 CTCATGGTTTAGTCCCGATCATTTCATTTTTTGACTCAC-GTTTAATCTCAATCTCTTTATCCTC
* ** * * *
31035894 TAATTCGCTGTTCAATCTTGATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTGTTGTTATC
65 T-ATT--CTATTCAATCCCGATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATC
31035959 CTCTGA
127 CTCTGA
* **
31035965 CTCATGGTTTAGTCCCAATCATTTCATTTTTTGACTCACAGTTTAATC-CTGGTCTCTTTA----
1 CTCATGGTTTAGTCCCGATCATTTCATTTTTTGACTCAC-GTTTAATCTC-AATCTCTTTATCCT
**
31036025 C----C---T--ATCCCGATCTCTTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATCCT
64 CTATTCTATTCAATCCCGATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATCCT
*
31036081 CTAA
129 CTGA
* * * * * *
31036085 CTCGTGGTTTAGTCCCGGTTATTTCATTTTTTGACTCGCGATTTAATCTCAATCTTTTTACCCTT
1 CTCATGGTTTAGTCCCGATCATTTCATTTTTTGACTCACG-TTTAATCTCAATCTCTTTATCC-T
* *
31036150 CGATTTCTAGTTCAATCTCGATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATC
64 CTA-TTCTA-TTCAATCCCGATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATC
*
31036215 TTCTGA
127 CTCTGA
*
31036221 CTCGTGGTT
1 CTCATGGTT
31036230 CAATCCCAGT
Statistics
Matches: 544, Mismatches: 70, Indels: 84
0.78 0.10 0.12
Matches are distributed among these distances:
119 16 0.03
120 172 0.32
121 2 0.00
122 1 0.00
124 4 0.01
125 6 0.01
126 1 0.00
127 6 0.01
128 6 0.01
129 1 0.00
130 5 0.01
131 4 0.01
132 1 0.00
134 2 0.00
135 74 0.14
136 242 0.44
138 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (132 bp):
CTCATGGTTTAGTCCCGATCATTTCATTTTTTGACTCACGTTTAATCTCAATCTCTTTATCCTCT
ATTCTATTCAATCCCGATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATCCTCT
GA
Found at i:31035704 original size:68 final size:68
Alignment explanation
Indices: 31035495--31035709 Score: 220
Period size: 68 Copynumber: 3.2 Consensus size: 68
31035485 CCCAATCTCT
* * *
31035495 TTATCCTCTTATTCATGATTCAATCCCGATCTCTTTAATTTAAAATCACAGTTTAATCTCGATTG
1 TTATCCTCTGATTCATGATTCAATCCCGATCTTTTTAATTTAAAATCATAGTTTAATCTCGATTG
31035560 TTG
66 TTG
* * * * * * * ** *
31035563 TTATCCTCTAACTCATGATTTAGTCCCGATCATTTCATTTTTTGACTCAT-GATTTAATCTCGAT
1 TTATCCTCTGATTCATGATTCAATCCCGATCTTTTTA-ATTTAAAATCATAG-TTTAATCTCGAT
*
31035627 CT-CT-
64 -TGTTG
* * * *
31035631 TTATCCTCTGATTCACGATTCAATCCTGATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTG
1 TTATCCTCTGATTCATGATTCAATCCCGATCTTTTTAATTTAAAATCATAGTTTAATCTCGATTG
31035696 TTG
66 TTG
31035699 TTATCCTCTGA
1 TTATCCTCTGA
31035710 CTTGTTGTTT
Statistics
Matches: 113, Mismatches: 28, Indels: 12
0.74 0.18 0.08
Matches are distributed among these distances:
66 1 0.01
67 19 0.17
68 72 0.64
69 20 0.18
70 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (68 bp):
TTATCCTCTGATTCATGATTCAATCCCGATCTTTTTAATTTAAAATCATAGTTTAATCTCGATTG
TTG
Found at i:31035977 original size:255 final size:256
Alignment explanation
Indices: 31035517--31036229 Score: 1067
Period size: 255 Copynumber: 2.8 Consensus size: 256
31035507 TCATGATTCA
* *
31035517 ATCCCGATCTCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTATCCTCTAACTCATGAT
1 ATCCCGATCTCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTATCCTCTAACTCGTGGT
* *
31035582 TTAGTCCCGATCATTTCATTTTTTGACTCATGATTTAATCTCGATCTCTTTATCCTCTGATTCAC
66 TTAGTCCCGGTCATTTCATTTTTTGACTCACGATTTAATCTCGATCTCTTTATCCTCTGATTCAC
*
31035647 -GATTCAATCCTGATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTGTTGTTATCCTCTGAC
131 TG-TTCAATCTTGATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTGTTGTTATCCTCTGAC
* * * * *
31035711 TTGTTGTTTAGTCCCGATCATTTCATTTTTTGACTCGC-GATTTAATCCTAGTCTCTTTATCT
195 TCGTGGTTTAGTCCCAATCATTTCATTTTTTGACTCACAG-TTTAATCCTAGTCTCTTTACCT
* * *
31035773 ATCCCAATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATCCTCTGACTCGTGGT
1 ATCCCGATCTCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTATCCTCTAACTCGTGGT
* * * * *
31035838 TTAGTCCCGGTCA-TTCATTTTTTAACTCACGGTTTAATTTCGATCTCTTTATCCTCTAATTCGC
66 TTAGTCCCGGTCATTTCATTTTTTGACTCACGATTTAATCTCGATCTCTTTATCCTCTGATTCAC
31035902 TGTTCAATCTTGATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTGTTGTTATCCTCTGACT
131 TGTTCAATCTTGATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTGTTGTTATCCTCTGACT
* *
31035967 CATGGTTTAGTCCCAATCATTTCATTTTTTGACTCACAGTTTAATCCTGGTCTCTTTACCT
196 CGTGGTTTAGTCCCAATCATTTCATTTTTTGACTCACAGTTTAATCCTAGTCTCTTTACCT
*
31036028 ATCCCGATCTCTTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATCCTCTAACTCGTGGT
1 ATCCCGATCTCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTATCCTCTAACTCGTGGT
* * * * * *
31036093 TTAGTCCCGGTTATTTCATTTTTTGACTCGCGATTTAATCTCAATCTTTTTACCCT-TCGATT-T
66 TTAGTCCCGGTCATTTCATTTTTTGACTCACGATTTAATCTCGATCTCTTTATCCTCT-GATTCA
* * * * *
31036156 CTAGTTCAATCTCGATCTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATCTTCTGA
130 CT-GTTCAATCTTGATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTGTTGTTATCCTCTGA
31036221 CTCGTGGTT
194 CTCGTGGTT
31036230 CAATCCCAGT
Statistics
Matches: 412, Mismatches: 40, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
255 235 0.57
256 177 0.43
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.46
Consensus pattern (256 bp):
ATCCCGATCTCTTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTATCCTCTAACTCGTGGT
TTAGTCCCGGTCATTTCATTTTTTGACTCACGATTTAATCTCGATCTCTTTATCCTCTGATTCAC
TGTTCAATCTTGATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTGTTGTTATCCTCTGACT
CGTGGTTTAGTCCCAATCATTTCATTTTTTGACTCACAGTTTAATCCTAGTCTCTTTACCT
Found at i:31036145 original size:120 final size:120
Alignment explanation
Indices: 31035913--31036146 Score: 328
Period size: 120 Copynumber: 1.9 Consensus size: 120
31035903 GTTCAATCTT
* * * *
31035913 GATCTTTTTAATTTAAAATCGTAGTTTAATCTTGATTGTTGTTATCCTCTGACTCATGGTTTAGT
1 GATCTCTTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATCCTCTAACTCATGGTTTAGT
**
31035978 CCCAATCATTTCATTTTTTGACTCACAGTTTAATCCTGGTCTCTTTACCTATCCC
66 CCCAATCATTTCATTTTTTGACTCACAGTTTAATCCTAATCTCTTTACCTATCCC
*
31036033 GATCTCTTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATCCTCTAACTCGTGGTTTAGT
1 GATCTCTTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATCCTCTAACTCATGGTTTAGT
** * * *
31036098 CCCGGTTATTTCATTTTTTGACTCGC-GATTTAAT-CTCAATCTTTTTACC
66 CCCAATCATTTCATTTTTTGACTCACAG-TTTAATCCT-AATCTCTTTACC
31036147 CTTCGATTTC
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
119 3 0.03
120 97 0.97
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (120 bp):
GATCTCTTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATCCTCTAACTCATGGTTTAGT
CCCAATCATTTCATTTTTTGACTCACAGTTTAATCCTAATCTCTTTACCTATCCC
Found at i:31036397 original size:171 final size:170
Alignment explanation
Indices: 31036108--31036479 Score: 507
Period size: 171 Copynumber: 2.2 Consensus size: 170
31036098 CCCGGTTATT
**
31036108 TCATTTTTTGACTCGCGATTTAATCTCAATCTTTTTACCCTTCGATTTCTAGTTCAATCTCGATC
1 TCATTTTTTGACTAACGATTTAATCTCAATCTTTTTACCCTTCGATTTCTAGTTCAATCTCGATC
* *
31036173 TCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTATCTTCTGACTCGTGGTTCAATCCCA
66 TCTTTAATTTAAAATCATAATTTAATCTCGATTATTGTTATCTTCTGACTCGTGGTTCAATCCCA
* *
31036238 GTTTTCTTATTTTCAAACTTGTGATTCAATCCAAATTAACG
131 GTCTTCTTA-TTTCAAACTTGTGATTCAATCCAAATTAACA
* ** * *
31036279 TCATTTTCTGACTAACGATTTAATCTTGATCTTTTTA-TCTTCTGA-TTC-ATGATTCAATCTTG
1 TCATTTTTTGACTAACGATTTAATCTCAATCTTTTTACCCTTC-GATTTCTA-G-TTCAATCTCG
*
31036341 ATCTCTTTAATTTAAAATCATAATTTAATCTCGATTATTGTTATCTTCTTACTCGTGGTTCAATC
63 ATCTCTTTAATTTAAAATCATAATTTAATCTCGATTATTGTTATCTTCTGACTCGTGGTTCAATC
** * *
31036406 CTGGTCTTCTTATTTCGAACTTGTGATTCAATCCAAGTTAACA
128 CCAGTCTTCTTATTTCAAACTTGTGATTCAATCCAAATTAACA
** * *
31036449 TCATTTTTTGACTTGCGGTTTAATCCCAATC
1 TCATTTTTTGACTAACGATTTAATCTCAATC
31036480 ATTCCTATAA
Statistics
Matches: 175, Mismatches: 23, Indels: 7
0.85 0.11 0.03
Matches are distributed among these distances:
169 1 0.01
170 60 0.34
171 114 0.65
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (170 bp):
TCATTTTTTGACTAACGATTTAATCTCAATCTTTTTACCCTTCGATTTCTAGTTCAATCTCGATC
TCTTTAATTTAAAATCATAATTTAATCTCGATTATTGTTATCTTCTGACTCGTGGTTCAATCCCA
GTCTTCTTATTTCAAACTTGTGATTCAATCCAAATTAACA
Found at i:31042347 original size:3 final size:3
Alignment explanation
Indices: 31042339--31042371 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
31042329 TTAAAGTTTA
31042339 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31042372 CTCACCATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:31042742 original size:11 final size:11
Alignment explanation
Indices: 31042726--31042757 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
31042716 AAATCCCATA
31042726 AGAGATTTGTT
1 AGAGATTTGTT
31042737 AGAGATTTGTT
1 AGAGATTTGTT
*
31042748 TGAGATTTGT
1 AGAGATTTGT
31042758 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:31042869 original size:52 final size:52
Alignment explanation
Indices: 31042782--31042937 Score: 208
Period size: 51 Copynumber: 3.0 Consensus size: 52
31042772 TGGACAAGAA
* *
31042782 GACTTGCAAAAGAAGAATTCTAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGCAAGTTT
* * *
31042834 GACTTGTAAGAGAAGAATTTTAAAAGGAAAGGGATTCTTAATAGGCAAG-TT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
* * **
31042885 GACTTACAGGAGAAGAATTCTAAGAGGAGTGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
31042937 G
1 G
31042938 TATGGTTATA
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
51 44 0.49
52 41 0.46
53 5 0.06
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.27
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:31043469 original size:25 final size:25
Alignment explanation
Indices: 31043435--31043546 Score: 111
Period size: 25 Copynumber: 4.5 Consensus size: 25
31043425 AAATGATATC
*
31043435 AGAGCTGAAGGTTCGAAACGTGAAA
1 AGAGCTGAAGGTTCGAAATGTGAAA
* *
31043460 AGAGTTGAAGATTC-AAGATGTGAAA
1 AGAGCTGAAGGTTCGAA-ATGTGAAA
* * *
31043485 AAAGCCGAAGGTTCGAGATGTG-AA
1 AGAGCTGAAGGTTCGAAATGTGAAA
* * *
31043509 AGAGCTGAAAGTTCGAGATGTGAGA
1 AGAGCTGAAGGTTCGAAATGTGAAA
*
31043534 AGAGCTAAAGGTT
1 AGAGCTGAAGGTT
31043547 TGGGAAGTGC
Statistics
Matches: 70, Mismatches: 14, Indels: 6
0.78 0.16 0.07
Matches are distributed among these distances:
24 23 0.33
25 46 0.66
26 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.32, T:0.20
Consensus pattern (25 bp):
AGAGCTGAAGGTTCGAAATGTGAAA
Found at i:31043545 original size:49 final size:50
Alignment explanation
Indices: 31043435--31043546 Score: 129
Period size: 49 Copynumber: 2.3 Consensus size: 50
31043425 AAATGATATC
*
31043435 AGAGCTGAAGGTTCGAAACGTGAAAAGAGTTGAAGATTCAAGATGTGAAA
1 AGAGCTGAAGGTTCGAAACGTGAAAAGAGCTGAAGATTCAAGATGTGAAA
* * * * * *
31043485 AAAGCCGAAGGTTCGAGATGTG-AAAGAGCTGAA-AGTTCGAGATGTGAGA
1 AGAGCTGAAGGTTCGAAACGTGAAAAGAGCTGAAGA-TTCAAGATGTGAAA
*
31043534 AGAGCTAAAGGTT
1 AGAGCTGAAGGTT
31043547 TGGGAAGTGC
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
48 1 0.02
49 32 0.63
50 18 0.35
ACGTcount: A:0.39, C:0.09, G:0.32, T:0.20
Consensus pattern (50 bp):
AGAGCTGAAGGTTCGAAACGTGAAAAGAGCTGAAGATTCAAGATGTGAAA
Found at i:31043809 original size:11 final size:11
Alignment explanation
Indices: 31043793--31043824 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
31043783 AAATCCCATA
31043793 AGAGATTTGTT
1 AGAGATTTGTT
31043804 AGAGATTTGTT
1 AGAGATTTGTT
*
31043815 TGAGATTTGT
1 AGAGATTTGT
31043825 CAGATATTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (11 bp):
AGAGATTTGTT
Found at i:31043936 original size:52 final size:52
Alignment explanation
Indices: 31043849--31044005 Score: 217
Period size: 52 Copynumber: 3.0 Consensus size: 52
31043839 TGGACAAGAA
* *
31043849 GACTTGCAAAAGAAGAATTCTAAGA-GAAAGAGGATTCTTAATAGGTAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAG-GGATTCTTAATAGGCAAGTTT
* * *
31043901 GACTTGTAAGAGAAGAATTTTAAAAGGAAAGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
* * **
31043953 GACTTACAGGAGAAGAATTCTAAGAGGAGTGGGATTCTTAATAGGCAAGTTT
1 GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
31044005 G
1 G
31044006 TATGGTTATA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 87 0.95
53 5 0.05
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.27
Consensus pattern (52 bp):
GACTTGCAAGAGAAGAATTCTAAGAGGAAAGGGATTCTTAATAGGCAAGTTT
Found at i:31049169 original size:12 final size:13
Alignment explanation
Indices: 31049152--31049180 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
31049142 AACTTTGATA
31049152 ATTATCATTA-TC
1 ATTATCATTATTC
31049164 ATTATCATTATTC
1 ATTATCATTATTC
31049177 ATTA
1 ATTA
31049181 ATTAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTATCATTATTC
Found at i:31052608 original size:21 final size:22
Alignment explanation
Indices: 31052584--31052625 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
31052574 AAATTATCTT
*
31052584 ATCAACATAAAT-AATTTATTG
1 ATCAACAAAAATAAATTTATTG
*
31052605 ATCAATAAAAATAAATTTATT
1 ATCAACAAAAATAAATTTATT
31052626 TTTTTAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (22 bp):
ATCAACAAAAATAAATTTATTG
Found at i:31053209 original size:13 final size:14
Alignment explanation
Indices: 31053191--31053241 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 14
31053181 TATATGATTA
31053191 TTATTTTTTAA-TT
1 TTATTTTTTAACTT
31053204 TTATTTTTTATACTT
1 TTATTTTTTA-ACTT
*
31053219 ATATTTTGTATAACTT
1 TTATTTT-T-TAACTT
31053235 TTATTTT
1 TTATTTT
31053242 AAGACTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 10 0.31
14 1 0.03
15 8 0.25
16 11 0.34
17 2 0.06
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (14 bp):
TTATTTTTTAACTT
Found at i:31053223 original size:15 final size:15
Alignment explanation
Indices: 31053191--31053241 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
31053181 TATATGATTA
31053191 TTATTTTTTA-A-TT
1 TTATTTTTTATACTT
31053204 TTATTTTTTATACTT
1 TTATTTTTTATACTT
* *
31053219 ATATTTTGTATAACTT
1 TTATTTTTTAT-ACTT
31053235 TTATTTT
1 TTATTTT
31053242 AAGACTAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 10 0.31
14 1 0.03
15 11 0.34
16 10 0.31
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.71
Consensus pattern (15 bp):
TTATTTTTTATACTT
Found at i:31066140 original size:28 final size:25
Alignment explanation
Indices: 31066072--31066129 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
31066062 TCGTCGTCGA
31066072 AAAAATATTTATTATTTTTTTTGTT
1 AAAAATATTTATTATTTTTTTTGTT
31066097 AAAAATATTTATTATTTTTTTTGTT
1 AAAAATATTTATTATTTTTTTTGTT
31066122 AAAAATAT
1 AAAAATAT
31066130 ATCTAATTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (25 bp):
AAAAATATTTATTATTTTTTTTGTT
Found at i:31066522 original size:26 final size:23
Alignment explanation
Indices: 31066487--31066538 Score: 59
Period size: 26 Copynumber: 2.1 Consensus size: 23
31066477 ATCTAGAGAA
*
31066487 AATTTCTCATCTAGAGATTTCTTAAG
1 AATTTATCAT-TAGA-ATTT-TTAAG
*
31066513 AATTTATCATTTGAATTTTTAAG
1 AATTTATCATTAGAATTTTTAAG
31066536 AAT
1 AAT
31066539 CTCATTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.33
24 4 0.17
25 3 0.12
26 9 0.38
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.46
Consensus pattern (23 bp):
AATTTATCATTAGAATTTTTAAG
Found at i:31066865 original size:15 final size:15
Alignment explanation
Indices: 31066842--31066871 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31066832 AACACATAAA
*
31066842 TAAATAAAAAAACAT
1 TAAAAAAAAAAACAT
31066857 TAAAAAAAAAAACAT
1 TAAAAAAAAAAACAT
31066872 ACCAAAGGAC
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:0.77, C:0.07, G:0.00, T:0.17
Consensus pattern (15 bp):
TAAAAAAAAAAACAT
Found at i:31067868 original size:42 final size:42
Alignment explanation
Indices: 31067819--31068112 Score: 396
Period size: 42 Copynumber: 7.0 Consensus size: 42
31067809 AGTAAACAAA
31067819 GCTCCTCTAAATAGAGGCGAA-ACAACTTTGAAAAAATAAATT
1 GCTCCTCTAAATAGAGGC-AACACAACTTTGAAAAAATAAATT
* * ** *
31067861 GTTCCTCTAAATAGAGGTAACTTAACTTTGGAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATT
*
31067903 GCTCCTCTAAATAGAGGCAACATAACTTTGAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATT
* **
31067945 GCTCATCTAAATAGAGGCAACATGACTTT-AGAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACACAACTTTGA-AAAAATAAATT
* *
31067987 ACTCCTCTAAATAGAGGTAACACAACTTT-AGAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACACAACTTTGA-AAAAATAAATT
*
31068029 GCTCCTTTAAATAGAGGCAACACAACTTTGAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATT
* * * *
31068071 GCTTCTCGAAATAGAGGTAACATAACTTTGAAAAAATAAATT
1 GCTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATT
31068113 ACTTATTGAC
Statistics
Matches: 225, Mismatches: 24, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
41 3 0.01
42 221 0.98
43 1 0.00
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (42 bp):
GCTCCTCTAAATAGAGGCAACACAACTTTGAAAAAATAAATT
Found at i:31089625 original size:21 final size:21
Alignment explanation
Indices: 31089601--31089653 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
31089591 TATTATTGAT
31089601 TTTAATTTTATTATGATAATA
1 TTTAATTTTATTATGATAATA
* * *
31089622 TTTAATCTCATTATTATAATA
1 TTTAATTTTATTATGATAATA
* *
31089643 ATTAGTTTTAT
1 TTTAATTTTAT
31089654 CTTTATTATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (21 bp):
TTTAATTTTATTATGATAATA
Found at i:31089659 original size:24 final size:22
Alignment explanation
Indices: 31089601--31089662 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
31089591 TATTATTGAT
*
31089601 TTTAAT-TTTATTATGATAATA
1 TTTAATCTTTATTATAATAATA
31089622 TTTAATCTCATTATTATAATAATTA
1 TTTAATCT--TTATTATAATAA-TA
*
31089647 GTTTTATCTTTATTAT
1 -TTTAATCTTTATTAT
31089663 TATTTTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
21 6 0.18
22 1 0.03
24 18 0.53
25 2 0.06
26 7 0.21
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (22 bp):
TTTAATCTTTATTATAATAATA
Found at i:31090339 original size:7 final size:7
Alignment explanation
Indices: 31090329--31090362 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
31090319 TTTTAAAAAA
31090329 TAATATT
1 TAATATT
31090336 TAATAAATT
1 TAAT--ATT
31090345 TAATATT
1 TAATATT
31090352 TAATATT
1 TAATATT
31090359 TAAT
1 TAAT
31090363 TTTTTTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 18 0.72
9 7 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (7 bp):
TAATATT
Found at i:31090348 original size:16 final size:16
Alignment explanation
Indices: 31090312--31090356 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
31090302 TGATTTATGT
*
31090312 ATTTAATTTTTAA-AA
1 ATTTAATATTTAATAA
*
31090327 A-ATAATATTTAATAA
1 ATTTAATATTTAATAA
31090342 ATTTAATATTTAATA
1 ATTTAATATTTAATA
31090357 TTTAATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 9 0.36
15 4 0.16
16 12 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTAATATTTAATAA
Found at i:31097822 original size:68 final size:70
Alignment explanation
Indices: 31097713--31097851 Score: 230
Period size: 68 Copynumber: 2.0 Consensus size: 70
31097703 CGTCCGTACA
*
31097713 TCGATTAATATTATACTGTTTTTTGAAAATTTTAATTCTTA-TT-TGATCTTTTAGGGTTAAAAA
1 TCGATTAATATTATACTGTTTTTTGAAAATTTTAATTCTTATTTATGATATTTTAGGGTTAAAAA
31097776 TTGAT
66 TTGAT
*
31097781 TCGATTAATATTATACTGTTTTTTGAAAA-TTTATGTTCTTATTTATGATATTTTAGGGTTAAAA
1 TCGATTAATATTATACTGTTTTTTGAAAATTTTA-ATTCTTATTTATGATATTTTAGGGTTAAAA
31097845 ATTGAT
65 ATTGAT
31097851 T
1 T
31097852 TTTTTTAAAA
Statistics
Matches: 66, Mismatches: 2, Indels: 4
0.92 0.03 0.06
Matches are distributed among these distances:
67 4 0.06
68 35 0.53
69 2 0.03
70 25 0.38
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (70 bp):
TCGATTAATATTATACTGTTTTTTGAAAATTTTAATTCTTATTTATGATATTTTAGGGTTAAAAA
TTGAT
Found at i:31103684 original size:17 final size:17
Alignment explanation
Indices: 31103658--31103691 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31103648 TTAAACATAT
*
31103658 TATTTCAAAATCAATAA
1 TATTTCAAAATAAATAA
*
31103675 TATTTTAAAATAAATAA
1 TATTTCAAAATAAATAA
31103692 AAAATAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
TATTTCAAAATAAATAA
Found at i:31105622 original size:16 final size:17
Alignment explanation
Indices: 31105591--31105633 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
31105581 GATATATTAA
31105591 AATATTTAAA-ACTATT
1 AATATTTAAATACTATT
31105607 AATATTTAAATA-TATT
1 AATATTTAAATACTATT
*
31105623 AA-AATTAAATA
1 AATATTTAAATA
31105634 AAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 16 0.64
17 1 0.04
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATTTAAATACTATT
Found at i:31106683 original size:22 final size:22
Alignment explanation
Indices: 31106658--31106729 Score: 92
Period size: 22 Copynumber: 3.2 Consensus size: 22
31106648 TCCGAAATTA
31106658 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
31106680 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
* * *
31106701 ATAAATATATAATTATATAAATAT
1 ATAAA-ATATTATTTTTTAAA-AT
31106725 ATAAA
1 ATAAA
31106730 TAAAAAATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
21 9 0.20
22 26 0.59
23 2 0.05
24 7 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:31106712 original size:8 final size:8
Alignment explanation
Indices: 31106699--31106731 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
31106689 TATTTTTTAA
31106699 ATATAAAT
1 ATATAAAT
*
31106707 ATATAATT
1 ATATAAAT
31106715 ATATAAAT
1 ATATAAAT
31106723 ATATAAAT
1 ATATAAAT
31106731 A
1 A
31106732 AAAAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATAAAT
Found at i:31107034 original size:16 final size:16
Alignment explanation
Indices: 31107015--31107060 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
31107005 AAAAATTAAT
31107015 AATTTAAATTTAAATA
1 AATTTAAATTTAAATA
*
31107031 AATTTAAA-TGAAA-A
1 AATTTAAATTTAAATA
*
31107045 ATATTTAAATATAAAT
1 A-ATTTAAATTTAAAT
31107061 GCTTTGAAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
14 2 0.08
15 11 0.46
16 11 0.46
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:31116564 original size:16 final size:18
Alignment explanation
Indices: 31116543--31116575 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
31116533 CACAAACTTT
31116543 ACAAAA-AAAA-AAAAAG
1 ACAAAATAAAACAAAAAG
31116559 ACAAAATAAAACAAAAA
1 ACAAAATAAAACAAAAA
31116576 TATTTCTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.85, C:0.09, G:0.03, T:0.03
Consensus pattern (18 bp):
ACAAAATAAAACAAAAAG
Found at i:31120717 original size:2 final size:2
Alignment explanation
Indices: 31120712--31120740 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31120702 AGATTAACAA
31120712 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31120741 CATACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31121070 original size:48 final size:49
Alignment explanation
Indices: 31121005--31121131 Score: 157
Period size: 48 Copynumber: 2.6 Consensus size: 49
31120995 CAGAAGTCAC
* * *
31121005 CTTATCCAGATGCTGTTCCTCTTTATTGTTTAAGATAGCAGT-AGGTGT
1 CTTATCCAGATGATGTTCCTCTTCATTATTTAAGATAGCAGTAAGGTGT
* * *
31121053 CTTATCCGGATGATGTTCCTCTTCATTATTTATGATATCAGTAGAAGGTGT
1 CTTATCCAGATGATGTTCCTCTTCATTATTTAAGATAGCAGT--AAGGTGT
* *
31121104 CTTATCAAGATGACGTTCCTCTTCATTA
1 CTTATCCAGATGATGTTCCTCTTCATTA
31121132 GTTATGACTT
Statistics
Matches: 67, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 36 0.54
51 31 0.46
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.41
Consensus pattern (49 bp):
CTTATCCAGATGATGTTCCTCTTCATTATTTAAGATAGCAGTAAGGTGT
Found at i:31121107 original size:51 final size:48
Alignment explanation
Indices: 31121005--31121138 Score: 160
Period size: 51 Copynumber: 2.7 Consensus size: 48
31120995 CAGAAGTCAC
* * * *
31121005 CTTATCCAGATGCTGTTCCTCTTTATTGTTTAAGATAGCAGTAGGTGT
1 CTTATCCAGATGATGTTCCTCTTCATTATTTATGATAGCAGTAGGTGT
* *
31121053 CTTATCCGGATGATGTTCCTCTTCATTATTTATGATATCAGTAGAAGGTGT
1 CTTATCCAGATGATGTTCCTCTTCATTATTTATGATAGCAGT---AGGTGT
* * *
31121104 CTTATCAAGATGACGTTCCTCTTCATTAGTTATGA
1 CTTATCCAGATGATGTTCCTCTTCATTATTTATGA
31121139 CTTCCCTTCG
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
48 36 0.49
51 37 0.51
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (48 bp):
CTTATCCAGATGATGTTCCTCTTCATTATTTATGATAGCAGTAGGTGT
Found at i:31123922 original size:25 final size:26
Alignment explanation
Indices: 31123856--31123923 Score: 72
Period size: 24 Copynumber: 2.8 Consensus size: 26
31123846 AATATAATTG
*
31123856 TTATACATTTA-ATAAT-TTAATAAT
1 TTATATATTTATATAATATTAATAAT
* *
31123880 TTATAT-TATATAAAATATTAA-AAT
1 TTATATATTTATATAATATTAATAAT
*
31123904 TTATATATTTATATTATATT
1 TTATATATTTATATAATATT
31123924 TTATGCAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
23 3 0.09
24 18 0.51
25 14 0.40
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (26 bp):
TTATATATTTATATAATATTAATAAT
Found at i:31127187 original size:3 final size:3
Alignment explanation
Indices: 31127179--31127224 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
31127169 TCAAGCCATA
31127179 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
31127225 TTCTCTAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31137532 original size:2 final size:2
Alignment explanation
Indices: 31137527--31137563 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31137517 CACACACACG
31137527 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
31137564 TTACTATTAG
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:31140294 original size:2 final size:2
Alignment explanation
Indices: 31140289--31140328 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
31140279 ATCAAAAAAA
*
31140289 TC TC TC CC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31140329 GGGAAAGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:31140666 original size:6 final size:6
Alignment explanation
Indices: 31140651--31140682 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
31140641 CCCTCACCTT
31140651 CACAAGC CACAAC CACAAC CACAAC CACAAC C
1 CACAA-C CACAAC CACAAC CACAAC CACAAC C
31140683 CTTCATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.47, C:0.50, G:0.03, T:0.00
Consensus pattern (6 bp):
CACAAC
Found at i:31141929 original size:3 final size:3
Alignment explanation
Indices: 31141921--31141950 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31141911 ATTGTAGAGG
31141921 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
31141951 GGATACAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:31143311 original size:15 final size:15
Alignment explanation
Indices: 31143293--31143494 Score: 104
Period size: 15 Copynumber: 13.5 Consensus size: 15
31143283 CAATTTATGC
31143293 AACTGCAGCTCATGT
1 AACTGCAGCTCATGT
* * *
31143308 AACTGCAGGTCCTGC
1 AACTGCAGCTCATGT
31143323 AA-TAGCAGCTCATGT
1 AACT-GCAGCTCATGT
* * *
31143338 GACTGCAGTTCATGC
1 AACTGCAGCTCATGT
* *
31143353 AAATGCAGCTCGTGT
1 AACTGCAGCTCATGT
* * *
31143368 GATTGCAGATCATGT
1 AACTGCAGCTCATGT
* * *
31143383 AAATGCA-TTCCCTGT
1 AACTGCAGCT-CATGT
* *
31143398 GACTGCAGATCATGT
1 AACTGCAGCTCATGT
* * *
31143413 AAATGCATCTCTTGT
1 AACTGCAGCTCATGT
* * *
31143428 GACTGCAGATCGTGT
1 AACTGCAGCTCATGT
* *
31143443 AAATGCATCTCATGT
1 AACTGCAGCTCATGT
* *
31143458 GACTGCAGTTCATGT
1 AACTGCAGCTCATGT
* *
31143473 AAATGCTA-TTCATGT
1 AACTGC-AGCTCATGT
31143488 AACTGCA
1 AACTGCA
31143495 ATCCCATTTC
Statistics
Matches: 134, Mismatches: 48, Indels: 11
0.69 0.25 0.06
Matches are distributed among these distances:
14 3 0.02
15 128 0.96
16 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (15 bp):
AACTGCAGCTCATGT
Found at i:31143375 original size:60 final size:59
Alignment explanation
Indices: 31143275--31143478 Score: 212
Period size: 60 Copynumber: 3.4 Consensus size: 59
31143265 CTGTAATATG
* * * * * * *
31143275 TGTGACTGCAATTTATGCAACTGCAGCTCATGTAACTGCAGGTCCTG-CAATAGCAGCTCA
1 TGTGACTGCAGTTCATGCAAATGCAGCTCATGTGACTGCAGATCATGTAAAT-GCA-CTCA
* * * *
31143335 TGTGACTGCAGTTCATGCAAATGCAGCTCGTGTGATTGCAGATCATGTAAATGCATTCCC
1 TGTGACTGCAGTTCATGCAAATGCAGCTCATGTGACTGCAGATCATGTAAATGCACT-CA
* * * * *
31143395 TGTGACTGCAGATCATGTAAATGCATCTCTTGTGACTGCAGATCGTGTAAATGCATCTCA
1 TGTGACTGCAGTTCATGCAAATGCAGCTCATGTGACTGCAGATCATGTAAATGCA-CTCA
*
31143455 TGTGACTGCAGTTCATGTAAATGC
1 TGTGACTGCAGTTCATGCAAATGC
31143479 TATTCATGTA
Statistics
Matches: 121, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 116 0.96
61 4 0.03
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.30
Consensus pattern (59 bp):
TGTGACTGCAGTTCATGCAAATGCAGCTCATGTGACTGCAGATCATGTAAATGCACTCA
Found at i:31155116 original size:6 final size:6
Alignment explanation
Indices: 31155105--31155129 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
31155095 GAGAGGAAGT
31155105 GGTTAG GGTTAG GGTTAG GGTTAG G
1 GGTTAG GGTTAG GGTTAG GGTTAG G
31155130 CACCCCAGGC
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:0.16, C:0.00, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTTAG
Found at i:31160298 original size:13 final size:13
Alignment explanation
Indices: 31160263--31160298 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
31160253 TATAAGTCTC
* *
31160263 TAAAATAAAAATG
1 TAAAATAAATATA
31160276 TAAAATAAATATA
1 TAAAATAAATATA
31160289 TAAAATAAAT
1 TAAAATAAAT
31160299 GCATATAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (13 bp):
TAAAATAAATATA
Found at i:31160577 original size:13 final size:13
Alignment explanation
Indices: 31160559--31160584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31160549 CATCTACTTC
31160559 ATAAAAAATAAAA
1 ATAAAAAATAAAA
31160572 ATAAAAAATAAAA
1 ATAAAAAATAAAA
31160585 TCTTAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
ATAAAAAATAAAA
Found at i:31160689 original size:29 final size:29
Alignment explanation
Indices: 31160630--31160689 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
31160620 AAACCATAGT
* *
31160630 AAAATATTTAATATTATATTTAAATTTTA
1 AAAATATTTAATATGATATTTAAATTATA
* *
31160659 AAAATTTTTAATATGATATTTAAGTTATA
1 AAAATATTTAATATGATATTTAAATTATA
31160688 AA
1 AA
31160690 TTTATTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (29 bp):
AAAATATTTAATATGATATTTAAATTATA
Found at i:31161636 original size:183 final size:183
Alignment explanation
Indices: 31161328--31161689 Score: 591
Period size: 183 Copynumber: 2.0 Consensus size: 183
31161318 CCCATATTAT
*
31161328 ATGATTAATATTGTATGCTTCATAATTTGTCTAGTCAAGTAGTATATTCGAAAAATTACTTTAAA
1 ATGATTAATATTGTATGCTTCATAATTTGTCTAGTCAAGTAGTATATCCGAAAAATTACTTTAAA
* * * *
31161393 CACATGTATCATGCTATGTGAGTAAAGACTTTGAGTCTTTGATTTATACATTTTATAACAATTTT
66 AACATGTATCATACTATGTGAGTAAAGACTTGGAGTCTTTGATTTATACATTTTATAACAAATTT
*
31161458 TTAGAATATTTAAATTTTTACAATTAAAAATATTGTATATTATTTTATATTTC
131 TTAAAATATTTAAATTTTTACAATTAAAAATATTGTATATTATTTTATATTTC
* * *
31161511 ATGATTAATATTGTTTGCTTTATAATTTGTCTAGTCAAGTAGTATATCCGACAAATTACTTTAAA
1 ATGATTAATATTGTATGCTTCATAATTTGTCTAGTCAAGTAGTATATCCGAAAAATTACTTTAAA
* * *
31161576 AACATGTGTCATAC-ACTTTGGGTAAAGACTTGGAGTCTTTGATTTATACATTTTATAACAAATT
66 AACATGTATCATACTA-TGTGAGTAAAGACTTGGAGTCTTTGATTTATACATTTTATAACAAATT
*
31161640 TTTAAAATATTTAATTTTTTACAATTAAAAATATTGTATATTATTTTATA
130 TTTAAAATATTTAAATTTTTACAATTAAAAATATTGTATATTATTTTATA
31161690 ATTTGTTTTG
Statistics
Matches: 165, Mismatches: 13, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
182 1 0.01
183 164 0.99
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (183 bp):
ATGATTAATATTGTATGCTTCATAATTTGTCTAGTCAAGTAGTATATCCGAAAAATTACTTTAAA
AACATGTATCATACTATGTGAGTAAAGACTTGGAGTCTTTGATTTATACATTTTATAACAAATTT
TTAAAATATTTAAATTTTTACAATTAAAAATATTGTATATTATTTTATATTTC
Found at i:31161674 original size:24 final size:27
Alignment explanation
Indices: 31161643--31161692 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
31161633 ACAAATTTTT
31161643 AAAATATT-TA-ATT-TTTTACAATTA
1 AAAATATTGTATATTATTTTACAATTA
*
31161667 AAAATATTGTATATTATTTTATAATT
1 AAAATATTGTATATTATTTTACAATT
31161693 TGTTTTGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 8 0.36
25 2 0.09
26 3 0.14
27 9 0.41
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
AAAATATTGTATATTATTTTACAATTA
Found at i:31161769 original size:20 final size:19
Alignment explanation
Indices: 31161744--31161782 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
31161734 GATATTTTAT
31161744 AAAAGAAAGGTTATAATTAA
1 AAAAG-AAGGTTATAATTAA
*
31161764 AAAAGAATGTTATAATTAA
1 AAAAGAAGGTTATAATTAA
31161783 CCATTCTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.59, C:0.00, G:0.13, T:0.28
Consensus pattern (19 bp):
AAAAGAAGGTTATAATTAA
Found at i:31163664 original size:21 final size:24
Alignment explanation
Indices: 31163629--31163675 Score: 64
Period size: 21 Copynumber: 2.1 Consensus size: 24
31163619 AATTTTTTAT
*
31163629 TTTTTATATATTATTTTAATA-AA
1 TTTTTATATATTATTTAAATAGAA
31163652 TTTTTA-ATA-TATTTAAATAGAA
1 TTTTTATATATTATTTAAATAGAA
31163674 TT
1 TT
31163676 AGATATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 9 0.41
22 7 0.32
23 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTTTATATATTATTTAAATAGAA
Found at i:31168763 original size:2 final size:2
Alignment explanation
Indices: 31168756--31168791 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
31168746 CAATAACTTC
31168756 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31168792 AAAGATTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31181486 original size:2 final size:2
Alignment explanation
Indices: 31181479--31181503 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31181469 AGAAAAGTTT
31181479 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 T
31181504 CTTAATTGTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31191005 original size:15 final size:16
Alignment explanation
Indices: 31190985--31191014 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31190975 AATTATTTAA
31190985 AATTTTAA-AAATAAT
1 AATTTTAATAAATAAT
31191000 AATTTTAATAAATAA
1 AATTTTAATAAATAA
31191015 ATAAATAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTTTAATAAATAAT
Found at i:31205887 original size:11 final size:12
Alignment explanation
Indices: 31205848--31205890 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 12
31205838 AATTTAATAA
31205848 AAATAATACATT
1 AAATAATACATT
**
31205860 AAATATATATTTT
1 AAATA-ATACATT
31205873 AAATAATA-ATT
1 AAATAATACATT
31205884 AAATAAT
1 AAATAAT
31205891 TCTTAACCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 9 0.33
12 8 0.30
13 10 0.37
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAATACATT
Found at i:31214401 original size:2 final size:2
Alignment explanation
Indices: 31214389--31214462 Score: 121
Period size: 2 Copynumber: 37.0 Consensus size: 2
31214379 TTTATACTTC
*
31214389 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
31214431 AT AT GT AT AT AC 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
31214463 GGCGATAAGA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31215136 original size:11 final size:11
Alignment explanation
Indices: 31215120--31215144 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
31215110 AGGTTGATGT
31215120 AAAGAGTTAGA
1 AAAGAGTTAGA
31215131 AAAGAGTTAGA
1 AAAGAGTTAGA
31215142 AAA
1 AAA
31215145 TCGATCTAGT
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:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (11 bp):
AAAGAGTTAGA
Found at i:31221733 original size:12 final size:10
Alignment explanation
Indices: 31221709--31221746 Score: 51
Period size: 11 Copynumber: 3.7 Consensus size: 10
31221699 TGCTGACACG
31221709 TAATTTTTTT
1 TAATTTTTTT
31221719 TAAATTTTTTAT
1 T-AATTTTTT-T
31221731 TAATTTTTTT
1 TAATTTTTTT
31221741 T-ATTTT
1 TAATTTT
31221747 AGATATGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 16 0.62
12 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TAATTTTTTT
Found at i:31229268 original size:19 final size:19
Alignment explanation
Indices: 31229244--31229287 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
31229234 CAGCTGAGGT
31229244 AAATATCTAATCTATCTGC
1 AAATATCTAATCTATCTGC
31229263 AAATATCTAATCTATCTGC
1 AAATATCTAATCTATCTGC
31229282 AAATAT
1 AAATAT
31229288 AGCTAGCGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (19 bp):
AAATATCTAATCTATCTGC
Found at i:31230220 original size:19 final size:20
Alignment explanation
Indices: 31230171--31230222 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
31230161 TAAATTAATT
31230171 AAAATTAATATATTTATATTTAA
1 AAAATT-ATATATTTATA--TAA
*
31230194 TAAA-TATATATTTATA-AA
1 AAAATTATATATTTATATAA
31230212 AAAATTATATA
1 AAAATTATATA
31230223 AATATTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
18 5 0.19
19 6 0.23
21 11 0.42
22 1 0.04
23 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATTATATATTTATATAA
Found at i:31232020 original size:61 final size:61
Alignment explanation
Indices: 31231945--31232063 Score: 238
Period size: 61 Copynumber: 2.0 Consensus size: 61
31231935 AAATTGATCT
31231945 GTCCAAAGAAAAATGGACTCGGTGAAAGCTAATCGACTAGGAATAATCTTGGTGTCACACG
1 GTCCAAAGAAAAATGGACTCGGTGAAAGCTAATCGACTAGGAATAATCTTGGTGTCACACG
31232006 GTCCAAAGAAAAATGGACTCGGTGAAAGCTAATCGACTAGGAATAATCTTGGTGTCAC
1 GTCCAAAGAAAAATGGACTCGGTGAAAGCTAATCGACTAGGAATAATCTTGGTGTCAC
31232064 TAGGACGCGT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (61 bp):
GTCCAAAGAAAAATGGACTCGGTGAAAGCTAATCGACTAGGAATAATCTTGGTGTCACACG
Found at i:31236285 original size:21 final size:20
Alignment explanation
Indices: 31236260--31236307 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
31236250 GTCAATATAT
*
31236260 TATATTTTATATAAAAAATCA
1 TATATTTTAAATAAAAAAT-A
* *
31236281 TATATTATAAATATAAAATA
1 TATATTTTAAATAAAAAATA
31236301 TATATTT
1 TATATTT
31236308 AATTTTACTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TATATTTTAAATAAAAAATA
Found at i:31236991 original size:17 final size:18
Alignment explanation
Indices: 31236969--31237004 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
31236959 ACTAATAAAC
31236969 TTAA-TTATATATTTTTA
1 TTAATTTATATATTTTTA
31236986 TTAATTTTATATATTTTTA
1 TTAA-TTTATATATTTTTA
31237005 AATTTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
19 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTAATTTATATATTTTTA
Found at i:31237003 original size:10 final size:10
Alignment explanation
Indices: 31236973--31237013 Score: 50
Period size: 9 Copynumber: 4.3 Consensus size: 10
31236963 ATAAACTTAA
31236973 TTATATATTT
1 TTATATATTT
*
31236983 TTAT-TAATT
1 TTATATATTT
31236992 TTATATATTT
1 TTATATATTT
*
31237002 TTAAAT-TTT
1 TTATATATTT
31237011 TTA
1 TTA
31237014 AAATAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 14 0.52
10 13 0.48
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATATATTT
Found at i:31237008 original size:17 final size:18
Alignment explanation
Indices: 31236973--31237010 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
31236963 ATAAACTTAA
31236973 TTATATATTTTTATTAATT
1 TTATATATTTTTA-TAATT
31236992 TTATATATTTTTA-AATT
1 TTATATATTTTTATAATT
31237009 TT
1 TT
31237011 TTAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTATATATTTTTATAATT
Found at i:31237057 original size:22 final size:24
Alignment explanation
Indices: 31237011--31237073 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
31237001 TTTAAATTTT
* * *
31237011 TTAAAATAAAATAAAAATATTATA
1 TTAAAATAATATATAAACATTATA
*
31237035 TTTAAAT-ATAT-TAAACATTATA
1 TTAAAATAATATATAAACATTATA
31237057 TTAAAATAATATATAAA
1 TTAAAATAATATATAAA
31237074 AATAAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 15 0.47
23 7 0.22
24 10 0.31
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAATAATATATAAACATTATA
Found at i:31237130 original size:12 final size:12
Alignment explanation
Indices: 31237113--31237141 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
31237103 CATATAAAAA
31237113 TTTAATTTAAAT
1 TTTAATTTAAAT
31237125 TTTAA-TTAAAT
1 TTTAATTTAAAT
31237136 TTTAAT
1 TTTAAT
31237142 GATTTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
TTTAATTTAAAT
Found at i:31237190 original size:16 final size:16
Alignment explanation
Indices: 31237171--31237201 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31237161 CATAAAAAAA
*
31237171 TTAAATCAAATTCAAT
1 TTAAATCAAAATCAAT
31237187 TTAAATCAAAATCAA
1 TTAAATCAAAATCAA
31237202 AATCATTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (16 bp):
TTAAATCAAAATCAAT
Found at i:31237912 original size:22 final size:22
Alignment explanation
Indices: 31237885--31237937 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
31237875 ATTTGATAAA
*
31237885 AATTTATTAATCAATACAAAAT
1 AATTTATTAATCAATAAAAAAT
*
31237907 AATTTAATAATCAATAAAAAAT
1 AATTTATTAATCAATAAAAAAT
*
31237929 -ATTTTTTAA
1 AATTTATTAA
31237938 AATTAATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 7 0.26
22 20 0.74
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.40
Consensus pattern (22 bp):
AATTTATTAATCAATAAAAAAT
Found at i:31266351 original size:97 final size:97
Alignment explanation
Indices: 31266204--31266397 Score: 352
Period size: 97 Copynumber: 2.0 Consensus size: 97
31266194 GCATAATATT
*
31266204 CATCGATTTCTGCAAAACAAAAATACTACAATCAAATCATGCAGATAACAATTTATCAGTTAAAA
1 CATCGATTTCTGCAAAACAAAAATACTACAATCAAATCATGCAGATAACAACTTATCAGTTAAAA
31266269 CAAATTCAATAAAATCAGTAACATCGAAGTAC
66 CAAATTCAATAAAATCAGTAACATCGAAGTAC
* *
31266301 CATCGATTTCTTCAAAACAAAAATAGTACAATCAAATCATGCAGATAACAACTTATCAGTTAAAA
1 CATCGATTTCTGCAAAACAAAAATACTACAATCAAATCATGCAGATAACAACTTATCAGTTAAAA
*
31266366 CAAATTCAATAAGATCAGTAACATCGAAGTAC
66 CAAATTCAATAAAATCAGTAACATCGAAGTAC
31266398 TAAAGTAAGG
Statistics
Matches: 93, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
97 93 1.00
ACGTcount: A:0.48, C:0.19, G:0.09, T:0.25
Consensus pattern (97 bp):
CATCGATTTCTGCAAAACAAAAATACTACAATCAAATCATGCAGATAACAACTTATCAGTTAAAA
CAAATTCAATAAAATCAGTAACATCGAAGTAC
Found at i:31268342 original size:18 final size:19
Alignment explanation
Indices: 31268304--31268338 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
31268294 AGTGGGTAGA
31268304 GTTCATTGCATTTTTGGAT
1 GTTCATTGCATTTTTGGAT
31268323 GTTCA-TGC-TTTTTGGA
1 GTTCATTGCATTTTTGGA
31268339 ATGTCAAGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 3 0.19
19 5 0.31
ACGTcount: A:0.14, C:0.11, G:0.23, T:0.51
Consensus pattern (19 bp):
GTTCATTGCATTTTTGGAT
Found at i:31278213 original size:34 final size:34
Alignment explanation
Indices: 31278175--31278244 Score: 81
Period size: 34 Copynumber: 2.1 Consensus size: 34
31278165 TATTATATAT
31278175 TAATAAATAATAT-TTATATT-TTAATAAATATAAA
1 TAAT-AATAATATATTATATTATTAA-AAATATAAA
* * *
31278209 TAATAATTATTTATTATATTATTAAATATATAAA
1 TAATAATAATATATTATATTATTAAAAATATAAA
31278243 TA
1 TA
31278245 TTATTTCTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
33 6 0.19
34 21 0.68
35 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (34 bp):
TAATAATAATATATTATATTATTAAAAATATAAA
Found at i:31278220 original size:31 final size:32
Alignment explanation
Indices: 31278171--31278250 Score: 80
Period size: 31 Copynumber: 2.6 Consensus size: 32
31278161 TAATTATTAT
*
31278171 ATATTAATAAATAA-TATTTATAT-T-TTAATAA
1 ATATAAAT-AATAATTATTTAT-TATATTAATAA
*
31278202 ATATAAATAATAATTATTTATTATATTATTAA
1 ATATAAATAATAATTATTTATTATATTAATAA
*
31278234 ATATATA-AAT-ATTATTT
1 ATATAAATAATAATTATTT
31278251 CTAACTATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
30 13 0.30
31 18 0.42
32 12 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (32 bp):
ATATAAATAATAATTATTTATTATATTAATAA
Found at i:31278452 original size:17 final size:17
Alignment explanation
Indices: 31278427--31278463 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
31278417 AAGTTTGAAT
31278427 TTTAAATTTTTAAAATA
1 TTTAAATTTTTAAAATA
* *
31278444 TTTATATTTTTATAATA
1 TTTAAATTTTTAAAATA
31278461 TTT
1 TTT
31278464 TTTATTAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAATTTTTAAAATA
Found at i:31279411 original size:13 final size:13
Alignment explanation
Indices: 31279390--31279439 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
31279380 TAGTCACGAA
*
31279390 ATAATAATATAAT
1 ATAAAAATATAAT
*
31279403 ATAAAAATATATT
1 ATAAAAATATAAT
31279416 ATTAAAAAT-TAAT
1 A-TAAAAATATAAT
31279429 A-AAAATATATA
1 ATAAAA-ATATA
31279440 TTTGATAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
11 4 0.13
12 2 0.06
13 18 0.58
14 7 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAAAAATATAAT
Found at i:31279438 original size:26 final size:26
Alignment explanation
Indices: 31279403--31279478 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 26
31279393 ATAATATAAT
*
31279403 ATAAAAATATAT-TAT-TAAAAATTA
1 ATAAAAATATATATTTATAAAAATTA
31279427 ATAAAAATATATATTTGATAAAAATTA
1 ATAAAAATATATATTT-ATAAAAATTA
* *
31279454 A-AAAAA-AT-TAGTTATAAATATTA
1 ATAAAAATATATATTTATAAAAATTA
31279477 AT
1 AT
31279479 TATGCTATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
23 10 0.22
24 16 0.36
25 4 0.09
26 5 0.11
27 10 0.22
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (26 bp):
ATAAAAATATATATTTATAAAAATTA
Found at i:31279470 original size:23 final size:24
Alignment explanation
Indices: 31279390--31279478 Score: 83
Period size: 27 Copynumber: 3.5 Consensus size: 24
31279380 TAGTCACGAA
*
31279390 ATAATAATATAATATAAAAATATATT
1 ATAAAAAT-TAATA-AAAAATATATT
31279416 ATTAAAAATTAATAAAAATATATATTT
1 A-TAAAAATTAATAAAAA-ATATA-TT
31279443 GATAAAAATTAA-AAAAAAT-TAGTT
1 -ATAAAAATTAATAAAAAATATA-TT
*
31279467 ATAAATATTAAT
1 ATAAAAATTAAT
31279479 TATGCTATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
23 10 0.18
24 4 0.07
25 6 0.11
26 16 0.29
27 18 0.33
28 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
ATAAAAATTAATAAAAAATATATT
Found at i:31280194 original size:23 final size:24
Alignment explanation
Indices: 31280168--31280223 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
31280158 TTGATAAAAT
* *
31280168 TATAAAGAAA-TTAATTTTTTTAA
1 TATAAAGAAATTTAATCTTCTTAA
31280191 TATAAA-AAATTTAATCTTCTTAA
1 TATAAAGAAATTTAATCTTCTTAA
*
31280214 AATAAAGAAA
1 TATAAAGAAA
31280224 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 22 0.79
24 3 0.11
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (24 bp):
TATAAAGAAATTTAATCTTCTTAA
Found at i:31280321 original size:16 final size:17
Alignment explanation
Indices: 31280302--31280339 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
31280292 AAATTATATA
*
31280302 AAATTTGAAGAAT-AAT
1 AAATTTGAACAATAAAT
*
31280318 AAATTTGATCAATAAAT
1 AAATTTGAACAATAAAT
31280335 AAATT
1 AAATT
31280340 ATTTTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.55, C:0.03, G:0.08, T:0.34
Consensus pattern (17 bp):
AAATTTGAACAATAAAT
Found at i:31284153 original size:2 final size:2
Alignment explanation
Indices: 31284142--31284180 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
31284132 ACCCTCCCCC
*
31284142 CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
31284181 GCAGATGGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
CT
Found at i:31290575 original size:19 final size:18
Alignment explanation
Indices: 31290517--31290574 Score: 68
Period size: 19 Copynumber: 3.3 Consensus size: 18
31290507 TAAATATAAA
31290517 ATATAAAAT-TTTAAATT
1 ATATAAAATATTTAAATT
31290534 AT-TAAAAATTATTTAAATT
1 ATAT-AAAA-TATTTAAATT
*
31290553 ATATAAAATAATTAAATT
1 ATATAAAATATTTAAATT
31290571 -TATA
1 ATATA
31290575 TTTATATTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
16 1 0.03
17 10 0.28
18 10 0.28
19 14 0.39
20 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATAAAATATTTAAATT
Found at i:31296347 original size:58 final size:59
Alignment explanation
Indices: 31296257--31296599 Score: 403
Period size: 59 Copynumber: 5.9 Consensus size: 59
31296247 TCTTGTGTAG
* * *
31296257 GAAAAATTGATACTTTTAATTTTTTCTCAAAAAATATTTTTTT-AAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTGAAAATTTATTTTTAA
* * * *
31296315 GAAAAATTGATACTTTCAATTTTTCC-CCAAAAATATTTTTTTGAAATTTTGATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTGAAAATTT-ATTTTTAA
* **
31296374 -AGAAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTTTTAAATTTATTTTTAA
1 GA-AAAATTGATACTTTCAACTTTTCCTCAAAAA-ATATTTTTTTGAAAATTTATTTTTAA
* * * *
31296433 GAAAAATTGATATTTTCAACTTTTCTTC-AAAAATATTTTTTTGAAATTTTGATTTTCAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTGAAAATTT-ATTTTTAA
* * * ***
31296492 GGAAAATTGATAATTTCAATTTTTCCTC-AAAAACCCTTTTTTGAAAATTTATTTTTAA
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTGAAAATTTATTTTTAA
* *
31296550 GAAAAATTAATACTTTCAACTTTTCC-CTAAAAATATTTTTTTGAAAATTT
1 GAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTGAAAATTT
31296600 TGATTTTAAT
Statistics
Matches: 241, Mismatches: 35, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
57 17 0.07
58 95 0.39
59 110 0.46
60 18 0.07
61 1 0.00
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.48
Consensus pattern (59 bp):
GAAAAATTGATACTTTCAACTTTTCCTCAAAAAATATTTTTTTGAAAATTTATTTTTAA
Found at i:31296450 original size:118 final size:118
Alignment explanation
Indices: 31296259--31296606 Score: 529
Period size: 118 Copynumber: 3.0 Consensus size: 118
31296249 TTGTGTAGGA
* * *
31296259 AAAATTGATACTTTTAATTTTTTCTCAAAAA-ATATTTTTTTAAAATTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAATTTTTCCTCAAAAACCTATTTTTTTAAAATTTATTTTTAAGAAAAATT
*
31296323 GATACTTTCAATTTTTCCCCAAAAATATTTTTTTGAAATTTTGATTTTCAAAG
66 GATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTTTGATTTTCAAAG
* * *
31296376 AAAATTGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTTTTAAATTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAATTTTTCCTCAAAAACCTATTTTTTTAAAATTTATTTTTAAGAAAAATT
* ** *
31296441 GATATTTTCAACTTTTCTTCAAAAATATTTTTTTGAAATTTTGATTTTCAAGG
66 GATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTTTGATTTTCAAAG
* * *
31296494 AAAATTGATAATTTCAATTTTTCCTCAAAAACC-CTTTTTTGAAAATTTATTTTTAAGAAAAATT
1 AAAATTGATACTTTCAATTTTTCCTCAAAAACCTATTTTTTTAAAATTTATTTTTAAGAAAAATT
* *
31296558 AATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAAATTTTGATTTT
66 GATACTTTCAACTTTTCCCCAAAAATATTTTTTTG-AAATTTTGATTTT
31296607 AATTTTAAAA
Statistics
Matches: 208, Mismatches: 21, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
117 86 0.41
118 122 0.59
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.48
Consensus pattern (118 bp):
AAAATTGATACTTTCAATTTTTCCTCAAAAACCTATTTTTTTAAAATTTATTTTTAAGAAAAATT
GATACTTTCAACTTTTCCCCAAAAATATTTTTTTGAAATTTTGATTTTCAAAG
Found at i:31296663 original size:17 final size:17
Alignment explanation
Indices: 31296615--31296790 Score: 107
Period size: 17 Copynumber: 10.4 Consensus size: 17
31296605 TTAATTTTAA
*
31296615 AAAAAATAGAATAATAA-
1 AAAAAATA-AATAAAAAT
31296632 AAAAAATAAATAAAAAT
1 AAAAAATAAATAAAAAT
* *
31296649 AAAAAATAAAGAAAAGT
1 AAAAAATAAATAAAAAT
31296666 AAAACAA-AAATAAAAAT
1 AAAA-AATAAATAAAAAT
*
31296683 AAAATAA-AGATAAAAA-
1 AAAA-AATAAATAAAAAT
* * * *
31296699 GAATATTAAATAAACAT
1 AAAAAATAAATAAAAAT
**
31296716 AATCTAATAAATAAAAA-
1 AA-AAAATAAATAAAAAT
*
31296733 AGATAAAA-AAA-ACAAAT
1 A-A-AAAATAAATAAAAAT
*
31296750 AAACAAATAAATGAAAAT
1 AAA-AAATAAATAAAAAT
*
31296768 AAAAAAAAAATTAAAAA-
1 AAAAAATAAA-TAAAAAT
31296785 AAAAAA
1 AAAAAA
31296791 CCTGGAGCGG
Statistics
Matches: 125, Mismatches: 23, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
15 2 0.02
16 24 0.19
17 70 0.56
18 29 0.23
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.16
Consensus pattern (17 bp):
AAAAAATAAATAAAAAT
Found at i:31296663 original size:27 final size:25
Alignment explanation
Indices: 31296612--31296790 Score: 96
Period size: 27 Copynumber: 6.9 Consensus size: 25
31296602 ATTTTAATTT
*
31296612 TAAAAAAAATAGAATAATAAAAAAAA
1 TAAAAAAAATA-AAAAATAAAAAAAA
*
31296638 TAAATAAAAATAAAAAATAAAGAAAAG
1 TAAA-AAAAATAAAAAATAAA-AAAAA
31296665 TAAAACAAAA-ATAAAAATAAAATAAAGA
1 TAAAA-AAAATA-AAAAATAAAA-AAA-A
* ** * *
31296693 TAAAAAGAATATTAAATAAACATAA
1 TAAAAAAAATAAAAAATAAAAAAAA
** *
31296718 TCTAATAAATAAAAAAGATAAAAAAAA
1 TAAAAAAAAT-AAAAA-ATAAAAAAAA
* * * * *
31296745 CAAATAAACA-AATAAATGAAAATAA
1 TAAA-AAAAATAAAAAATAAAAAAAA
*
31296770 -AAAAAAAATTAAAAA-AAAAAA
1 TAAAAAAAATAAAAAATAAAAAA
31296791 CCTGGAGCGG
Statistics
Matches: 113, Mismatches: 29, Indels: 25
0.68 0.17 0.15
Matches are distributed among these distances:
23 8 0.07
24 7 0.06
25 15 0.13
26 24 0.21
27 50 0.44
28 9 0.08
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.16
Consensus pattern (25 bp):
TAAAAAAAATAAAAAATAAAAAAAA
Found at i:31296787 original size:12 final size:11
Alignment explanation
Indices: 31296614--31296789 Score: 66
Period size: 11 Copynumber: 14.9 Consensus size: 11
31296604 TTTAATTTTA
31296614 AAAAAAATAGAAT
1 AAAAAAA-A-AAT
31296627 AATAAAAAAAAT
1 AA-AAAAAAAAT
*
31296639 -AAATAAAAAT
1 AAAAAAAAAAT
* *
31296649 AAAAAATAAAG
1 AAAAAAAAAAT
** *
31296660 AAAAGTAAAAC
1 AAAAAAAAAAT
31296671 AAAAATAAAAAT
1 AAAAA-AAAAAT
* *
31296683 AAAATAAAGAT
1 AAAAAAAAAAT
* *
31296694 AAAAAGAATAT
1 AAAAAAAAAAT
* * *
31296705 TAAATAAACAT
1 AAAAAAAAAAT
** *
31296716 AATCTAATAAAT
1 AA-AAAAAAAAT
*
31296728 AAAAAAGATAAAA
1 AAAAAA-A-AAAT
*
31296741 AAAACAAATAAAC
1 AAAA-AAA-AAAT
31296754 AAATAAATGAAAAT
1 AAA-AAA--AAAAT
31296768 AAAAAAAAAATT
1 AAAAAAAAAA-T
31296780 AAAAAAAAAA
1 AAAAAAAAAA
31296790 ACCTGGAGCG
Statistics
Matches: 120, Mismatches: 32, Indels: 23
0.69 0.18 0.13
Matches are distributed among these distances:
10 8 0.07
11 46 0.38
12 28 0.23
13 23 0.19
14 14 0.12
15 1 0.01
ACGTcount: A:0.77, C:0.03, G:0.04, T:0.16
Consensus pattern (11 bp):
AAAAAAAAAAT
Found at i:31297702 original size:10 final size:10
Alignment explanation
Indices: 31297684--31297811 Score: 59
Period size: 10 Copynumber: 12.4 Consensus size: 10
31297674 ATATTACAAG
*
31297684 ATAAAAAATA
1 ATAATAAATA
31297694 ATAATAAATAA
1 ATAATAAAT-A
*
31297705 ATTATAATATA
1 ATAATAA-ATA
31297716 ATAATAAATA
1 ATAATAAATA
*
31297726 TATAACTATATA
1 -ATAA-TAAATA
* *
31297738 AAAATACAT-
1 ATAATAAATA
*
31297747 ATACAT-ATTA
1 ATA-ATAAATA
* *
31297757 ACAGA-AAAGA
1 ATA-ATAAATA
*
31297767 AAAATAAATAA
1 ATAATAAAT-A
31297778 ATAA-AAAT-
1 ATAATAAATA
31297786 ATACATATAATA
1 ATA-ATA-AATA
31297798 ATAATAAATA
1 ATAATAAATA
31297808 ATAA
1 ATAA
31297812 AATACATAAA
Statistics
Matches: 89, Mismatches: 16, Indels: 26
0.68 0.12 0.20
Matches are distributed among these distances:
8 3 0.03
9 5 0.06
10 40 0.45
11 31 0.35
12 10 0.11
ACGTcount: A:0.66, C:0.04, G:0.02, T:0.28
Consensus pattern (10 bp):
ATAATAAATA
Found at i:31297718 original size:19 final size:21
Alignment explanation
Indices: 31297694--31297749 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 21
31297684 ATAAAAAATA
31297694 ATAATAAATAAAT-TATAA-T
1 ATAATAAATAAATATATAACT
31297713 ATAAT-AATAAATATATAACT
1 ATAATAAATAAATATATAACT
* *
31297733 ATATAAAAATACATATA
1 ATA-ATAAATAAATATA
31297750 CATATTAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 7 0.23
19 10 0.32
20 4 0.13
21 1 0.03
22 9 0.29
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAATAAATAAATATATAACT
Found at i:31297736 original size:22 final size:22
Alignment explanation
Indices: 31297691--31297833 Score: 66
Period size: 22 Copynumber: 6.5 Consensus size: 22
31297681 AAGATAAAAA
* *
31297691 ATAATAATAAATAAATTATAAT
1 ATAATAATAAATATATAATAAT
31297713 ATAATAATAAATATATAACT-AT
1 ATAATAATAAATATATAA-TAAT
* * * *
31297735 ATAAAAATACATATACATATTAAC
1 ATAATAATA-A-ATATATAATAAT
* * *
31297759 AGAA-AAGAAAAATA-AATAA-
1 ATAATAATAAATATATAATAAT
*
31297778 ATAAAAATATACATATAATAATAAT
1 ATAATAATA-A-ATAT-ATAATAAT
*
31297803 A-AATAATAAAATACATAA-AAT
1 ATAATAAT-AAATATATAATAAT
*
31297824 ACAA-AATAAA
1 ATAATAATAAA
31297834 AATACAAAAT
Statistics
Matches: 93, Mismatches: 16, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
19 3 0.03
20 10 0.11
21 11 0.12
22 36 0.39
23 10 0.11
24 21 0.23
25 2 0.02
ACGTcount: A:0.66, C:0.05, G:0.01, T:0.27
Consensus pattern (22 bp):
ATAATAATAAATATATAATAAT
Found at i:31297785 original size:6 final size:6
Alignment explanation
Indices: 31297761--31297849 Score: 54
Period size: 6 Copynumber: 13.8 Consensus size: 6
31297751 ATATTAACAG
* * * * *
31297761 AAAAGA AAAATAA ATAAATA AAAATA TACAT- ATAATA ATAATA AATAATA
1 AAAATA AAAAT-A A-AAATA AAAATA AAAATA AAAATA AAAATA AA-AATA
*
31297811 AAATACA TAAAATA CAAAATA AAAATA CAAAATA AAAAT
1 AAA-ATA -AAAATA -AAAATA AAAATA -AAAATA AAAAT
31297850 TACATTGGGC
Statistics
Matches: 66, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
5 2 0.03
6 31 0.47
7 26 0.39
8 7 0.11
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:31297805 original size:27 final size:28
Alignment explanation
Indices: 31297772--31297837 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
31297762 AAAGAAAAAT
*
31297772 AAATAAATAA-AAATATACATATAATA-A
1 AAATAAATAATAAA-ATACATAAAATACA
*
31297799 TAATAAATAATAAAATACATAAAATACA
1 AAATAAATAATAAAATACATAAAATACA
31297827 AAATAAA-AATA
1 AAATAAATAATA
31297838 CAAAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (28 bp):
AAATAAATAATAAAATACATAAAATACA
Found at i:31297838 original size:13 final size:13
Alignment explanation
Indices: 31297819--31297849 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
31297809 TAAAATACAT
31297819 AAAATACAAAATA
1 AAAATACAAAATA
31297832 AAAATACAAAATA
1 AAAATACAAAATA
31297845 AAAAT
1 AAAAT
31297850 TACATTGGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAATACAAAATA
Found at i:31300430 original size:2 final size:2
Alignment explanation
Indices: 31300423--31300449 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31300413 AGGAAGGGAA
31300423 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
31300450 GACACACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31301700 original size:15 final size:15
Alignment explanation
Indices: 31301665--31301699 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
31301655 TTATTACATG
*
31301665 TATTTTATTTTATTA
1 TATTTTAATTTATTA
31301680 TATTTTAATTTATTA
1 TATTTTAATTTATTA
31301695 -ATTTT
1 TATTTT
31301700 TCTCATGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTTAATTTATTA
Found at i:31305662 original size:20 final size:20
Alignment explanation
Indices: 31305639--31305677 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31305629 ATATTTAGTT
31305639 TTTGAAATATATATGTTGTA
1 TTTGAAATATATATGTTGTA
** *
31305659 TTTGAGGTATATATTTTGT
1 TTTGAAATATATATGTTGT
31305678 CATCTAAATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.18, T:0.54
Consensus pattern (20 bp):
TTTGAAATATATATGTTGTA
Found at i:31306313 original size:2 final size:2
Alignment explanation
Indices: 31306308--31306338 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
31306298 GGAGAGAGCT
31306308 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 T
31306339 GTGTGTGTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31314797 original size:22 final size:19
Alignment explanation
Indices: 31314769--31314820 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 19
31314759 TGTATTCAAA
31314769 ATAAAAAATAAATTTAAAATAT
1 ATAAAAAATAAATTT--AAT-T
*
31314791 ATAAAAAAGAAATTTAATT
1 ATAAAAAATAAATTTAATT
31314810 ATAAAAAATAA
1 ATAAAAAATAA
31314821 TGACATAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 11 0.39
20 3 0.11
22 14 0.50
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
ATAAAAAATAAATTTAATT
Found at i:31315037 original size:26 final size:26
Alignment explanation
Indices: 31315008--31315067 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
31314998 ATTGTTTAAG
*
31315008 TAAATAAATTTGTAT-TTTTATTTATA
1 TAAATAAA-TTGAATATTTTATTTATA
*
31315034 TAAATAAA-TGAATATTTTATTTATT
1 TAAATAAATTGAATATTTTATTTATA
31315059 TAAATAAAT
1 TAAATAAAT
31315068 AAATGAAGTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.13
25 18 0.60
26 8 0.27
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (26 bp):
TAAATAAATTGAATATTTTATTTATA
Found at i:31316761 original size:2 final size:2
Alignment explanation
Indices: 31316754--31316778 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31316744 AAACATTTGG
31316754 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
31316779 GAGAATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31333120 original size:18 final size:19
Alignment explanation
Indices: 31333086--31333122 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
31333076 ATGGTATTAA
*
31333086 AATAAATTATTTTATATTT
1 AATAAATTATTTAATATTT
31333105 AATAAA-TATTTAATATTT
1 AATAAATTATTTAATATTT
31333123 TTATTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATAAATTATTTAATATTT
Found at i:31333126 original size:26 final size:24
Alignment explanation
Indices: 31333095--31333155 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 24
31333085 AAATAAATTA
31333095 TTTTATATTTA-ATAAATATTTAATAT
1 TTTTATATTTATATAAA-A-TTAA-AT
* *
31333121 TTTTATTTTTATATTAAATTAAAT
1 TTTTATATTTATATAAAATTAAAT
31333145 TTTT-TATTTAT
1 TTTTATATTTAT
31333156 TATTAATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 6 0.19
24 6 0.19
25 4 0.13
26 11 0.35
27 4 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATATTTATATAAAATTAAAT
Found at i:31333146 original size:24 final size:23
Alignment explanation
Indices: 31333120--31333169 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
31333110 ATATTTAATA
*
31333120 TTTTTATTTTTATATTAAATTAAAT
1 TTTTTATTTAT-TATT-AATTAAAT
31333145 TTTTTATTTATTATTAATT-AAT
1 TTTTTATTTATTATTAATTAAAT
31333167 TTT
1 TTT
31333170 AAGTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 4 0.17
24 4 0.17
25 10 0.42
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TTTTTATTTATTATTAATTAAAT
Found at i:31333154 original size:23 final size:24
Alignment explanation
Indices: 31333095--31333169 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
31333085 AAATAAATTA
* * *
31333095 TTTTATATTTAATAAATATTTAATAT
1 TTTTATATTT-ATTATTAATTAA-AT
*
31333121 TTTTATTTTTA-TATTAAATTAAAT
1 TTTTATATTTATTATT-AATTAAAT
31333145 TTTT-TATTTATTATTAATT-AAT
1 TTTTATATTTATTATTAATTAAAT
31333167 TTT
1 TTT
31333170 AAGTTAAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 6 0.14
23 9 0.21
24 12 0.29
25 6 0.14
26 9 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTTATATTTATTATTAATTAAAT
Done.