Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 13 of 20
Found at i:4851327 original size:18 final size:17
Alignment explanation
Indices: 4851304--4851341 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
4851294 TTTAAAATAA
4851304 AAATAT-ACAAATATAATT
1 AAATATAACAAA-A-AATT
4851322 AAATATAACAAAAAATT
1 AAATATAACAAAAAATT
4851339 AAA
1 AAA
4851342 ATTTATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 7 0.37
19 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATATAACAAAAAATT
Found at i:4863499 original size:18 final size:18
Alignment explanation
Indices: 4863476--4863510 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4863466 AGAGAAGGCC
4863476 CCTTTCTCTCTCTCTCTT
1 CCTTTCTCTCTCTCTCTT
*
4863494 CCTTTCTTTCTCTCTCT
1 CCTTTCTCTCTCTCTCT
4863511 ACACTCCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.43, G:0.00, T:0.57
Consensus pattern (18 bp):
CCTTTCTCTCTCTCTCTT
Found at i:4864776 original size:17 final size:18
Alignment explanation
Indices: 4864754--4864789 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
4864744 CCTCCCATTC
4864754 TCTTTCTTT-TCCTCCTT
1 TCTTTCTTTATCCTCCTT
*
4864771 TCTTTCTTTATCTTCCTT
1 TCTTTCTTTATCCTCCTT
4864789 T
1 T
4864790 TCTTCATGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.67
Consensus pattern (18 bp):
TCTTTCTTTATCCTCCTT
Found at i:4868293 original size:18 final size:18
Alignment explanation
Indices: 4868240--4868295 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
4868230 ATAATTTATT
4868240 TTTTTGTT-T-TATTTT-
1 TTTTTGTTATATATTTTA
* ** *
4868255 TTTTTGTTATAAAAGTGA
1 TTTTTGTTATATATTTTA
4868273 TTTTTGTTATATATTTTA
1 TTTTTGTTATATATTTTA
4868291 TTTTT
1 TTTTT
4868296 TTAAGAACAA
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
15 8 0.27
16 1 0.03
17 2 0.07
18 19 0.63
ACGTcount: A:0.20, C:0.00, G:0.09, T:0.71
Consensus pattern (18 bp):
TTTTTGTTATATATTTTA
Found at i:4873533 original size:2 final size:2
Alignment explanation
Indices: 4873520--4873549 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4873510 ATAGATAAAG
*
4873520 AT AT AG 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
4873550 TAATTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4873535 original size:12 final size:12
Alignment explanation
Indices: 4873510--4873548 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
4873500 AATCTCATGC
* *
4873510 ATAGATAAAGAT
1 ATAGATATATAT
4873522 ATAGATATATAT
1 ATAGATATATAT
*
4873534 ATATATATATAT
1 ATAGATATATAT
4873546 ATA
1 ATA
4873549 TTAATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (12 bp):
ATAGATATATAT
Found at i:4875279 original size:31 final size:31
Alignment explanation
Indices: 4875244--4875303 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
4875234 ACCCTAACCG
** * *
4875244 ACCTATTTGCTGCCTCTAATTTTAGTTGACC
1 ACCTATTTGCCACCTCCAATTTCAGTTGACC
4875275 ACCTATTTGCCACCTCCAATTTCAGTTGA
1 ACCTATTTGCCACCTCCAATTTCAGTTGA
4875304 TTCATACATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (31 bp):
ACCTATTTGCCACCTCCAATTTCAGTTGACC
Found at i:4886702 original size:29 final size:30
Alignment explanation
Indices: 4886660--4886740 Score: 101
Period size: 30 Copynumber: 2.7 Consensus size: 30
4886650 TACCTTTTTC
* *
4886660 ATAAGTTTTTATATTTTTATTAT-ATTTAA
1 ATAAATTTTTATATTTTTATTATAAATTAA
* * *
4886689 TTAATTTTTTATATTTTTATTTTAAATTAA
1 ATAAATTTTTATATTTTTATTATAAATTAA
*
4886719 ATAAATTTTTATATTTGTATTA
1 ATAAATTTTTATATTTTTATTA
4886741 CGTCTATCAA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 20 0.47
30 23 0.53
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (30 bp):
ATAAATTTTTATATTTTTATTATAAATTAA
Found at i:4886728 original size:59 final size:57
Alignment explanation
Indices: 4886660--4886792 Score: 158
Period size: 57 Copynumber: 2.3 Consensus size: 57
4886650 TACCTTTTTC
* * * * * * *
4886660 ATAAGTTTTTATATTTTTATTATATTTAATTAATTTTTTATATTTTTATTTTAAATTAA
1 ATAAATTTTTATATTTTTATTACATCT-ATCAA-ATTTTATATTATTATTTTAAATCAA
* *
4886719 ATAAATTTTTATATTTGTATTACGTCTATCAAATTTTATATTATTATTTTAAATCAA
1 ATAAATTTTTATATTTTTATTACATCTATCAAATTTTATATTATTATTTTAAATCAA
*
4886776 ATAAATTCTTATATTTT
1 ATAAATTTTTATATTTT
4886793 ATTTTGAATC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
57 37 0.59
58 4 0.06
59 22 0.35
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (57 bp):
ATAAATTTTTATATTTTTATTACATCTATCAAATTTTATATTATTATTTTAAATCAA
Found at i:4886794 original size:29 final size:28
Alignment explanation
Indices: 4886695--4886808 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 28
4886685 TTAATTAATT
*
4886695 TTTTATATTTTTATTTTAAATTAAATAAA
1 TTTTATA-TTTTATTTTAAATCAAATAAA
** *
4886724 TTTTTATATTTGTA--TTACGTC-TATCAAA
1 -TTTTATATTT-TATTTTAAATCAAAT-AAA
4886752 TTTTATATTATTATTTTAAATCAAATAAA
1 TTTTATATT-TTATTTTAAATCAAATAAA
*
4886781 TTCTTATATTTTATTTTGAATCAAATAA
1 TT-TTATATTTTATTTTAAATCAAATAA
4886809 TCTTCTATGA
Statistics
Matches: 69, Mismatches: 8, Indels: 15
0.75 0.09 0.16
Matches are distributed among these distances:
27 13 0.19
28 8 0.12
29 30 0.43
30 18 0.26
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.54
Consensus pattern (28 bp):
TTTTATATTTTATTTTAAATCAAATAAA
Found at i:4898904 original size:16 final size:17
Alignment explanation
Indices: 4898872--4898904 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4898862 AATATATCAG
*
4898872 AATTAGAAAATTAATAA
1 AATTACAAAATTAATAA
4898889 AATTACAAAA-TAATAA
1 AATTACAAAATTAATAA
4898905 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (17 bp):
AATTACAAAATTAATAA
Found at i:4899136 original size:19 final size:19
Alignment explanation
Indices: 4899112--4899149 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4899102 ATCGAGGTAG
4899112 ACTCGAACTAAGGTGAGTA
1 ACTCGAACTAAGGTGAGTA
4899131 ACTCGAACTAAGGTGAGTA
1 ACTCGAACTAAGGTGAGTA
4899150 TCTCTTCCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.26, T:0.21
Consensus pattern (19 bp):
ACTCGAACTAAGGTGAGTA
Found at i:4900184 original size:54 final size:54
Alignment explanation
Indices: 4900097--4900236 Score: 271
Period size: 54 Copynumber: 2.6 Consensus size: 54
4900087 NNNNNNNNNN
4900097 GGCATGTTTCCTCCACCCATGTTTGGAGGTGGAACATGGTTATTCTGGTAATGA
1 GGCATGTTTCCTCCACCCATGTTTGGAGGTGGAACATGGTTATTCTGGTAATGA
*
4900151 GGCACGTTTCCTCCACCCATGTTTGGAGGTGGAACATGGTTATTCTGGTAATGA
1 GGCATGTTTCCTCCACCCATGTTTGGAGGTGGAACATGGTTATTCTGGTAATGA
4900205 GGCATGTTTCCTCCACCCATGTTTGGAGGTGG
1 GGCATGTTTCCTCCACCCATGTTTGGAGGTGG
4900237 NNNNNNNNNN
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 84 1.00
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.32
Consensus pattern (54 bp):
GGCATGTTTCCTCCACCCATGTTTGGAGGTGGAACATGGTTATTCTGGTAATGA
Found at i:4904750 original size:40 final size:40
Alignment explanation
Indices: 4904691--4904769 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
4904681 TTGACTATTT
*
4904691 TTCACCATAGTGAGATTTTCAACCTTGCCAAGATTGGTGA
1 TTCACCATAGTGAGATTTTCAACCTCGCCAAGATTGGTGA
* * *
4904731 TTCACCTTAGTG-GAGTTTTCAACCTCGCCACGGTTGGTG
1 TTCACCATAGTGAGA-TTTTCAACCTCGCCAAGATTGGTG
4904770 TCTTTCACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 2 0.06
40 32 0.94
ACGTcount: A:0.22, C:0.23, G:0.23, T:0.33
Consensus pattern (40 bp):
TTCACCATAGTGAGATTTTCAACCTCGCCAAGATTGGTGA
Found at i:4913098 original size:14 final size:16
Alignment explanation
Indices: 4913079--4913112 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
4913069 ATTGAAATTA
4913079 TTTTCTTTT-TC-TTT
1 TTTTCTTTTCTCGTTT
4913093 TTTTCTTTTCTCGTTT
1 TTTTCTTTTCTCGTTT
4913109 TTTT
1 TTTT
4913113 TCTTGATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 2 0.11
16 7 0.39
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTCTTTTCTCGTTT
Found at i:4920295 original size:20 final size:19
Alignment explanation
Indices: 4920270--4920319 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
4920260 TAAAAATTTT
4920270 AATTTTTATTATATTTAATA
1 AATTTTTATTAT-TTTAATA
* *
4920290 AATTTTTATAATTTTAATT
1 AATTTTTATTATTTTAATA
*
4920309 AATTATTATTA
1 AATTTTTATTA
4920320 ATTAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTATTATTTTAATA
Found at i:4920305 original size:19 final size:19
Alignment explanation
Indices: 4920270--4920322 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
4920260 TAAAAATTTT
*
4920270 AATTTTTATTATATTTAATA
1 AATTTTTATAAT-TTTAATA
*
4920290 AATTTTTATAATTTTAATT
1 AATTTTTATAATTTTAATA
*
4920309 AATTATTATTAATT
1 AATTTTTA-TAATT
4920323 AAAATATTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTTTATAATTTTAATA
Found at i:4921243 original size:15 final size:15
Alignment explanation
Indices: 4921223--4921266 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
4921213 TTATTTTTTC
* *
4921223 TACAATCATATTGCT
1 TACAATCACATTACT
4921238 TACAATCACATTACT
1 TACAATCACATTACT
*
4921253 TGCAATCACATTAC
1 TACAATCACATTAC
4921267 CTGTAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (15 bp):
TACAATCACATTACT
Found at i:4924845 original size:21 final size:21
Alignment explanation
Indices: 4924806--4924844 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4924796 GAAAACAACG
4924806 TTATTGATTTATCTATTTTAA
1 TTATTGATTTATCTATTTTAA
*
4924827 TTATTTATTTATC-ATTTT
1 TTATTGATTTATCTATTTT
4924845 TCCTAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.67
Consensus pattern (21 bp):
TTATTGATTTATCTATTTTAA
Found at i:4926553 original size:17 final size:17
Alignment explanation
Indices: 4926485--4926553 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
4926475 ATTATAAAAA
4926485 AATAATATTTCAAATT-T
1 AATAATATTT-AAATTAT
*
4926502 AA-AATTAATTAAAATTAT
1 AATAA-T-ATTTAAATTAT
* *
4926520 --TAATATTTTAATCAT
1 AATAATATTTAAATTAT
4926535 AATAATATTTAAATTAT
1 AATAATATTTAAATTAT
4926552 AA
1 AA
4926554 ATAAAATATT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
15 8 0.20
16 3 0.08
17 25 0.62
18 4 0.10
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAATATTTAAATTAT
Found at i:4926588 original size:43 final size:41
Alignment explanation
Indices: 4926496--4926604 Score: 103
Period size: 43 Copynumber: 2.5 Consensus size: 41
4926486 ATAATATTTC
* * **
4926496 AAATTTAAA-ATTAATTAAAATTATTAATATTTTAATCATAAT
1 AAATTTAAATA-TAAATAAAA-TATTAATATTTAAAAAATAAT
*
4926538 AATATTTAAATTATAAATAAAATATTAATATTTAAAAAAATTAT
1 AA-ATTTAAA-TATAAATAAAATATTAATATTT-AAAAAATAAT
*
4926582 AAATTTAAAAATAAAATAAAATA
1 AAATTTAAATAT-AAATAAAATA
4926605 GATAATCATA
Statistics
Matches: 56, Mismatches: 6, Indels: 9
0.79 0.08 0.13
Matches are distributed among these distances:
42 4 0.07
43 35 0.62
44 16 0.29
45 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (41 bp):
AAATTTAAATATAAATAAAATATTAATATTTAAAAAATAAT
Found at i:4926592 original size:18 final size:19
Alignment explanation
Indices: 4926538--4926592 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 19
4926528 TAATCATAAT
4926538 AATATT-TAAATTATAAATAA
1 AATATTATAAATT-TAAA-AA
*
4926558 AATATTA-ATATTT-AAAA
1 AATATTATAAATTTAAAAA
4926575 AA-ATTATAAATTTAAAAA
1 AATATTATAAATTTAAAAA
4926593 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
16 4 0.13
17 9 0.30
18 6 0.20
19 1 0.03
20 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATATTATAAATTTAAAAA
Found at i:4926600 original size:17 final size:17
Alignment explanation
Indices: 4926544--4926601 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
4926534 TAATAATATT
*
4926544 TAAATTATAAATAAAATAT
1 TAAATT-TAAA-AAAATAA
*
4926563 TAATATTTAAAAAAATTA
1 TAA-ATTTAAAAAAATAA
4926581 TAAATTTAAAAATAA-AA
1 TAAATTTAAAAA-AATAA
4926598 TAAA
1 TAAA
4926602 ATAGATAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 14 0.41
18 10 0.29
19 7 0.21
20 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAATTTAAAAAAATAA
Found at i:4926603 original size:18 final size:18
Alignment explanation
Indices: 4926552--4926603 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
4926542 TTTAAATTAT
4926552 AAATAAAATATTAATATTTA
1 AAATAAAATA-TAA-ATTTA
*
4926572 AAA-AAATTATAAATTTAA
1 AAATAAAATATAAATTT-A
4926590 AAATAAAATA-AAAT
1 AAATAAAATATAAAT
4926604 AGATAATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 4 0.14
18 11 0.39
19 10 0.36
20 3 0.11
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATAAAATATAAATTTA
Found at i:4926977 original size:269 final size:263
Alignment explanation
Indices: 4926575--4927055 Score: 727
Period size: 269 Copynumber: 1.8 Consensus size: 263
4926565 ATATTTAAAA
* *
4926575 AAATTATAAATTTAAAAATAAAATAAAATAGATAATCATATATTGTAATAAACAGTTTAAGTTTT
1 AAATTATAAATTTAAAAATAAAATAAAATAGATAATCATATATTATAATAAACAGTTCAAGTTTT
* * *
4926640 TAATTATATATTATAAAAACTTGATATTTTAAATTTAAATTTAATTAAAATTATTAATATTTTAA
66 TAATTATATATTATAAAAAATTGATATTTTAAATTTAAAATTAATTAAAATTATTAATATTGTAA
* *
4926705 TCATAATAATTTTTAAATAATAAATAAAATAGTAATATTTTAAAATGTTAATGATTAAATTA-TA
131 TCATAATAATATTTAAATAATAAATAAAATAGTAATATTTTAAAATATTAATGATTAAATTATTA
*
4926769 AGTAAAACATTAATATTGAAAAATTTTATTATTTAAATGATCAATTAGTAATATTTTAAATTAAT
196 AATAAAACATTAATATTGAAAAATTTTATTATTTAAATGATCAATTAGTAATATTTTAAATTAAT
4926834 TAT
261 TAT
4926837 AAATTATTAATATTTAAAAAATAAAATAAAATAGATAATTAATCATATATTATAATAAA-A-TTC
1 AAATTA-TAA-ATTT-AAAAATAAAATAAAATAG---A-TAATCATATATTATAATAAACAGTTC
*
4926900 AAGTTTTTAATTATATATTATAAAAAAATT-AGTATTTTAAATTTAAAAATTAATTAAATTTATT
59 AAGTTTTTAATTATATATTAT-AAAAAATTGA-TATTTTAAATTT-AAAATTAATTAAAATTATT
* * *
4926964 AATATTGTAATCATAATAATATTTAAATTATAAATAAGATATTAATATTTTAAAATATTAATGAT
121 AATATTGTAATCATAATAATATTTAAATAATAAATAAAATAGTAATATTTTAAAATATTAATGAT
*
4927029 TAAATTATTAAATAAAATATTAATATT
186 TAAATTATTAAATAAAACATTAATATT
4927056 TTTAAAAAAT
Statistics
Matches: 195, Mismatches: 13, Indels: 14
0.88 0.06 0.06
Matches are distributed among these distances:
262 6 0.03
263 3 0.02
264 4 0.02
265 18 0.09
267 24 0.12
268 21 0.11
269 102 0.52
270 17 0.09
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (263 bp):
AAATTATAAATTTAAAAATAAAATAAAATAGATAATCATATATTATAATAAACAGTTCAAGTTTT
TAATTATATATTATAAAAAATTGATATTTTAAATTTAAAATTAATTAAAATTATTAATATTGTAA
TCATAATAATATTTAAATAATAAATAAAATAGTAATATTTTAAAATATTAATGATTAAATTATTA
AATAAAACATTAATATTGAAAAATTTTATTATTTAAATGATCAATTAGTAATATTTTAAATTAAT
TAT
Found at i:4927023 original size:16 final size:16
Alignment explanation
Indices: 4927002--4927081 Score: 55
Period size: 17 Copynumber: 5.2 Consensus size: 16
4926992 TATAAATAAG
4927002 ATATTAATATTTTAAA
1 ATATTAATATTTTAAA
4927018 ATATTAATGA--TTAAA
1 ATATTAAT-ATTTTAAA
*
4927033 TTATTAA-A---TAAA
1 ATATTAATATTTTAAA
4927045 ATATTAATATTTTTAAA
1 ATATTAATA-TTTTAAA
* * *
4927062 AAATTATAAATTTAAAA
1 ATATTA-ATATTTTAAA
4927079 ATA
1 ATA
4927082 AAATAAAATA
Statistics
Matches: 51, Mismatches: 6, Indels: 13
0.73 0.09 0.19
Matches are distributed among these distances:
12 10 0.20
13 2 0.04
15 11 0.22
16 8 0.16
17 18 0.35
18 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (16 bp):
ATATTAATATTTTAAA
Found at i:4927056 original size:43 final size:42
Alignment explanation
Indices: 4926960--4927544 Score: 158
Period size: 43 Copynumber: 13.3 Consensus size: 42
4926950 TAATTAAATT
* * * *
4926960 TATTAATATTGTAATCATAATAATATTTAAATTATAAATAAGA
1 TATTAATATTTTAA-AATATTAATATTTAAATTATAAATAAAA
4927003 TATTAATATTTTAAAATATTAATGA-TTAAATTATTAAATAAAA
1 TATTAATATTTTAAAATATTAAT-ATTTAAATTA-TAAATAAAA
* * *
4927046 TATTAATATTTTTAAAAAATTATAAATTTAAA-AATAAAATAAAA
1 TATTAATA-TTTTAAAATATTA-ATATTTAAATTAT-AAATAAAA
* ** * * * * * *
4927090 TAGATAATCATATATTGTAATA--AACAGTTTAAGTTTTTAATTATA
1 TA-TTAAT-AT-T-TTAAAATATTAATA-TTTAAATTATAAATAAAA
* ** * * * * *
4927135 TATTATAAAAACTTGATATTTTAA-ATTTAAA-AATTAATTAAAA
1 TA-T-TAATATTTTAAAATATTAATATTTAAATTA-TAAATAAAA
* * * * *
4927178 TTTTAATATTTTAATCATAATAATTTTTAAATAATAAATAAAA
1 TATTAATATTTTAA-AATATTAATATTTAAATTATAAATAAAA
* * *
4927221 TAGTAATATTTTAAAATGTTATTGA-TTAAATTATAAATAAAA
1 TATTAATATTTTAAAATATTAAT-ATTTAAATTATAAATAAAA
* * * * * *
4927263 CATTAATA-TTGAAAAGTTTTATTATTTAAATGATCAATTAGTAATA
1 TATTAATATTTTAAAA-TATTAATATTTAAATTAT-AA--A-TAAAA
* **
4927309 TTTTAAATAAATTATAAATCATTAATATTT-AA--A-AAATAAAA
1 TATT-AATATTTTA-AAAT-ATTAATATTTAAATTATAAATAAAA
* ** * * * *
4927350 TA-AAATA-GAT-AAATAATCATATATTATAATAATAGATAAAA
1 TATTAATATTTTAAAATATTAATAT-TTA-AATTATAAATAAAA
* * *
4927391 TTTTTAATTATATATTATAAAAAATTAATATTTTAAATTTAAAAATTAAATAAATT
1 ----T-ATTA-ATATTTTAAAATATTAATA-TTTAAA-TT----A-TAAATAAA-A
* * * * *
4927447 TATTAATATTGTAATCATAATAATATTTAAATTACAAATAAGA
1 TATTAATATTTTAA-AATATTAATATTTAAATTATAAATAAAA
4927490 TATTAATATTTTAAAATATTAATGA-TTAAATTATAAAATAAAA
1 TATTAATATTTTAAAATATTAAT-ATTTAAATTAT-AAATAAAA
*
4927533 TATTAAAATTTT
1 TATTAATATTTT
4927545 GGAATGTTAG
Statistics
Matches: 394, Mismatches: 92, Indels: 112
0.66 0.15 0.19
Matches are distributed among these distances:
35 6 0.02
36 6 0.02
38 3 0.01
39 4 0.01
40 1 0.00
41 26 0.07
42 78 0.20
43 107 0.27
44 37 0.09
45 30 0.08
46 14 0.04
47 10 0.03
48 8 0.02
49 17 0.04
50 26 0.07
51 12 0.03
52 1 0.00
54 1 0.00
55 7 0.02
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.42
Consensus pattern (42 bp):
TATTAATATTTTAAAATATTAATATTTAAATTATAAATAAAA
Found at i:4927086 original size:44 final size:43
Alignment explanation
Indices: 4926980--4927091 Score: 113
Period size: 44 Copynumber: 2.6 Consensus size: 43
4926970 GTAATCATAA
* * * *
4926980 TAATATTTAAATTAT-AAATAAGATATTAATATTTTAAAATAT
1 TAATAATTAAATAATAAAATAAAATATTAATATTTTAAAAAAT
* * *
4927022 TAATGATTAAATTATTAAATAAAATATTAATATTTTTAAAAAAT
1 TAATAATTAAATAATAAAATAAAATATTAATA-TTTTAAAAAAT
4927066 T-ATAAATTTAAA-AATAAAATAAAATA
1 TAAT-AA-TTAAATAATAAAATAAAATA
4927092 GATAATCATA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 13 0.22
43 17 0.29
44 24 0.41
45 5 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (43 bp):
TAATAATTAAATAATAAAATAAAATATTAATATTTTAAAAAAT
Found at i:4927195 original size:218 final size:222
Alignment explanation
Indices: 4926837--4927272 Score: 654
Period size: 218 Copynumber: 2.0 Consensus size: 222
4926827 AATTAATTAT
4926837 AAATTATTAATATTTAAAAAATAAAATAAAATAGATAATTAATCATATATTATAATAAAATTCAA
1 AAATTATTAATATTTAAAAAATAAAATAAAATAG--AATTAATCATATATTATAATAAAATTCAA
*
4926902 GTTTTTAATTATATATTATAAAAAAATTAGTATTTTAAATTTAAAAATTAATTAAATTTATTAAT
64 GTTTTTAATTATATATTATAAAAAAATTAGTATTTTAAATTTAAAAATTAATTAAAATTATTAAT
* * *
4926967 ATTGTAATCATAATAATATTTAAATTATAAATAAGATATTAATATTTTAAAATATTAATGATTAA
129 ATTGTAATCATAATAATATTTAAATAATAAATAAAATAGTAATATTTTAAAATATTAATGATTAA
*
4927032 ATTATTAAATAAAATATTAATATTTTTAAA
194 ATTA-TAAATAAAACATTAATATTTTTAAA
* *
4927062 AAATTA-TAA-ATTT-AAAAATAAAATAAAATAG-A-TAATCATATATTGTAATAAACAGTTTAA
1 AAATTATTAATATTTAAAAAATAAAATAAAATAGAATTAATCATATATTATAATAAA-A-TTCAA
*
4927122 GTTTTTAATTATATATTAT-AAAAACTT-GATATTTTAAATTTAAAAATTAATTAAAATT-TTAA
64 GTTTTTAATTATATATTATAAAAAAATTAG-TATTTTAAATTTAAAAATTAATTAAAATTATTAA
* * * *
4927184 TATTTTAATCATAATAATTTTTAAATAATAAATAAAATAGTAATATTTTAAAATGTTATTGATTA
128 TATTGTAATCATAATAATATTTAAATAATAAATAAAATAGTAATATTTTAAAATATTAATGATTA
4927249 AATTATAAATAAAACATTAATATT
193 AATTATAAATAAAACATTAATATT
4927273 GAAAAGTTTT
Statistics
Matches: 196, Mismatches: 12, Indels: 14
0.88 0.05 0.06
Matches are distributed among these distances:
217 18 0.09
218 87 0.44
219 37 0.19
220 23 0.12
222 18 0.09
223 4 0.02
224 3 0.02
225 6 0.03
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (222 bp):
AAATTATTAATATTTAAAAAATAAAATAAAATAGAATTAATCATATATTATAATAAAATTCAAGT
TTTTAATTATATATTATAAAAAAATTAGTATTTTAAATTTAAAAATTAATTAAAATTATTAATAT
TGTAATCATAATAATATTTAAATAATAAATAAAATAGTAATATTTTAAAATATTAATGATTAAAT
TATAAATAAAACATTAATATTTTTAAA
Found at i:4927285 original size:42 final size:42
Alignment explanation
Indices: 4927203--4927293 Score: 105
Period size: 42 Copynumber: 2.2 Consensus size: 42
4927193 CATAATAATT
* *
4927203 TTTAAATAATAAATAAAATAGTAATATTTTAAAATGTTATTGA
1 TTTAAATAATAAATAAAACAGTAATATTTGAAAATGTTATT-A
* * *
4927246 -TTAAATTATAAATAAAACATTAATA-TTGAAAAGTTTTATTA
1 TTTAAATAATAAATAAAACAGTAATATTTGAAAA-TGTTATTA
4927287 TTTAAAT
1 TTTAAAT
4927294 GATCAATTAG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 7 0.17
42 34 0.83
ACGTcount: A:0.51, C:0.01, G:0.05, T:0.43
Consensus pattern (42 bp):
TTTAAATAATAAATAAAACAGTAATATTTGAAAATGTTATTA
Found at i:4927320 original size:27 final size:26
Alignment explanation
Indices: 4927289--4927345 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
4927279 TTTTATTATT
* *
4927289 TAAATGATCAATTAGTAATATTTTAAA
1 TAAATGATAAATCAGTAATA-TTTAAA
* *
4927316 TAAATTATAAATCATTAATATTTAAA
1 TAAATGATAAATCAGTAATATTTAAA
4927342 -AAAT
1 TAAAT
4927346 AAAATAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 4 0.15
26 6 0.23
27 16 0.62
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (26 bp):
TAAATGATAAATCAGTAATATTTAAA
Found at i:4927488 original size:487 final size:487
Alignment explanation
Indices: 4926517--4927544 Score: 1816
Period size: 487 Copynumber: 2.1 Consensus size: 487
4926507 TAATTAAAAT
* *
4926517 TATTAATATTTTAATCATAATAAT-ATTTAAATTA-TAAATAAAATATTAATA-TTTAAAAAAAT
1 TATTAATATTTTAA-AATATTAATGA-TTAAATTATTAAATAAAATATTAATATTTTAAAAAAAT
4926579 TATAAATTTAAAAATAAAATAAAATAGATAATCATATATTGTAATAAACAGTTTAAGTTTTTAAT
64 TATAAATTTAAAAATAAAATAAAATAGATAATCATATATTGTAATAAACAGTTTAAGTTTTTAAT
*
4926644 TATATATTATAAAAACTTGATATTTTAAATTTAAATTTAATTAAAATTATTAATATTTTAATCAT
129 TATATATTATAAAAACTTGATATTTTAAATTTAAAATTAATTAAAATTATTAATATTTTAATCAT
*
4926709 AATAATTTTTAAATAATAAATAAAATAGTAATATTTTAAAATGTTAATGATTAAATTATAAGTAA
194 AATAATTTTTAAATAATAAATAAAATAGTAATATTTTAAAATGTTAATGATTAAATTATAAATAA
*
4926774 AACATTAATATTGAAAAATTTTATTATTTAAATGATCAATTAGTAATATTTTAAATTAATTATAA
259 AACATTAATATTGAAAAATTTTATTATTTAAATGATCAATTAGTAATATTTTAAATAAATTATAA
* * * *
4926839 ATTATTAATATTTAAAAAATAAAATAAAATAGATAATTAATCATATATTATAATAAAATTCAAGT
324 ATCATTAATATTTAAAAAATAAAATAAAATAGATAAATAATCATATATTATAATAAAATTAAAAT
* *
4926904 TTTTAATTATATATTATAAAAAAATTAGTATTTTAAATTTAAAAATTAATTAAATTTATTAATAT
389 TTTTAATTATATATTATAAAAAAATTAATATTTTAAATTTAAAAATTAAATAAATTTATTAATAT
*
4926969 TGTAATCATAATAATATTTAAATTATAAATAAGA
454 TGTAATCATAATAATATTTAAATTACAAATAAGA
*
4927003 TATTAATATTTTAAAATATTAATGATTAAATTATTAAATAAAATATTAATATTTTTAAAAAATTA
1 TATTAATATTTTAAAATATTAATGATTAAATTATTAAATAAAATATTAATATTTTAAAAAAATTA
4927068 TAAATTTAAAAATAAAATAAAATAGATAATCATATATTGTAATAAACAGTTTAAGTTTTTAATTA
66 TAAATTTAAAAATAAAATAAAATAGATAATCATATATTGTAATAAACAGTTTAAGTTTTTAATTA
4927133 TATATTATAAAAACTTGATATTTTAAATTTAAAAATTAATTAAAATT-TTAATATTTTAATCATA
131 TATATTATAAAAACTTGATATTTTAAATTT-AAAATTAATTAAAATTATTAATATTTTAATCATA
*
4927197 ATAATTTTTAAATAATAAATAAAATAGTAATATTTTAAAATGTTATTGATTAAATTATAAATAAA
195 ATAATTTTTAAATAATAAATAAAATAGTAATATTTTAAAATGTTAATGATTAAATTATAAATAAA
*
4927262 ACATTAATATTGAAAAGTTTTATTATTTAAATGATCAATTAGTAATATTTTAAATAAATTATAAA
260 ACATTAATATTGAAAAATTTTATTATTTAAATGATCAATTAGTAATATTTTAAATAAATTATAAA
4927327 TCATTAATATTTAAAAAATAAAATAAAATAGATAAATAATCATATATTATAATAATAGA-TAAAA
325 TCATTAATATTTAAAAAATAAAATAAAATAGATAAATAATCATATATTATAATAA-A-ATTAAAA
4927391 TTTTTAATTATATATTAT-AAAAAATTAATATTTTAAATTTAAAAATTAAATAAATTTATTAATA
388 TTTTTAATTATATATTATAAAAAAATTAATATTTTAAATTTAAAAATTAAATAAATTTATTAATA
4927455 TTGTAATCATAATAATATTTAAATTACAAATAAGA
453 TTGTAATCATAATAATATTTAAATTACAAATAAGA
* *
4927490 TATTAATATTTTAAAATATTAATGATTAAATTATAAAATAAAATATTAAAATTTT
1 TATTAATATTTTAAAATATTAATGATTAAATTATTAAATAAAATATTAATATTTT
4927545 GGAATGTTAG
Statistics
Matches: 519, Mismatches: 17, Indels: 11
0.95 0.03 0.02
Matches are distributed among these distances:
485 15 0.03
486 32 0.06
487 434 0.84
488 37 0.07
489 1 0.00
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (487 bp):
TATTAATATTTTAAAATATTAATGATTAAATTATTAAATAAAATATTAATATTTTAAAAAAATTA
TAAATTTAAAAATAAAATAAAATAGATAATCATATATTGTAATAAACAGTTTAAGTTTTTAATTA
TATATTATAAAAACTTGATATTTTAAATTTAAAATTAATTAAAATTATTAATATTTTAATCATAA
TAATTTTTAAATAATAAATAAAATAGTAATATTTTAAAATGTTAATGATTAAATTATAAATAAAA
CATTAATATTGAAAAATTTTATTATTTAAATGATCAATTAGTAATATTTTAAATAAATTATAAAT
CATTAATATTTAAAAAATAAAATAAAATAGATAAATAATCATATATTATAATAAAATTAAAATTT
TTAATTATATATTATAAAAAAATTAATATTTTAAATTTAAAAATTAAATAAATTTATTAATATTG
TAATCATAATAATATTTAAATTACAAATAAGA
Found at i:4927499 original size:269 final size:268
Alignment explanation
Indices: 4927071--4927657 Score: 735
Period size: 269 Copynumber: 2.2 Consensus size: 268
4927061 AAAATTATAA
* * * *
4927071 ATTT-AAAAATAAAATAAAATAG----ATAATCATATATTGTAATAAACAGTTTAAGTTTTTAAT
1 ATTTAAAAAATAAAATAAAATAGATAAATAATCATATATTATAATAAA-AGATAAAATTTTTAAT
* * * *
4927131 TATATATTATAAAAACTTGATATTTTAAATTTAAAAATTAATTAAAATTTTAATATTTTAATCAT
65 TATATATTATAAAAAATTAATATTTTAAATTTAAAAATTAAATAAAATTTTAATATTGTAATCAT
* * * *
4927196 AATAATTTTTAAATAATAAATAAAATAGTAATATTTTAAAATGTTATTGATTAAATTAT-AAATA
130 AATAATATTTAAATAACAAATAAAATAGTAATATTTTAAAATATTAATGATTAAATTATAAAATA
* **
4927260 AAACATT-AATATTGAAAAGTTTTATTATTTAAATGATCAATTAGTAATATTTTAAATAAATTAT
195 AAACATTAAATATTG-AAA-TGTTAGCATTTAAATGATCAATTAGTAATATTTTAAATAAATTAT
4927324 AAATCATTAAT
258 AAATCATTAAT
*
4927335 ATTTAAAAAATAAAATAAAATAGATAAATAATCATATATTATAATAATAGATAAAATTTTTAATT
1 ATTTAAAAAATAAAATAAAATAGATAAATAATCATATATTATAATAAAAGATAAAATTTTTAATT
*
4927400 ATATATTATAAAAAATTAATATTTTAAATTTAAAAATTAAATAAATTTATTAATATTGTAATCAT
66 ATATATTATAAAAAATTAATATTTTAAATTTAAAAATTAAATAAAATT-TTAATATTGTAATCAT
* * *
4927465 AATAATATTTAAATTACAAATAAGATATTAATATTTTAAAATATTAATGATTAAATTATAAAATA
130 AATAATATTTAAATAACAAATAAAATAGTAATATTTTAAAATATTAATGATTAAATTATAAAATA
* * * * * * * *
4927530 AAATATTAAAATTTTGGAATGTTAGCATTTAAATTATCAGTTATTAATATTTTAGATAAATTTTA
195 AAACATT-AAATATTGAAATGTTAGCATTTAAATGATCAATTAGTAATATTTTAAATAAATTATA
* * **
4927595 ATTTATTTTT
259 AATCATTAAT
* *
4927605 ATTTTAAAAAA-ATAGATTAAA-A-ATAAATAATCATATATTATAATAAAAGATAA
1 A-TTTAAAAAATA-AAATAAAATAGATAAATAATCATATATTATAATAAAAGATAA
4927658 TTTTTATCTT
Statistics
Matches: 277, Mismatches: 35, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
264 4 0.01
265 18 0.06
268 58 0.21
269 116 0.42
270 58 0.21
271 17 0.06
272 6 0.02
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.42
Consensus pattern (268 bp):
ATTTAAAAAATAAAATAAAATAGATAAATAATCATATATTATAATAAAAGATAAAATTTTTAATT
ATATATTATAAAAAATTAATATTTTAAATTTAAAAATTAAATAAAATTTTAATATTGTAATCATA
ATAATATTTAAATAACAAATAAAATAGTAATATTTTAAAATATTAATGATTAAATTATAAAATAA
AACATTAAATATTGAAATGTTAGCATTTAAATGATCAATTAGTAATATTTTAAATAAATTATAAA
TCATTAAT
Found at i:4927539 original size:20 final size:20
Alignment explanation
Indices: 4927463--4927539 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
4927453 TATTGTAATC
*
4927463 ATAATAATATTTAAATTA-CAA
1 ATAA-AATA-TTAAATTATAAA
* *
4927484 ATAAGATATTAATATTTTAAA
1 ATAAAATATTAA-ATTATAAA
*
4927505 ATATTAATGATTAAATTATAAA
1 ATA-AAAT-ATTAAATTATAAA
4927527 ATAAAATATTAAA
1 ATAAAATATTAAA
4927540 ATTTTGGAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
19 4 0.09
20 12 0.27
21 12 0.27
22 12 0.27
23 5 0.11
ACGTcount: A:0.57, C:0.01, G:0.03, T:0.39
Consensus pattern (20 bp):
ATAAAATATTAAATTATAAA
Found at i:4928222 original size:45 final size:46
Alignment explanation
Indices: 4928088--4928241 Score: 206
Period size: 46 Copynumber: 3.4 Consensus size: 46
4928078 ACTTGAGAGT
* *
4928088 GAACGACGTTGGTGACGGCTGTCATTGCCACCCCTCAGTTAATC-GG
1 GAACGACGTTGGTGACGGCTGTCATTGTCACCCCTTAGTTAA-CAGG
4928134 GAACGACGTTGGTGACGGCTGTCATTGTCACCCCTTAGTTAACAGG
1 GAACGACGTTGGTGACGGCTGTCATTGTCACCCCTTAGTTAACAGG
** * *
4928180 GAACGACCATGGTGACGGC-GCCATTGTCACCCCTTAGCTAACAGG
1 GAACGACGTTGGTGACGGCTGTCATTGTCACCCCTTAGTTAACAGG
* *
4928225 GAAC-AAGTTGGAGACGG
1 GAACGACGTTGGTGACGG
4928242 ATAGAACGAA
Statistics
Matches: 97, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
44 9 0.09
45 29 0.30
46 59 0.61
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.21
Consensus pattern (46 bp):
GAACGACGTTGGTGACGGCTGTCATTGTCACCCCTTAGTTAACAGG
Found at i:4933132 original size:18 final size:18
Alignment explanation
Indices: 4933111--4933149 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
4933101 TTTTATTTTA
4933111 AATTAAATAAATATTAAT
1 AATTAAATAAATATTAAT
* *
4933129 AATTAATTAATTATTAAT
1 AATTAAATAAATATTAAT
4933147 AAT
1 AAT
4933150 CAATATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTAAATAAATATTAAT
Found at i:4941538 original size:34 final size:35
Alignment explanation
Indices: 4941500--4941568 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
4941490 GTTCGTGTTT
*
4941500 GTTTCACAAGTTTTAC-TGCAAGACATTCCTTTAA
1 GTTTCACAAGTTTTACTTCCAAGACATTCCTTTAA
*
4941534 GTTTCACGAGTTTTACTTCCAAGACATTCCTTTAA
1 GTTTCACAAGTTTTACTTCCAAGACATTCCTTTAA
4941569 ATTTGCGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 15 0.47
35 17 0.53
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (35 bp):
GTTTCACAAGTTTTACTTCCAAGACATTCCTTTAA
Found at i:4945735 original size:4 final size:4
Alignment explanation
Indices: 4945723--4945767 Score: 63
Period size: 4 Copynumber: 11.2 Consensus size: 4
4945713 GCATGTCTTC
* * *
4945723 ATGT TTGT ATGT ATGT ATGA ATGT ATGT ATGT ATGT ATGT TTGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
4945768 AGTGAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
ATGT
Found at i:4946377 original size:13 final size:13
Alignment explanation
Indices: 4946346--4946376 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
4946336 AAATTGCTTT
4946346 TCTTTTCTTCAAG
1 TCTTTTCTTCAAG
4946359 TCTTTTCTTCAAG
1 TCTTTTCTTCAAG
4946372 T-TTTT
1 TCTTTT
4946377 TGAGTGTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.22
13 14 0.78
ACGTcount: A:0.13, C:0.19, G:0.06, T:0.61
Consensus pattern (13 bp):
TCTTTTCTTCAAG
Found at i:4974422 original size:18 final size:18
Alignment explanation
Indices: 4974399--4974448 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
4974389 ACACGTTTAA
4974399 TTAATCATGTTATCCTGT
1 TTAATCATGTTATCCTGT
* * * *
4974417 TTAATCATATAAACGTGT
1 TTAATCATGTTATCCTGT
*
4974435 TTAATCGTGTTATC
1 TTAATCATGTTATC
4974449 ATATTTAAAT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (18 bp):
TTAATCATGTTATCCTGT
Found at i:4984098 original size:63 final size:63
Alignment explanation
Indices: 4983999--4984125 Score: 245
Period size: 63 Copynumber: 2.0 Consensus size: 63
4983989 CTTTTTGCCG
*
4983999 GCTTTGAAGACAAAATAAATACCCCACCAATCCAAGTTCAGTTCATGTTAGGCTAAAGATTAA
1 GCTTTGAAGACAAAATAAATACCCCACCAATCCAAGTTCAATTCATGTTAGGCTAAAGATTAA
4984062 GCTTTGAAGACAAAATAAATACCCCACCAATCCAAGTTCAATTCATGTTAGGCTAAAGATTAA
1 GCTTTGAAGACAAAATAAATACCCCACCAATCCAAGTTCAATTCATGTTAGGCTAAAGATTAA
4984125 G
1 G
4984126 TAAAGAATAT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.40, C:0.20, G:0.14, T:0.25
Consensus pattern (63 bp):
GCTTTGAAGACAAAATAAATACCCCACCAATCCAAGTTCAATTCATGTTAGGCTAAAGATTAA
Found at i:4992784 original size:64 final size:64
Alignment explanation
Indices: 4992672--4992816 Score: 179
Period size: 64 Copynumber: 2.3 Consensus size: 64
4992662 TTTCTATCAC
* ** * *
4992672 GTATGTTTAATTTAAATTTATATATTATTAACATAAATTTATACGAATTAACGTAAAATATAAT
1 GTATCTTTAATTTAAATTTATATATTATTAACATAAACGTATAAGAATTAACATAAAATATAAT
* *
4992736 GTATCTTTAATTTGAATTTATATATTATTAATC-TAAACGTATAAGAATTAACATAAAATGT--T
1 GTATCTTTAATTTAAATTTATATATTATTAA-CATAAACGTATAAGAATTAACATAAAATATAAT
4992798 GTATCTTGATAATTTAAAT
1 GTATCTT--TAATTTAAAT
4992817 GAAAAATTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
62 8 0.11
64 61 0.87
65 1 0.01
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.44
Consensus pattern (64 bp):
GTATCTTTAATTTAAATTTATATATTATTAACATAAACGTATAAGAATTAACATAAAATATAAT
Found at i:4999372 original size:2 final size:2
Alignment explanation
Indices: 4999365--4999389 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4999355 NNNNNNNNNN
4999365 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
4999390 AATGATCAGA
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:5004154 original size:11 final size:11
Alignment explanation
Indices: 5004127--5004160 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
5004117 TGTTATATAA
5004127 AATTATT-ATT
1 AATTATTAATT
*
5004137 TATTATTAATT
1 AATTATTAATT
5004148 AATTATTAATT
1 AATTATTAATT
5004159 AA
1 AA
5004161 ATTTAATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTATTAATT
Found at i:5015743 original size:2 final size:2
Alignment explanation
Indices: 5015736--5015772 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
5015726 AGCTGAGTTT
5015736 AG AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5015773 GGGCAGAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5024232 original size:34 final size:35
Alignment explanation
Indices: 5024189--5024257 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
5024179 CTCATCTCTA
5024189 AGTCATATCC-TTACAATTCACATACATGACTTGC
1 AGTCATATCCTTTACAATTCACATACATGACTTGC
5024223 AGTCATATCCTTTACAATTCACATACATGACTTGC
1 AGTCATATCCTTTACAATTCACATACATGACTTGC
5024258 GTGGATTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (35 bp):
AGTCATATCCTTTACAATTCACATACATGACTTGC
Found at i:5024771 original size:10 final size:10
Alignment explanation
Indices: 5024733--5024773 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
5024723 ATTTTCTTAT
5024733 TACATATATA
1 TACATATATA
*
5024743 TATATATATA
1 TACATATATA
*
5024753 TATATATATA
1 TACATATATA
*
5024763 TACACATATA
1 TACATATATA
5024773 T
1 T
5024774 CCATTGTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (10 bp):
TACATATATA
Found at i:5024773 original size:2 final size:2
Alignment explanation
Indices: 5024736--5024764 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5024726 TTCTTATTAC
5024736 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
5024765 CACATATATC
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:5027182 original size:67 final size:66
Alignment explanation
Indices: 5027047--5027182 Score: 161
Period size: 67 Copynumber: 2.0 Consensus size: 66
5027037 TCATTGAATG
* * *
5027047 TAAAGTTTTCCCATTTTAGAAAAATTTTAACAATTTTGGGTTATAATAGAAGTCATTAATAAGGG
1 TAAAGTTTTCCCATTTTAGAAAAATTTCAACAATTTTGGGTTATAATAGAAGTCACTAACAAGGG
5027112 A
66 A
* *
5027113 TAAAGTTTT-CCTTTATTAGTAAAAATTTCAA-AATTTTTGGG-TATAATAGAAGTTCCCTAACA
1 TAAAGTTTTCCCATT-TTAG-AAAAATTTCAACAA-TTTTGGGTTATAATAGAAG-TCACTAACA
*
5027175 TGGGA
62 AGGGA
5027180 TAA
1 TAA
5027183 TTTTGGGTTA
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
65 4 0.07
66 26 0.43
67 30 0.50
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (66 bp):
TAAAGTTTTCCCATTTTAGAAAAATTTCAACAATTTTGGGTTATAATAGAAGTCACTAACAAGGG
A
Found at i:5028766 original size:3 final size:3
Alignment explanation
Indices: 5028758--5028793 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
5028748 TTCAAAGATC
*
5028758 TCT TCT TCT TCT TCT TCT TCT TCG TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
5028794 CTCTCTGTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:5028798 original size:2 final size:2
Alignment explanation
Indices: 5028791--5028829 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5028781 GTCTTCTTCT
*
5028791 TC TC TC TC TG 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 T
5028830 AAATCTCTTT
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:0.46, G:0.03, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5041716 original size:27 final size:28
Alignment explanation
Indices: 5041658--5041731 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
5041648 ATAATATATA
* * *
5041658 ATTAATTATTTTTATTTTATTTTAAAAT
1 ATTAATAATTTATAATTTATTTTAAAAT
* *
5041686 ATTAATAATTTATAGTTTA-TTTAAGAT
1 ATTAATAATTTATAATTTATTTTAAAAT
*
5041713 ATTAATAATTAATAATTTA
1 ATTAATAATTTATAATTTA
5041732 AATATTAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 24 0.60
28 16 0.40
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (28 bp):
ATTAATAATTTATAATTTATTTTAAAAT
Found at i:5041732 original size:15 final size:14
Alignment explanation
Indices: 5041714--5041761 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 14
5041704 ATTTAAGATA
*
5041714 TTAATAATTAATAAT
1 TTAA-AATTAATATT
*
5041729 TTAAATATTAACATT
1 TTAAA-ATTAATATT
5041744 TTAAAAATTAATATT
1 TT-AAAATTAATATT
5041759 TTA
1 TTA
5041762 TTTATAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 2 0.07
15 23 0.82
16 3 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAAAATTAATATT
Found at i:5042140 original size:41 final size:39
Alignment explanation
Indices: 5042030--5042136 Score: 115
Period size: 41 Copynumber: 2.7 Consensus size: 39
5042020 AATTAAAAAT
* * * *
5042030 TTAAAATATTAATAATATAATAAGTTAAACATTAATATT
1 TTAAAATATTAATATTTTAATAATTTAAACATTAATATA
* * *
5042069 TTAAAATATTATTATTTATTTATAATTTAAACATTATTATGA
1 TTAAAATATTAATA-TT-TTAATAATTTAAACATTAATAT-A
*
5042111 TTAAAATATTAAGATTTTAATAATTT
1 TTAAAATATTAATATTTTAATAATTT
5042137 TAAAATTTTT
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
39 13 0.24
40 10 0.18
41 20 0.36
42 12 0.22
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.48
Consensus pattern (39 bp):
TTAAAATATTAATATTTTAATAATTTAAACATTAATATA
Found at i:5043223 original size:29 final size:29
Alignment explanation
Indices: 5043186--5043262 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
5043176 AAATTTAAAT
* *
5043186 AAGTTTTTATATTTTTATTGCGTTCAATC
1 AAGTCTTTATATTTTTATTACGTTCAATC
*
5043215 AAGTCTTTATATTTTTATTATGTTCAATC
1 AAGTCTTTATATTTTTATTACGTTCAATC
*
5043244 AAGCCTTTATATTTTTATT
1 AAGTCTTTATATTTTTATT
5043263 TTTGAACAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.26, C:0.10, G:0.08, T:0.56
Consensus pattern (29 bp):
AAGTCTTTATATTTTTATTACGTTCAATC
Found at i:5043314 original size:30 final size:31
Alignment explanation
Indices: 5043182--5043314 Score: 93
Period size: 29 Copynumber: 4.5 Consensus size: 31
5043172 AAAAAAATTT
* ** *
5043182 AAAT-AAGTTTTTATATTTTTATTGCG-TTC
1 AAATAAAGTCTTTATATTTTTATTTTGAATC
* * *
5043211 -AATCAAGTCTTTATATTTTTATTATG-TTC
1 AAATAAAGTCTTTATATTTTTATTTTGAATC
* *
5043240 -AATCAAGCCTTTATATTTTTATTTTTGAA-C
1 AAATAAAGTCTTTATATTTTTA-TTTTGAATC
* *
5043270 AAAATAAAAT-TTTATACTTTTATTTTGAATC
1 -AAATAAAGTCTTTATATTTTTATTTTGAATC
5043301 AAAT-AAGTCTTTAT
1 AAATAAAGTCTTTAT
5043315 GATAAATAAT
Statistics
Matches: 86, Mismatches: 11, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
28 3 0.03
29 45 0.52
30 21 0.24
31 12 0.14
32 5 0.06
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (31 bp):
AAATAAAGTCTTTATATTTTTATTTTGAATC
Found at i:5045290 original size:14 final size:15
Alignment explanation
Indices: 5045271--5045300 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5045261 ATCTCTCATA
5045271 TAAAATTTTA-ATTT
1 TAAAATTTTACATTT
5045285 TAAAATTTTACATTT
1 TAAAATTTTACATTT
5045300 T
1 T
5045301 GATGATTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAAATTTTACATTT
Found at i:5046363 original size:16 final size:18
Alignment explanation
Indices: 5046335--5046371 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
5046325 TAATTTTTAA
5046335 TTATAATTTAG-TTATTT
1 TTATAATTTAGTTTATTT
5046352 TTATAA-TTAGTTTATTT
1 TTATAATTTAGTTTATTT
5046369 TTA
1 TTA
5046372 GTGAGTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
TTATAATTTAGTTTATTT
Found at i:5048742 original size:33 final size:30
Alignment explanation
Indices: 5048704--5048785 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 30
5048694 TAGTATTGAA
* *
5048704 TAAATTAAATATTAATATTTTAATTTATTTTT
1 TAAATTAAATATTAATATTTT--TTAATATTT
**
5048736 TAAAATTAAATATTTTTATTTTTTAATATTT
1 T-AAATTAAATATTAATATTTTTTAATATTT
*
5048767 TGAATTAAATATTAATATT
1 TAAATTAAATATTAATATT
5048786 CATCAAAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
30 15 0.36
31 8 0.19
32 1 0.02
33 18 0.43
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (30 bp):
TAAATTAAATATTAATATTTTTTAATATTT
Found at i:5061044 original size:13 final size:13
Alignment explanation
Indices: 5061028--5061055 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
5061018 AAAGTTAGAC
5061028 ATAACATCATTAA
1 ATAACATCATTAA
5061041 ATAACATCATTAA
1 ATAACATCATTAA
5061054 AT
1 AT
5061056 TGCTTTAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAACATCATTAA
Found at i:5069475 original size:24 final size:24
Alignment explanation
Indices: 5069445--5069502 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
5069435 GCGTTCAATC
5069445 AAATTTTTATTTTTTTTATTAAAT
1 AAATTTTTATTTTTTTTATTAAAT
5069469 AAATTTTTATTTTTTTTATTAAAT
1 AAATTTTTATTTTTTTTATTAAAT
5069493 AAATTTTTAT
1 AAATTTTTAT
5069503 AGTTAATGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
AAATTTTTATTTTTTTTATTAAAT
Found at i:5069477 original size:15 final size:15
Alignment explanation
Indices: 5069457--5069502 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
5069447 ATTTTTATTT
5069457 TTTTTATTAAATAAA
1 TTTTTATTAAATAAA
5069472 TTTTTATT---T---
1 TTTTTATTAAATAAA
5069481 TTTTTATTAAATAAA
1 TTTTTATTAAATAAA
5069496 TTTTTAT
1 TTTTTAT
5069503 AGTTAATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
9 8 0.32
12 2 0.08
15 15 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTTATTAAATAAA
Found at i:5070264 original size:20 final size:17
Alignment explanation
Indices: 5070239--5070277 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 17
5070229 ATCTCTAAAC
5070239 AAATTAATAAACATAGAATA
1 AAATTAA-AAA-ATA-AATA
5070259 AAATTAAAAAATAAATA
1 AAATTAAAAAATAAATA
5070276 AA
1 AA
5070278 TAAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 3 0.16
20 7 0.37
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
AAATTAAAAAATAAATA
Found at i:5070890 original size:3 final size:3
Alignment explanation
Indices: 5070884--5070918 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5070874 CGACGTCTGC
*
5070884 TGT TGT TGC TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
5070919 CGGTGGTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.03, G:0.34, T:0.63
Consensus pattern (3 bp):
TGT
Found at i:5070895 original size:9 final size:9
Alignment explanation
Indices: 5070881--5070919 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
5070871 CGACGACGTC
5070881 TGCTGTTGT
1 TGCTGTTGT
5070890 TGCTGTTGT
1 TGCTGTTGT
*
5070899 TGTTGTTGT
1 TGCTGTTGT
*
5070908 TGTTGTTGT
1 TGCTGTTGT
5070917 TGC
1 TGC
5070920 GGTGGTGGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.00, C:0.08, G:0.33, T:0.59
Consensus pattern (9 bp):
TGCTGTTGT
Found at i:5074073 original size:2 final size:2
Alignment explanation
Indices: 5074066--5074114 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
5074056 TAATGGGAGA
* * *
5074066 AT AT AT AT AG AT AT AG AT AA AT -T 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
5074107 AT AT AT AT
1 AT AT AT AT
5074115 TGGTGTTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5074298 original size:2 final size:2
Alignment explanation
Indices: 5074293--5074317 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5074283 TTTTCTCCCC
5074293 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 C
5074318 AAGTTTCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:5076976 original size:2 final size:2
Alignment explanation
Indices: 5076969--5077002 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5076959 AGGCATACAT
5076969 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5077003 TCAAATGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5087305 original size:2 final size:2
Alignment explanation
Indices: 5087298--5087342 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
5087288 TGACAATCAA
*
5087298 TC TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5087340 TC T
1 TC T
5087343 TAATCATAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.47, G:0.02, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5092445 original size:26 final size:26
Alignment explanation
Indices: 5092392--5092459 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 26
5092382 TAATATAAAA
* *
5092392 TACATATATTTATTATTAATTTTCATT
1 TACATAT-TTTATAATTAATTTTAATT
*
5092419 T-CATATTTTATAATTATTTTTAAATT
1 TACATATTTTATAATTAATTTT-AATT
*
5092445 TACAGATTTT-TAATT
1 TACATATTTTATAATT
5092460 TAATCAATTC
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 13 0.37
26 14 0.40
27 8 0.23
ACGTcount: A:0.34, C:0.06, G:0.01, T:0.59
Consensus pattern (26 bp):
TACATATTTTATAATTAATTTTAATT
Found at i:5097253 original size:34 final size:34
Alignment explanation
Indices: 5097210--5097277 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
5097200 TGTCCTTCGC
5097210 TAATGCTGGCTTTGATGGAACCCAAGATCAAGTT
1 TAATGCTGGCTTTGATGGAACCCAAGATCAAGTT
5097244 TAATGCTGGCTTTGATGGAACCCAAGATCAAGTT
1 TAATGCTGGCTTTGATGGAACCCAAGATCAAGTT
5097278 GAAGACATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (34 bp):
TAATGCTGGCTTTGATGGAACCCAAGATCAAGTT
Found at i:5098697 original size:21 final size:21
Alignment explanation
Indices: 5098668--5098708 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5098658 TTACATATTA
*
5098668 TAAATAAAATCAAATAAAATT
1 TAAAAAAAATCAAATAAAATT
* *
5098689 TAAAAAAAATGACATAAAAT
1 TAAAAAAAATCAAATAAAAT
5098709 ACACGCCTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAAAAAAATCAAATAAAATT
Found at i:5102481 original size:29 final size:26
Alignment explanation
Indices: 5102437--5102496 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 26
5102427 TCATAAAACT
* *
5102437 TATTTGATTAAAAATATAAATATAAA
1 TATTTGATTAAAAATAAAAAAATAAA
5102463 TATTTGATTGAATATAATAAAAAAATAAA
1 TATTTGATT-AA-A-AATAAAAAAATAAA
*
5102492 GATTT
1 TATTT
5102497 ACACATGTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.32
27 2 0.07
28 1 0.04
29 16 0.57
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (26 bp):
TATTTGATTAAAAATAAAAAAATAAA
Found at i:5103428 original size:8 final size:8
Alignment explanation
Indices: 5103392--5103441 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
5103382 CTGACGTAAC
*
5103392 ATATTAAC
1 ATATTAAT
5103400 ATATTAAT
1 ATATTAAT
5103408 GATGATATAAT
1 -AT-AT-TAAT
5103419 ATATTAAT
1 ATATTAAT
5103427 ATATT-AT
1 ATATTAAT
5103434 A-ATTAAT
1 ATATTAAT
5103441 A
1 A
5103442 ATGATCTGAT
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
6 3 0.08
7 6 0.16
8 16 0.43
9 4 0.11
10 4 0.11
11 4 0.11
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (8 bp):
ATATTAAT
Found at i:5122332 original size:6 final size:6
Alignment explanation
Indices: 5122316--5122364 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
5122306 CTTAATCTTT
* * * * *
5122316 TATATA CATATG TATATA TACATA TATATA TATACA TATATG TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
5122364 T
1 T
5122365 TCTTTTTTGA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:5122335 original size:14 final size:14
Alignment explanation
Indices: 5122316--5122364 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
5122306 CTTAATCTTT
5122316 TATATACATATGTA
1 TATATACATATGTA
*
5122330 TATATACATATATA
1 TATATACATATGTA
5122344 TATATACATATATGTA
1 TATATAC--ATATGTA
5122360 TATAT
1 TATAT
5122365 TCTTTTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 20 0.65
16 11 0.35
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (14 bp):
TATATACATATGTA
Found at i:5122362 original size:8 final size:8
Alignment explanation
Indices: 5122316--5122364 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
5122306 CTTAATCTTT
*
5122316 TATATACA
1 TATATATA
*
5122324 TATGTATA
1 TATATATA
*
5122332 TATACATA
1 TATATATA
5122340 TATATATA
1 TATATATA
*
5122348 TACATATA
1 TATATATA
*
5122356 TGTATATA
1 TATATATA
5122364 T
1 T
5122365 TCTTTTTTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (8 bp):
TATATATA
Found at i:5122364 original size:10 final size:10
Alignment explanation
Indices: 5122316--5122364 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
5122306 CTTAATCTTT
*
5122316 TATATACATA
1 TATATATATA
*
5122326 TGTATATATA
1 TATATATATA
*
5122336 CATATATATA
1 TATATATATA
*
5122346 TATACATATA
1 TATATATATA
*
5122356 TGTATATAT
1 TATATATAT
5122365 TCTTTTTTGA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (10 bp):
TATATATATA
Found at i:5129134 original size:19 final size:20
Alignment explanation
Indices: 5129110--5129147 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
5129100 CTCTAAATAT
5129110 TTTCTTT-ATAGTTATTCTC
1 TTTCTTTCATAGTTATTCTC
5129129 TTTCTTTCATAGTTATTCT
1 TTTCTTTCATAGTTATTCT
5129148 TTCAATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.16, C:0.16, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTCTTTCATAGTTATTCTC
Found at i:5135117 original size:14 final size:15
Alignment explanation
Indices: 5135088--5135120 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5135078 ATATTGTGTT
*
5135088 TTTTTTTCATTAAAG
1 TTTTTTTCACTAAAG
5135103 TTTTTTTCACT-AAG
1 TTTTTTTCACTAAAG
5135117 TTTT
1 TTTT
5135121 CCTTGATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (15 bp):
TTTTTTTCACTAAAG
Found at i:5152735 original size:3 final size:3
Alignment explanation
Indices: 5152729--5152771 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
5152719 TAAAGATGAT
* *
5152729 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAG GAA GAG GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
5152772 GAGCTGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5153339 original size:3 final size:3
Alignment explanation
Indices: 5153331--5153362 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
5153321 AGCTATAGCT
5153331 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
5153363 GAGTTCAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5172989 original size:34 final size:34
Alignment explanation
Indices: 5172951--5173119 Score: 144
Period size: 34 Copynumber: 5.0 Consensus size: 34
5172941 AAAACTTTGG
* * *
5172951 CATCAGATGTTACACATCAAGGCCAAAGTTTCAA
1 CATCAGATGTTACACACCAAGGTCAAAGCTTCAA
* * *
5172985 CATCAGATGTTATATACCAAGGTCAAAGCTTCAC
1 CATCAGATGTTACACACCAAGGTCAAAGCTTCAA
* * *
5173019 CATCAGATATTACACACCAAGGTCAAAACTTCAG
1 CATCAGATGTTACACACCAAGGTCAAAGCTTCAA
* * ** *
5173053 CATTAGATATTACATGCCAAGGCCAAAGCTTCAGTA
1 CATCAGATGTTACACACCAAGGTCAAAGCTTCA--A
* ** *
5173089 C-T-GGATGTTACATGCTAAGGTCAAAGCTTCA
1 CATCAGATGTTACACACCAAGGTCAAAGCTTCA
5173120 CCACTAAATG
Statistics
Matches: 112, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
34 110 0.98
35 1 0.01
36 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (34 bp):
CATCAGATGTTACACACCAAGGTCAAAGCTTCAA
Found at i:5173100 original size:68 final size:68
Alignment explanation
Indices: 5172951--5173085 Score: 171
Period size: 68 Copynumber: 2.0 Consensus size: 68
5172941 AAAACTTTGG
* * * * * *
5172951 CATCAGATGTTACACATCAAGGCCAAAGTTTCAACATCAGATGTTATATACCAAGGTCAAAGCTT
1 CATCAGATGTTACACACCAAGGTCAAAGCTTCAACATCAGATATTACATACCAAGGCCAAAGCTT
5173016 CAC
66 CAC
* * * * *
5173019 CATCAGATATTACACACCAAGGTCAAAACTTCAGCATTAGATATTACATGCCAAGGCCAAAGCTT
1 CATCAGATGTTACACACCAAGGTCAAAGCTTCAACATCAGATATTACATACCAAGGCCAAAGCTT
5173084 CA
66 CA
5173086 GTACTGGATG
Statistics
Matches: 56, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (68 bp):
CATCAGATGTTACACACCAAGGTCAAAGCTTCAACATCAGATATTACATACCAAGGCCAAAGCTT
CAC
Found at i:5173131 original size:34 final size:34
Alignment explanation
Indices: 5173001--5173139 Score: 136
Period size: 34 Copynumber: 4.1 Consensus size: 34
5172991 ATGTTATATA
**
5173001 CCAAGGTCAAAGCTTCACCA-TCAGATATTACACA
1 CCAAGGTCAAAGCTTCACCACT-AGATATTACATG
* * *
5173035 CCAAGGTCAAAACTTCAGCATTAGATATTACATG
1 CCAAGGTCAAAGCTTCACCACTAGATATTACATG
* ** * *
5173069 CCAAGGCCAAAGCTTCAGTACTGGATGTTACATG
1 CCAAGGTCAAAGCTTCACCACTAGATATTACATG
* * * *
5173103 CTAAGGTCAAAGCTTCACCACTAAATGTTACGTG
1 CCAAGGTCAAAGCTTCACCACTAGATATTACATG
5173137 CCA
1 CCA
5173140 TGCCTTATAC
Statistics
Matches: 86, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
34 85 0.99
35 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.24
Consensus pattern (34 bp):
CCAAGGTCAAAGCTTCACCACTAGATATTACATG
Found at i:5192626 original size:3 final size:3
Alignment explanation
Indices: 5192618--5192645 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5192608 CTCCAAACCA
5192618 TCC TCC TCC TCC TCC TCC TCC TCC TCC T
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC T
5192646 TCACACGCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.64, G:0.00, T:0.36
Consensus pattern (3 bp):
TCC
Found at i:5193398 original size:16 final size:16
Alignment explanation
Indices: 5193367--5193397 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
5193357 AGAAATAAAA
5193367 ATACTAATACATTTTT
1 ATACTAATACATTTTT
5193383 ATACTAATA-ATTTTT
1 ATACTAATACATTTTT
5193398 TTTGTTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (16 bp):
ATACTAATACATTTTT
Found at i:5197406 original size:2 final size:2
Alignment explanation
Indices: 5197399--5197440 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
5197389 GTAAGAAGAG
* * *
5197399 AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AA 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
5197441 TCTAAAAATA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:5197673 original size:24 final size:24
Alignment explanation
Indices: 5197641--5197689 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
5197631 TATATTGATG
* *
5197641 ATAAACTCCCATCGAGACAATCGA
1 ATAAACTCCAACCGAGACAATCGA
5197665 ATAAACTCCAACCGAGACAATCGA
1 ATAAACTCCAACCGAGACAATCGA
5197689 A
1 A
5197690 GTCTCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.29, G:0.12, T:0.14
Consensus pattern (24 bp):
ATAAACTCCAACCGAGACAATCGA
Found at i:5203592 original size:216 final size:218
Alignment explanation
Indices: 5203213--5203648 Score: 639
Period size: 216 Copynumber: 2.0 Consensus size: 218
5203203 TATAGAAAAT
* * * * *
5203213 ATTTTATTTGGATGTTTTATGACAAATATTTTTCATTATTTATTTTTAAAAAAGTAAAACCTTAC
1 ATTTTATTTGAACGTTTTATGAAAAATATTTTTCACTATTTATTTTTAAAAAAGCAAAACCTTAC
* * *
5203278 GAATTTACTTAAACTTAACGAACATTATCCAAATACAATAGAAAAAAAACAAAAAGAAAGATTAC
66 GAATTTAATTAAACTCAACAAACATTATCCAAATACAATAGAAAAAAAACAAAAAGAAAGATTAC
* * *
5203343 TCAAATTACATACATGTTAAAAAAAAAACTTATTTTTGAGGGATTAAGTATTATAGTTAATTAG-
131 ACAAATTACATACATGTTAAAAAAAAAACTTATTTTTGAGGGATTAAGTACTATAGTTAACTAGC
5203407 TCTCCAAGCTTCAAATTGATATTG
196 T-TCCAAGCTTCAAATTGATATTG
*
5203431 ATTTTATTTGAACGTTTTATGAAAAATGTTTTTCACTATTTA-TTTTAAAAAA-CAAATACCTTA
1 ATTTTATTTGAACGTTTTATGAAAAATATTTTTCACTATTTATTTTTAAAAAAGCAAA-ACCTTA
* *
5203494 -GCAATTTAATTAAACTCAACAAATATTATCCAAATACAATAG-AAAAAAATAAAAAGAAAGATT
65 CG-AATTTAATTAAACTCAACAAACATTATCCAAATACAATAGAAAAAAAACAAAAAGAAAGATT
* *
5203557 ACACAAATTACATACATGTTAAAAATAATACTTATTTTTGAGGGATTAAGTACTATAGTTAACTA
129 ACACAAATTACATACATGTTAAAAAAAAAACTTATTTTTGAGGGATTAAGTACTATAGTTAACTA
** *
5203622 GCTTGTAAGCTTTAAATTGATATTG
194 GCTTCCAAGCTTCAAATTGATATTG
5203647 AT
1 AT
5203649 AACTTGAATC
Statistics
Matches: 196, Mismatches: 19, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
216 106 0.54
217 53 0.27
218 37 0.19
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.36
Consensus pattern (218 bp):
ATTTTATTTGAACGTTTTATGAAAAATATTTTTCACTATTTATTTTTAAAAAAGCAAAACCTTAC
GAATTTAATTAAACTCAACAAACATTATCCAAATACAATAGAAAAAAAACAAAAAGAAAGATTAC
ACAAATTACATACATGTTAAAAAAAAAACTTATTTTTGAGGGATTAAGTACTATAGTTAACTAGC
TTCCAAGCTTCAAATTGATATTG
Found at i:5205009 original size:22 final size:21
Alignment explanation
Indices: 5204959--5205010 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5204949 ACAAGTCGCC
* *
5204959 AACAAA-TCGATATATAATTG
1 AACAAATTCAATATAAAATTG
5204979 AACAAATTCAATATAAAATTG
1 AACAAATTCAATATAAAATTG
5205000 AATCAAATTCA
1 AA-CAAATTCA
5205011 CAAGATCTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 6 0.21
21 14 0.50
22 8 0.29
ACGTcount: A:0.54, C:0.12, G:0.06, T:0.29
Consensus pattern (21 bp):
AACAAATTCAATATAAAATTG
Found at i:5205198 original size:2 final size:2
Alignment explanation
Indices: 5205191--5205231 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5205181 TCTAATTTGA
5205191 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5205232 ATCCTTGACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5208373 original size:2 final size:2
Alignment explanation
Indices: 5208362--5208395 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5208352 AACAAAGATG
5208362 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5208396 GATAGATAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5210482 original size:17 final size:16
Alignment explanation
Indices: 5210448--5210497 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
5210438 TAATTTTTAA
*
5210448 TTATAATTTAGTTGTTT
1 TTATAA-TTAGTTATTT
5210465 TTATAATTAGTTTATTT
1 TTATAATTAG-TTATTT
*
5210482 TTA-AATGAGTTATTT
1 TTATAATTAGTTATTT
5210497 T
1 T
5210498 AATTTTATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 7 0.23
16 9 0.30
17 14 0.47
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (16 bp):
TTATAATTAGTTATTT
Found at i:5221517 original size:6 final size:6
Alignment explanation
Indices: 5221506--5221543 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
5221496 TAATTTAGAA
5221506 AAAAAT AAAAAT AAAAA- ATAAAAT -AAAAT AAAAAT AAA
1 AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAA
5221544 CACTCAGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 6 0.21
6 23 0.79
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:5228815 original size:29 final size:29
Alignment explanation
Indices: 5228773--5228830 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
5228763 TGTGCCAAAA
5228773 TCAAATATCATTGAAGGTTCTAGTGATTT
1 TCAAATATCATTGAAGGTTCTAGTGATTT
5228802 TCAAATATCATTGAAGGTTCTAGTGATTT
1 TCAAATATCATTGAAGGTTCTAGTGATTT
5228831 GTGTAAAGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.41
Consensus pattern (29 bp):
TCAAATATCATTGAAGGTTCTAGTGATTT
Found at i:5240530 original size:94 final size:92
Alignment explanation
Indices: 5240358--5240531 Score: 249
Period size: 94 Copynumber: 1.9 Consensus size: 92
5240348 TTTATGGAAG
** *
5240358 ATCAAAATCTTTAATTATTATTTTTTATTATCTTGCAAGAGTCGTTGTCTCCACGGAGAAAATAA
1 ATCAAAATCTTTAATTATTATTTTTTATTATCTTGCAAGACCCGTTGTCTCAACGGAGAAAATAA
* *
5240423 AAGGTTTAGAATTTTCAGATTTTAAAT
66 AAAGTTTAAAATTTTCAGATTTTAAAT
* * * *
5240450 ATCAAAATCTTTAATTATTGTTTTTTATTATTTTTTGCGAGACCCGTTGTCTCAATGGAGAAAAT
1 ATCAAAATCTTTAATTATTATTTTTTATTA--TCTTGCAAGACCCGTTGTCTCAACGGAGAAAAT
5240515 AAAAAGTTTAAAATTTT
64 AAAAAGTTTAAAATTTT
5240532 TGAATTTCAA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
92 29 0.41
94 42 0.59
ACGTcount: A:0.34, C:0.10, G:0.13, T:0.43
Consensus pattern (92 bp):
ATCAAAATCTTTAATTATTATTTTTTATTATCTTGCAAGACCCGTTGTCTCAACGGAGAAAATAA
AAAGTTTAAAATTTTCAGATTTTAAAT
Found at i:5251140 original size:18 final size:18
Alignment explanation
Indices: 5251101--5251140 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
5251091 CTATATATTT
5251101 ATATTTTAATTTTAGTTGA
1 ATATTTTAATTTTAG-TGA
5251120 ATATTTTAAATTTTA-TGA
1 ATATTTT-AATTTTAGTGA
5251138 ATA
1 ATA
5251141 ATTAGTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 7 0.35
20 7 0.35
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (18 bp):
ATATTTTAATTTTAGTGA
Found at i:5267315 original size:22 final size:24
Alignment explanation
Indices: 5267287--5267332 Score: 78
Period size: 22 Copynumber: 2.0 Consensus size: 24
5267277 TCAAATACTG
5267287 AAAACATATAAACAC-ATA-CTTA
1 AAAACATATAAACACGATATCTTA
5267309 AAAACATATAAACACGATATCTTA
1 AAAACATATAAACACGATATCTTA
5267333 TTAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 15 0.68
23 3 0.14
24 4 0.18
ACGTcount: A:0.57, C:0.17, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAACATATAAACACGATATCTTA
Found at i:5269996 original size:41 final size:40
Alignment explanation
Indices: 5269927--5270011 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 40
5269917 TTTCCCTTCA
* *
5269927 AATTTGGAACACAAAGCGAAGTAAATCATGGCTTTGGATG
1 AATTTGGAACACAAAGAGAAGTAAATCATGACTTTGGATG
* *
5269967 CAATTTGGAATACAAAGAGAAAG-AGATCATGACTTTGGATG
1 -AATTTGGAACACAAAGAG-AAGTAAATCATGACTTTGGATG
5270008 AATT
1 AATT
5270012 CGACAACGTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
40 4 0.10
41 32 0.82
42 3 0.08
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.26
Consensus pattern (40 bp):
AATTTGGAACACAAAGAGAAGTAAATCATGACTTTGGATG
Found at i:5276472 original size:213 final size:213
Alignment explanation
Indices: 5276105--5276531 Score: 755
Period size: 213 Copynumber: 2.0 Consensus size: 213
5276095 ACTGTTATTT
*
5276105 CCATGTCCCTTATGAGATTTTTCTTTTTGGGATGGAAGGGACTGGCAGATGTTAAGATTTTCCAT
1 CCATGTCCCTTATGAGATTTTTCTTTTTGGGATGGAAGGGACTGGCAGATGTTAAGATTTGCCAT
* * * * *
5276170 GCGGAATAAGAATGTTGCTTGATTTGTTGTTACTAATATGGCCGTGGAACTCTATGAGCAAAGGA
66 GAGGAATAAGAATGTTGCCTGATTTGTTGTTACTAATATGGCCATGGAACTCTATAAGCAAAGCA
* * *
5276235 GGACATGTGTGTTGAGACAAAATTAATGTACCATTGCAAACTAACATTTCTTTGAATGTTGACAA
131 GGACATGTATGTTCAGACAAAATTAATATACCATTGCAAACTAACATTTCTTTGAATGTTGACAA
5276300 CTTCATCCAGGTTTCATC
196 CTTCATCCAGGTTTCATC
5276318 CCATGTCCCTTATGAGATTTTTCTTTTTGGGATGGAAGGGACTGGCAGATGTTAAGATTTGCCAT
1 CCATGTCCCTTATGAGATTTTTCTTTTTGGGATGGAAGGGACTGGCAGATGTTAAGATTTGCCAT
*
5276383 GAGGAATAAGAATGTTGCCTGATTTGTTGTTACTAATATGGCCATGGGACTCTATAAGCAAAGCA
66 GAGGAATAAGAATGTTGCCTGATTTGTTGTTACTAATATGGCCATGGAACTCTATAAGCAAAGCA
*
5276448 GGCCATGTATGTTCAGACAAAATTAATATACCATTGCAAACTAACATTTCTTTGAATGTTGACAA
131 GGACATGTATGTTCAGACAAAATTAATATACCATTGCAAACTAACATTTCTTTGAATGTTGACAA
5276513 CTTCATCCAGGTTTCATC
196 CTTCATCCAGGTTTCATC
5276531 C
1 C
5276532 TTTTTAGAGA
Statistics
Matches: 203, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
213 203 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (213 bp):
CCATGTCCCTTATGAGATTTTTCTTTTTGGGATGGAAGGGACTGGCAGATGTTAAGATTTGCCAT
GAGGAATAAGAATGTTGCCTGATTTGTTGTTACTAATATGGCCATGGAACTCTATAAGCAAAGCA
GGACATGTATGTTCAGACAAAATTAATATACCATTGCAAACTAACATTTCTTTGAATGTTGACAA
CTTCATCCAGGTTTCATC
Found at i:5277361 original size:61 final size:61
Alignment explanation
Indices: 5277284--5277406 Score: 212
Period size: 61 Copynumber: 2.0 Consensus size: 61
5277274 TGATAGGAGT
*
5277284 TACTTAACTGTATTTTTTACCTATCAAATTGTATTAACGATAAGGATTCTGAAAATACTTC
1 TACTTAACTGTATTTTTTACCTATCAAATTGTATTAACAATAAGGATTCTGAAAATACTTC
*
5277345 TACTTAAGCT-TATTTTTTCCCTATCAAATTGTATTAACAATAAGGATTCTGAAAATACTTC
1 TACTTAA-CTGTATTTTTTACCTATCAAATTGTATTAACAATAAGGATTCTGAAAATACTTC
5277406 T
1 T
5277407 GCTCCCCCTC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 57 0.97
62 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.41
Consensus pattern (61 bp):
TACTTAACTGTATTTTTTACCTATCAAATTGTATTAACAATAAGGATTCTGAAAATACTTC
Found at i:5282439 original size:21 final size:21
Alignment explanation
Indices: 5282414--5282453 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5282404 AATTTATCTC
*
5282414 TTTTGAGTCGAGAATGTATAT
1 TTTTGAATCGAGAATGTATAT
*
5282435 TTTTGAATCGAGAGTGTAT
1 TTTTGAATCGAGAATGTAT
5282454 GTGTTTATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.05, G:0.25, T:0.42
Consensus pattern (21 bp):
TTTTGAATCGAGAATGTATAT
Found at i:5289797 original size:14 final size:13
Alignment explanation
Indices: 5289769--5289794 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5289759 TTCTTTTATA
5289769 ATAAATTATTTTT
1 ATAAATTATTTTT
5289782 ATAAATTATTTTT
1 ATAAATTATTTTT
5289795 TATTTAAAGG
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:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATAAATTATTTTT
Found at i:5294645 original size:23 final size:22
Alignment explanation
Indices: 5294619--5294666 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
5294609 AATAAAAATT
5294619 AATTTAATTAAAATTTTAAAAAA
1 AATTTAATT-AAATTTTAAAAAA
**
5294642 AATTTAATTATTTTTTAAAAAA
1 AATTTAATTAAATTTTAAAAAA
5294664 AAT
1 AAT
5294667 CTAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATTTAATTAAATTTTAAAAAA
Found at i:5294825 original size:22 final size:22
Alignment explanation
Indices: 5294798--5294839 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5294788 AATACACCTT
*
5294798 TTTTTATATTATATAAAAATAC
1 TTTTTATATTATAAAAAAATAC
*
5294820 TTTTTATATTTTAAAAAAAT
1 TTTTTATATTATAAAAAAAT
5294840 TATTCTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTTATATTATAAAAAAATAC
Found at i:5297807 original size:79 final size:79
Alignment explanation
Indices: 5297676--5297833 Score: 221
Period size: 79 Copynumber: 2.0 Consensus size: 79
5297666 TTGGAAATAG
* * *
5297676 GACAATACAAGAATCACCAAGATTGATCCCCAATCCGATTATTTATGGAGATGGTTTCCACC-CT
1 GACAACACAAGAATCACCAAGATTCATCCCCAATCCCATTATTTATGGAGATGGTTTCCACCTCT
5297740 TCTCAATGACCCCAT
66 TC-CAATGACCCCAT
* * * *
5297755 GACAACACAAGAATTACCAAGA-TCATTTCCCAATCCCATTTTTTGTGGAGATGGTTTCCACCTC
1 GACAACACAAGAATCACCAAGATTCA-TCCCCAATCCCATTATTTATGGAGATGGTTTCCACCTC
5297819 TTCCAATGACCCCAT
65 TTCCAATGACCCCAT
5297834 TCAAGATTAA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
78 2 0.03
79 64 0.91
80 4 0.06
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (79 bp):
GACAACACAAGAATCACCAAGATTCATCCCCAATCCCATTATTTATGGAGATGGTTTCCACCTCT
TCCAATGACCCCAT
Found at i:5298034 original size:44 final size:44
Alignment explanation
Indices: 5297971--5298054 Score: 168
Period size: 44 Copynumber: 1.9 Consensus size: 44
5297961 ACATGTATGT
5297971 AGATGTACTTTTAGACCACTGCAGAGTATCAATCGTTATTACCA
1 AGATGTACTTTTAGACCACTGCAGAGTATCAATCGTTATTACCA
5298015 AGATGTACTTTTAGACCACTGCAGAGTATCAATCGTTATT
1 AGATGTACTTTTAGACCACTGCAGAGTATCAATCGTTATT
5298055 GCTAATTATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (44 bp):
AGATGTACTTTTAGACCACTGCAGAGTATCAATCGTTATTACCA
Found at i:5310235 original size:2 final size:2
Alignment explanation
Indices: 5310228--5310284 Score: 51
Period size: 2 Copynumber: 28.5 Consensus size: 2
5310218 AAAGGGTCAG
* * ** *
5310228 AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT AT GC AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
5310270 AT AC AT GT AT AT AT A
1 AT AT AT AT AT AT AT A
5310285 GGATAGGTGT
Statistics
Matches: 43, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (2 bp):
AT
Found at i:5310245 original size:12 final size:12
Alignment explanation
Indices: 5310228--5310284 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
5310218 AAAGGGTCAG
*
5310228 ATATATATATAT
1 ATATATATACAT
*
5310240 ATATATACACAT
1 ATATATATACAT
*
5310252 ATATATATGCAT
1 ATATATATACAT
*
5310264 ATACATATACAT
1 ATATATATACAT
*
5310276 GTATATATA
1 ATATATATA
5310285 GGATAGGTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (12 bp):
ATATATATACAT
Found at i:5311834 original size:2 final size:2
Alignment explanation
Indices: 5311827--5311854 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5311817 AGCTTTAAAT
5311827 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5311855 AGACAAATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5323238 original size:14 final size:13
Alignment explanation
Indices: 5323203--5323245 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
5323193 TTATAAAAAT
5323203 AATTATACTATATA
1 AATTATA-TATATA
*
5323217 TATATATATATATCA
1 AAT-TATATATAT-A
5323232 AATTATATATATA
1 AATTATATATATA
5323245 A
1 A
5323246 TAATAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
13 2 0.08
14 16 0.64
15 7 0.28
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTATATATATA
Found at i:5324262 original size:2 final size:2
Alignment explanation
Indices: 5324255--5324291 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5324245 GATCTTGGAA
5324255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5324292 ACCAGCTTGT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5326952 original size:16 final size:19
Alignment explanation
Indices: 5326921--5326960 Score: 59
Period size: 16 Copynumber: 2.3 Consensus size: 19
5326911 GACTGACTAT
5326921 ATAAAAATTATTTAAAT-A
1 ATAAAAATTATTTAAATAA
5326939 ATAAAAA-T-TTTAAATAA
1 ATAAAAATTATTTAAATAA
5326956 ATAAA
1 ATAAA
5326961 TAAACTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 7 0.33
18 7 0.33
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATAAAAATTATTTAAATAA
Found at i:5330822 original size:10 final size:11
Alignment explanation
Indices: 5330807--5330831 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5330797 AAAGGTTGAT
5330807 AAAAAAAGAAA
1 AAAAAAAGAAA
5330818 AAAAAAAGAAA
1 AAAAAAAGAAA
5330829 AAA
1 AAA
5330832 CAAACTAACT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:5331096 original size:12 final size:12
Alignment explanation
Indices: 5331079--5331114 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5331069 ACTTGAAAGA
5331079 GAGGGAGGAAGG
1 GAGGGAGGAAGG
5331091 GAGGGAGGAAGG
1 GAGGGAGGAAGG
* *
5331103 AAGGAAGGAAGG
1 GAGGGAGGAAGG
5331115 AAGGAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (12 bp):
GAGGGAGGAAGG
Found at i:5331103 original size:4 final size:4
Alignment explanation
Indices: 5331084--5331121 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
5331074 AAAGAGAGGG
* *
5331084 AGGA AGGG AGGG AGGA AGGA AGGA AGGA AGGA AGGA AG
1 AGGA AGGA AGGA AGGA AGGA AGGA AGGA AGGA AGGA AG
5331122 AAAGAAAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (4 bp):
AGGA
Found at i:5338746 original size:6 final size:6
Alignment explanation
Indices: 5338735--5338773 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
5338725 GAGGCCCCGC
* *
5338735 TTCTGG TTCTGG TTCTGG TTCTGG TTCAGG TTCAGG TTC
1 TTCTGG TTCTGG TTCTGG TTCTGG TTCTGG TTCTGG TTC
5338774 AGGATCTAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.05, C:0.18, G:0.31, T:0.46
Consensus pattern (6 bp):
TTCTGG
Found at i:5343075 original size:16 final size:15
Alignment explanation
Indices: 5343033--5343075 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
5343023 TTATTATTTT
*
5343033 ATATTATTTTAATTA
1 ATATTATTTTAATAA
*
5343048 ATATTAAATTTAATAA
1 ATATT-ATTTTAATAA
5343064 ATAATTATTTTA
1 AT-ATTATTTTA
5343076 TCATATTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 15 0.65
17 3 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTATTTTAATAA
Found at i:5352717 original size:21 final size:22
Alignment explanation
Indices: 5352693--5352746 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
5352683 CGTTATTAAT
* *
5352693 TTTTAAGCATTGTTTGA-TTGA
1 TTTTAAGCATTGTGTGACTAGA
* *
5352714 TTTTAGGCATTGTGTGACTAGT
1 TTTTAAGCATTGTGTGACTAGA
5352736 TTTTAAGCATT
1 TTTTAAGCATT
5352747 ACGTAATTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 15 0.56
22 12 0.44
ACGTcount: A:0.22, C:0.07, G:0.20, T:0.50
Consensus pattern (22 bp):
TTTTAAGCATTGTGTGACTAGA
Done.