Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 16 of 143
Found at i:4923946 original size:17 final size:17
Alignment explanation
Indices: 4923924--4923958 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4923914 ACTTAAAAAA
*
4923924 ATAAATTAATTGTAATT
1 ATAAATCAATTGTAATT
*
4923941 ATAAATCAATTTTAATT
1 ATAAATCAATTGTAATT
4923958 A
1 A
4923959 ACTAAACAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
ATAAATCAATTGTAATT
Found at i:4943633 original size:39 final size:39
Alignment explanation
Indices: 4943579--4943656 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
4943569 AGGATGAATA
4943579 TATAAAATTTATTAAATAAAAGGATCATTATCAATCATT
1 TATAAAATTTATTAAATAAAAGGATCATTATCAATCATT
* * *
4943618 TATAAAATTTGTTAAATAAAAGGGTGATTATCAATCATT
1 TATAAAATTTATTAAATAAAAGGATCATTATCAATCATT
4943657 ATCTATTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.38
Consensus pattern (39 bp):
TATAAAATTTATTAAATAAAAGGATCATTATCAATCATT
Found at i:4947685 original size:24 final size:23
Alignment explanation
Indices: 4947658--4947717 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
4947648 TCATTAACAT
4947658 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* **
4947682 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
4947705 TGTTCGTGAACAT
1 TGTTCGTGAACAT
4947718 TAAACAAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:4949538 original size:34 final size:34
Alignment explanation
Indices: 4949473--4949539 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
4949463 ATAATTCAAA
*
4949473 AATTATTAAAAAATAAAAAAATATATCAAAATTT
1 AATTATTAAAAAATAAAAAAATATATAAAAATTT
*
4949507 AATT-TTAAAAAATATAAGAAAT-TCATAAAAATT
1 AATTATTAAAAAATA-AAAAAATAT-ATAAAAATT
4949540 CAAGAAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 11 0.38
34 18 0.62
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (34 bp):
AATTATTAAAAAATAAAAAAATATATAAAAATTT
Found at i:4949670 original size:31 final size:31
Alignment explanation
Indices: 4949634--4949698 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
4949624 AAACAATCAT
*
4949634 TTTGACTTTTTTCAAAAAATTGATGATCAAA
1 TTTGACTTTTTTCAAAAAATTGAGGATCAAA
* *
4949665 TTTGACTTTTTTTAAAAAATTGAGGATGAAA
1 TTTGACTTTTTTCAAAAAATTGAGGATCAAA
4949696 TTT
1 TTT
4949699 AACACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.37, C:0.06, G:0.12, T:0.45
Consensus pattern (31 bp):
TTTGACTTTTTTCAAAAAATTGAGGATCAAA
Found at i:4957745 original size:28 final size:28
Alignment explanation
Indices: 4957687--4957747 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
4957677 TAAGATAGTG
* * *
4957687 TTTAGTGACATAGATATTACATTTATTT
1 TTTAGTGACATAAATATTAAATTTATAT
*
4957715 TTTATTGACATAAATATTTAAATTTA-AT
1 TTTAGTGACATAAATA-TTAAATTTATAT
4957743 TTTAG
1 TTTAG
4957748 AGTTATTCGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (28 bp):
TTTAGTGACATAAATATTAAATTTATAT
Found at i:4974734 original size:3 final size:3
Alignment explanation
Indices: 4974726--4974751 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4974716 GCCGCTGATT
4974726 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
4974752 GCCGGCATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:4976379 original size:20 final size:20
Alignment explanation
Indices: 4976351--4976388 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4976341 TACATCAATA
4976351 ATTTCATTT-TAAATTTGAGG
1 ATTTCATTTGT-AATTTGAGG
*
4976371 ATTTTATTTGTAATTTGA
1 ATTTCATTTGTAATTTGA
4976389 TTTTTTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.29, C:0.03, G:0.13, T:0.55
Consensus pattern (20 bp):
ATTTCATTTGTAATTTGAGG
Found at i:4978354 original size:2 final size:2
Alignment explanation
Indices: 4978347--4978385 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
4978337 CAGATCCCAC
4978347 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
4978386 AAAGCCAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:4993613 original size:21 final size:21
Alignment explanation
Indices: 4993573--4993613 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4993563 TCAGTTCAGC
* *
4993573 CTCTTTTGCTTTAAGTTCCTT
1 CTCTCTTGCTTTAAGATCCTT
*
4993594 CTCTCTTGCTTTTAGATCCT
1 CTCTCTTGCTTTAAGATCCT
4993614 AGATTTGATA
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:0.10, C:0.27, G:0.10, T:0.54
Consensus pattern (21 bp):
CTCTCTTGCTTTAAGATCCTT
Found at i:4997101 original size:29 final size:29
Alignment explanation
Indices: 4997068--4997127 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
4997058 ACATCAAATT
4997068 TTAAT-GTAGAAATCAAGTCATTTTCATAA
1 TTAATCGTA-AAATCAAGTCATTTTCATAA
* **
4997097 TTAATCTTAAAATTGAGTCATTTTCATAA
1 TTAATCGTAAAATCAAGTCATTTTCATAA
4997126 TT
1 TT
4997128 TTCTAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.43
Consensus pattern (29 bp):
TTAATCGTAAAATCAAGTCATTTTCATAA
Found at i:5001309 original size:51 final size:52
Alignment explanation
Indices: 5001233--5001336 Score: 192
Period size: 51 Copynumber: 2.0 Consensus size: 52
5001223 GAAGGTACAT
5001233 TAATTCATGAAACCAGACAAAGTCTTAATTGTGGTTTAAC-TTTTATTATTA
1 TAATTCATGAAACCAGACAAAGTCTTAATTGTGGTTTAACTTTTTATTATTA
*
5001284 TAATTCATGGAACCAGACAAAGTCTTAATTGTGGTTTAACTTTTTATTATTA
1 TAATTCATGAAACCAGACAAAGTCTTAATTGTGGTTTAACTTTTTATTATTA
5001336 T
1 T
5001337 TATATTGTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 39 0.76
52 12 0.24
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (52 bp):
TAATTCATGAAACCAGACAAAGTCTTAATTGTGGTTTAACTTTTTATTATTA
Found at i:5003852 original size:22 final size:22
Alignment explanation
Indices: 5003822--5003866 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
5003812 TTATATATAA
*
5003822 TATGGACCAACACTTTGAATGT
1 TATGCACCAACACTTTGAATGT
5003844 TATGCACCAACACTTTGAATGT
1 TATGCACCAACACTTTGAATGT
5003866 T
1 T
5003867 CTTTGCCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (22 bp):
TATGCACCAACACTTTGAATGT
Found at i:5006404 original size:29 final size:29
Alignment explanation
Indices: 5006362--5006438 Score: 154
Period size: 29 Copynumber: 2.7 Consensus size: 29
5006352 TTTATCTCGG
5006362 GTTACATTTTAGTCACTTATGTTTAAAAT
1 GTTACATTTTAGTCACTTATGTTTAAAAT
5006391 GTTACATTTTAGTCACTTATGTTTAAAAT
1 GTTACATTTTAGTCACTTATGTTTAAAAT
5006420 GTTACATTTTAGTCACTTA
1 GTTACATTTTAGTCACTTA
5006439 CATTAATGTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (29 bp):
GTTACATTTTAGTCACTTATGTTTAAAAT
Found at i:5010760 original size:18 final size:19
Alignment explanation
Indices: 5010711--5010760 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
5010701 ATTTGTTACT
* *
5010711 TAAAAATTCAAAACTTCTT
1 TAAAAATGCAAAACTTCTG
5010730 TAAAATATG-AAAACTT-TG
1 TAAAA-ATGCAAAACTTCTG
5010748 TAAAAATGCAAAA
1 TAAAAATGCAAAA
5010761 AATCCCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 3 0.11
18 10 0.37
19 12 0.44
20 2 0.07
ACGTcount: A:0.54, C:0.10, G:0.06, T:0.30
Consensus pattern (19 bp):
TAAAAATGCAAAACTTCTG
Found at i:5010842 original size:18 final size:19
Alignment explanation
Indices: 5010804--5010846 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
5010794 CAATTTCTTA
**
5010804 AAAATTTTCATAAAATTCT
1 AAAATTTTCATAAAAACCT
5010823 AAAATTTTC-TAAAAACCT
1 AAAATTTTCATAAAAACCT
5010841 AAAATT
1 AAAATT
5010847 CCAAACAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTTTCATAAAAACCT
Found at i:5010943 original size:23 final size:24
Alignment explanation
Indices: 5010897--5010945 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
5010887 TTGCATATAC
*
5010897 TTATATATTTTCTAAAAATTATTT
1 TTATATATTTTCTAAAAATGATTT
5010921 TTATA-ATTTTC-AAAAATAGATTT
1 TTATATATTTTCTAAAAAT-GATTT
5010944 TT
1 TT
5010946 TTTAGTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 12 0.52
24 5 0.22
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (24 bp):
TTATATATTTTCTAAAAATGATTT
Found at i:5012201 original size:30 final size:30
Alignment explanation
Indices: 5012165--5012325 Score: 135
Period size: 30 Copynumber: 5.5 Consensus size: 30
5012155 ACCCGGGGGC
5012165 AAAATGGTAATTTTGGTGAAATCGGGGTTA
1 AAAATGGTAATTTTGGTGAAATCGGGGTTA
***
5012195 AAAATGG-AATTTTTGG-GGCTTCGAGGG-T-
1 AAAATGGTAA-TTTTGGTGAAATCG-GGGTTA
*
5012223 AAAATGGTAATTTGTGGTGAAATCGAGGTTA
1 AAAATGGTAATTT-TGGTGAAATCGGGGTTA
*
5012254 AAAAT-GAAATTTT-G-GAAAGTTCGAGGG-T-
1 AAAATGGTAATTTTGGTGAAA--TCG-GGGTTA
*
5012282 AAAATGGTAATTTTTGGTGAAACCGGGGTTA
1 AAAATGGTAA-TTTTGGTGAAATCGGGGTTA
5012313 AAAATGG-AATTTT
1 AAAATGGTAATTTT
5012326 AGAAGGTTCG
Statistics
Matches: 104, Mismatches: 11, Indels: 33
0.70 0.07 0.22
Matches are distributed among these distances:
27 4 0.04
28 16 0.15
29 29 0.28
30 38 0.37
31 13 0.12
32 4 0.04
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTGAAATCGGGGTTA
Found at i:5012355 original size:59 final size:59
Alignment explanation
Indices: 5012165--5012355 Score: 287
Period size: 59 Copynumber: 3.3 Consensus size: 59
5012155 ACCCGGGGGC
* *
5012165 AAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGGAATTTTTG-GGGCTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGG-TTCGAGGGT
* * * * *
5012223 AAAATGGTAATTTGTGGTGAAATCGAGGTTAAAAATGAAATTTTGGAAAGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGAGGGT
*
5012282 AAAATGGTAATTTTTGGTGAAACCGGGGTTAAAAATGGAATTTTAGAAGGTTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGAGGGT
5012341 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
5012356 AGAAGTTTTG
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
58 10 0.08
59 108 0.91
60 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGAGGGT
Found at i:5012358 original size:30 final size:30
Alignment explanation
Indices: 5012313--5012384 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
5012303 ACCGGGGTTA
5012313 AAAATGG-AA-TTTTAGAAGGTTCGAGGGT-
1 AAAATGGTAATTTTTAGAAGGTTCG-GGGTC
* *
5012341 AAAATGGTAATTTTTAGAAGTTTTGGGGTC
1 AAAATGGTAATTTTTAGAAGGTTCGGGGTC
5012371 AAAAT-GTAATTTTT
1 AAAATGGTAATTTTT
5012385 GGACTGTTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
28 7 0.18
29 15 0.38
30 17 0.44
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (30 bp):
AAAATGGTAATTTTTAGAAGGTTCGGGGTC
Found at i:5014205 original size:17 final size:16
Alignment explanation
Indices: 5014185--5014262 Score: 72
Period size: 17 Copynumber: 4.9 Consensus size: 16
5014175 AATTTTAATT
*
5014185 TAAATTAAAATTTAAAG
1 TAAATTTAAATTT-AAG
*
5014202 TAAATTTAAA--TAAT
1 TAAATTTAAATTTAAG
5014216 TAAATTTAAATTTAAG
1 TAAATTTAAATTTAAG
* *
5014232 ATAGATTTAAATTTAAA
1 -TAAATTTAAATTTAAG
*
5014249 TAAAATT-AATTTAA
1 TAAATTTAAATTTAA
5014263 CTCCAAATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
14 12 0.24
15 8 0.16
16 8 0.16
17 23 0.45
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
TAAATTTAAATTTAAG
Found at i:5014219 original size:31 final size:29
Alignment explanation
Indices: 5014175--5014255 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 29
5014165 TTAGTGTTTT
*
5014175 AATTTTAATTTAAATTAAAATTTAA-AGTA
1 AATTTAAATTTAAATTAAAATTTAAGA-TA
*
5014204 AATTTAAATAATTAAATTTAAATTTAAGATA
1 AATTTAAAT--TTAAATTAAAATTTAAGATA
*
5014235 GATTTAAATTTAAA-TAAAATT
1 AATTTAAATTTAAATTAAAATT
5014256 AATTTAACTC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
28 6 0.13
29 13 0.29
31 25 0.56
32 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (29 bp):
AATTTAAATTTAAATTAAAATTTAAGATA
Found at i:5014227 original size:11 final size:11
Alignment explanation
Indices: 5014181--5014262 Score: 59
Period size: 11 Copynumber: 7.6 Consensus size: 11
5014171 TTTTAATTTT
5014181 AATTTAAATTAA
1 AATTTAAATT-A
*
5014193 AATTTAAAGTA
1 AATTTAAATTA
5014204 AATTTAAA-T-
1 AATTTAAATTA
5014213 AA-TTAAATTTA
1 AATTTAAA-TTA
5014224 AATTTAAGA-TA
1 AATTTAA-ATTA
*
5014235 GATTTAAATTTA
1 AATTTAAA-TTA
*
5014247 AA-TAAAATT-
1 AATTTAAATTA
5014256 AATTTAA
1 AATTTAA
5014263 CTCCAAATTA
Statistics
Matches: 57, Mismatches: 5, Indels: 18
0.71 0.06 0.22
Matches are distributed among these distances:
8 5 0.09
9 4 0.07
10 8 0.14
11 23 0.40
12 16 0.28
13 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (11 bp):
AATTTAAATTA
Found at i:5014245 original size:6 final size:6
Alignment explanation
Indices: 5014175--5014249 Score: 66
Period size: 6 Copynumber: 12.5 Consensus size: 6
5014165 TTAGTGTTTT
* * *
5014175 AATTTT AATTTA AATTAA AATTTA AA-GTA AATTTA AATAATTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT--TTA AATTTA
*
5014224 AATTTA AGA--TA GATTTA AATTTA AAT
1 AATTTA A-ATTTA AATTTA AATTTA AAT
5014250 AAAATTAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
4 1 0.02
5 6 0.11
6 42 0.75
7 1 0.02
8 6 0.11
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (6 bp):
AATTTA
Found at i:5014682 original size:76 final size:76
Alignment explanation
Indices: 5014550--5015514 Score: 1399
Period size: 76 Copynumber: 12.8 Consensus size: 76
5014540 GCTTCTTTAG
* * * * *
5014550 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAGAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
5014615 ACTTCAGTTTC
66 ACTTCAATTTC
* ** * * * * *
5014626 AGAGATAAAGACGTAATATCCAGCTTTACTTCAATTTCAAAAGGATAGGAAAAGATCTTACTCTT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
5014691 ACTACAATTTC
66 ACTTCAATTTC
* * * * *
5014702 AGAGATAAAGACGTGCTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGTTCTT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
5014767 ACTTCATTTTC
66 ACTTCAATTTC
* * * *
5014778 AAAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCCT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5014843 ACTTCAATTTC
66 ACTTCAATTTC
5014854 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5014919 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
5014930 AGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGTTCTT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5014995 ACTTCAATTTC
66 ACTTCAATTTC
* * *
5015006 AGAGATAAAAACTTGTCGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCCT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5015071 ACTTCAATTTC
66 ACTTCAATTTC
*
5015082 AAAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
*
5015147 ACTTCAATTTT
66 ACTTCAATTTC
* *
5015158 AGAGATAAAAACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCCT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5015223 ACTTCAATTTC
66 ACTTCAATTTC
5015234 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5015299 ACTTCAATTTC
66 ACTTCAATTTC
* *
5015310 AGAGATAAAGACTTGTTGTCTC-ACTCTACTTCAATTTCAAGGGGAT--G--ACG---TTGCTCT
1 AGAGATAAAGACTTGTTGTC-CAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCT
*
5015367 TTCTTCAATTTC
65 TACTTCAATTTC
* * * * * *
5015379 AGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGTGGATTGGAAATGATCTTTGCTCC
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATC-TTGCTCT
5015444 TACTTCAATTTC
65 TACTTCAATTTC
* * * * *
5015456 AGAGATGAAGACTTGTTATCC-ACTCTACTTCAATTTCAAGCGGATTGGAAATGATCTTG
1 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG
5015515 TTTGGTCTGA
Statistics
Matches: 813, Mismatches: 66, Indels: 21
0.90 0.07 0.02
Matches are distributed among these distances:
68 1 0.00
69 59 0.07
71 1 0.00
72 2 0.00
73 2 0.00
74 1 0.00
75 3 0.00
76 705 0.87
77 39 0.05
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:5015405 original size:69 final size:69
Alignment explanation
Indices: 5015287--5015500 Score: 279
Period size: 69 Copynumber: 3.0 Consensus size: 69
5015277 GATAGGAAAA
* *
5015287 GATC-TTGCTCTTACTTCAATTTCAGAGATAAAGACTTGTTGTCTCACTCTACTTCAATTTCAAG
1 GATCGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATC-CACTCTACTTCAATTTCAAG
5015351 GGGAT
65 GGGAT
*
5015356 GA-CGTTGCTCTTTCTTCAATTTCAGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAG
1 GATCGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCC-ACTCTACTTCAATTTCAA-
5015420 TGGATTGGAAAT
64 -GG---GG--AT
* * *
5015432 GATCTTTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGC
1 GATCGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGG
5015497 GGAT
66 GGAT
5015501 TGGAAATGAT
Statistics
Matches: 128, Mismatches: 7, Indels: 20
0.83 0.05 0.13
Matches are distributed among these distances:
68 2 0.02
69 58 0.45
71 4 0.03
74 3 0.02
76 22 0.17
77 39 0.30
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.37
Consensus pattern (69 bp):
GATCGTTGCTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGG
GGAT
Found at i:5027361 original size:29 final size:29
Alignment explanation
Indices: 5027321--5027596 Score: 128
Period size: 29 Copynumber: 9.4 Consensus size: 29
5027311 ACTCGGGGGC
5027321 AAAATGGTAATTTTGGTAAAATGGGGGTTA
1 AAAATGG-AATTTTGGTAAAATGGGGGTTA
* * ***
5027351 AAAATGAAATTTTTG-AGGCTTCGGGGG-T-
1 AAAATGGAATTTTGGTA-AAAT-GGGGGTTA
* *
5027379 AAAATGGTAATTTTGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTGGTAAAATGGGGGTTA
*
5027409 AAAATGGAATTTTGG-AAAGTTTGGGGG-T-
1 AAAATGGAATTTTGGTAAA--ATGGGGGTTA
* *
5027437 AAAATGGTAATTTTGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTGGTAAAATGGGGGTTA
* ** * *
5027467 AAAATGGAATTTTAG-AAGGTTCGGGGAT-
1 AAAATGGAATTTTGGTAA-AATGGGGGTTA
* * * *
5027495 AAAATGGTAATTTATGATGAAATCGAGGTTA
1 AAAATGG-AATTT-TGGTAAAATGGGGGTTA
* *
5027526 AAAATGGAATTTTGG-AAAGTTCGAGGG-T-
1 AAAATGGAATTTTGGTAAA-AT-GGGGGTTA
*
5027554 AAAATGGTAATTTTTGGTGAAACT-GGGGTT-
1 AAAATGG-AA-TTTTGGT-AAAATGGGGGTTA
5027584 AAAATGGAATTTT
1 AAAATGGAATTTT
5027597 AAAAGGTTTG
Statistics
Matches: 184, Mismatches: 38, Indels: 50
0.68 0.14 0.18
Matches are distributed among these distances:
28 46 0.25
29 66 0.36
30 60 0.33
31 9 0.05
32 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTGGTAAAATGGGGGTTA
Found at i:5027393 original size:58 final size:58
Alignment explanation
Indices: 5027313--5027625 Score: 425
Period size: 58 Copynumber: 5.4 Consensus size: 58
5027303 TTTTGGATAC
* * * * *
5027313 TCGGGGGCAAAATGGTAATTTTGGTAAAATGGGGGTTAAAAATGAAATTTTTG-AGGCT
1 TCGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGG-T
* *
5027371 TCGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGT
*
5027429 TTGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGT
1 TCGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGT
* * * * *
5027487 TCGGGGATAAAATGGTAATTTATGATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGT
1 TCGGGGGTAAAATGGTAATTT-TGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGT
* *
5027546 TCGAGGGTAAAATGGTAATTTTTGGTGAAA-CTGGGGTT-AAAATGGAATTTTAAAAGGT
1 TCGGGGGTAAAATGGTAA-TTTTGGTGAAATC-GGGGTTAAAAATGGAATTTTAGAAGGT
*
5027604 TTGGGGGTAAAATGGTAATTTT
1 TCGGGGGTAAAATGGTAATTTT
5027626 TTAAAAGTTT
Statistics
Matches: 227, Mismatches: 24, Indels: 9
0.87 0.09 0.03
Matches are distributed among these distances:
57 4 0.02
58 157 0.69
59 63 0.28
60 3 0.01
ACGTcount: A:0.34, C:0.03, G:0.31, T:0.32
Consensus pattern (58 bp):
TCGGGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGT
Found at i:5027588 original size:117 final size:116
Alignment explanation
Indices: 5027277--5027625 Score: 463
Period size: 117 Copynumber: 3.0 Consensus size: 116
5027267 AAAAAGAAAC
* * * * * * * *
5027277 GATGAAATTGAGGTTGAAAACGTGACTTTTGGATA-CTCGGGGGCAAAATGGTAATTTTGGTAAA
1 GATGAAATCGAGGTTAAAAATG-GAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGTGAA
* * *
5027341 ATGGGGGTTAAAAATGAAATTTTTG-AGGCTTCGGGGGTAAAATGGTAATTTT
65 ATCGGGGTTAAAAATGGAATTTTAGAAGG-TTCGGGGGTAAAATGGTAATTTT
* * *
5027393 GGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTGGTGAAA
1 GATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGTGAAA
*
5027458 TCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGATAAAATGGTAATTTAT
66 TCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGTAAAATGGTAATTT-T
*
5027510 GATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGAGGGTAAAATGGTAATTTTTGGTGAA
1 GATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAA-TTTTGGTGAA
* *
5027575 A-CTGGGGTT-AAAATGGAATTTTAAAAGGTTTGGGGGTAAAATGGTAATTTT
65 ATC-GGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGTAAAATGGTAATTTT
5027626 TTAAAAGTTT
Statistics
Matches: 206, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
115 10 0.05
116 86 0.42
117 93 0.45
118 17 0.08
ACGTcount: A:0.34, C:0.04, G:0.30, T:0.32
Consensus pattern (116 bp):
GATGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTCGGGGGTAAAATGGTAATTTTGGTGAAA
TCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGTAAAATGGTAATTTT
Found at i:5027631 original size:31 final size:27
Alignment explanation
Indices: 5027577--5027654 Score: 84
Period size: 28 Copynumber: 2.7 Consensus size: 27
5027567 TTGGTGAAAC
*
5027577 TGGGGTTAAAATGGAATTTTAAAAGGTT
1 TGGGGGTAAAATGGAATTTTAAAA-GTT
5027605 TGGGGGTAAAATGGTAATTTTTTAAAAGTT
1 TGGGGGTAAAATGG-AA--TTTTAAAAGTT
* *
5027635 TTGGGGTCAAAATGCAATTT
1 TGGGGGT-AAAATGGAATTT
5027655 CTGGACTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
28 16 0.37
29 2 0.05
30 11 0.26
31 14 0.33
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (27 bp):
TGGGGGTAAAATGGAATTTTAAAAGTT
Found at i:5027654 original size:30 final size:30
Alignment explanation
Indices: 5027577--5027654 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
5027567 TTGGTGAAAC
*
5027577 TGGGGTTAAAATGGAA--TTTTAAAAGGTTT
1 TGGGG-TAAAATGCAATTTTTTAAAAGGTTT
* *
5027606 GGGGGTAAAATGGTAATTTTTTAAAA-GTTT
1 TGGGGTAAAAT-GCAATTTTTTAAAAGGTTT
5027636 TGGGGTCAAAATGCAATTT
1 TGGGGT-AAAATGCAATTT
5027655 CTGGACTGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 6 0.15
29 7 0.17
30 15 0.37
31 13 0.32
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (30 bp):
TGGGGTAAAATGCAATTTTTTAAAAGGTTT
Found at i:5029507 original size:20 final size:20
Alignment explanation
Indices: 5029463--5029516 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
5029453 TTTTAATTTT
*
5029463 AATTTAAA-TTAAA-ATTTA
1 AATTTAAATTTAAATAATTA
*
5029481 AA-GTAAATTTAAATAATTA
1 AATTTAAATTTAAATAATTA
5029500 AATTTAAATTTAAATAA
1 AATTTAAATTTAAATAA
5029517 AATCAATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 4 0.13
18 7 0.23
19 6 0.20
20 13 0.43
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AATTTAAATTTAAATAATTA
Found at i:5029514 original size:6 final size:6
Alignment explanation
Indices: 5029452--5029514 Score: 65
Period size: 6 Copynumber: 10.3 Consensus size: 6
5029442 AATGTTTAGT
* * * *
5029452 ATTTTA ATTTTA ATTTAA ATTAAA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
5029501 ATTTAA ATTTAA AT
1 ATTTAA ATTTAA AT
5029515 AAAATCAATT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
5 4 0.08
6 39 0.80
8 6 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:5029524 original size:26 final size:26
Alignment explanation
Indices: 5029469--5029524 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
5029459 TTTTAATTTA
*
5029469 AATTAAAATTTAAAGTAAATTTAAAT
1 AATTAAAATTTAAAGTAAATTAAAAT
*
5029495 AATT-AAATTTAAATTTAAA-TAAAAT
1 AATTAAAATTTAAA-GTAAATTAAAAT
5029520 CAATT
1 -AATT
5029525 TAACTCCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 14 0.54
26 12 0.46
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (26 bp):
AATTAAAATTTAAAGTAAATTAAAAT
Found at i:5032788 original size:13 final size:13
Alignment explanation
Indices: 5032761--5032794 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
5032751 AAACTAAAAA
5032761 TTTTAAAATTACT
1 TTTTAAAATTACT
5032774 TTTATAAAA-TACT
1 TTT-TAAAATTACT
5032787 TTTTAAAA
1 TTTTAAAA
5032795 GCACTTCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 5 0.25
13 10 0.50
14 5 0.25
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTTAAAATTACT
Found at i:5033493 original size:3 final size:3
Alignment explanation
Indices: 5033485--5033518 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5033475 TACTTTTTTA
5033485 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5033519 TATCATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5034492 original size:12 final size:12
Alignment explanation
Indices: 5034475--5034500 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5034465 AAACATAAAA
5034475 TATATTAATTTT
1 TATATTAATTTT
5034487 TATATTAATTTT
1 TATATTAATTTT
5034499 TA
1 TA
5034501 CAAATTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATATTAATTTT
Found at i:5039392 original size:16 final size:16
Alignment explanation
Indices: 5039356--5039394 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5039346 AATTGTTTTT
5039356 ATTTTTATTTTTAGTA
1 ATTTTTATTTTTAGTA
*
5039372 CTTTTTATTTTTA-TAA
1 ATTTTTATTTTTAGT-A
5039388 ATTTTTA
1 ATTTTTA
5039395 ATAATTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 1 0.05
16 19 0.95
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
ATTTTTATTTTTAGTA
Found at i:5053845 original size:21 final size:23
Alignment explanation
Indices: 5053819--5053860 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5053809 TAAAAGCTAT
*
5053819 TTACAA-ATCCAATC-TCTAAGA
1 TTACAAGATCAAATCTTCTAAGA
5053840 TTACAAGATCAAATCTTCTAA
1 TTACAAGATCAAATCTTCTAA
5053861 ATATTACATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.31
Consensus pattern (23 bp):
TTACAAGATCAAATCTTCTAAGA
Found at i:5055226 original size:14 final size:15
Alignment explanation
Indices: 5055209--5055237 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5055199 CAGCTATGTT
5055209 AATATTT-AAATATA
1 AATATTTAAAATATA
5055223 AATATTTAAAATATA
1 AATATTTAAAATATA
5055238 GTTTATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATTTAAAATATA
Found at i:5055630 original size:3 final size:3
Alignment explanation
Indices: 5055622--5055646 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5055612 TCATTTTTCA
5055622 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
5055647 CAGATATATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5057562 original size:16 final size:17
Alignment explanation
Indices: 5057543--5057575 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5057533 GAGAAAATAT
5057543 ACTT-AAACAAAAAAAA
1 ACTTCAAACAAAAAAAA
*
5057559 ACTTCAAAGAAAAAAAA
1 ACTTCAAACAAAAAAAA
5057576 GCACCAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.12, G:0.03, T:0.12
Consensus pattern (17 bp):
ACTTCAAACAAAAAAAA
Found at i:5062847 original size:17 final size:17
Alignment explanation
Indices: 5062827--5062871 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
5062817 GTCAATGCTC
5062827 GAAGGAAGTGAGGAGAA
1 GAAGGAAGTGAGGAGAA
*
5062844 GAAGGAAGTAAGGAGAA
1 GAAGGAAGTGAGGAGAA
5062861 GAAGGAAGTGA
1 GAAGGAAGTGA
5062872 AACCTGCAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.44, T:0.07
Consensus pattern (17 bp):
GAAGGAAGTGAGGAGAA
Found at i:5063459 original size:31 final size:33
Alignment explanation
Indices: 5063421--5063486 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
5063411 CAAAATAAAT
5063421 TTTTTTAT-CT-AAAGTTAAAATATA-TATATAG
1 TTTTTTATACTAAAAGTTAAAATATATTAT-TAG
*
5063452 TTTTTTATAGTAAAAGTTAAAATATATTATTAG
1 TTTTTTATACTAAAAGTTAAAATATATTATTAG
5063485 TT
1 TT
5063487 GCTGCATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 8 0.26
32 1 0.03
33 19 0.61
34 3 0.10
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.50
Consensus pattern (33 bp):
TTTTTTATACTAAAAGTTAAAATATATTATTAG
Found at i:5069569 original size:18 final size:18
Alignment explanation
Indices: 5069546--5069588 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
5069536 GAATAAAATT
5069546 TTAATTAAACAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
5069564 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
5069582 TTAATTA
1 TTAATTA
5069589 CAACTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:5070947 original size:48 final size:48
Alignment explanation
Indices: 5070888--5070998 Score: 138
Period size: 48 Copynumber: 2.3 Consensus size: 48
5070878 AACATTTATA
*
5070888 AAAATCTAATTTAATAATTATCTTGTTA-ATA-T-TTTATTAATTTAAT
1 AAAATTTAATTTAATAATTATCTTG-TAGATAGTATTTATTAATTTAAT
* *
5070934 ATTAAATTTAATTTAATATTTATTTTGTAGATAGTATTTATTAATTTAAT
1 A--AAATTTAATTTAATAATTATCTTGTAGATAGTATTTATTAATTTAAT
5070984 AAAATTTAATATTAA
1 AAAATTTAAT-TTAA
5070999 ATTTAATCTA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
46 1 0.02
47 2 0.04
48 33 0.59
49 5 0.09
50 15 0.27
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (48 bp):
AAAATTTAATTTAATAATTATCTTGTAGATAGTATTTATTAATTTAAT
Found at i:5070995 original size:60 final size:59
Alignment explanation
Indices: 5070926--5071043 Score: 184
Period size: 60 Copynumber: 2.0 Consensus size: 59
5070916 ATATTTTATT
* *
5070926 AATTTAATATTAAATTTAATTTAATATTTATTTTGTAGATAGTATT-TATTAATTTAATAA
1 AATTTAATATTAAATTTAATCTAATATTTATCTTG-AGA-AGTATTATATTAATTTAATAA
*
5070986 AATTTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 AATTTAATATTAAATTTAATCTAATATTTATCTTGAGAAGTATTATATTAATTTAATA
5071044 TTAAAGTGAT
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
58 6 0.11
59 15 0.28
60 33 0.61
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (59 bp):
AATTTAATATTAAATTTAATCTAATATTTATCTTGAGAAGTATTATATTAATTTAATAA
Found at i:5072349 original size:23 final size:23
Alignment explanation
Indices: 5072320--5072381 Score: 81
Period size: 24 Copynumber: 2.7 Consensus size: 23
5072310 AAAATATTTT
5072320 AATAATATTTTATAAAGTTTTGA
1 AATAATATTTTATAAAGTTTTGA
* *
5072343 AATAATATATTTACAAGGTTTTGA
1 AATAATAT-TTTATAAAGTTTTGA
*
5072367 AATAATGTTTT-TAAA
1 AATAATATTTTATAAA
5072382 CATTATATAT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 2 0.06
23 11 0.33
24 20 0.61
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.45
Consensus pattern (23 bp):
AATAATATTTTATAAAGTTTTGA
Found at i:5072490 original size:12 final size:13
Alignment explanation
Indices: 5072467--5072495 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
5072457 AAAATAAAAG
5072467 TATTATTTTAATA
1 TATTATTTTAATA
5072480 TATTA-TTTAATA
1 TATTATTTTAATA
5072492 TATT
1 TATT
5072496 GTTTGCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATTTTAATA
Found at i:5079363 original size:24 final size:24
Alignment explanation
Indices: 5079331--5079382 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
5079321 CTTTCAACCA
5079331 CAATCGGTTGCTGTACATCGCAAT
1 CAATCGGTTGCTGTACATCGCAAT
5079355 CAATCGGTTGCTGTACATCGCAAT
1 CAATCGGTTGCTGTACATCGCAAT
5079379 CAAT
1 CAAT
5079383 AAATCTTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (24 bp):
CAATCGGTTGCTGTACATCGCAAT
Found at i:5083181 original size:49 final size:49
Alignment explanation
Indices: 5083124--5083222 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
5083114 AGGGGTTGAG
5083124 AAAGATGAGAGTTATGGTGGTGGTTGTGATTGTAGAAAGAAAGTTGTAA
1 AAAGATGAGAGTTATGGTGGTGGTTGTGATTGTAGAAAGAAAGTTGTAA
*
5083173 AAAGATGAGAGTTATGGTGGTTGTTGTGATTGTAGAAAGAAAGTTGTAA
1 AAAGATGAGAGTTATGGTGGTGGTTGTGATTGTAGAAAGAAAGTTGTAA
5083222 A
1 A
5083223 GAGAATTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.31
Consensus pattern (49 bp):
AAAGATGAGAGTTATGGTGGTGGTTGTGATTGTAGAAAGAAAGTTGTAA
Found at i:5084416 original size:29 final size:29
Alignment explanation
Indices: 5084365--5084420 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
5084355 GTTTAATATT
*
5084365 CAATTTGATACATCAAGTTTAATTTTATG
1 CAATTTGATACATCAAGTCTAATTTTATG
*
5084394 CAATTTGATACATGAA-TACTAATTTTA
1 CAATTTGATACATCAAGT-CTAATTTTA
5084421 GTTTTCAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.43
Consensus pattern (29 bp):
CAATTTGATACATCAAGTCTAATTTTATG
Found at i:5095906 original size:18 final size:18
Alignment explanation
Indices: 5095874--5095925 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
5095864 CTGGGATGAG
5095874 AATAAATTT--TTAATTA
1 AATAAATTTAATTAATTA
*
5095890 AATAAATTTAATTAATTG
1 AATAAATTTAATTAATTA
*
5095908 AA-AATTTTAAATTAATTA
1 AATAAATTT-AATTAATTA
5095926 CAACTGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 9 0.30
17 5 0.17
18 16 0.53
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AATAAATTTAATTAATTA
Found at i:5102223 original size:281 final size:281
Alignment explanation
Indices: 5101720--5102281 Score: 1079
Period size: 281 Copynumber: 2.0 Consensus size: 281
5101710 GAATCAAAAG
5101720 ACTGAACGCCTATGAATCCATGAAACTCAGAAAAAAATAACTGCATAACTTCATCTTATGAGGAA
1 ACTGAACGCCTATGAATCCATGAAACTCAGAAAAAAATAACTGCATAACTTCATCTTATGAGGAA
5101785 AAACTTCAAAATTATCATACATAAGAGGAAATTATTTTGCATTAGCCTGTATTTCCAGAAAATCA
66 AAACTTCAAAATTATCATACATAAGAGGAAATTATTTTGCATTAGCCTGTATTTCCAGAAAATCA
*
5101850 TACAAGGTGATGCATAGTGAACTCTAATCAACAATATTTGAAGTGTATAAATTATAAACGAACGT
131 TACAAGGTGATGCATAGTGAACTCTAATCAACAATATTTGAAGTGTATAAATTATAAACGAAAGT
* * *
5101915 CAAATTCTGCACCTACTGTACATGTACACATGCATCTACTGTCATATCAATTGTGATGGTAACAT
196 CAAATTCTGCACCTACCGTACATGTACACATGCATCTACAGTCATATCAAATGTGATGGTAACAT
5101980 TCAAGGTTAAGCTTTAATTAC
261 TCAAGGTTAAGCTTTAATTAC
5102001 ACTGAACGCCTATGAATCCATGAAACTCAGAAAAAAATAACTGCATAACTTCATCTTATGAGGAA
1 ACTGAACGCCTATGAATCCATGAAACTCAGAAAAAAATAACTGCATAACTTCATCTTATGAGGAA
5102066 AAACTTCAAAATTATCATACATAAGAGGAAATTATTTTGCATTAGCCTGTATTTCCAGAAAATCA
66 AAACTTCAAAATTATCATACATAAGAGGAAATTATTTTGCATTAGCCTGTATTTCCAGAAAATCA
*
5102131 TACAAGGTGATTCATAGTGAACTCTAATCAACAATATTTGAAGTGTATAAATTATAAACGAAAGT
131 TACAAGGTGATGCATAGTGAACTCTAATCAACAATATTTGAAGTGTATAAATTATAAACGAAAGT
5102196 CAAATTCTGCACCTACCGTACATGTACACATGCATCTACAGTCATATCAAATGTGATGGTAACAT
196 CAAATTCTGCACCTACCGTACATGTACACATGCATCTACAGTCATATCAAATGTGATGGTAACAT
5102261 TCAAGGTTAAGCTTTAATTAC
261 TCAAGGTTAAGCTTTAATTAC
5102282 CTTCCCAAGT
Statistics
Matches: 276, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
281 276 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (281 bp):
ACTGAACGCCTATGAATCCATGAAACTCAGAAAAAAATAACTGCATAACTTCATCTTATGAGGAA
AAACTTCAAAATTATCATACATAAGAGGAAATTATTTTGCATTAGCCTGTATTTCCAGAAAATCA
TACAAGGTGATGCATAGTGAACTCTAATCAACAATATTTGAAGTGTATAAATTATAAACGAAAGT
CAAATTCTGCACCTACCGTACATGTACACATGCATCTACAGTCATATCAAATGTGATGGTAACAT
TCAAGGTTAAGCTTTAATTAC
Found at i:5104649 original size:23 final size:23
Alignment explanation
Indices: 5104622--5104668 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
5104612 TGTTTATAAA
5104622 AATTAATTTAT-TAATA-TATTAAT
1 AATT-ATTTATCT-ATACTATTAAT
5104645 AATTATTTATCTATACTATTAAT
1 AATTATTTATCTATACTATTAAT
5104668 A
1 A
5104669 TAACCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (23 bp):
AATTATTTATCTATACTATTAAT
Found at i:5104902 original size:23 final size:23
Alignment explanation
Indices: 5104872--5104926 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
5104862 TTCTTGAGTA
5104872 AACATAAAAAACAATTAACTTTT
1 AACATAAAAAACAATTAACTTTT
5104895 AACATAAAAAACAATTAACTTTT
1 AACATAAAAAACAATTAACTTTT
5104918 AACATAAAA
1 AACATAAAA
5104927 TGTTCTCTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.60, C:0.13, G:0.00, T:0.27
Consensus pattern (23 bp):
AACATAAAAAACAATTAACTTTT
Found at i:5105322 original size:30 final size:30
Alignment explanation
Indices: 5105286--5105368 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 30
5105276 GTCACCACTA
* **
5105286 ACCATTTTCCGTTACAGACATAAAGGGGCT
1 ACCATTTTTCGTTACAGACATAAAGACGCT
* * *
5105316 ACCATTTTTTGTTACAAACGTAAAGACGCT
1 ACCATTTTTCGTTACAGACATAAAGACGCT
**
5105346 GTCATTTTTCGTTACAGACATAA
1 ACCATTTTTCGTTACAGACATAA
5105369 CGGAGTTGTC
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (30 bp):
ACCATTTTTCGTTACAGACATAAAGACGCT
Found at i:5107181 original size:30 final size:30
Alignment explanation
Indices: 5107147--5107207 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
5107137 CATGATCTGG
**
5107147 CACATGGTTGTGTGCCCAACCCGTGTGGCT
1 CACATGGCCGTGTGCCCAACCCGTGTGGCT
* *
5107177 CACATGGCCGTGTGTCCAGCCCGTGTGGCT
1 CACATGGCCGTGTGCCCAACCCGTGTGGCT
5107207 C
1 C
5107208 CTAAAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.11, C:0.33, G:0.31, T:0.25
Consensus pattern (30 bp):
CACATGGCCGTGTGCCCAACCCGTGTGGCT
Found at i:5109379 original size:4 final size:4
Alignment explanation
Indices: 5109372--5109416 Score: 54
Period size: 4 Copynumber: 10.8 Consensus size: 4
5109362 AAATAAATGG
* *
5109372 GAAA GAAA GAAAA GAAA GAAA GAAA GAAG GAGAG GAAA GAAA GAA
1 GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAA
5109417 GAAGGAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 29 0.78
5 8 0.22
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:5109398 original size:21 final size:21
Alignment explanation
Indices: 5109372--5109424 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
5109362 AAATAAATGG
*
5109372 GAAAGAAAGAAAAGAAAGAAA
1 GAAAGAAGGAAAAGAAAGAAA
* *
5109393 GAAAGAAGGAGAGGAAAGAAA
1 GAAAGAAGGAAAAGAAAGAAA
5109414 G-AAGAAGGAAA
1 GAAAGAAGGAAA
5109425 TAAATGTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 9 0.32
21 19 0.68
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (21 bp):
GAAAGAAGGAAAAGAAAGAAA
Found at i:5109409 original size:17 final size:18
Alignment explanation
Indices: 5109371--5109420 Score: 68
Period size: 17 Copynumber: 2.9 Consensus size: 18
5109361 CAAATAAATG
5109371 GGAAAGAAAGAA-AAGAA
1 GGAAAGAAAGAAGAAGAA
* *
5109388 AGAAAGAAAGAAGGAG-A
1 GGAAAGAAAGAAGAAGAA
5109405 GGAAAGAAAGAAGAAG
1 GGAAAGAAAGAAGAAG
5109421 GAAATAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 26 0.93
18 2 0.07
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (18 bp):
GGAAAGAAAGAAGAAGAA
Found at i:5112498 original size:14 final size:13
Alignment explanation
Indices: 5112479--5112509 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
5112469 AAGTGTCGAG
5112479 TTTAGGGTTTAAGT
1 TTTAGGGTTTAA-T
5112493 TTTAGGGTTTAAT
1 TTTAGGGTTTAAT
5112506 TTTA
1 TTTA
5112510 TGAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (13 bp):
TTTAGGGTTTAAT
Found at i:5112750 original size:21 final size:21
Alignment explanation
Indices: 5112724--5112764 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5112714 TAGGGTCCAT
5112724 TTACCCCAGAAGAGTAGAGTG
1 TTACCCCAGAAGAGTAGAGTG
** *
5112745 TTACCCGGGAGGAGTAGAGT
1 TTACCCCAGAAGAGTAGAGT
5112765 ATTGCGGTGG
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:0.29, C:0.17, G:0.34, T:0.20
Consensus pattern (21 bp):
TTACCCCAGAAGAGTAGAGTG
Found at i:5115317 original size:20 final size:21
Alignment explanation
Indices: 5115292--5115334 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5115282 TACTTACTAC
5115292 TACTAA-TAACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
5115312 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
5115333 TA
1 TA
5115335 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:5115518 original size:18 final size:18
Alignment explanation
Indices: 5115495--5115529 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5115485 AAAATATTTT
5115495 AAAATTAACTAAACTTAA
1 AAAATTAACTAAACTTAA
*
5115513 AAAATTAATTAAACTTA
1 AAAATTAACTAAACTTA
5115530 CCTTTCTTTC
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:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAATTAACTAAACTTAA
Found at i:5115691 original size:17 final size:17
Alignment explanation
Indices: 5115669--5115724 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
5115659 ATTTTTTTCC
5115669 TTCTCCTCTTTCTTTTT
1 TTCTCCTCTTTCTTTTT
5115686 TTCTCCT-TCTTCTTTCTT
1 TTCTCCTCT-TTCTTT-TT
* *
5115704 CTTC-CTTCTTTCTTTCT
1 -TTCTCCTCTTTCTTTTT
5115721 TTCT
1 TTCT
5115725 TTGTCTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
16 4 0.12
17 14 0.44
18 10 0.31
19 4 0.12
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (17 bp):
TTCTCCTCTTTCTTTTT
Found at i:5115699 original size:21 final size:20
Alignment explanation
Indices: 5115660--5115747 Score: 74
Period size: 21 Copynumber: 4.3 Consensus size: 20
5115650 ACACATTACA
5115660 TTTTTTTCCTTCTCCTCTTTCT
1 TTTTTTTCCTTCT--TCTTTCT
5115682 TTTTTTCTCCTTCTTCTTTC-
1 TTTTTT-TCCTTCTTCTTTCT
*
5115702 --TTCTTCCTTCTTTCTTTCT
1 TTTTTTTCCTTC-TTCTTTCT
* * *
5115721 TTCTTTGTCTTTTTTCTTTCT
1 TT-TTTTTCCTTCTTCTTTCT
5115742 TTTTTT
1 TTTTTT
5115748 CTTTAAATTT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
17 6 0.11
18 10 0.19
20 3 0.06
21 16 0.30
22 12 0.22
23 7 0.13
ACGTcount: A:0.00, C:0.26, G:0.01, T:0.73
Consensus pattern (20 bp):
TTTTTTTCCTTCTTCTTTCT
Found at i:5115702 original size:4 final size:4
Alignment explanation
Indices: 5115675--5115751 Score: 63
Period size: 4 Copynumber: 19.2 Consensus size: 4
5115665 TTCCTTCTCC
* *
5115675 TCTT TCTT TTTT TCTCCT TC-T TCTT TC-T TC-T TCCT TCTT TCTT TCTT
1 TCTT TCTT TCTT TCT--T TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT
*
5115722 TCTTT GTCTT T-TT TCTT TCTT TTTT TCTT T
1 TC-TT -TCTT TCTT TCTT TCTT TCTT TCTT T
5115752 AAATTTCGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
3 12 0.20
4 40 0.66
5 4 0.07
6 5 0.08
ACGTcount: A:0.00, C:0.25, G:0.01, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:5115711 original size:14 final size:13
Alignment explanation
Indices: 5115685--5115751 Score: 52
Period size: 14 Copynumber: 5.2 Consensus size: 13
5115675 TCTTTCTTTT
*
5115685 TTTCTCCTTCTTC
1 TTTCTTCTTCTTC
5115698 TTTCTTCTTCCTTC
1 TTTCTTCTT-CTTC
5115712 TTTCTTTCTTTCTT-
1 TTTC-TTC-TTCTTC
*
5115726 TGTCTT-TT-TTC
1 TTTCTTCTTCTTC
*
5115737 TTTCTT-TTTTTC
1 TTTCTTCTTCTTC
5115749 TTT
1 TTT
5115752 AAATTTCGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
10 2 0.04
11 9 0.20
12 6 0.13
13 10 0.22
14 11 0.24
15 6 0.13
16 2 0.04
ACGTcount: A:0.00, C:0.25, G:0.01, T:0.73
Consensus pattern (13 bp):
TTTCTTCTTCTTC
Found at i:5115720 original size:25 final size:25
Alignment explanation
Indices: 5115703--5115751 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5115693 TCTTCTTTCT
5115703 TCTTCCTTCTTTCTTTCTTTCTTTG
1 TCTTCCTTCTTTCTTTCTTTCTTTG
** *
5115728 TCTTTTTTCTTTCTTTTTTTCTTT
1 TCTTCCTTCTTTCTTTCTTTCTTT
5115752 AAATTTCGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (25 bp):
TCTTCCTTCTTTCTTTCTTTCTTTG
Found at i:5115738 original size:17 final size:18
Alignment explanation
Indices: 5115710--5115751 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
5115700 TCTTCTTCCT
5115710 TCTTTCTTTCTTTCTTTG
1 TCTTTCTTTCTTTCTTTG
5115728 TCTTT-TTTCTTTCTTT-
1 TCTTTCTTTCTTTCTTTG
5115744 T-TTTCTTT
1 TCTTTCTTT
5115752 AAATTTCGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.13
16 4 0.17
17 11 0.48
18 5 0.22
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (18 bp):
TCTTTCTTTCTTTCTTTG
Found at i:5117381 original size:20 final size:22
Alignment explanation
Indices: 5117356--5117403 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
5117346 TTTATATTGT
5117356 TGTTTTGG-TG-CTTTTTTTAC
1 TGTTTTGGTTGACTTTTTTTAC
*
5117376 TGTTTTGGTTGATTTTTTTTAC
1 TGTTTTGGTTGACTTTTTTTAC
5117398 TGTTTT
1 TGTTTT
5117404 TGAGTTGTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
22 15 0.60
ACGTcount: A:0.06, C:0.06, G:0.19, T:0.69
Consensus pattern (22 bp):
TGTTTTGGTTGACTTTTTTTAC
Found at i:5117395 original size:22 final size:22
Alignment explanation
Indices: 5117367--5117439 Score: 87
Period size: 22 Copynumber: 3.3 Consensus size: 22
5117357 GTTTTGGTGC
5117367 TTTTTTTACTGTTTTG-GTTGAT
1 TTTTTTTACTGTTTTGAGTTG-T
5117389 TTTTTTTACTGTTTTTGAGTTGT
1 TTTTTTTACTG-TTTTGAGTTGT
*
5117412 TGTTTTTTATTGTTTTGA-TTGT
1 T-TTTTTTACTGTTTTGAGTTGT
*
5117434 TATTTT
1 TTTTTT
5117440 CGTGTTATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
21 4 0.09
22 16 0.35
23 13 0.28
24 13 0.28
ACGTcount: A:0.10, C:0.03, G:0.16, T:0.71
Consensus pattern (22 bp):
TTTTTTTACTGTTTTGAGTTGT
Found at i:5117410 original size:24 final size:22
Alignment explanation
Indices: 5117358--5117427 Score: 81
Period size: 24 Copynumber: 3.1 Consensus size: 22
5117348 TATATTGTTG
*
5117358 TTTTGG-TGCTTTTTTTACTG-
1 TTTTGGTTGTTTTTTTTACTGT
5117378 TTTTGGTTGATTTTTTTTACTGT
1 TTTTGGTTG-TTTTTTTTACTGT
*
5117401 TTTTGAGTTGTTGTTTTTTATTGT
1 TTTTG-GTTGTT-TTTTTTACTGT
5117425 TTT
1 TTT
5117428 GATTGTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.14
21 2 0.05
22 11 0.26
23 7 0.16
24 17 0.40
ACGTcount: A:0.07, C:0.04, G:0.19, T:0.70
Consensus pattern (22 bp):
TTTTGGTTGTTTTTTTTACTGT
Found at i:5117451 original size:12 final size:12
Alignment explanation
Indices: 5117431--5117464 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
5117421 TTGTTTTGAT
*
5117431 TGTTATTTTCG-
1 TGTTATTTTTGC
5117442 TGTTATTTTTGC
1 TGTTATTTTTGC
5117454 TGTTATTTTTG
1 TGTTATTTTTG
5117465 TTGCTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.09, C:0.06, G:0.18, T:0.68
Consensus pattern (12 bp):
TGTTATTTTTGC
Found at i:5117548 original size:20 final size:20
Alignment explanation
Indices: 5117499--5117562 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
5117489 TTCTTTTTAA
*
5117499 TGTTGTTTTAATGTTATTTT
1 TGTTGTTTTGATGTTATTTT
*
5117519 TGCTACTGTTTTGTTGTTATTTT
1 TG-T--TGTTTTGATGTTATTTT
*
5117542 TGTTGTTTGGATGTTATTTT
1 TGTTGTTTTGATGTTATTTT
5117562 T
1 T
5117563 TATGAGTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
20 18 0.49
21 1 0.03
22 1 0.03
23 17 0.46
ACGTcount: A:0.11, C:0.03, G:0.19, T:0.67
Consensus pattern (20 bp):
TGTTGTTTTGATGTTATTTT
Found at i:5117725 original size:24 final size:24
Alignment explanation
Indices: 5117675--5117725 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
5117665 CTTAATATAA
*
5117675 TTTTTTAATGTATTTTAAATTTAT
1 TTTTTTAATGTATTTTAAATGTAT
5117699 TTTTTTAATGTTTATTTT-AATGT-T
1 TTTTTTAATG--TATTTTAAATGTAT
5117723 TTT
1 TTT
5117726 AAGTGTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 14 0.58
25 4 0.17
26 6 0.25
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (24 bp):
TTTTTTAATGTATTTTAAATGTAT
Found at i:5118595 original size:158 final size:158
Alignment explanation
Indices: 5118299--5118602 Score: 432
Period size: 158 Copynumber: 1.9 Consensus size: 158
5118289 TTACAGATAC
* *
5118299 AGCTCATGTGAGCATTACATGTTATATGGGTGCTGGTCTTAGATGCCCTACCGATGGCTGAGGTC
1 AGCTCATGTGAGCATTACATGTTATATGAGTGCTGGTCTTAGATACCCTACCGATGGCTGAGGTC
** *
5118364 CTGCATTGGTTGCGGATTCTCCACAGCTCGTGTGAGTAGCATCGTGTAGCCCCACATCTCGACCC
66 CTGCATTGAATGCGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCCCACATCTCGACCC
5118429 ACAACTCGTGTGAGCAGGCCCATTTCAT
131 ACAACTCGTGTGAGCAGGCCCATTTCAT
* * * * * *
5118457 AGCTCGTGTGAGCATTATATGTTATATGAGTGCTGGTTTTAGATATCTTATCGATGGCTGAGGTC
1 AGCTCATGTGAGCATTACATGTTATATGAGTGCTGGTCTTAGATACCCTACCGATGGCTGAGGTC
* * *
5118522 C-GACATTTAATGCGGATTCTCCTCAGCTCGTGTGAGCAGCATCGTGTAGCCCCATATCTC-AGC
66 CTG-CATTGAATGCGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCCCACATCTCGA-C
* *
5118585 CCATAGCTCGTGTGAGCA
129 CCACAACTCGTGTGAGCA
5118603 TATATGATTA
Statistics
Matches: 128, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
157 2 0.02
158 126 0.98
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.30
Consensus pattern (158 bp):
AGCTCATGTGAGCATTACATGTTATATGAGTGCTGGTCTTAGATACCCTACCGATGGCTGAGGTC
CTGCATTGAATGCGGATTCTCCACAGCTCGTGTGAGCAGCATCGTGTAGCCCCACATCTCGACCC
ACAACTCGTGTGAGCAGGCCCATTTCAT
Found at i:5120785 original size:8 final size:8
Alignment explanation
Indices: 5120772--5120798 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5120762 GAAACAATGT
5120772 TCTCTTTC
1 TCTCTTTC
5120780 TCTCTTTC
1 TCTCTTTC
5120788 TCTCTTTC
1 TCTCTTTC
5120796 TCT
1 TCT
5120799 TATATTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (8 bp):
TCTCTTTC
Found at i:5124008 original size:31 final size:31
Alignment explanation
Indices: 5123973--5124043 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
5123963 ACCATTTAGT
5123973 TAAATTAAAGGTAAATTATAC-TATTAGTCAC
1 TAAATTAAAGGTAAATT-TACATATTAGTCAC
** * *
5124004 TAAATTATGGGTAAATTTTCATTTTAGTCAC
1 TAAATTAAAGGTAAATTTACATATTAGTCAC
*
5124035 TTAATTAAA
1 TAAATTAAA
5124044 AAAGTTACAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.41
Consensus pattern (31 bp):
TAAATTAAAGGTAAATTTACATATTAGTCAC
Found at i:5132431 original size:59 final size:59
Alignment explanation
Indices: 5132360--5132476 Score: 180
Period size: 59 Copynumber: 2.0 Consensus size: 59
5132350 TATTTTCTGT
*
5132360 CAAATCACCCCAAAATAGATGAAAAAATTAATATTTGTTAACTTTGCTGATGTGGAAGA
1 CAAATCACCCCAAAATAGATGAAAAAATTAATATTTGTTAACTTTGCTGACGTGGAAGA
** * * *
5132419 CAAATCACCCCAAAATTTATGGAAAAGTTAATGTTTGTTAACTTTGCTGACGTGGAAG
1 CAAATCACCCCAAAATAGATGAAAAAATTAATATTTGTTAACTTTGCTGACGTGGAAG
5132477 GAATTTGAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (59 bp):
CAAATCACCCCAAAATAGATGAAAAAATTAATATTTGTTAACTTTGCTGACGTGGAAGA
Found at i:5133824 original size:17 final size:17
Alignment explanation
Indices: 5133802--5133859 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
5133792 AGAAGATGAA
5133802 AGGTTAAAGGTTAAGGG
1 AGGTTAAAGGTTAAGGG
*
5133819 AGGTT--AGG-GAAGATGG
1 AGGTTAAAGGTTAAG--GG
*
5133835 AAGGTTAAAAGTTAAGGG
1 -AGGTTAAAGGTTAAGGG
5133853 AGGTTAA
1 AGGTTAA
5133860 GGAAAATGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 12
0.68 0.06 0.26
Matches are distributed among these distances:
14 3 0.09
15 3 0.09
16 2 0.06
17 17 0.53
18 2 0.06
19 2 0.06
20 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.40, T:0.22
Consensus pattern (17 bp):
AGGTTAAAGGTTAAGGG
Found at i:5133839 original size:34 final size:34
Alignment explanation
Indices: 5133793--5133880 Score: 140
Period size: 34 Copynumber: 2.6 Consensus size: 34
5133783 GTAGTTACAA
* * *
5133793 GAAGATGAAAGGTTAAAGGTTAAGGGAGGTTAGG
1 GAAGATGGAAGGTTAAAAGTTAAGGGAGGTTAAG
5133827 GAAGATGGAAGGTTAAAAGTTAAGGGAGGTTAAG
1 GAAGATGGAAGGTTAAAAGTTAAGGGAGGTTAAG
*
5133861 GAAAATGGAAGGTTAAAAGT
1 GAAGATGGAAGGTTAAAAGT
5133881 CAATGGAGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 50 1.00
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (34 bp):
GAAGATGGAAGGTTAAAAGTTAAGGGAGGTTAAG
Found at i:5137041 original size:38 final size:38
Alignment explanation
Indices: 5136966--5137043 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
5136956 TTACTAATAA
5136966 ATCACTATGGTTAGATAATATATATTTTTATATATACC
1 ATCACTATGGTTAGATAATATATATTTTTATATATACC
5137004 ATCACTATGGTTAGATAATATATATTTTTATATATACC
1 ATCACTATGGTTAGATAATATATATTTTTATATATACC
5137042 AT
1 AT
5137044 AACAAAACAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (38 bp):
ATCACTATGGTTAGATAATATATATTTTTATATATACC
Found at i:5139265 original size:34 final size:34
Alignment explanation
Indices: 5139222--5139325 Score: 163
Period size: 34 Copynumber: 3.1 Consensus size: 34
5139212 AGAATATGAA
*
5139222 AGGTTAAGGAAGATGAAAGGTTAAAGGTCAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAGGG
*
5139256 AGGTTAAGGAAGATGGAAGATTAAAGGTCAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAGGG
* * *
5139290 AGGTTAAGGAAAATGGAAGGTTAAAAGTTAAGGG
1 AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAGGG
5139324 AG
1 AG
5139326 ATGAAAGGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.42, C:0.02, G:0.38, T:0.18
Consensus pattern (34 bp):
AGGTTAAGGAAGATGGAAGGTTAAAGGTCAAGGG
Found at i:5139310 original size:17 final size:17
Alignment explanation
Indices: 5139221--5139313 Score: 64
Period size: 17 Copynumber: 5.5 Consensus size: 17
5139211 AAGAATATGA
* *
5139221 AAGGTTAAGGAAGATGA
1 AAGGTTAAGGAAAATGG
**
5139238 AAGGTTAAAGGTCAA-GG
1 AAGGTT-AAGGAAAATGG
* *
5139255 GAGGTTAAGGAAGATGG
1 AAGGTTAAGGAAAATGG
* **
5139272 AAGATTAAAGGTCAA-GG
1 AAGGTT-AAGGAAAATGG
*
5139289 GAGGTTAAGGAAAATGG
1 AAGGTTAAGGAAAATGG
5139306 AAGGTTAA
1 AAGGTTAA
5139314 AAGTTAAGGG
Statistics
Matches: 54, Mismatches: 18, Indels: 8
0.68 0.22 0.10
Matches are distributed among these distances:
16 11 0.20
17 33 0.61
18 10 0.19
ACGTcount: A:0.43, C:0.02, G:0.37, T:0.18
Consensus pattern (17 bp):
AAGGTTAAGGAAAATGG
Found at i:5142171 original size:11 final size:11
Alignment explanation
Indices: 5142138--5142172 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
5142128 ACTTAGGTTG
5142138 TGTACTAATTT
1 TGTACTAATTT
*
5142149 TGTATCTTATTT
1 TGTA-CTAATTT
5142161 TGTACTAATTT
1 TGTACTAATTT
5142172 T
1 T
5142173 ATTTTTTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.60
Consensus pattern (11 bp):
TGTACTAATTT
Found at i:5145964 original size:20 final size:22
Alignment explanation
Indices: 5145938--5145988 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 22
5145928 AACAAGTCAA
5145938 ATTAAAAACAT-TA-ATTTAAAT
1 ATTAAAAA-ATATATATTTAAAT
*
5145959 -TTAAAAATTATATATTTAAAT
1 ATTAAAAAATATATATTTAAAT
5145980 ATTAAAAAA
1 ATTAAAAAA
5145989 ATACCTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 1 0.04
20 9 0.36
21 8 0.32
22 7 0.28
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTAAAAAATATATATTTAAAT
Found at i:5152102 original size:2 final size:2
Alignment explanation
Indices: 5152095--5152120 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5152085 GACTCCGTGG
5152095 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
5152121 GTTGATCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5158387 original size:22 final size:22
Alignment explanation
Indices: 5158359--5158402 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5158349 ATATATTAAT
5158359 AATCATACCTAATTAGCTGATG
1 AATCATACCTAATTAGCTGATG
5158381 AATCATACCTAATTAGCTGATG
1 AATCATACCTAATTAGCTGATG
5158403 CTTAGTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (22 bp):
AATCATACCTAATTAGCTGATG
Found at i:5160710 original size:6 final size:6
Alignment explanation
Indices: 5160699--5160804 Score: 86
Period size: 6 Copynumber: 16.2 Consensus size: 6
5160689 TTGAAAACAA
*
5160699 GAAAGG GAAAGG AGAAAGGG GGAAGG GAAAGG GAAAGG GAAAGG AGAAAGG
1 GAAAGG GAAAGG -GAAA-GG GAAAGG GAAAGG GAAAGG GAAAGG -GAAAGG
* * *
5160750 AGAAAGGG GAAGGG GGAAGC GAAAGG AGAAAGG AGAAAAGAG GAAAGG
1 -GAAA-GG GAAAGG GAAAGG GAAAGG -GAAAGG -G-AAAG-G GAAAGG
*
5160798 GGAAGG G
1 GAAAGG G
5160805 GGAAGGGGGA
Statistics
Matches: 84, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
6 41 0.49
7 33 0.39
8 9 0.11
9 1 0.01
ACGTcount: A:0.48, C:0.01, G:0.51, T:0.00
Consensus pattern (6 bp):
GAAAGG
Found at i:5160717 original size:7 final size:7
Alignment explanation
Indices: 5160698--5160797 Score: 86
Period size: 7 Copynumber: 15.0 Consensus size: 7
5160688 ATTGAAAACA
5160698 AGAAAGG
1 AGAAAGG
5160705 -GAAAGG
1 AGAAAGG
5160711 AGAAAGG
1 AGAAAGG
* *
5160718 GGGAAGG
1 AGAAAGG
5160725 -GAAAGG
1 AGAAAGG
5160731 -GAAAGG
1 AGAAAGG
5160737 -GAAAGG
1 AGAAAGG
5160743 AGAAAGG
1 AGAAAGG
5160750 AGAAAGG
1 AGAAAGG
*
5160757 -GGAAGG
1 AGAAAGG
* *
5160763 GGGAA-G
1 AGAAAGG
*
5160769 CGAAAGG
1 AGAAAGG
5160776 AGAAAGG
1 AGAAAGG
*
5160783 AGAAAAG
1 AGAAAGG
5160790 AGGAAAGG
1 A-GAAAGG
5160798 GGAAGGGGGA
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
6 32 0.41
7 42 0.53
8 5 0.06
ACGTcount: A:0.50, C:0.01, G:0.49, T:0.00
Consensus pattern (7 bp):
AGAAAGG
Found at i:5160735 original size:26 final size:25
Alignment explanation
Indices: 5160699--5160787 Score: 84
Period size: 26 Copynumber: 3.7 Consensus size: 25
5160689 TTGAAAACAA
5160699 GAAAGG-GAAAGGAGAAAGGGGGAAGG
1 GAAAGGAGAAAGG-GAAAGGGGGAA-G
5160725 GAAAGG-GAAAGGGAAA---GG-A-
1 GAAAGGAGAAAGGGAAAGGGGGAAG
*
5160744 GAAAGGAGAAAGGGGAAGGGGGAAG
1 GAAAGGAGAAAGGGAAAGGGGGAAG
5160769 CGAAAGGAGAAAGGAGAAA
1 -GAAAGGAGAAAGG-GAAA
5160788 AGAGGAAAGG
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
19 6 0.11
20 9 0.17
21 1 0.02
22 2 0.04
23 2 0.04
24 1 0.02
25 4 0.08
26 25 0.47
27 3 0.06
ACGTcount: A:0.49, C:0.01, G:0.49, T:0.00
Consensus pattern (25 bp):
GAAAGGAGAAAGGGAAAGGGGGAAG
Found at i:5160740 original size:32 final size:33
Alignment explanation
Indices: 5160700--5160804 Score: 131
Period size: 33 Copynumber: 3.2 Consensus size: 33
5160690 TGAAAACAAG
* *
5160700 AAAGGGAAAGGAGAAAGGGGGAA-GGGAAAGGG
1 AAAGGGAAAGGAGAAAGGAGAAAGGGGAAAGGG
*
5160732 AAAGGGAAAGGAGAAAGGAGAAAGGGGAAGGGG
1 AAAGGGAAAGGAGAAAGGAGAAAGGGGAAAGGG
* * *
5160765 GAAGCGAAAGGAGAAAGGAGAAAAGAGGAAAGGG
1 AAAGGGAAAGGAGAAAGGAG-AAAGGGGAAAGGG
*
5160799 GAAGGG
1 AAAGGG
5160805 GGAAGGGGGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
32 21 0.33
33 26 0.41
34 16 0.25
ACGTcount: A:0.49, C:0.01, G:0.50, T:0.00
Consensus pattern (33 bp):
AAAGGGAAAGGAGAAAGGAGAAAGGGGAAAGGG
Found at i:5160801 original size:7 final size:7
Alignment explanation
Indices: 5160699--5160815 Score: 84
Period size: 7 Copynumber: 17.4 Consensus size: 7
5160689 TTGAAAACAA
5160699 GAAA-GG
1 GAAAGGG
*
5160705 GAAAGGA
1 GAAAGGG
5160712 GAAAGGG
1 GAAAGGG
*
5160719 GGAA-GG
1 GAAAGGG
5160725 GAAA-GG
1 GAAAGGG
5160731 GAAA-GG
1 GAAAGGG
*
5160737 GAAAGGA
1 GAAAGGG
*
5160744 GAAAGGA
1 GAAAGGG
5160751 GAAAGGG
1 GAAAGGG
5160758 G-AAGGG
1 GAAAGGG
* *
5160764 GGAA-GC
1 GAAAGGG
*
5160770 GAAAGGA
1 GAAAGGG
5160777 GAAAGGAG
1 GAAAGG-G
* *
5160785 AAAAGAG
1 GAAAGGG
5160792 GAAAGGG
1 GAAAGGG
*
5160799 GAAGGGG
1 GAAAGGG
*
5160806 GAAGGGG
1 GAAAGGG
5160813 GAA
1 GAA
5160816 GGGAAATGGA
Statistics
Matches: 91, Mismatches: 15, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
6 31 0.34
7 56 0.62
8 4 0.04
ACGTcount: A:0.47, C:0.01, G:0.52, T:0.00
Consensus pattern (7 bp):
GAAAGGG
Found at i:5161967 original size:20 final size:22
Alignment explanation
Indices: 5161928--5161967 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
5161918 CTTCTTGATC
*
5161928 TAGACTTTTAACTTCAGTCATA
1 TAGACTTTTAACTCCAGTCATA
5161950 TAGACTTTT-A-TCCAGTCA
1 TAGACTTTTAACTCCAGTCA
5161968 GCGGTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 1 0.06
22 9 0.53
ACGTcount: A:0.30, C:0.20, G:0.10, T:0.40
Consensus pattern (22 bp):
TAGACTTTTAACTCCAGTCATA
Found at i:5163258 original size:23 final size:25
Alignment explanation
Indices: 5163232--5163277 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5163222 CCAATTAGGG
5163232 AATTA-TTGTTTAG-ATTTAATTCA
1 AATTATTTGTTTAGAATTTAATTCA
*
5163255 AATTATTTTTTTAGAATTTAATT
1 AATTATTTGTTTAGAATTTAATT
5163278 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 5 0.25
24 7 0.35
25 8 0.40
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATTTGTTTAGAATTTAATTCA
Found at i:5172420 original size:44 final size:43
Alignment explanation
Indices: 5172353--5172442 Score: 171
Period size: 44 Copynumber: 2.1 Consensus size: 43
5172343 ATGTGTGTTA
5172353 TTAAAAATCTCCATCGTGTCCGGTTCAGCCATGCACTTTAAGT
1 TTAAAAATCTCCATCGTGTCCGGTTCAGCCATGCACTTTAAGT
5172396 TTAACAAATCTCCATCGTGTCCGGTTCAGCCATGCACTTTAAGT
1 TTAA-AAATCTCCATCGTGTCCGGTTCAGCCATGCACTTTAAGT
5172440 TTA
1 TTA
5172443 GATAGCTGAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 4 0.09
44 42 0.91
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.33
Consensus pattern (43 bp):
TTAAAAATCTCCATCGTGTCCGGTTCAGCCATGCACTTTAAGT
Found at i:5174295 original size:55 final size:55
Alignment explanation
Indices: 5174225--5174367 Score: 214
Period size: 55 Copynumber: 2.6 Consensus size: 55
5174215 ATTGCTTCTT
* *
5174225 CTTCTTTTGAATCGATTGTTTATATGTTTAAATCGGTTGTTATATTGGAATACTA
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTATTATATTGGAATACTA
* * * *
5174280 TTTCTTTTGAATCGATTATTTATATGTTTAAATCGATTATTATGTTGGAATATTA
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTATTATATTGGAATACTA
* *
5174335 CTTCTTTTAAATCGATTGTTTGTATGTTTAAAT
1 CTTCTTTTGAATCGATTGTTTATATGTTTAAAT
5174368 TTAGGGTTAC
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 78 1.00
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.52
Consensus pattern (55 bp):
CTTCTTTTGAATCGATTGTTTATATGTTTAAATCGATTATTATATTGGAATACTA
Found at i:5182500 original size:21 final size:21
Alignment explanation
Indices: 5182474--5182516 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
5182464 ACCTTTTTTA
5182474 AAGTTAAAAGTCAAAATCATT
1 AAGTTAAAAGTCAAAATCATT
*
5182495 AAGTTAAAAGTTAAAATCATT
1 AAGTTAAAAGTCAAAATCATT
5182516 A
1 A
5182517 TATTGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.09, T:0.30
Consensus pattern (21 bp):
AAGTTAAAAGTCAAAATCATT
Found at i:5184536 original size:13 final size:13
Alignment explanation
Indices: 5184518--5184543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5184508 CATTCAAACA
5184518 CAACGGAGTGACT
1 CAACGGAGTGACT
5184531 CAACGGAGTGACT
1 CAACGGAGTGACT
5184544 GGTGATGCAA
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:0.31, C:0.23, G:0.31, T:0.15
Consensus pattern (13 bp):
CAACGGAGTGACT
Found at i:5205468 original size:27 final size:26
Alignment explanation
Indices: 5205414--5205469 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
5205404 GCACATCGGA
*
5205414 TTGGGGTCAAATTTACTCGATTGAGT
1 TTGGGGTCAAATTTACTCGATCGAGT
*
5205440 TTGGGGTTCAAATTTACTCGATCGGGT
1 TTGGGG-TCAAATTTACTCGATCGAGT
5205467 TTG
1 TTG
5205470 AGGTGTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.20, C:0.12, G:0.29, T:0.39
Consensus pattern (26 bp):
TTGGGGTCAAATTTACTCGATCGAGT
Found at i:5208379 original size:6 final size:6
Alignment explanation
Indices: 5208365--5208416 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
5208355 AGTCCGGCAA
* *
5208365 CAGCTC CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC GAGCAC
1 CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC CAGCAC
5208413 CAGC
1 CAGC
5208417 TTCTACTGCA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 43 1.00
ACGTcount: A:0.31, C:0.48, G:0.19, T:0.02
Consensus pattern (6 bp):
CAGCAC
Found at i:5210899 original size:14 final size:14
Alignment explanation
Indices: 5210880--5210911 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
5210870 GTTAACTTCC
5210880 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
5210894 TTTCTTTTTCTTTT
1 TTTCTTTTTCTTTT
5210908 TTTC
1 TTTC
5210912 CGAAGGATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTCTTTTTCTTTT
Found at i:5211269 original size:19 final size:19
Alignment explanation
Indices: 5211247--5211308 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
5211237 AAAACATAAA
5211247 AATTACAAGAAAATAATTT
1 AATTACAAGAAAATAATTT
**
5211266 AATTA-ATTAGAAAAT-ATAAA
1 AATTACA--AGAAAATAAT-TT
*
5211286 AATTACAAGAAAAGAATTT
1 AATTACAAGAAAATAATTT
5211305 AATT
1 AATT
5211309 GCTGTAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
18 1 0.03
19 17 0.52
20 14 0.42
21 1 0.03
ACGTcount: A:0.60, C:0.03, G:0.06, T:0.31
Consensus pattern (19 bp):
AATTACAAGAAAATAATTT
Found at i:5218014 original size:60 final size:60
Alignment explanation
Indices: 5217921--5218040 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
5217911 TTAGTAGGAG
*
5217921 AGATCTTGAGTTTTTTCTTGTTTTCCTTTGCATACTTGTAATATCTTGAATAATGTCTTT
1 AGATCATGAGTTTTTTCTTGTTTTCCTTTGCATACTTGTAATATCTTGAATAATGTCTTT
5217981 AGATCATGAGTTTTTTCTTGTTTTCCTTTGCATACTTGTAATATCTTGAATAATGTCTTT
1 AGATCATGAGTTTTTTCTTGTTTTCCTTTGCATACTTGTAATATCTTGAATAATGTCTTT
5218041 GGAAACAGGT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 59 1.00
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (60 bp):
AGATCATGAGTTTTTTCTTGTTTTCCTTTGCATACTTGTAATATCTTGAATAATGTCTTT
Found at i:5219342 original size:7 final size:7
Alignment explanation
Indices: 5219332--5219358 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5219322 TATTTTTTTT
5219332 CCTTTCA
1 CCTTTCA
5219339 CCTTTCA
1 CCTTTCA
5219346 CCTTTCA
1 CCTTTCA
5219353 CCTTTC
1 CCTTTC
5219359 TTTAATGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.11, C:0.44, G:0.00, T:0.44
Consensus pattern (7 bp):
CCTTTCA
Found at i:5220231 original size:12 final size:12
Alignment explanation
Indices: 5220210--5220241 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5220200 GTTAACTTCC
5220210 TTTC-TTTTTTT
1 TTTCTTTTTTTT
5220221 TTTCTTTTTTTT
1 TTTCTTTTTTTT
5220233 TTTCTTTTT
1 TTTCTTTTT
5220242 ATTTCCGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:5222299 original size:22 final size:24
Alignment explanation
Indices: 5222274--5222318 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
5222264 GAGAGTACCG
5222274 AAGTACT-G-AATAGAGAGCACAT
1 AAGTACTGGCAATAGAGAGCACAT
*
5222296 AAGTGCTGGGCAATAGAGAGCAC
1 AAGTACT-GGCAATAGAGAGCAC
5222319 GCAAAGTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 6 0.32
24 1 0.05
25 12 0.63
ACGTcount: A:0.40, C:0.16, G:0.29, T:0.16
Consensus pattern (24 bp):
AAGTACTGGCAATAGAGAGCACAT
Found at i:5222382 original size:23 final size:23
Alignment explanation
Indices: 5222352--5222472 Score: 149
Period size: 23 Copynumber: 5.2 Consensus size: 23
5222342 ACAAAGTACT
5222352 GAGCACACGAAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
5222375 GAGCACACGAAGTGCTAATCAGA
1 GAGCACACGAAGTGCTAATCAGA
5222398 GAGCACAC-ACAGTGCTAATAACAGA
1 GAGCACACGA-AGTGCTAAT--CAGA
* * *
5222423 GAGCACGA-GACGTACTAAACAGA
1 GAGCAC-ACGAAGTGCTAATCAGA
5222446 GAGCACAC-ACAGTGCTAATCAGA
1 GAGCACACGA-AGTGCTAATCAGA
5222469 GAGC
1 GAGC
5222473 TCGCTAGTGT
Statistics
Matches: 85, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
22 3 0.04
23 64 0.75
25 16 0.19
26 2 0.02
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (23 bp):
GAGCACACGAAGTGCTAATCAGA
Found at i:5222427 original size:48 final size:46
Alignment explanation
Indices: 5222352--5222472 Score: 165
Period size: 48 Copynumber: 2.6 Consensus size: 46
5222342 ACAAAGTACT
* *
5222352 GAGCACACGA-AGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCAGA
1 GAGCACAC-ACAGTGCTAATCAGAGAGCACGA-GAAGTACTAAACAGA
*
5222398 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTACTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTACTAAACAGA
5222446 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
5222473 TCGCTAGTGT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
45 1 0.01
46 25 0.37
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTACTAAACAGA
Found at i:5225478 original size:53 final size:53
Alignment explanation
Indices: 5225415--5225521 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
5225405 CCATGTGATA
5225415 GGCTAATGATTAAGGACTTTTATCGTTTTAAATGTGACTTGAGTTCGAATTGT
1 GGCTAATGATTAAGGACTTTTATCGTTTTAAATGTGACTTGAGTTCGAATTGT
5225468 GGCTAATGATTAAGGACTTTTATCGTTTTAAATGTGACTTGAGTTCGAATTGT
1 GGCTAATGATTAAGGACTTTTATCGTTTTAAATGTGACTTGAGTTCGAATTGT
5225521 G
1 G
5225522 TTAATCGTGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.26, C:0.09, G:0.23, T:0.41
Consensus pattern (53 bp):
GGCTAATGATTAAGGACTTTTATCGTTTTAAATGTGACTTGAGTTCGAATTGT
Found at i:5226775 original size:5 final size:5
Alignment explanation
Indices: 5226765--5226792 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
5226755 TAAGAGGAAA
5226765 GGGTT GGGTT GGGTT GGGTT GGGTT GGG
1 GGGTT GGGTT GGGTT GGGTT GGGTT GGG
5226793 CAGGATTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (5 bp):
GGGTT
Found at i:5232080 original size:158 final size:158
Alignment explanation
Indices: 5231782--5232088 Score: 352
Period size: 158 Copynumber: 1.9 Consensus size: 158
5231772 TTGTAACATG
* ** * * *
5231782 TAACCATATATGCTCACACTAGCTATGAAATGGTTCTACTCACACGAACTGCTGGTTGGGATGTT
1 TAACCATATATGCTCACACGAGCTATGAAATGGGCCTACTCACACGAACTGATGGTCGAGATGTT
** *
5231847 AGGCTATGCGATGCTGCTCACACGAGCTGTAGAGAATCCGCAACAAATGCAGGACCTCAATCATC
66 AGGCTACACGATGCTGCTCACACGAGCTGTAGAGAATCCGCAACAAATGCAGGACCTCAAACATC
**
5231912 GGTAGGACATCTAAGACCAGCACCCGTA
131 AATAGGACATCTAAGACCAGCACCCGTA
* * *
5231940 TAACC-TATAATGCTCACACGAGCTGTGAAATGGGCCTGCTCACACGAGCT-ATGGGTCGAGATG
1 TAACCATAT-ATGCTCACACGAGCTATGAAATGGGCCTACTCACACGAACTGAT-GGTCGAGATG
* * * * * * *
5232003 TTGGGCTACACGATGCTGCTCACACGAGCTAG-GGAGAATTCGTAAGAATTGTC-GGATCTCAAA
64 TTAGGCTACACGATGCTGCTCACACGAGCT-GTAGAGAATCCGCAACAAATG-CAGGACCTCAAA
*
5232066 CATCAATAGTACATCTAAGACCA
127 CATCAATAGGACATCTAAGACCA
5232089 ACATCCAGAA
Statistics
Matches: 123, Mismatches: 22, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
157 4 0.03
158 117 0.95
159 2 0.02
ACGTcount: A:0.30, C:0.24, G:0.23, T:0.23
Consensus pattern (158 bp):
TAACCATATATGCTCACACGAGCTATGAAATGGGCCTACTCACACGAACTGATGGTCGAGATGTT
AGGCTACACGATGCTGCTCACACGAGCTGTAGAGAATCCGCAACAAATGCAGGACCTCAAACATC
AATAGGACATCTAAGACCAGCACCCGTA
Found at i:5233232 original size:13 final size:14
Alignment explanation
Indices: 5233208--5233255 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
5233198 TTAATATTTC
*
5233208 AATATTATTTTAAT
1 AATATAATTTTAAT
*
5233222 AATA-AATTTTAAA
1 AATATAATTTTAAT
5233235 AATAATAATTTTAAAT
1 AAT-ATAATTTT-AAT
5233251 AATAT
1 AATAT
5233256 TCTTAATACA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 10 0.36
14 5 0.18
15 8 0.29
16 5 0.18
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATATAATTTTAAT
Found at i:5233240 original size:16 final size:16
Alignment explanation
Indices: 5233218--5233254 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
5233208 AATATTATTT
5233218 TAATAATAAATTTTAAA
1 TAATAAT-AATTTTAAA
5233235 -AATAATAATTTTAAA
1 TAATAATAATTTTAAA
5233250 TAATA
1 TAATA
5233255 TTCTTAATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATAATTTTAAA
Found at i:5243237 original size:6 final size:6
Alignment explanation
Indices: 5243226--5243269 Score: 79
Period size: 6 Copynumber: 7.3 Consensus size: 6
5243216 TTGAGGCAGC
*
5243226 AGCTGG AGCTGG AGCTGG AGCTGG AGCTGG AGCTGG AGCAGG AG
1 AGCTGG AGCTGG AGCTGG AGCTGG AGCTGG AGCTGG AGCTGG AG
5243270 GAGATGGGGT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.20, C:0.16, G:0.50, T:0.14
Consensus pattern (6 bp):
AGCTGG
Found at i:5253888 original size:14 final size:15
Alignment explanation
Indices: 5253862--5253895 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5253852 AAATTTATAA
5253862 TATTTTATATTATGT
1 TATTTTATATTATGT
5253877 TATTTT-TATTATGT
1 TATTTTATATTATGT
*
5253891 AATTT
1 TATTT
5253896 AAAACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (15 bp):
TATTTTATATTATGT
Found at i:5257691 original size:15 final size:15
Alignment explanation
Indices: 5257671--5257704 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5257661 CCTCCAAACG
*
5257671 CCACAAGCATCGCCA
1 CCACAAACATCGCCA
*
5257686 CCACAAACATCGTCA
1 CCACAAACATCGCCA
5257701 CCAC
1 CCAC
5257705 CGCCACCGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.35, C:0.47, G:0.09, T:0.09
Consensus pattern (15 bp):
CCACAAACATCGCCA
Found at i:5259238 original size:54 final size:55
Alignment explanation
Indices: 5259180--5259364 Score: 182
Period size: 54 Copynumber: 3.4 Consensus size: 55
5259170 GGGAGATTTA
* * *
5259180 TGGTGAGAGGAGAAGGGAGAGGGAGCGAGCA-AGGAGTAGAGATAGAG-ACAT-GAG
1 TGGTGAAAGGAGAAGGGAGAAGGAGCGAG-AGAGGAGTAGAGAAAGAGAAC-TGGAG
*
5259234 TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAGGAGTAGGGAAAGAGAACTGGAG
1 TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAGGAGTAGAGAAAGAGAACTGGAG
* * * * ** * * * * *
5259289 -AGAGAAAGGAGAAGGGAGAAGGAGCGAGGGAAGAGCCGGGACAGGGATCTAGA-
1 TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAGGAGTAGAGAAAGAGAACTGGAG
5259342 TGGTGAAAGGAGAAGGGAGAAGG
1 TGGTGAAAGGAGAAGGGAGAAGG
5259365 TGCATGACAG
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
53 1 0.01
54 105 0.95
55 5 0.05
ACGTcount: A:0.39, C:0.05, G:0.49, T:0.07
Consensus pattern (55 bp):
TGGTGAAAGGAGAAGGGAGAAGGAGCGAGAGAGGAGTAGAGAAAGAGAACTGGAG
Done.