Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008656.1 Hibiscus syriacus cultivar Beakdansim tig00111650_pilon, 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: 2456495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 12
Found at i:811049 original size:32 final size:32
Alignment explanation
Indices: 811004--811245 Score: 224
Period size: 32 Copynumber: 8.5 Consensus size: 32
810994 CAAAACATGG
811004 ATTGATTTATTTTAAATAATTTATTAGTATGA
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
*
811036 ATTAATTTATTTT-AA-AA--TA-T-G---G-
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
811058 ATTGATTTATTTTAAATAATTTATTAGTATGA
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
811090 ATTGATTTATTTT-AA-AA--TA-T-G---G-
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
811112 ATTGATTTATTTTAAATAATTTATTAGTAT-A
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
811143 GATTGATTTA-TTT---TAA---A--A-TATGA
1 -ATTGATTTATTTTAAATAATTTATTAGTATGA
811166 ATTGATTTATTTTAAATAATTTATTAGTAT-A
1 ATTGATTTATTTTAAATAATTTATTAGTATGA
*
811197 GATTGATTTATTTTAAATAATTTATTTGTATGA
1 -ATTGATTTATTTTAAATAATTTATTAGTATGA
811230 ATTGATTTATTTTAAA
1 ATTGATTTATTTTAAA
811246 ATATGGATTT
Statistics
Matches: 173, Mismatches: 3, Indels: 68
0.71 0.01 0.28
Matches are distributed among these distances:
22 37 0.21
23 11 0.06
24 4 0.02
25 1 0.01
26 9 0.05
27 4 0.02
28 9 0.05
29 1 0.01
30 4 0.02
31 10 0.06
32 82 0.47
33 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (32 bp):
ATTGATTTATTTTAAATAATTTATTAGTATGA
Found at i:811056 original size:22 final size:22
Alignment explanation
Indices: 811031--811073 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
811021 AATTTATTAG
811031 TATGAATTAATTTATTTTAAAA
1 TATGAATTAATTTATTTTAAAA
* *
811053 TATGGATTGATTTATTTTAAA
1 TATGAATTAATTTATTTTAAA
811074 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATGAATTAATTTATTTTAAAA
Found at i:811060 original size:54 final size:54
Alignment explanation
Indices: 810995--811357 Score: 459
Period size: 54 Copynumber: 6.6 Consensus size: 54
810985 TTTTCAGATC
* *
810995 AAAACATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTAATTTATTTT
1 AAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
811049 AAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
1 AAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
811103 AAAATATGGATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTT
1 AAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTT
*
811157 AAAATATGAATTGATTTATTTTAAATAATTTATTAGTAT-AGATTGATTTATTTT
1 AAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTT
* * * * * * * * *
811211 -AAATA---ATTTATTTGTATGAATTGATTTATTTTAAAATATGGATTTATTTATTATTGT
1 AAAATATGGATTGATTTATTTTAAATAATTTA--TT--AGTATGAATTGATTTA-T-TT-T
** *
811268 AGTTATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTT
1 A-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
811323 AAAATATGGATTGATTTATTTTAAATAATTTATTA
1 AAAATATGGATTGATTTATTTTAAATAATTTATTA
811358 TTGTAGTTGT
Statistics
Matches: 271, Mismatches: 24, Indels: 28
0.84 0.07 0.09
Matches are distributed among these distances:
50 17 0.06
52 2 0.01
53 6 0.02
54 201 0.74
55 3 0.01
56 4 0.01
57 2 0.01
58 14 0.05
59 3 0.01
60 2 0.01
62 17 0.06
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (54 bp):
AAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
Found at i:811110 original size:22 final size:22
Alignment explanation
Indices: 811085--811127 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
811075 AATTTATTAG
811085 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
811107 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
811128 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:811149 original size:86 final size:81
Alignment explanation
Indices: 811096--811342 Score: 290
Period size: 80 Copynumber: 3.0 Consensus size: 81
811086 ATGAATTGAT
*
811096 TTATTTTA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAA
1 TTATTTTAGTAATATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAA
*
811160 ATATGAATTGATTTATT-
65 ATATGAATTG-TATATTA
* * * *
811177 TTAAATAATTTATTAGTATAGATTGATTTATTTTAAATAATTTATTTGTATGAATTGATTTATTT
1 TT--AT--TTTAGTAATATGGATTGATTTATTTTAAATAATTTATTAGTATG-ATTGATTTATTT
*
811242 TAAAATATGGATT-TAT-TTA
61 TAAAATATGAATTGTATATTA
* *
811261 TTATTGTAGTTATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
1 TTATTTTAGTAATATGGATTGATTTATTTTAAATAATTTATTAGTAT-GATTGATTTATTTTAAA
*
811326 ATATGGATTG-AT-TTA
65 ATATGAATTGTATATTA
811341 TT
1 TT
811343 TTAAATAATT
Statistics
Matches: 145, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
80 69 0.48
81 3 0.02
82 2 0.01
83 4 0.03
84 4 0.03
85 5 0.03
86 58 0.40
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.53
Consensus pattern (81 bp):
TTATTTTAGTAATATGGATTGATTTATTTTAAATAATTTATTAGTATGATTGATTTATTTTAAAA
TATGAATTGTATATTA
Found at i:811189 original size:14 final size:14
Alignment explanation
Indices: 811170--811223 Score: 54
Period size: 14 Copynumber: 3.6 Consensus size: 14
811160 ATATGAATTG
811170 ATTTATTTTAAATA
1 ATTTATTTTAAATA
* *
811184 ATTTATTAGTATAGATTG
1 ATTTATT--T-TA-AATA
811202 ATTTATTTTAAATA
1 ATTTATTTTAAATA
811216 ATTTATTT
1 ATTTATTT
811224 GTATGAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 17 0.53
15 2 0.06
16 2 0.06
17 2 0.06
18 9 0.28
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTTAAATA
Found at i:811241 original size:18 final size:16
Alignment explanation
Indices: 811058--811259 Score: 78
Period size: 18 Copynumber: 11.8 Consensus size: 16
811048 TAAAATATGG
811058 ATTGATTTATTTTA-A
1 ATTGATTTATTTTATA
* *
811073 A-TAATTTATTAGTATGA
1 ATTGATTTATT-TTAT-A
811090 ATTGATTTATTTTAAAATA
1 ATTGATTTATTTT---ATA
811109 TGGATTGATTTATTTTA-A
1 ---ATTGATTTATTTTATA
* *
811127 A-TAATTTATTAGTATA
1 ATTGATTTATT-TTATA
811143 GATTGATTTATTTTAAAATATGA
1 -ATTGATTTA-TTT----TAT-A
811166 ATTGATTTATTTTA-A
1 ATTGATTTATTTTATA
* *
811181 A-TAATTTATTAGTATA
1 ATTGATTTATT-TTATA
811197 GATTGATTTATTTTA-A
1 -ATTGATTTATTTTATA
*
811213 A-TAATTTATTTGTATGA
1 ATTGATTTATTT-TAT-A
*
811230 ATTGATTTATTTTAAA
1 ATTGATTTATTTTATA
811246 ATATGGATTTATTT
1 AT-T-GATTTATTT
811260 ATTATTGTAG
Statistics
Matches: 142, Mismatches: 15, Indels: 57
0.66 0.07 0.27
Matches are distributed among these distances:
14 33 0.23
15 13 0.09
16 6 0.04
17 14 0.10
18 41 0.29
19 4 0.03
20 2 0.01
21 3 0.02
22 25 0.18
23 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (16 bp):
ATTGATTTATTTTATA
Found at i:811330 original size:22 final size:22
Alignment explanation
Indices: 811305--811347 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
811295 AATTTATTAG
811305 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
811327 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
811348 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:811407 original size:31 final size:31
Alignment explanation
Indices: 811372--811430 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
811362 AGTTGTATAG
*
811372 ATTATTTAAATTTAAGTATTGTAAAACTAAA
1 ATTATTTAAATTTAAGTATTGCAAAACTAAA
*
811403 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTAAGTATTGCAAAACT
811431 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (31 bp):
ATTATTTAAATTTAAGTATTGCAAAACTAAA
Found at i:812303 original size:18 final size:18
Alignment explanation
Indices: 812280--812314 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
812270 ATTTTTATTG
812280 AATAAAAATAATATTTCT
1 AATAAAAATAATATTTCT
* *
812298 AATAAAAGTATTATTTC
1 AATAAAAATAATATTTC
812315 GTATTTCATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.06, G:0.03, T:0.40
Consensus pattern (18 bp):
AATAAAAATAATATTTCT
Found at i:813524 original size:18 final size:18
Alignment explanation
Indices: 813501--813537 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
813491 ATAAAGTAAA
813501 AAAATTAAAATAAAAAAG
1 AAAATTAAAATAAAAAAG
* *
813519 AAAATTTAAATTAAAAAG
1 AAAATTAAAATAAAAAAG
813537 A
1 A
813538 TTAAATTGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAATTAAAATAAAAAAG
Found at i:814944 original size:5 final size:5
Alignment explanation
Indices: 814926--815285 Score: 443
Period size: 5 Copynumber: 73.6 Consensus size: 5
814916 AATATTAGTA
814926 ATAA- ATAA- ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-A- ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
814972 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT ATAAT AT-A-
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
815019 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT AT-AT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
815068 AT-AT ATAAT ATAAT ATAAT ATAAT ATATAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATAAT ATAAT ATAAT ATAAT
815118 ATAAT ATAAT ATAAT ATAAT AT-AT ATATAT ATATAT ATAAT AT-AT AT-AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT ATAAT ATAAT ATAAT
* * *
815167 ATATAT ATATAT ATGAT ATGAT AT-AT ATGAT AT-AT ATAAT AT-AT AT-AT
1 ATA-AT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
* *
815215 ATATAT ATATAT ATGAT AT-AT ATGAT AT-AT AT-AT ATATAT ATATAT
1 ATA-AT ATA-AT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT ATA-AT
815261 ATATAT ATATAT ATAAT ATAAT ATA
1 ATA-AT ATA-AT ATAAT ATAAT ATA
815286 TTTATTTTAA
Statistics
Matches: 334, Mismatches: 2, Indels: 39
0.89 0.01 0.10
Matches are distributed among these distances:
3 4 0.01
4 64 0.19
5 207 0.62
6 59 0.18
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (5 bp):
ATAAT
Found at i:815303 original size:31 final size:30
Alignment explanation
Indices: 815268--815340 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 30
815258 TATATATATA
**
815268 TATATATA-ATATAATATATTTATTTTAAAAC
1 TATATATACATATAATATA-TT-TTCAAAAAC
*
815299 TATATA-ACATATATTATATTTTCAAAAAC
1 TATATATACATATAATATATTTTCAAAAAC
*
815328 TATATATATATAT
1 TATATATACATAT
815341 TTCAAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 13 0.36
30 8 0.22
31 15 0.42
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (30 bp):
TATATATACATATAATATATTTTCAAAAAC
Found at i:815303 original size:33 final size:32
Alignment explanation
Indices: 815266--815372 Score: 85
Period size: 29 Copynumber: 3.3 Consensus size: 32
815256 TATATATATA
*
815266 TATATATATAATATAATATATTTATTTTAAAAC
1 TATATATATAATATAATATATTT-TTTAAAAAC
* * *
815299 TATATA-A-CATATATTATA-TTTTCAAAAAC
1 TATATATATAATATAATATATTTTTTAAAAAC
* * * *
815328 TATATATATATATTTCAAAATATGTTTTCAAAAC
1 TATATATATA-ATAT-AATATATTTTTTAAAAAC
815362 TATATTATATA
1 TATA-TATATA
815373 CGCTTTCAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 10
0.73 0.14 0.13
Matches are distributed among these distances:
29 13 0.23
30 3 0.05
31 9 0.16
32 4 0.07
33 10 0.18
34 12 0.21
35 6 0.11
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.46
Consensus pattern (32 bp):
TATATATATAATATAATATATTTTTTAAAAAC
Found at i:815303 original size:35 final size:33
Alignment explanation
Indices: 815264--815372 Score: 93
Period size: 34 Copynumber: 3.4 Consensus size: 33
815254 TATATATATA
*
815264 TATATATATATAATATAATATATTTATTTTAAAAC
1 TATATATATAT-ATATAATATATTT-TTTAAAAAC
* *
815299 TATATA-ACATATAT--TATA-TTTTCAAAAAC
1 TATATATATATATATAATATATTTTTTAAAAAC
* * * *
815328 TATATATATATATTTCAAAATATGTTTTCAAAAC
1 TATATATATATATAT-AATATATTTTTTAAAAAC
815362 TATAT-TATATA
1 TATATATATATA
815373 CGCTTTCAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
29 13 0.22
30 8 0.13
31 4 0.07
33 13 0.22
34 16 0.27
35 6 0.10
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (33 bp):
TATATATATATATATAATATATTTTTTAAAAAC
Found at i:815304 original size:2 final size:2
Alignment explanation
Indices: 814937--815286 Score: 368
Period size: 2 Copynumber: 193.0 Consensus size: 2
814927 TAAATAAATA
814937 AT AT A- AT AT A- AT AT A- AT AT A- AT AT A- AT AT A- AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
814972 AT A- AT AT A- AT AT A- AT AT A- AT AT A- AT AT A- 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
815008 A- AT AT A- AT AT A- AT A- AT AT A- AT AT A- AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
815042 AT AT A- AT AT A- AT AT A- AT AT AT AT A- AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
815079 A- AT AT A- AT AT A- AT AT AT AT AT A- AT AT A- AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
815115 A- AT AT A- AT AT A- AT AT A- AT AT A- 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
815152 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT GAT AT GAT 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
815195 GAT AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT GAT 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
815238 GAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
815280 A- AT AT AT
1 AT AT AT AT
815287 TTATTTTAAA
Statistics
Matches: 302, Mismatches: 0, Indels: 92
0.77 0.00 0.23
Matches are distributed among these distances:
1 41 0.14
2 251 0.83
3 10 0.03
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (2 bp):
AT
Found at i:815390 original size:36 final size:35
Alignment explanation
Indices: 815317--815475 Score: 114
Period size: 36 Copynumber: 4.4 Consensus size: 35
815307 ATATATTATA
815317 TTTTCAAAAACTATATATATATATTTCAAAATATG
1 TTTTCAAAAACTATATATATATATTTCAAAATATG
815352 TTTTC-AAAACTATAT-TATATACGCTTTCAAAA-ATTG
1 TTTTCAAAAACTATATATATATA---TTTCAAAATA-TG
* * *
815388 TTTTTTAAAAACTATATATTTTATGTTTTCAAAA-ACT-
1 -TTTTCAAAAACTATATA-TATAT-ATTTCAAAATA-TG
* * **
815425 TTTTAAAAAACTATATATTATATGTTTTCAAAA-AAA
1 TTTTCAAAAACTATATA-TATAT-ATTTCAAAATATG
*
815461 ATTTCAAAAACTATA
1 TTTTCAAAAACTATA
815476 CTACATTTTA
Statistics
Matches: 105, Mismatches: 9, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
33 6 0.06
34 10 0.10
35 6 0.06
36 55 0.52
37 4 0.04
38 20 0.19
40 4 0.04
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (35 bp):
TTTTCAAAAACTATATATATATATTTCAAAATATG
Found at i:823591 original size:12 final size:12
Alignment explanation
Indices: 823572--823604 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
823562 AGTGGGAGTA
823572 ATTTTCAAAATT
1 ATTTTCAAAATT
823584 GA-TTTCAAAATT
1 -ATTTTCAAAATT
823596 ATTTTCAAA
1 ATTTTCAAA
823605 GAAAATCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.05
12 17 0.89
13 1 0.05
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (12 bp):
ATTTTCAAAATT
Found at i:829382 original size:52 final size:52
Alignment explanation
Indices: 829317--829444 Score: 177
Period size: 53 Copynumber: 2.4 Consensus size: 52
829307 AGTTGTTATG
* * *
829317 GCAATACTACTCAGCATTAATTACAACCCTT-GTTTGTCAGACTATTTTTGTA
1 GCAATACT-CTCAGCATAAACTACAACCCTTGGTTTGTCAGACTATTGTTGTA
* *
829369 GCAATACCTCTCAGCATAAACTACAACCCTTGGTTTGTCAGATTGTTGTTGTA
1 GCAATA-CTCTCAGCATAAACTACAACCCTTGGTTTGTCAGACTATTGTTGTA
829422 GCAATAGCTCTCAGCATAAACTA
1 GCAATA-CTCTCAGCATAAACTA
829445 TAATCATTGT
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
52 26 0.38
53 42 0.62
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.34
Consensus pattern (52 bp):
GCAATACTCTCAGCATAAACTACAACCCTTGGTTTGTCAGACTATTGTTGTA
Found at i:842776 original size:24 final size:24
Alignment explanation
Indices: 842744--842793 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
842734 GTTAGTTATA
*
842744 GAAGCTTGTTG-TTTTACAGCCGAT
1 GAAGCTTG-TGCTTTTACAGCAGAT
842768 GAAGCTTGTGCTTTTACAGCAGAT
1 GAAGCTTGTGCTTTTACAGCAGAT
842792 GA
1 GA
842794 GTCTCCTTGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (24 bp):
GAAGCTTGTGCTTTTACAGCAGAT
Found at i:849145 original size:17 final size:17
Alignment explanation
Indices: 849118--849156 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
849108 ATCATAATGA
849118 ATTTT-GGTCAAAATTG
1 ATTTTCGGTCAAAATTG
849134 ATTTTCGGTCAAAATTG
1 ATTTTCGGTCAAAATTG
849151 ATTTTC
1 ATTTTC
849157 AATGCAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.46
Consensus pattern (17 bp):
ATTTTCGGTCAAAATTG
Found at i:850266 original size:20 final size:21
Alignment explanation
Indices: 850241--850281 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
850231 TGCATATATT
*
850241 TCATCCTCAAAAGCTA-AAAA
1 TCATCCCCAAAAGCTAGAAAA
*
850261 TCATCCCCAACAGCTAGAAAA
1 TCATCCCCAAAAGCTAGAAAA
850282 GGCCACAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.46, C:0.29, G:0.07, T:0.17
Consensus pattern (21 bp):
TCATCCCCAAAAGCTAGAAAA
Found at i:851038 original size:18 final size:18
Alignment explanation
Indices: 851015--851050 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
851005 AAAATTAAAT
851015 AAATTTAAATTAAAAAGA
1 AAATTTAAATTAAAAAGA
851033 AAATTTAAATTAAAAAGA
1 AAATTTAAATTAAAAAGA
851051 TTAAATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.28
Consensus pattern (18 bp):
AAATTTAAATTAAAAAGA
Found at i:851068 original size:15 final size:14
Alignment explanation
Indices: 851006--851070 Score: 51
Period size: 15 Copynumber: 4.2 Consensus size: 14
850996 AATAAAGTAA
851006 AAATTAAATAA-ATTT
1 AAATTAAA-AAGA-TT
851021 AAATTAAAAAGAAAATTT
1 AAATTAAAAAG---A-TT
851039 AAATTAAAAAGATT
1 AAATTAAAAAGATT
*
851053 AAATTGAAAAGAATT
1 AAATTAAAAAG-ATT
851068 AAA
1 AAA
851071 ATTCAAGAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
14 14 0.32
15 15 0.34
18 15 0.34
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (14 bp):
AAATTAAAAAGATT
Found at i:852600 original size:5 final size:5
Alignment explanation
Indices: 852461--852599 Score: 179
Period size: 5 Copynumber: 27.8 Consensus size: 5
852451 TAATATATAA
* * * * * *
852461 CATAA CATAA CATAA CATAA CATAA CATAA CATAG CATAG CATAG CATAG
1 CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG
* *
852511 CATAG CATAG CATAG CATAG CATAG AATAG CATAG CATAG AATAG CATAG
1 CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATAG
* * *
852561 CATAG CATAG CATAG CATAG CATAA CATAA CATAA CATA
1 CATAG CATAG CATAG CATAG CATAG CATAG CATAG CATA
852600 ATTTTTTTTT
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 128 1.00
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.20
Consensus pattern (5 bp):
CATAG
Found at i:852696 original size:37 final size:38
Alignment explanation
Indices: 852648--852791 Score: 129
Period size: 37 Copynumber: 3.7 Consensus size: 38
852638 ATATGTTTTC
*
852648 AAAACTATATTATATAGGTTTTCAAAAAC-C-CTTTTAA
1 AAAAATATATTATATA-GTTTTCAAAAACACTCTTTTAA
*
852685 AAAAATATATTATAT-GTTTTCAAAAACACTTTTTTAA
1 AAAAATATATTATATAGTTTTCAAAAACACTCTTTTAA
* *
852722 AAAAAAACTATATATTATATGTTTTC-AAAACAAT-TTTTAA
1 AAAAATA-TAT-TA-TATA-GTTTTCAAAAACACTCTTTTAA
*
852762 AAAAA-ATATATATTATAATTCTTCAAAAAC
1 AAAAATATAT-TA-TATAGTT-TTCAAAAAC
852792 TATACTATAT
Statistics
Matches: 93, Mismatches: 5, Indels: 16
0.82 0.04 0.14
Matches are distributed among these distances:
35 12 0.13
36 1 0.01
37 28 0.30
38 17 0.18
39 8 0.09
40 14 0.15
41 7 0.08
42 6 0.06
ACGTcount: A:0.49, C:0.10, G:0.03, T:0.39
Consensus pattern (38 bp):
AAAAATATATTATATAGTTTTCAAAAACACTCTTTTAA
Found at i:852709 original size:35 final size:38
Alignment explanation
Indices: 852648--852772 Score: 134
Period size: 37 Copynumber: 3.3 Consensus size: 38
852638 ATATGTTTTC
*
852648 AAAACTATATTATATAGGTTTTCAAAAAC-C-CTTTT-AA
1 AAAAATATATTATAT--GTTTTCAAAAACACTCTTTTAAA
*
852685 AAAAATATATTATATGTTTTCAAAAACACTTTTTTAAAAA
1 AAAAATATATTATATGTTTTCAAAAACACTCTTTT--AAA
*
852725 AAAACTATATATTATATGTTTTC-AAAACAAT-TTTTAAA
1 AAAA--ATATATTATATGTTTTCAAAAACACTCTTTTAAA
852763 AAAAATATAT
1 AAAAATATAT
852773 ATTATAATTC
Statistics
Matches: 78, Mismatches: 3, Indels: 15
0.81 0.03 0.16
Matches are distributed among these distances:
35 12 0.15
36 7 0.09
37 18 0.23
38 7 0.09
40 10 0.13
41 7 0.09
42 17 0.22
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.39
Consensus pattern (38 bp):
AAAAATATATTATATGTTTTCAAAAACACTCTTTTAAA
Found at i:852759 original size:40 final size:40
Alignment explanation
Indices: 852653--852791 Score: 150
Period size: 42 Copynumber: 3.5 Consensus size: 40
852643 TTTTCAAAAC
*
852653 TATATTATATAGGTTTTCAAAAAC-C-CTTTT--AAAAAA-A
1 TATATTATAT--GTTTTCAAAAACACATTTTTAAAAAAAATA
*
852690 TATATTATATGTTTTCAAAAACACTTTTTTAAAAAAAAACTA
1 TATATTATATGTTTTCAAAAACACATTTTT-AAAAAAAA-TA
852732 TATATTATATGTTTTC-AAAACA-ATTTTTAAAAAAAATA
1 TATATTATATGTTTTCAAAAACACATTTTTAAAAAAAATA
*
852770 TATATTATAAT-TCTTCAAAAAC
1 TATATTAT-ATGTTTTCAAAAAC
852792 TATACTATAT
Statistics
Matches: 90, Mismatches: 3, Indels: 16
0.83 0.03 0.15
Matches are distributed among these distances:
35 12 0.13
36 1 0.01
37 14 0.16
38 14 0.16
39 15 0.17
40 11 0.12
41 6 0.07
42 17 0.19
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.40
Consensus pattern (40 bp):
TATATTATATGTTTTCAAAAACACATTTTTAAAAAAAATA
Found at i:852936 original size:2 final size:2
Alignment explanation
Indices: 852929--853022 Score: 188
Period size: 2 Copynumber: 47.0 Consensus size: 2
852919 TGTGAAAAGA
852929 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
852971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
853013 AT AT AT AT AT
1 AT AT AT AT AT
853023 GGTAAGAGTA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 92 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:855951 original size:4 final size:4
Alignment explanation
Indices: 855942--855976 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
855932 TTCAACTATA
855942 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
855977 ACATGCATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:859543 original size:25 final size:25
Alignment explanation
Indices: 859512--859578 Score: 134
Period size: 25 Copynumber: 2.7 Consensus size: 25
859502 CGTTCTTAAA
859512 ATATTATAAATTCGTTCCTTCTAAG
1 ATATTATAAATTCGTTCCTTCTAAG
859537 ATATTATAAATTCGTTCCTTCTAAG
1 ATATTATAAATTCGTTCCTTCTAAG
859562 ATATTATAAATTCGTTC
1 ATATTATAAATTCGTTC
859579 AATAACATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 42 1.00
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (25 bp):
ATATTATAAATTCGTTCCTTCTAAG
Found at i:860663 original size:17 final size:19
Alignment explanation
Indices: 860640--860686 Score: 71
Period size: 17 Copynumber: 2.6 Consensus size: 19
860630 CATTTTTTTG
860640 TTATTTTATTTTATC-TCA
1 TTATTTTATTTTATCATCA
*
860658 TT-TTTTATTTTATCATTA
1 TTATTTTATTTTATCATCA
860676 TTATTTTATTT
1 TTATTTTATTT
860687 CTTATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 12 0.46
18 6 0.23
19 8 0.31
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTTATTTTATCATCA
Found at i:860828 original size:13 final size:13
Alignment explanation
Indices: 860812--860841 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
860802 AGATTAGTTA
860812 TATTTATTATAAT
1 TATTTATTATAAT
*
860825 TATTTATTATTAT
1 TATTTATTATAAT
860838 TATT
1 TATT
860842 AAATGTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTATTATAAT
Found at i:882423 original size:17 final size:17
Alignment explanation
Indices: 882386--882427 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
882376 AGTGTTTGTT
* * *
882386 TCTCGAACGAGAGTTTT
1 TCTCGAAAGAGAATTTC
882403 TCTCGAAAGAGAATTTC
1 TCTCGAAAGAGAATTTC
882420 TCTC-AAAG
1 TCTCGAAAG
882428 TAAGGGAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 4 0.18
17 18 0.82
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (17 bp):
TCTCGAAAGAGAATTTC
Found at i:887901 original size:32 final size:32
Alignment explanation
Indices: 887860--887925 Score: 114
Period size: 32 Copynumber: 2.1 Consensus size: 32
887850 AGAAGATCAT
* *
887860 TATCCCTTTACTAGTTGGCTCGCTTTTGAATG
1 TATCCCTTTACTAGTTGGATCGATTTTGAATG
887892 TATCCCTTTACTAGTTGGATCGATTTTGAATG
1 TATCCCTTTACTAGTTGGATCGATTTTGAATG
887924 TA
1 TA
887926 CAAACAACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.20, C:0.18, G:0.18, T:0.44
Consensus pattern (32 bp):
TATCCCTTTACTAGTTGGATCGATTTTGAATG
Found at i:891939 original size:23 final size:23
Alignment explanation
Indices: 891909--891977 Score: 99
Period size: 23 Copynumber: 3.1 Consensus size: 23
891899 TCGAAGGCAT
891909 GCACGAGCTCTCCTGCTTTCCAC
1 GCACGAGCTCTCCTGCTTTCCAC
891932 GCACGAGCTCTCCTGC-TTCCTAC
1 GCACGAGCTCTCCTGCTTTCC-AC
*
891955 G--CGAGCTCTCCTGCTTCCCAC
1 GCACGAGCTCTCCTGCTTTCCAC
891976 GC
1 GC
891978 GCGCCCAAGT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
21 16 0.38
22 7 0.17
23 19 0.45
ACGTcount: A:0.12, C:0.45, G:0.19, T:0.25
Consensus pattern (23 bp):
GCACGAGCTCTCCTGCTTTCCAC
Found at i:891961 original size:21 final size:20
Alignment explanation
Indices: 891912--891978 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 20
891902 AAGGCATGCA
891912 CGAGCTCTCCTGCTTTCCACG
1 CGAGCTCTCCTGC-TTCCACG
891933 CACGAGCTCTCCTGCTTCCTACG
1 --CGAGCTCTCCTGCTTCC-ACG
891956 CGAGCTCTCCTGCTTCCCACG
1 CGAGCTCTCCTGCTT-CCACG
891977 CG
1 CG
891979 CGCCCAAGTC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
21 20 0.48
22 6 0.14
23 16 0.38
ACGTcount: A:0.10, C:0.45, G:0.19, T:0.25
Consensus pattern (20 bp):
CGAGCTCTCCTGCTTCCACG
Found at i:896846 original size:13 final size:13
Alignment explanation
Indices: 896828--896852 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
896818 TATTCCATGT
896828 TTCCTTTCAACTA
1 TTCCTTTCAACTA
896841 TTCCTTTCAACT
1 TTCCTTTCAACT
896853 CCCATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.32, G:0.00, T:0.48
Consensus pattern (13 bp):
TTCCTTTCAACTA
Found at i:898290 original size:2 final size:2
Alignment explanation
Indices: 898283--898311 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
898273 TCAATCTACA
898283 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
898312 ATTTACGAAA
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:898479 original size:85 final size:85
Alignment explanation
Indices: 898329--898496 Score: 221
Period size: 85 Copynumber: 2.0 Consensus size: 85
898319 AAATACAATC
* * * *
898329 ATGAAACACAAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACACGCAATGTAAGTCA
1 ATGAAACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGCAAGTCA
*
898394 TACATGCGTGTCATAAATTT
66 TAAATGCGTGTCATAAATTT
* * * * *
898414 ATGACACATAAATGTGTGTCATCTTCATTT-ATGACGGGGGCTTCAATGACGCTCAATGCACGTC
1 ATGAAACACAAATGTGTGTCATCTT-ATTTAATGACGGGGGCTTCAATGACACGCAATGCAAGTC
*
898478 ATAAATGTGTGTCATAAAT
65 ATAAATGCGTGTCATAAAT
898497 GTGCGCCATA
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
85 68 0.96
86 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (85 bp):
ATGAAACACAAATGTGTGTCATCTTATTTAATGACGGGGGCTTCAATGACACGCAATGCAAGTCA
TAAATGCGTGTCATAAATTT
Found at i:898491 original size:13 final size:13
Alignment explanation
Indices: 898474--898510 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
898464 GCTCAATGCA
898474 CGTCATAAATGTG
1 CGTCATAAATGTG
*
898487 TGTCATAAATGTG
1 CGTCATAAATGTG
*
898500 CGCCATAAATG
1 CGTCATAAATG
898511 CACGTCATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (13 bp):
CGTCATAAATGTG
Found at i:898519 original size:13 final size:13
Alignment explanation
Indices: 898468--898519 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
898458 AATGACGCTC
898468 AATGCACGTCATA
1 AATGCACGTCATA
***
898481 AATGTGTGTCATA
1 AATGCACGTCATA
** *
898494 AATGTGCGCCATA
1 AATGCACGTCATA
898507 AATGCACGTCATA
1 AATGCACGTCATA
898520 GATTTATGAC
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (13 bp):
AATGCACGTCATA
Found at i:907720 original size:62 final size:63
Alignment explanation
Indices: 907612--907731 Score: 224
Period size: 64 Copynumber: 1.9 Consensus size: 63
907602 TTTCCTTAAT
907612 TTTGTGTGTCATGCATTGAAGGTAAACTGCAAAATATATTCCCATCTCAAATGAAATAAGGAAA
1 TTTGTGTGTCATGCATTGAAGGTAAACTGC-AAATATATTCCCATCTCAAATGAAATAAGGAAA
907676 TTTGTGTGTCATGCATTGAAGGTAAACTGC-AATATATTCCCATCTCAAATGAAATA
1 TTTGTGTGTCATGCATTGAAGGTAAACTGCAAATATATTCCCATCTCAAATGAAATA
907732 TAGGCTGTTG
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 26 0.46
64 30 0.54
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.32
Consensus pattern (63 bp):
TTTGTGTGTCATGCATTGAAGGTAAACTGCAAATATATTCCCATCTCAAATGAAATAAGGAAA
Found at i:919742 original size:112 final size:111
Alignment explanation
Indices: 919541--919770 Score: 334
Period size: 112 Copynumber: 2.1 Consensus size: 111
919531 GTTATAGGTT
** * * *
919541 CATTTCAACATACTTTGTGTATGATAGTATCGATCGATTTTGTTTAATGCATAACGGTGCATTTT
1 CATTTCAACATACTTCATGTATGAAAGTATCGATCAATTTTGCTTAATGCATAACGGTGCATTTT
** * *
919606 TGGCATAAAAGGTGCCACCCATGGTATTCTTAATAAGGTGAATTAC
66 CAGCATAAAAGGTGCCACCAATGGTATTCATAATAAGGTGAATTAC
* **
919652 CATTTCGACATACTTCATGTATGAAAGTTATCGATCAATTTTGCTTAATGCATAATTGTGCATTT
1 CATTTCAACATACTTCATGTATGAAAG-TATCGATCAATTTTGCTTAATGCATAACGGTGCATTT
*
919717 TCAGCATAAAAGGTGCCACCAATGGTATTCATAATGAGGTGAATTAC
65 TCAGCATAAAAGGTGCCACCAATGGTATTCATAATAAGGTGAATTAC
919764 CATTTCA
1 CATTTCA
919771 GCACTTCGGT
Statistics
Matches: 104, Mismatches: 14, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
111 23 0.22
112 81 0.78
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.36
Consensus pattern (111 bp):
CATTTCAACATACTTCATGTATGAAAGTATCGATCAATTTTGCTTAATGCATAACGGTGCATTTT
CAGCATAAAAGGTGCCACCAATGGTATTCATAATAAGGTGAATTAC
Found at i:925200 original size:23 final size:22
Alignment explanation
Indices: 925162--925232 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
925152 GGGTTATCGA
*
925162 TTCCCCTAC-AGGGGGAATTGG
1 TTCCCCTTCAAGGGGGAATTGG
*
925183 TTCCCCTTCAAAGGGGGAATCGG
1 TTCCCCTTC-AAGGGGGAATTGG
* *
925206 TTCCCCTTCAAGGGGGTATTGA
1 TTCCCCTTCAAGGGGGAATTGG
925228 TTCCC
1 TTCCC
925233 TCTGCACTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
21 8 0.19
22 15 0.35
23 20 0.47
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (22 bp):
TTCCCCTTCAAGGGGGAATTGG
Found at i:934801 original size:111 final size:112
Alignment explanation
Indices: 934670--934897 Score: 368
Period size: 112 Copynumber: 2.0 Consensus size: 112
934660 CTTATAGGTT
* * * * *
934670 CATTTCGACATACTTTGTGTATGATAG-TATCGATCGATTTTGTTTAATGCATAACGGTGCATTT
1 CATTTCGACATACTCTGTGTATGAAAGTTATCGATCAATTTCGCTTAATGCATAACGGTGCATTT
* * *
934734 TCGGCATAAAAGGTGCCACCCATGGTATTTATAATTAGGTGAATTAC
66 TCGACATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
*
934781 CATTTCGACATACTCTGTGTATGAAAGTTATCGATCAATTTCGCTTAATGCATAATGGTGCATTT
1 CATTTCGACATACTCTGTGTATGAAAGTTATCGATCAATTTCGCTTAATGCATAACGGTGCATTT
934846 TCGACATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
66 TCGACATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
934893 CATTT
1 CATTT
934898 TAGCACGTTG
Statistics
Matches: 107, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
111 25 0.23
112 82 0.77
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (112 bp):
CATTTCGACATACTCTGTGTATGAAAGTTATCGATCAATTTCGCTTAATGCATAACGGTGCATTT
TCGACATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGAATTAC
Found at i:936148 original size:4 final size:4
Alignment explanation
Indices: 936139--936164 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
936129 CACTAACTTG
936139 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
936165 TATGTTCGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:936352 original size:14 final size:14
Alignment explanation
Indices: 936333--936368 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
936323 TTTTTATTTA
*
936333 TTTAATTTCAGTCC
1 TTTAATTTCAGTAC
*
936347 TTTAATTTCATTAC
1 TTTAATTTCAGTAC
936361 TTTAATTT
1 TTTAATTT
936369 TCTATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.03, T:0.58
Consensus pattern (14 bp):
TTTAATTTCAGTAC
Found at i:936474 original size:2 final size:2
Alignment explanation
Indices: 936467--936524 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
936457 AGTCCCACGA
936467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
936509 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
936525 GTATGTTTCA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:940738 original size:19 final size:19
Alignment explanation
Indices: 940712--940756 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
940702 TTATATTTAA
940712 TTAT-TTAT-TTTATTAT-T
1 TTATCTTATCTTT-TTATCT
940729 TTATTCTTATCTTTTTATCT
1 TTA-TCTTATCTTTTTATCT
940749 TTATCTTA
1 TTATCTTA
940757 AATTATCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
17 3 0.12
18 1 0.04
19 13 0.54
20 7 0.29
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATCTTATCTTTTTATCT
Found at i:946262 original size:30 final size:30
Alignment explanation
Indices: 946226--946285 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
946216 AGAAATAGGT
946226 GCACGTTAGCATAGCCCAATCCCATGTGGC
1 GCACGTTAGCATAGCCCAATCCCATGTGGC
* * *
946256 GCACGTTAGCATAGCTCAATTCTATGTGGC
1 GCACGTTAGCATAGCCCAATCCCATGTGGC
946286 ACACACTAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (30 bp):
GCACGTTAGCATAGCCCAATCCCATGTGGC
Found at i:950058 original size:21 final size:22
Alignment explanation
Indices: 950034--950086 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
950024 AGTATTTTAA
*
950034 TTAGGATTTATTTTCATTA-TT
1 TTAGGATTTATTTACATTATTT
*
950055 TTAGGATTATATTTACCTTATTT
1 TTAGGATT-TATTTACATTATTT
950078 TTAGGATTT
1 TTAGGATTT
950087 TGAAGGCTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 8 0.29
22 10 0.36
23 10 0.36
ACGTcount: A:0.25, C:0.06, G:0.11, T:0.58
Consensus pattern (22 bp):
TTAGGATTTATTTACATTATTT
Found at i:950232 original size:20 final size:20
Alignment explanation
Indices: 950204--950241 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
950194 TCCTTTCAAG
*
950204 TTTTCAATTTTTTTATTTTA
1 TTTTAAATTTTTTTATTTTA
950224 TTTTAAATTTTTTTATTT
1 TTTTAAATTTTTTTATTT
950242 CAAATATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTAAATTTTTTTATTTTA
Found at i:957337 original size:35 final size:36
Alignment explanation
Indices: 957271--957345 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
957261 CAAAAAAGTT
* ** *
957271 AAAAAATTGTTCTTTGTTTCGAACAATAAAAGAAGA
1 AAAAAAATGTTCACTGTTTCGAACAAGAAAAGAAGA
*
957307 AAAAAAATGTTCACTGTTTCGAAC-AGAAAAGAAGG
1 AAAAAAATGTTCACTGTTTCGAACAAGAAAAGAAGA
957342 AAAA
1 AAAA
957346 TTGATTGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 13 0.38
36 21 0.62
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (36 bp):
AAAAAAATGTTCACTGTTTCGAACAAGAAAAGAAGA
Found at i:958283 original size:21 final size:22
Alignment explanation
Indices: 958259--958311 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
958249 AGTATTTTAA
*
958259 TTAGGATTTATTTTCATT-ATT
1 TTAGGATTTATTTACATTGATT
* *
958280 TTAGGATTATATTTACCTTGTTT
1 TTAGGATT-TATTTACATTGATT
958303 TTAGGATTT
1 TTAGGATTT
958312 TAAAGGCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 8 0.30
22 9 0.33
23 10 0.37
ACGTcount: A:0.23, C:0.06, G:0.13, T:0.58
Consensus pattern (22 bp):
TTAGGATTTATTTACATTGATT
Found at i:959215 original size:14 final size:13
Alignment explanation
Indices: 959177--959226 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 13
959167 ATTTTAAACA
*
959177 ATTTATATTTAATT
1 ATTT-TATTTTATT
959191 A-TTTATTTTATT
1 ATTTTATTTTATT
959203 ATTTTATTCTTATCT
1 ATTTTATT-TTAT-T
959218 -TTTTATTTT
1 ATTTTATTTT
959227 TATCTAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
12 9 0.28
13 10 0.31
14 12 0.38
15 1 0.03
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTATTTTATT
Found at i:959229 original size:14 final size:15
Alignment explanation
Indices: 959192--959232 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
959182 TATTTAATTA
959192 TTTA-TTTTAT-TAT
1 TTTATTTTTATCTAT
*
959205 TTTATTCTTATCT-T
1 TTTATTTTTATCTAT
959219 TTTATTTTTATCTA
1 TTTATTTTTATCTA
959233 AAATTCTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.17
14 18 0.78
15 1 0.04
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTTATCTAT
Found at i:961565 original size:8 final size:8
Alignment explanation
Indices: 961552--961619 Score: 58
Period size: 8 Copynumber: 9.0 Consensus size: 8
961542 AATTACACCT
961552 GAAGAAAA
1 GAAGAAAA
961560 GAAGAAAA
1 GAAGAAAA
961568 G-AG-AAA
1 GAAGAAAA
*
961574 -AA-ATAA
1 GAAGAAAA
961580 GAAGAAAA
1 GAAGAAAA
*
961588 TGAAAAAAA
1 -GAAGAAAA
961597 G-A-AAAA
1 GAAGAAAA
961603 GAAGAAAAA
1 GAAG-AAAA
961612 GAAGAAAA
1 GAAGAAAA
961620 AGAAAACAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
6 11 0.22
7 6 0.12
8 17 0.35
9 15 0.31
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (8 bp):
GAAGAAAA
Found at i:961574 original size:15 final size:15
Alignment explanation
Indices: 961554--961625 Score: 62
Period size: 14 Copynumber: 4.9 Consensus size: 15
961544 TTACACCTGA
961554 AGAAAAGAAGAAAAG
1 AGAAAAGAAGAAAAG
*
961569 AGAAAA-AATAAGAAG
1 AGAAAAGAAGAA-AAG
* *
961584 A-AAATGAAAAAAAG
1 AGAAAAGAAGAAAAG
961598 A-AAAAGAAGAAAA-
1 AGAAAAGAAGAAAAG
*
961611 AGAAGAAAAAGAAAA
1 AGAA-AAGAAGAAAA
961626 CAAACGAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
13 1 0.02
14 23 0.49
15 23 0.49
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AGAAAAGAAGAAAAG
Found at i:961600 original size:14 final size:15
Alignment explanation
Indices: 961556--961625 Score: 67
Period size: 15 Copynumber: 4.8 Consensus size: 15
961546 ACACCTGAAG
961556 AAAAGAAG-AAAAGA
1 AAAAGAAGAAAAAGA
* *
961570 GAAAA-AATAAGAAGA
1 -AAAAGAAGAAAAAGA
*
961585 AAATGAA-AAAAAGA
1 AAAAGAAGAAAAAGA
961599 AAAAGAAGAAAAAGA
1 AAAAGAAGAAAAAGA
961614 AGAAA-AAGAAAA
1 A-AAAGAAGAAAA
961626 CAAACGAATA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
14 17 0.37
15 26 0.57
16 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.03
Consensus pattern (15 bp):
AAAAGAAGAAAAAGA
Found at i:961602 original size:9 final size:9
Alignment explanation
Indices: 961556--961719 Score: 73
Period size: 9 Copynumber: 17.2 Consensus size: 9
961546 ACACCTGAAG
961556 AAAAGAAGAA
1 AAAAGAA-AA
*
961566 AAGAGAAAA
1 AAAAGAAAA
*
961575 AATAAGAAGA
1 AA-AAGAAAA
*
961585 AAATG-AAA
1 AAAAGAAAA
961593 AAAAGAAAA
1 AAAAGAAAA
*
961602 AGAAGAAAA
1 AAAAGAAAA
*
961611 AGAAGAAAA
1 AAAAGAAAA
961620 AGAAA-ACAAA
1 A-AAAGA-AAA
** *
961630 CGAATAATAA
1 AAAAGAA-AA
961640 AAAAGAAAA
1 AAAAGAAAA
*
961649 AAATGAATCAA
1 AAAAGAA--AA
961660 AAATA-AAAA
1 AAA-AGAAAA
*
961669 AGAAAGAGAA
1 A-AAAGAAAA
*
961679 AGAAGTAAAGA
1 AAAAG-AAA-A
961690 AAAAGACAAA
1 AAAAGA-AAA
** *
961700 TGAATAAAA
1 AAAAGAAAA
961709 AAAAGAAAA
1 AAAAGAAAA
961718 AA
1 AA
961720 GAAAATTGAA
Statistics
Matches: 115, Mismatches: 25, Indels: 29
0.68 0.15 0.17
Matches are distributed among these distances:
8 6 0.05
9 57 0.50
10 38 0.33
11 14 0.12
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.06
Consensus pattern (9 bp):
AAAAGAAAA
Found at i:961604 original size:23 final size:22
Alignment explanation
Indices: 961556--961649 Score: 79
Period size: 23 Copynumber: 4.2 Consensus size: 22
961546 ACACCTGAAG
*
961556 AAAAGAAGAAAA-GAGAAAA-A
1 AAAAGAAGAAAATGAAAAAAGA
*
961576 ATAAGAAGAAAATGAAAAAAAGA
1 AAAAGAAGAAAATG-AAAAAAGA
*
961599 AAAAGAAGAAAAAGAAGAAAAAGA
1 AAAAGAAGAAAATG-A-AAAAAGA
961623 AAACA-AACGAATAAT-AAAAAAGA
1 AAA-AGAA-GAA-AATGAAAAAAGA
961646 AAAA
1 AAAA
961650 AATGAATCAA
Statistics
Matches: 62, Mismatches: 5, Indels: 12
0.78 0.06 0.15
Matches are distributed among these distances:
20 11 0.18
21 1 0.02
22 6 0.10
23 25 0.40
24 13 0.21
25 4 0.06
26 2 0.03
ACGTcount: A:0.78, C:0.02, G:0.16, T:0.04
Consensus pattern (22 bp):
AAAAGAAGAAAATGAAAAAAGA
Found at i:961611 original size:18 final size:18
Alignment explanation
Indices: 961552--961718 Score: 78
Period size: 20 Copynumber: 9.0 Consensus size: 18
961542 AATTACACCT
*
961552 GAAG-AAAAGAAG-AAAA
1 GAAGAAAAAAAAGAAAAA
961568 G-AGAAAAAATAAGAAGAAA
1 GAAGAAAAAA-AAGAA-AAA
*
961587 -ATG-AAAAAAAGAAAAA
1 GAAGAAAAAAAAGAAAAA
*
961603 GAAGAAAAAGAAGAAAAA
1 GAAGAAAAAAAAGAAAAA
* *
961621 GAA-AACAAACGAATAATAAA
1 GAAGAA-AAA-AAAGAA-AAA
* *
961641 AAAGAAAAAAATGAATCAAA
1 GAAGAAAAAAAAGAA--AAA
* *
961661 -AATAAAAAAGAAAGAGAAA
1 GAA-GAAAAA-AAAGAAAAA
*
961680 GAAGTAAAGAAAAAGACAAAT
1 GAAG-AAA-AAAAAGA-AAAA
*
961701 GAATAAAAAAAAGAAAAA
1 GAAGAAAAAAAAGAAAAA
961719 AGAAAATTGA
Statistics
Matches: 115, Mismatches: 18, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
15 2 0.02
16 8 0.07
17 12 0.10
18 27 0.23
19 24 0.21
20 29 0.25
21 13 0.11
ACGTcount: A:0.75, C:0.02, G:0.16, T:0.06
Consensus pattern (18 bp):
GAAGAAAAAAAAGAAAAA
Found at i:961613 original size:29 final size:28
Alignment explanation
Indices: 961553--961614 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
961543 ATTACACCTG
* * *
961553 AAGAAAAGAAGAAAAGAGAAAAAATAAG
1 AAGAAAAGAAAAAAAGAGAAAAAAGAAA
961581 AAGAAAATGAAAAAAAGA-AAAAGAAGAAA
1 AAGAAAA-GAAAAAAAGAGAAAA-AAGAAA
961610 AAGAA
1 AAGAA
961615 GAAAAAGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 11 0.38
29 18 0.62
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (28 bp):
AAGAAAAGAAAAAAAGAGAAAAAAGAAA
Found at i:961643 original size:32 final size:31
Alignment explanation
Indices: 961553--961724 Score: 102
Period size: 32 Copynumber: 5.2 Consensus size: 31
961543 ATTACACCTG
*
961553 AAGAAAAGAAGAAAAGAGAAAAAATAAGAAGAAA
1 AAGAAAAAAAGAAAA-AG-AAAAA-AAGAAGAAA
*
961587 ATGAAAAAAAGAAAAAGAAGAAAAAGAAGAAA
1 AAGAAAAAAAGAAAAAGAA-AAAAAGAAGAAA
* *
961619 AAGAAAACAAACGAATAA-TAAAAAAGAA-AAA
1 AAGAAAA-AAA-GAAAAAGAAAAAAAGAAGAAA
* *
961650 AATGAATCAAAAATAAAAAAGAAAGAGAAAGAAG-TA
1 AA-GAA--AAAAA-GAAAAAGAAA-A-AAAGAAGAAA
* *
961686 AAG--AAAAAGACAAATGAATAAAAAAAAGAAAA
1 AAGAAAAAAAGA-AAAAGAA-AAAAAGAAG-AAA
961718 AAGAAAA
1 AAGAAAA
961725 TTGAAAGGAG
Statistics
Matches: 108, Mismatches: 14, Indels: 32
0.70 0.09 0.21
Matches are distributed among these distances:
30 7 0.06
31 17 0.16
32 33 0.31
33 16 0.15
34 24 0.22
35 2 0.02
36 9 0.08
ACGTcount: A:0.76, C:0.02, G:0.16, T:0.06
Consensus pattern (31 bp):
AAGAAAAAAAGAAAAAGAAAAAAAGAAGAAA
Found at i:961718 original size:68 final size:62
Alignment explanation
Indices: 961571--961724 Score: 168
Period size: 68 Copynumber: 2.3 Consensus size: 62
961561 AAGAAAAGAG
*
961571 AAAAAATAAGAAGAAAATGAAAAAAAGAAAAAGAAGAAAAAGAAGAAAAAGAAAACAAACGAAT
1 AAAAAA-AAGAA-AAAATGAAAAAAAAAAAAAGAAGAAAAAGAAGAAAAAGAAAACAAACGAAT
*
961635 AATAAAAAAGAAAAAAATGAATCAAAAATAAAAAAGAAAGAGAAAGAAGTAAAGAA-AAAGACAA
1 AA-AAAAAAG-AAAAAATGAA--AAAAA-AAAAAAG-AAGAAAAAGAAG-AAA-AAGAAA-ACAA
*
961699 ATGAAT
57 ACGAAT
961705 AAAAAAAAGAAAAAA-GAAAA
1 AAAAAAAAGAAAAAATGAAAA
961725 TTGAAAGGAG
Statistics
Matches: 78, Mismatches: 3, Indels: 17
0.80 0.03 0.17
Matches are distributed among these distances:
64 13 0.17
65 8 0.10
66 5 0.06
67 9 0.12
68 17 0.22
69 13 0.17
70 13 0.17
ACGTcount: A:0.77, C:0.03, G:0.14, T:0.06
Consensus pattern (62 bp):
AAAAAAAAGAAAAAATGAAAAAAAAAAAAAGAAGAAAAAGAAGAAAAAGAAAACAAACGAAT
Found at i:961725 original size:73 final size:65
Alignment explanation
Indices: 961573--961716 Score: 161
Period size: 69 Copynumber: 2.2 Consensus size: 65
961563 GAAAAGAGAA
*
961573 AAAATAAG-AAGAAAATGAAAAAAAGAAAAAGAAGAAAAAGAAGAAAAAGAAAACAAACGAATAA
1 AAAA-AAGAAAGAAAATGAAAAAAAAAAAAAGAAGAAAAAGAAGAAAAAGAAAACAAACGAATAA
961637 T
65 T
* *
961638 AAAAAAGAAA-AAAATGAATCAAAAATAAAAAAGAAAGAGAAAGAAGTAAAGAA-AAAGACAAAT
1 AAAAAAGAAAGAAAATGAA--AAAAA-AAAAAAG-AAGAAAAAGAAG-AAA-AAGAAA-ACAAAC
961701 GAATAA-
59 GAATAAT
961707 AAAAAAGAAA
1 AAAAAAGAAA
961717 AAAGAAAATT
Statistics
Matches: 68, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
64 11 0.16
65 6 0.09
66 5 0.07
67 6 0.09
68 11 0.16
69 16 0.24
70 13 0.19
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.07
Consensus pattern (65 bp):
AAAAAAGAAAGAAAATGAAAAAAAAAAAAAGAAGAAAAAGAAGAAAAAGAAAACAAACGAATAAT
Found at i:962944 original size:29 final size:28
Alignment explanation
Indices: 962910--963000 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 28
962900 TCAAATTACT
962910 ATAAAATACAAATTTTTTTAGAATTTATA
1 ATAAAATA-AAATTTTTTTAGAATTTATA
* * *
962939 ATAAAAGTTTAAA-CTTTTTAGAATTTACA
1 ATAAAA--TAAAATTTTTTTAGAATTTATA
** * * *
962968 ATAAAGGAAAATTATTTTATAAATTATA
1 ATAAAATAAAATTTTTTTAGAATTTATA
962996 ATAAA
1 ATAAA
963001 GGACGAAATT
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
27 3 0.06
28 16 0.33
29 25 0.52
30 3 0.06
31 1 0.02
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (28 bp):
ATAAAATAAAATTTTTTTAGAATTTATA
Found at i:962986 original size:28 final size:27
Alignment explanation
Indices: 962923--963003 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 27
962913 AAATACAAAT
**
962923 TTTTTTAGAATTTATAATAAAAGTTTAAA
1 TTTTTTAGAATTTATAAT-AAAG-GAAAA
* *
962952 CTTTTTAGAATTTACAATAAAGGAAAA
1 TTTTTTAGAATTTATAATAAAGGAAAA
* *
962979 TTATTTTATAAATTATAATAAAGGA
1 TT-TTTTAGAATTTATAATAAAGGA
963004 CGAAATTTGT
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
27 4 0.09
28 23 0.53
29 16 0.37
ACGTcount: A:0.47, C:0.02, G:0.09, T:0.42
Consensus pattern (27 bp):
TTTTTTAGAATTTATAATAAAGGAAAA
Found at i:963017 original size:29 final size:29
Alignment explanation
Indices: 962949--963145 Score: 188
Period size: 29 Copynumber: 6.8 Consensus size: 29
962939 ATAAAAGTTT
* * *
962949 AAACTTTTTAGAATTTACAATAAAGG--A
1 AAACTATTTATAAATTACAATAAAGGACA
* * *
962976 AAATTATTTTATAAATTATAATAAAGGACG
1 AAACTA-TTTATAAATTACAATAAAGGACA
* * *
963006 AAA-TTTGTTATAAACTACAATAAAGTACA
1 AAACTAT-TTATAAATTACAATAAAGGACA
*
963035 AAACTATTTATAAATTACAATAAAGTACA
1 AAACTATTTATAAATTACAATAAAGGACA
**
963064 AAA-TAATTTATAAATTACAATAAAATACA
1 AAACT-ATTTATAAATTACAATAAAGGACA
*
963093 AAACTATTTATAAATTACAATAAAGGATA
1 AAACTATTTATAAATTACAATAAAGGACA
* *
963122 AAACCT-TTCATAAATTATAATAAA
1 AAA-CTATTTATAAATTACAATAAA
963146 AGGAGACATT
Statistics
Matches: 143, Mismatches: 19, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.03
28 19 0.13
29 112 0.78
30 8 0.06
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (29 bp):
AAACTATTTATAAATTACAATAAAGGACA
Found at i:963086 original size:87 final size:85
Alignment explanation
Indices: 962949--963145 Score: 209
Period size: 87 Copynumber: 2.3 Consensus size: 85
962939 ATAAAAGTTT
* * * * * *
962949 AAACTTTT-TAGAATTTACAATAAAGGAAAATTATTTTATAAATTATAATAAAGGACGAAA-TTT
1 AAACTTTTATA-AA-TTACAATAAAGGAAAAATAATTTATAAATTACAATAAAAGACAAAACTAT
*
963012 GTTATAAACTACAATAAAGTACA
64 -TTATAAACTACAATAAAGGACA
* *
963035 AAACTATTTATAAATTACAATAAAGTACAAAATAATTTATAAATTACAATAAAATACAAAACTAT
1 AAACT-TTTATAAATTACAATAAAGGA-AAAATAATTTATAAATTACAATAAAAGACAAAACTAT
* *
963100 TTATAAATTACAATAAAGGATA
64 TTATAAACTACAATAAAGGACA
* *
963122 AAACCTTTCATAAATTATAATAAA
1 AAA-CTTTTATAAATTACAATAAA
963146 AGGAGACATT
Statistics
Matches: 93, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
86 17 0.18
87 70 0.75
88 6 0.06
ACGTcount: A:0.54, C:0.08, G:0.06, T:0.32
Consensus pattern (85 bp):
AAACTTTTATAAATTACAATAAAGGAAAAATAATTTATAAATTACAATAAAAGACAAAACTATTT
ATAAACTACAATAAAGGACA
Found at i:964505 original size:61 final size:61
Alignment explanation
Indices: 964358--964505 Score: 154
Period size: 61 Copynumber: 2.4 Consensus size: 61
964348 AAACACGTTG
* * * *
964358 AAACAAGGAGGACATGGTACGTGATTTACCCTTAAACATGTAACTAAACATGTAACACACT
1 AAACAGGGAGGACTTGATACGTGATTTACCCTTAAACATGTAACTAAACATGAAACACACT
* * * * * * *
964419 AAACAGGGAGGACTTGATGCATGATTTATCCTTTAAC-TAGTAACTAATCGTGAAACATACT
1 AAACAGGGAGGACTTGATACGTGATTTACCCTTAAACAT-GTAACTAAACATGAAACACACT
* * *
964480 AGATATGGAGGACTTGATACGTGATT
1 AAACAGGGAGGACTTGATACGTGATT
964506 AGCCCAAAAC
Statistics
Matches: 70, Mismatches: 16, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
60 1 0.01
61 69 0.99
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.27
Consensus pattern (61 bp):
AAACAGGGAGGACTTGATACGTGATTTACCCTTAAACATGTAACTAAACATGAAACACACT
Found at i:967980 original size:10 final size:10
Alignment explanation
Indices: 967960--968069 Score: 53
Period size: 9 Copynumber: 11.6 Consensus size: 10
967950 ATTTGATCGG
967960 CTTTCTTTCTT
1 CTTT-TTTCTT
967971 CTTTTTTC-T
1 CTTTTTTCTT
967980 -TTTTTTC-T
1 CTTTTTTCTT
967988 C-TTTTT-TT
1 CTTTTTTCTT
967996 CTATTTTT-TT
1 CT-TTTTTCTT
968006 CCTTTTTTC-T
1 -CTTTTTTCTT
* * *
968016 CTATCTTCAT
1 CTTTTTTCTT
968026 -TTTTTTCTT
1 CTTTTTTCTT
*
968035 -TTTTTTCCT
1 CTTTTTTCTT
*
968044 C-TTTTACTAT
1 CTTTTTTCT-T
968054 CTCTTTTT-TT
1 CT-TTTTTCTT
968064 CTTTTT
1 CTTTTT
968070 CTTTTTTGAT
Statistics
Matches: 79, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
8 15 0.19
9 30 0.38
10 23 0.29
11 7 0.09
12 4 0.05
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (10 bp):
CTTTTTTCTT
Found at i:967991 original size:28 final size:27
Alignment explanation
Indices: 967960--968069 Score: 105
Period size: 28 Copynumber: 3.9 Consensus size: 27
967950 ATTTGATCGG
967960 CTTTCTTTCTTCTTTTTTCTTTTTTTCT
1 CTTTCTTTCTT-TTTTTTCTTTTTTTCT
* *
967988 CTTTTTTTCTATTTTTTTCCTTTTTTCT
1 CTTTCTTTCT-TTTTTTTCTTTTTTTCT
* *
968016 CTATC-TTCATTTTTTTCTTTTTTTTCCT
1 CTTTCTTTCTTTTTTTTC-TTTTTTT-CT
*
968044 CTTTTACTATCTCTTTTTTTCTTTTT
1 C-TTT-CTTTCT-TTTTTTTCTTTTT
968070 CTTTTTTGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
26 8 0.12
27 9 0.14
28 30 0.45
29 3 0.05
30 1 0.02
31 7 0.11
32 8 0.12
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (27 bp):
CTTTCTTTCTTTTTTTTCTTTTTTTCT
Found at i:968037 original size:34 final size:32
Alignment explanation
Indices: 967985--968069 Score: 116
Period size: 35 Copynumber: 2.5 Consensus size: 32
967975 TTTCTTTTTT
* *
967985 TCTCTTTTTTTCTATTTTTTTCCTTTTTTCTCTA
1 TCTCTTTTTTTCT-TTTTTTTCCTCTTTT-ACTA
968019 TCTTCATTTTTTTCTTTTTTTTCCTCTTTTACTA
1 TC-TC-TTTTTTTCTTTTTTTTCCTCTTTTACTA
968053 TCTCTTTTTTTCTTTTT
1 TCTCTTTTTTTCTTTTT
968070 CTTTTTTGAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
32 13 0.28
33 2 0.04
34 7 0.15
35 16 0.34
36 9 0.19
ACGTcount: A:0.06, C:0.20, G:0.00, T:0.74
Consensus pattern (32 bp):
TCTCTTTTTTTCTTTTTTTTCCTCTTTTACTA
Found at i:968333 original size:2 final size:2
Alignment explanation
Indices: 968326--968363 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
968316 GGACAACAAG
968326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
968364 TCATGTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:972224 original size:18 final size:20
Alignment explanation
Indices: 972185--972224 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
972175 TGGCAAAAAG
972185 AAAACAAGTTAAGACGTATAA
1 AAAACAAGTTAAGAC-TATAA
972206 AAAACAAG-TAAGA-TATAA
1 AAAACAAGTTAAGACTATAA
972224 A
1 A
972225 GCCAAATGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
20 5 0.26
21 8 0.42
ACGTcount: A:0.62, C:0.07, G:0.12, T:0.17
Consensus pattern (20 bp):
AAAACAAGTTAAGACTATAA
Found at i:975245 original size:29 final size:29
Alignment explanation
Indices: 975191--975246 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
975181 TGTAAGAAAA
* *
975191 TAAAAGTTAGTAATTAATATGCAATAAAT
1 TAAAAGTTAGTAATTAAAATGAAATAAAT
*
975220 TAAAAGTTAGTAGTTAGAAAT-AAATAA
1 TAAAAGTTAGTAATTA-AAATGAAATAA
975247 CATAGCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.54, C:0.02, G:0.12, T:0.32
Consensus pattern (29 bp):
TAAAAGTTAGTAATTAAAATGAAATAAAT
Found at i:977182 original size:2 final size:2
Alignment explanation
Indices: 977175--977209 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
977165 AGTTTCCATA
977175 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 A
977210 GTATTTAGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:978454 original size:19 final size:19
Alignment explanation
Indices: 978430--978472 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
978420 AACGTCACGT
978430 TTATAGTATTTTTGTGACG
1 TTATAGTATTTTTGTGACG
978449 TTATAGTATTTTTGTGACG
1 TTATAGTATTTTTGTGACG
978468 TTATA
1 TTATA
978473 CATAGTGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.23, C:0.05, G:0.19, T:0.53
Consensus pattern (19 bp):
TTATAGTATTTTTGTGACG
Found at i:980667 original size:27 final size:26
Alignment explanation
Indices: 980637--980692 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 26
980627 TTGAAAACTC
980637 ATTTTAGTATTTC-TAAAATTTTTATAA
1 ATTTTA-TATTTCTTAAAA-TTTTATAA
*
980664 A-TTTATTTTTCTTTAAAATTTTATAA
1 ATTTTATATTTC-TTAAAATTTTATAA
980690 ATT
1 ATT
980693 CACCATTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
25 5 0.20
26 13 0.52
27 7 0.28
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTTATATTTCTTAAAATTTTATAA
Found at i:986484 original size:59 final size:59
Alignment explanation
Indices: 986320--986488 Score: 212
Period size: 59 Copynumber: 2.9 Consensus size: 59
986310 TGTACTCAAC
* * * * * * *
986320 TATGATCCTCATTCGAAATTGATAACTAAAATTTTGAATATTTCAACTACATCCCAAAT
1 TATGACCCTCATTCAAAATTGATACCCAAAATTTTGAATATTTCAATTTCACCCCAAAT
* *
986379 TATGACTCTCATTCAAAATTGATACCTAAAATTTTGAATATTTCAATTTCACCCCAAAT
1 TATGACCCTCATTCAAAATTGATACCCAAAATTTTGAATATTTCAATTTCACCCCAAAT
* * * * *
986438 TATGACCCTCATTCTAAATTTATCCCCAAACTTTTGAACATTTCAATTTCA
1 TATGACCCTCATTCAAAATTGATACCCAAAATTTTGAATATTTCAATTTCA
986489 TCCAAAACTA
Statistics
Matches: 96, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 96 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.37
Consensus pattern (59 bp):
TATGACCCTCATTCAAAATTGATACCCAAAATTTTGAATATTTCAATTTCACCCCAAAT
Found at i:986491 original size:29 final size:28
Alignment explanation
Indices: 986407--986491 Score: 75
Period size: 31 Copynumber: 2.9 Consensus size: 28
986397 TTGATACCTA
*
986407 AAATTTTGAATATTTCAATTTCA-CCCC
1 AAATTTTGAACATTTCAATTTCATCCCC
* * *
986434 AAATTATGACCCTCATTCTAAATTT-ATCCCC
1 AAATTTTGA---ACATT-TCAATTTCATCCCC
986465 AAACTTTTGAACATTTCAATTTCATCC
1 AAA-TTTTGAACATTTCAATTTCATCC
986492 AAAACTATCA
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
27 8 0.18
28 6 0.14
29 8 0.18
30 4 0.09
31 13 0.30
32 5 0.11
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.39
Consensus pattern (28 bp):
AAATTTTGAACATTTCAATTTCATCCCC
Found at i:987871 original size:60 final size:60
Alignment explanation
Indices: 987807--987920 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
987797 CTACAAAACA
* * ** *
987807 TTATTTTGTTGATTC-CACTGATTATTGAAAGTTATAAAATGGTC-CTTCAACTATAGGGTG
1 TTATTTTGTTGAGTCTCA-TGACTATCAAAAGTTACAAAATGGTCAC-TCAACTATAGGGTG
987867 TTATTTTGTTGAGTCTCATGACTATCAAAAGTTACAAAATGGTCACTCAACTAT
1 TTATTTTGTTGAGTCTCATGACTATCAAAAGTTACAAAATGGTCACTCAACTAT
987921 TCATATATTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 44 0.94
61 3 0.06
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (60 bp):
TTATTTTGTTGAGTCTCATGACTATCAAAAGTTACAAAATGGTCACTCAACTATAGGGTG
Found at i:989500 original size:2 final size:2
Alignment explanation
Indices: 989493--989533 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
989483 GAATATTTTC
989493 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
989534 AGCTACTAGA
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:990375 original size:27 final size:28
Alignment explanation
Indices: 990344--990403 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
990334 GGAATTGAAG
* *
990344 AAAATTAGG-GATCCAGTTATAAATATA
1 AAAATTAGGAGATACAATTATAAATATA
* *
990371 GAAATTAGGAGCTACAATTATAAATATA
1 AAAATTAGGAGATACAATTATAAATATA
990399 AAAAT
1 AAAAT
990404 CAGAGGCCTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 8 0.30
28 19 0.70
ACGTcount: A:0.52, C:0.07, G:0.13, T:0.28
Consensus pattern (28 bp):
AAAATTAGGAGATACAATTATAAATATA
Found at i:995343 original size:12 final size:13
Alignment explanation
Indices: 995328--995391 Score: 66
Period size: 12 Copynumber: 5.3 Consensus size: 13
995318 TTAAAATATA
995328 TATTATAT-TTAT
1 TATTATATATTAT
*
995340 TATTATATACTA-
1 TATTATATATTAT
* *
995352 TAGTAT-GATTAT
1 TATTATATATTAT
995364 TATTAT-TATTAT
1 TATTATATATTAT
995376 TATTAT-TATTAT
1 TATTATATATTAT
995388 TATT
1 TATT
995392 TTACAATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
11 3 0.07
12 39 0.89
13 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:995344 original size:3 final size:3
Alignment explanation
Indices: 995336--995391 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
995326 TATATTATAT
* * *
995336 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
995381 TTA TTA TTA TT
1 TTA TTA TTA TT
995392 TTACAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:996306 original size:8 final size:8
Alignment explanation
Indices: 996295--996350 Score: 66
Period size: 8 Copynumber: 7.2 Consensus size: 8
996285 AAGAAAAAAA
996295 AAAAAATG
1 AAAAAATG
996303 AAAAAATG
1 AAAAAATG
996311 AAAAAATG
1 AAAAAATG
996319 AAAAAA--
1 AAAAAATG
996325 AAATGAAA--
1 AAA--AAATG
996333 AAAAAATG
1 AAAAAATG
996341 AAAAAATG
1 AAAAAATG
996349 AA
1 AA
996351 GAGAGAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.14
8 38 0.86
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:996308 original size:11 final size:11
Alignment explanation
Indices: 996292--996346 Score: 68
Period size: 11 Copynumber: 5.5 Consensus size: 11
996282 TTGAAGAAAA
996292 AAAAAAAAATG
1 AAAAAAAAATG
996303 ---AAAAAATG
1 AAAAAAAAATG
996311 --AAA-AAATG
1 AAAAAAAAATG
996319 AAAAAAAAATG
1 AAAAAAAAATG
996330 AAAAAAAAATG
1 AAAAAAAAATG
996341 AAAAAA
1 AAAAAA
996347 TGAAGAGAGA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
8 13 0.32
9 2 0.05
10 3 0.08
11 22 0.55
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (11 bp):
AAAAAAAAATG
Found at i:996324 original size:30 final size:29
Alignment explanation
Indices: 996287--996350 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
996277 TATGCTTGAA
*
996287 GAAAAAAAAAAAAATGAAAAAATGAAAAAAT
1 GAAAAAAAAAGAAA--AAAAAATGAAAAAAT
996318 GAAAAAAAAATGAAAAAAAAATGAAAAAAT
1 GAAAAAAAAA-GAAAAAAAAATGAAAAAAT
996348 GAA
1 GAA
996351 GAGAGAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 18 0.58
31 10 0.32
32 3 0.10
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (29 bp):
GAAAAAAAAAGAAAAAAAAATGAAAAAAT
Found at i:997461 original size:136 final size:136
Alignment explanation
Indices: 997212--997693 Score: 734
Period size: 136 Copynumber: 3.5 Consensus size: 136
997202 GGAGGTGAAC
* *
997212 CAACATTTCCAATGGAGATTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
* * * ** *
997277 ATGAGAAGAGCTTGTTCAACCTATCACTCGATTCACGGCATTTCGAATCAGTGATGCCTCGCTTG
66 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGCATTTTGAATCAGTGACACCTCACTTG
997342 AGGGAT
131 AGGGAT
* * *
997348 CAACATTTCC-AGTGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAAGGAGAAGAAGTTCAT
1 CAACATTTCCAATTG-AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCAT
*
997412 AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGTATTTTGAATCAGTGACACCTCACTT
65 AATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGCATTTTGAATCAGTGACACCTCACTT
997477 GAGGGAT
130 GAGGGAT
**
997484 TGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
* * *
997549 ATGAGAAGAGCTTGTTTGACCTATCACTCGATTCA-TGACATTTTAAATCAGTGACACCTCACTT
66 ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAG-CATTTTGAATCAGTGACACCTCACTT
997613 GAGGGAT
130 GAGGGAT
*** * *
997620 TGGCATTTCCAATTGAGAGTTCTTAATGAGAAGAACTCATGCGACAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
997685 ATGAGAAGA
66 ATGAGAAGA
997694 ACTTATTCAA
Statistics
Matches: 319, Mismatches: 24, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
135 3 0.01
136 313 0.98
137 3 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.25
Consensus pattern (136 bp):
CAACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATA
ATGAGAAGAGCTTGTTCGACCTATCACTCGATTCACAGCATTTTGAATCAGTGACACCTCACTTG
AGGGAT
Found at i:998004 original size:9 final size:9
Alignment explanation
Indices: 997977--998006 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
997967 TATACTATAG
997977 TATGATTAT
1 TATGATTAT
*
997986 TATTATTAT
1 TATGATTAT
997995 TATGATTAT
1 TATGATTAT
998004 TAT
1 TAT
998007 TTTACAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (9 bp):
TATGATTAT
Found at i:998898 original size:8 final size:8
Alignment explanation
Indices: 998882--998998 Score: 181
Period size: 8 Copynumber: 15.1 Consensus size: 8
998872 ATGCTTGAAG
998882 AAAAA-GA
1 AAAAATGA
998889 AAAAATGAA
1 AAAAATG-A
998898 AAAAATGA
1 AAAAATGA
998906 AAAAATG-
1 AAAAATGA
998913 AAAAA--A
1 AAAAATGA
998919 AAAAATGA
1 AAAAATGA
998927 AAAAATGA
1 AAAAATGA
998935 AAAAATGA
1 AAAAATGA
998943 AAAAATGA
1 AAAAATGA
998951 AAAAATGA
1 AAAAATGA
998959 AAAAATGA
1 AAAAATGA
998967 AAAAATGA
1 AAAAATGA
998975 AAAAATGA
1 AAAAATGA
*
998983 AAAAA-AA
1 AAAAATGA
998990 AAAAATGA
1 AAAAATGA
998998 A
1 A
998999 GAGAGAAAAA
Statistics
Matches: 102, Mismatches: 2, Indels: 11
0.89 0.02 0.10
Matches are distributed among these distances:
6 5 0.05
7 16 0.16
8 73 0.72
9 8 0.08
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.10
Consensus pattern (8 bp):
AAAAATGA
Found at i:1000347 original size:136 final size:135
Alignment explanation
Indices: 999862--1000354 Score: 702
Period size: 136 Copynumber: 3.6 Consensus size: 135
999852 AGGTGAACCA
*
999862 ACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* * * * *
999927 GAGAAGAGCTTGTTCAACCTATCACTCGATTCACGACATTTCGAATCAGTGATGCCTCGCTTGAG
66 GAGAAGAGCTTATTCGACCTATCACTCGATTCA-GACATTTTGAATCAGTGATACCTCACTTGAG
**
999992 GGATCA
130 GGATTG
* * *
999998 ACATTTCC-AGTGAAGAGTTCATAATGAGAAGAACTCATCCGACAAAAGGAGAAGAAGTTCATAA
1 ACATTTCCAATTG-AGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAA
* * * *
1000062 TGAGAAGAGC-TAGTTCGACCTATTACTCGATTCACAGTATTTTGAATCAGTGACACCTCACTTG
65 TGAGAAGAGCTTA-TTCGACCTATCACTCGATTCAGA-CATTTTGAATCAGTGATACCTCACTTG
1000126 AGGGATTG
128 AGGGATTG
* *
1000134 ACATTTCCAATTGAGAGTTCATAATTAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCATAAT
1 ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* *
1000199 GAGAAGAGCTTATTTGACCTATCACTCGATTCATGACATTTTAAATCAGTGATACCTCACTTGAG
66 GAGAAGAGCTTATTCGACCTATCACTCGATTCA-GACATTTTGAATCAGTGATACCTCACTTGAG
1000264 GGATTG
130 GGATTG
* * * *
1000270 ATATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATGCGACAGAGGGAGAATAGGTTCATAAT
1 ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
* *
1000335 GAGAAGAACTTATTCAACCT
66 GAGAAGAGCTTATTCGACCT
1000355 TGGTTTCAAG
Statistics
Matches: 316, Mismatches: 35, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
135 4 0.01
136 306 0.97
137 6 0.02
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (135 bp):
ACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
GAGAAGAGCTTATTCGACCTATCACTCGATTCAGACATTTTGAATCAGTGATACCTCACTTGAGG
GATTG
Found at i:1013560 original size:9 final size:9
Alignment explanation
Indices: 1013546--1013590 Score: 83
Period size: 9 Copynumber: 5.1 Consensus size: 9
1013536 GAAGAAAAAT
1013546 AAAAAATGA
1 AAAAAATGA
1013555 AAAAAATGA
1 AAAAAATGA
1013564 AAAAAATGA
1 AAAAAATGA
1013573 AAAAAATG-
1 AAAAAATGA
1013581 AAAAAATGA
1 AAAAAATGA
1013590 A
1 A
1013591 GAGAGAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.23
9 27 0.77
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (9 bp):
AAAAAATGA
Found at i:1013569 original size:18 final size:17
Alignment explanation
Indices: 1013535--1013590 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 17
1013525 GTATTATGTT
1013535 TGAAGAAAAAT-AAAAAA
1 TGAA-AAAAATGAAAAAA
1013552 TGAAAAAAATGAAAAAAA
1 TGAAAAAAATG-AAAAAA
1013570 TGAAAAAAATGAAAAAA
1 TGAAAAAAATGAAAAAA
1013587 TGAA
1 TGAA
1013591 GAGAGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.16
17 14 0.38
18 17 0.46
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
TGAAAAAAATGAAAAAA
Found at i:1014700 original size:136 final size:135
Alignment explanation
Indices: 1014451--1014809 Score: 493
Period size: 136 Copynumber: 2.6 Consensus size: 135
1014441 GGAGGTGAAC
* * * *
1014451 CAACATTTCTAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAATAAGTTCCTA
1 CAACATTTCCAAT-GAGAGTTCATAATGAGAAGAACTTATCCGATAGAGGGAGAAGAAGTTCATA
* * ** *
1014516 ATGAGAAGAGCTTGTTCAACTTATCACTCGATTCACGACATTTCGAATCACTGATGCCTCGCTTG
65 ATGAGAAGAGCTTGTTCAACCTATCACTCGATTCACAACATTTCGAATCACTGACACCTCACTTG
1014581 AGGGAT
130 AGGGAT
* * * * *
1014587 CAACATTTCCAGTGAAGAGTTCATAATGAGAAGAACTTATCCGACAAAAGGAGAAGAAGTTGATA
1 CAACATTTCCAATG-AGAGTTCATAATGAGAAGAACTTATCCGATAGAGGGAGAAGAAGTTCATA
* * *
1014652 ATGAGAAGAGCTTGTTTAACCTATCACTCGATTCACAACATTTTGAATCAGTGACACCTCACTTG
65 ATGAGAAGAGCTTGTTCAACCTATCACTCGATTCACAACATTTCGAATCACTGACACCTCACTTG
1014717 AGGGAT
130 AGGGAT
** *
1014723 TGATATTTCCAATTGAGAGTTCATAATGAGAAGAACTTATCCGATAGAGGGAGAAGAAGTTCATA
1 CAACATTTCCAA-TGAGAGTTCATAATGAGAAGAACTTATCCGATAGAGGGAGAAGAAGTTCATA
* *
1014788 ATGAGAAGAACTTATTCAACCT
65 ATGAGAAGAGCTTGTTCAACCT
1014810 TGGTTTCAAG
Statistics
Matches: 193, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
135 1 0.01
136 190 0.98
137 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (135 bp):
CAACATTTCCAATGAGAGTTCATAATGAGAAGAACTTATCCGATAGAGGGAGAAGAAGTTCATAA
TGAGAAGAGCTTGTTCAACCTATCACTCGATTCACAACATTTCGAATCACTGACACCTCACTTGA
GGGAT
Found at i:1021756 original size:54 final size:54
Alignment explanation
Indices: 1021690--1022030 Score: 456
Period size: 54 Copynumber: 6.4 Consensus size: 54
1021680 TTTATTAAGA
* * *
1021690 TGCACACGTAGTGCCTATACGGTCGTTCATCAACACATGATGAATTCTGTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACACATGATGAATTCTGTGAGT
*
1021744 TGCACACATAGTGCCTGTACAGTTGTTCATCAACACATGATGAATT-TCGTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACACATGATGAATTCT-GTGAGT
* * * * *
1021798 AGCACATATAGTGCCTGTACAGTTTTTCATCAACACATGATGAATTCCGTGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACACATGATGAATTCTGTGAGT
* * *
1021852 TACAAACATAGTGCTTGTACGGTTGTTCATCAACACATGATGAATT-T-TGAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACACATGATGAATTCTGTGAGT
* * *
1021904 TGCACACATAGTGCTTGTACGGTTGTTCGTCAACACATGATGAATTCTGTAAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACACATGATGAATTCTGTGAGT
* * ** *
1021958 TGCACACATAGTGCCTATACGGTTGTTTATCAATGCATGATGAATTCCG-GTAGT
1 TGCACACATAGTGCCTGTACGGTTGTTCATCAACACATGATGAATTCTGTG-AGT
1022012 TGCACACATAGTGCCTGTA
1 TGCACACATAGTGCCTGTA
1022031 GTACATATAT
Statistics
Matches: 253, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
52 48 0.19
53 2 0.01
54 203 0.80
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.32
Consensus pattern (54 bp):
TGCACACATAGTGCCTGTACGGTTGTTCATCAACACATGATGAATTCTGTGAGT
Found at i:1021999 original size:160 final size:162
Alignment explanation
Indices: 1021698--1022030 Score: 469
Period size: 160 Copynumber: 2.1 Consensus size: 162
1021688 GATGCACACG
*
1021698 TAGTGCCTATACGGTCGTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCCTGTA
1 TAGTGCCTGTACGGTCGTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCCTGTA
* * *
1021763 CAGTTGTTCATCAACACATGATGAATTTCGTGAGTAGCACATATAGTGCCTGTACAGTTTTTCAT
66 CAGTTGTTCATCAACACATGATGAATTTCGTAAGTAGCACACATAGTGCCTATACAGTTTTTCAT
1021828 CAACACATGATGAATTCC-GTGAGTTACAAACA
131 CAACACATGATGAATTCCGGT-AGTTACAAACA
* * *
1021860 TAGTGCTTGTACGGTTGTTCATCAACACATGATGAATT-T-TGAGTTGCACACATAGTGCTTGTA
1 TAGTGCCTGTACGGTCGTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCCTGTA
* * * *
1021923 CGGTTGTTCGTCAACACATGATGAA-TTCTGTAAGTTGCACACATAGTGCCTATACGGTTGTTT-
66 CAGTTGTTCATCAACACATGATGAATTTC-GTAAGTAGCACACATAGTGCCTATACAGTT-TTTC
** * *
1021986 ATCAATGCATGATGAATTCCGGTAGTTGCACACA
129 ATCAACACATGATGAATTCCGGTAGTTACAAACA
1022020 TAGTGCCTGTA
1 TAGTGCCTGTA
1022031 GTACATATAT
Statistics
Matches: 152, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
159 3 0.02
160 108 0.71
161 6 0.04
162 35 0.23
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (162 bp):
TAGTGCCTGTACGGTCGTTCATCAACACATGATGAATTCTGTGAGTTGCACACATAGTGCCTGTA
CAGTTGTTCATCAACACATGATGAATTTCGTAAGTAGCACACATAGTGCCTATACAGTTTTTCAT
CAACACATGATGAATTCCGGTAGTTACAAACA
Found at i:1022451 original size:42 final size:41
Alignment explanation
Indices: 1022355--1022470 Score: 103
Period size: 42 Copynumber: 2.8 Consensus size: 41
1022345 TCCAAGCTCA
* * *
1022355 ATAGTATCGATAC-CCCTAC-CATGGTATCAATACTTCTATACT
1 ATAGTATCGATACTCCCT-CTCA--GTATCGATACTACTACACT
**
1022397 ATAGTATCGATACCTTTCTCTCAGTATCGATACTACTACACT
1 ATAGTATCGATA-CTCCCTCTCAGTATCGATACTACTACACT
* *
1022439 ATGGTA-CTGATACTCCCTTTCAGTATCGATAC
1 ATAGTATC-GATACTCCCTCTCAGTATCGATAC
1022471 CATTTCGACA
Statistics
Matches: 61, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
41 18 0.30
42 37 0.61
43 2 0.03
44 4 0.07
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.34
Consensus pattern (41 bp):
ATAGTATCGATACTCCCTCTCAGTATCGATACTACTACACT
Found at i:1029222 original size:17 final size:18
Alignment explanation
Indices: 1029186--1029223 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1029176 TACTACACTA
*
1029186 TGGTATCGATACATATTT
1 TGGTATCGATACACATTT
1029204 TGGTATCGATAC-CATTT
1 TGGTATCGATACACATTT
1029221 TGG
1 TGG
1029224 CATTCGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.24, C:0.13, G:0.21, T:0.42
Consensus pattern (18 bp):
TGGTATCGATACACATTT
Found at i:1032443 original size:16 final size:15
Alignment explanation
Indices: 1032414--1032463 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
1032404 TTTTTTTTTC
*
1032414 TTTTTTCTTATCATT
1 TTTTTTCTTTTCATT
1032429 TTTTTTCTTTTTCATT
1 TTTTTTC-TTTTCATT
1032445 TTTTTTCATTTT-ATT
1 TTTTTTC-TTTTCATT
1032460 TTTT
1 TTTT
1032464 GTAGTACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
15 14 0.44
16 18 0.56
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTTCTTTTCATT
Found at i:1034867 original size:37 final size:37
Alignment explanation
Indices: 1034823--1034896 Score: 132
Period size: 37 Copynumber: 2.0 Consensus size: 37
1034813 ATAACGAATG
1034823 TAAAAATGTATAAAATGATTG-GCACTTGAGAAATGAA
1 TAAAAATGTATAAAATGATTGCG-ACTTGAGAAATGAA
1034860 TAAAAATGTATAAAATGATTGCGACTTGAGAAATGAA
1 TAAAAATGTATAAAATGATTGCGACTTGAGAAATGAA
1034897 AGAAAGCATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 35 0.97
38 1 0.03
ACGTcount: A:0.49, C:0.05, G:0.19, T:0.27
Consensus pattern (37 bp):
TAAAAATGTATAAAATGATTGCGACTTGAGAAATGAA
Found at i:1036904 original size:59 final size:59
Alignment explanation
Indices: 1036812--1036945 Score: 241
Period size: 59 Copynumber: 2.3 Consensus size: 59
1036802 CAAATTATTT
*
1036812 CCTATATGGAAATTCATACAGTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGC
* *
1036871 CCTATATTGAAATTTATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGC
1 CCTATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGC
1036930 CCTATATGGAAATTCA
1 CCTATATGGAAATTCA
1036946 CACTACTAGA
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 70 1.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (59 bp):
CCTATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGC
Found at i:1037198 original size:13 final size:13
Alignment explanation
Indices: 1037182--1037211 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1037172 TTATGACACG
*
1037182 CATTTATGACTTA
1 CATTTACGACTTA
1037195 CATTTACGACTTA
1 CATTTACGACTTA
1037208 CATT
1 CATT
1037212 GCGTGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
CATTTACGACTTA
Found at i:1037198 original size:98 final size:99
Alignment explanation
Indices: 1037020--1037200 Score: 231
Period size: 98 Copynumber: 1.8 Consensus size: 99
1037010 CAAATGCACG
* ** * *
1037020 TCATTGAAGCCACCGTCATAAATCTCAGATGACACGCAATTGTGTGTCATAAATCTACGACGCGC
1 TCATTAAAGCCACCGTCATAAATCGAAGATGACACACAATTGTGTGTCATAAATCTACGACACGC
*
1037085 ATTTATTACACACATTTATGATGCGCATTGCGCA
66 ATTTATGACACACATTTATGATGCGCATTGCGCA
* * * *
1037119 TCATTAAAGCC-CCAGTCATAAAT-GAAGATGACACACATTTGTGTTTCATAAATTTATGACACG
1 TCATTAAAGCCACC-GTCATAAATCGAAGATGACACACAATTGTGTGTCATAAATCTACGACACG
**
1037182 CATTTATGACTTACATTTA
65 CATTTATGACACACATTTA
1037201 CGACTTACAT
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
98 50 0.72
99 19 0.28
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (99 bp):
TCATTAAAGCCACCGTCATAAATCGAAGATGACACACAATTGTGTGTCATAAATCTACGACACGC
ATTTATGACACACATTTATGATGCGCATTGCGCA
Found at i:1037221 original size:98 final size:99
Alignment explanation
Indices: 1037018--1037226 Score: 226
Period size: 98 Copynumber: 2.1 Consensus size: 99
1037008 AACAAATGCA
** * *
1037018 CGTCATTGAAGCCACCGTCATAAATCTCAGATGACACGCAATTGTGTGTCATAAATCTACGACGC
1 CGTCATTGAAGCCACCGTCATAAATCGAAGATGACACACAATTGTGTGTCATAAATCTACGACAC
* * *
1037083 GCATTTATTACACACATTTATGATGCGCATTGCG
66 GCATTTATGACACACATTTACGATGCACATTGCG
* * * * * *
1037117 CATCATTAAAGCC-CCAGTCATAAAT-GAAGATGACACACATTTGTGTTTCATAAATTTATGACA
1 CGTCATTGAAGCCACC-GTCATAAATCGAAGATGACACACAATTGTGTGTCATAAATCTACGACA
** *
1037180 CGCATTTATGACTTACATTTACGACT-TACATTGCG
65 CGCATTTATGACACACATTTACGA-TGCACATTGCG
*
1037215 TGTCATTGAAGC
1 CGTCATTGAAGC
1037227 ACACATCATT
Statistics
Matches: 89, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
98 68 0.76
99 21 0.24
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (99 bp):
CGTCATTGAAGCCACCGTCATAAATCGAAGATGACACACAATTGTGTGTCATAAATCTACGACAC
GCATTTATGACACACATTTACGATGCACATTGCG
Found at i:1038888 original size:25 final size:24
Alignment explanation
Indices: 1038820--1038888 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 24
1038810 TTGCAGTGTT
* * *
1038820 CCCTCCTCATTTTCTTTCTTTTTT
1 CCCTCTTCATTTTCTTTCTCTTTC
* * * *
1038844 CCCTCTTTAGTGTCCCTTCTCCTTTC
1 CCCTCTTCA-TTTTCTTTCT-CTTTC
1038870 CCCTCTTCATTTTCTTTCT
1 CCCTCTTCATTTTCTTTCT
1038889 TTTTTTCCGT
Statistics
Matches: 32, Mismatches: 11, Indels: 3
0.70 0.24 0.07
Matches are distributed among these distances:
24 7 0.22
25 14 0.44
26 11 0.34
ACGTcount: A:0.04, C:0.38, G:0.03, T:0.55
Consensus pattern (24 bp):
CCCTCTTCATTTTCTTTCTCTTTC
Found at i:1038892 original size:50 final size:50
Alignment explanation
Indices: 1038820--1038933 Score: 149
Period size: 50 Copynumber: 2.3 Consensus size: 50
1038810 TTGCAGTGTT
* * *
1038820 CCCTCCTCATTTTCTTTC-TTTTTTCCCTCTTTAGTGTCCCTTCTCCTTTC
1 CCCTCTTCATTTTCTTTCTTTTTTTCCCTC-TTAGTGTCACTTCTCCCTTC
* *
1038870 CCCTCTTCATTTTCTTTCTTTTTTTCCGTCTTGGTGTCACTTCTCCCTTC
1 CCCTCTTCATTTTCTTTCTTTTTTTCCCTCTTAGTGTCACTTCTCCCTTC
* *
1038920 TCCTCTTCCTTTTC
1 CCCTCTTCATTTTC
1038934 AACAAGTTCT
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 46 0.82
51 10 0.18
ACGTcount: A:0.04, C:0.37, G:0.05, T:0.54
Consensus pattern (50 bp):
CCCTCTTCATTTTCTTTCTTTTTTTCCCTCTTAGTGTCACTTCTCCCTTC
Found at i:1042458 original size:24 final size:25
Alignment explanation
Indices: 1042431--1042497 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 25
1042421 AACACACACC
1042431 TCATATTATAAAAACTCACA-CATT
1 TCATATTATAAAAACTCACACCATT
* * *
1042455 TCATATTA-ACAACACACACACCCTT
1 TCATATTATA-AAAACTCACACCATT
1042480 T-ATATTATAAAAACTCAC
1 TCATATTATAAAAACTCAC
1042498 TCACACACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
23 1 0.03
24 29 0.83
25 5 0.14
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (25 bp):
TCATATTATAAAAACTCACACCATT
Found at i:1042527 original size:54 final size:52
Alignment explanation
Indices: 1042433--1042566 Score: 170
Period size: 54 Copynumber: 2.6 Consensus size: 52
1042423 CACACACCTC
1042433 ATATTATAAAAACT----CACACATTTCATATTAACAACACACACACCCTTT
1 ATATTATAAAAACTCACACACACATTTCATATTAACAACACACACACCCTTT
*
1042481 ATATTATAAAAACTCACTCACACACATTTCATATTAA-AAGAGCACACACCCTTT
1 ATATTATAAAAACTCA--CACACACATTTCATATTAACAACA-CACACACCCTTT
* * *
1042535 ATATTATAATAAGTCACACACGCATTTCATAT
1 ATATTATAAAAACTCACACACACATTTCATAT
1042567 ATACATTAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
48 14 0.19
52 15 0.20
53 3 0.04
54 43 0.57
ACGTcount: A:0.43, C:0.25, G:0.03, T:0.30
Consensus pattern (52 bp):
ATATTATAAAAACTCACACACACATTTCATATTAACAACACACACACCCTTT
Found at i:1042552 original size:26 final size:25
Alignment explanation
Indices: 1042469--1042555 Score: 79
Period size: 26 Copynumber: 3.3 Consensus size: 25
1042459 ATTAACAACA
*
1042469 CACACACCCTTTATATTATAAAAACT
1 CACACACCCTTTATATTAT-AAAAGT
*
1042495 CACTCACACACATTTCATATTA-AAAGAG-
1 CA--CACAC-CCTTT-ATATTATAAA-AGT
1042523 CACACACCCTTTATATTATAATAAGT
1 CACACACCCTTTATATTATAA-AAGT
1042549 CACACAC
1 CACACAC
1042556 GCATTTCATA
Statistics
Matches: 50, Mismatches: 3, Indels: 16
0.72 0.04 0.23
Matches are distributed among these distances:
24 6 0.12
25 8 0.16
26 15 0.30
28 10 0.20
29 5 0.10
30 6 0.12
ACGTcount: A:0.41, C:0.28, G:0.03, T:0.28
Consensus pattern (25 bp):
CACACACCCTTTATATTATAAAAGT
Found at i:1042632 original size:25 final size:24
Alignment explanation
Indices: 1042565--1042635 Score: 65
Period size: 25 Copynumber: 2.9 Consensus size: 24
1042555 CGCATTTCAT
*
1042565 ATATACATTAAACACACACACATA
1 ATATAAATTAAACACACACACATA
* *
1042589 TTGCAT-AA-TAAAAAGCACACACATA
1 AT--ATAAATTAAACA-CACACACATA
1042614 CATATAAATTAAACACACACAC
1 -ATATAAATTAAACACACACAC
1042636 GTACTGCATA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
24 8 0.22
25 20 0.56
26 8 0.22
ACGTcount: A:0.54, C:0.24, G:0.03, T:0.20
Consensus pattern (24 bp):
ATATAAATTAAACACACACACATA
Found at i:1042741 original size:107 final size:105
Alignment explanation
Indices: 1042576--1042771 Score: 295
Period size: 107 Copynumber: 1.8 Consensus size: 105
1042566 TATACATTAA
*
1042576 ACACACACACATATTGCATAATAAAAAGCACACACATACATATAAATTAAACACACACACGTACT
1 ACACACACACATACTGCATAATAAAAAGCACACACATACATATAAATTAAACACACACACGTACT
**
1042641 GCATAATAAAAGAAGTATACACACATAAATATATATTAAAT
66 GCATAATAAAA-AAAAATACACACATAAATATATATTAAAT
* * * *
1042682 ACACACACACTTACTGCATAATAAAAAAGCACACACATGA-ATATATATTAAATACACACACTTA
1 ACACACACACATACTGCATAAT-AAAAAGCACACACAT-ACATATAAATTAAACACACACACGTA
1042746 CTGCATAATAAAAAAAAATACACACA
64 CTGCATAATAAAAAAAAATACACACA
1042772 CACACTTATT
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
106 31 0.38
107 49 0.60
108 1 0.01
ACGTcount: A:0.53, C:0.21, G:0.05, T:0.21
Consensus pattern (105 bp):
ACACACACACATACTGCATAATAAAAAGCACACACATACATATAAATTAAACACACACACGTACT
GCATAATAAAAAAAAATACACACATAAATATATATTAAAT
Found at i:1045598 original size:19 final size:19
Alignment explanation
Indices: 1045574--1045615 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
1045564 TTTCTGCGTT
1045574 GTGGTGAATGG-TGAAACTA
1 GTGGTGAATGGCT-AAACTA
1045593 GTGGTGAATGGCTAAACTA
1 GTGGTGAATGGCTAAACTA
1045612 GTGG
1 GTGG
1045616 ATCGGTCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.29, C:0.07, G:0.38, T:0.26
Consensus pattern (19 bp):
GTGGTGAATGGCTAAACTA
Found at i:1046145 original size:59 final size:59
Alignment explanation
Indices: 1046051--1046268 Score: 321
Period size: 59 Copynumber: 3.7 Consensus size: 59
1046041 CACTTAGTAA
* *
1046051 TTAGTATGAA-TCCTTTCTCATGTTAGCACATGAAGTGCCCTATATGGAAATTCAGACAC
1 TTAGTATGAATTCC-TTCTCATGTTAGCACACGAAGTGCCCTATATGGAAATTCATACAC
*
1046110 TTAGTATAAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAATTCATACAC
1 TTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAATTCATACAC
* * *
1046169 TTAGTATGAATTCCTTCTCATGTTATCACATGAAGTGCCCTATATGAAAATTCATACAC
1 TTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAATTCATACAC
* * ** *
1046228 TTCGTATGAATTTCTTGACATTTTAGCACACGAAGTGCCCT
1 TTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
1046269 TTTGGTAATC
Statistics
Matches: 144, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
59 141 0.98
60 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (59 bp):
TTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATATGGAAATTCATACAC
Found at i:1049116 original size:162 final size:162
Alignment explanation
Indices: 1048849--1049174 Score: 652
Period size: 162 Copynumber: 2.0 Consensus size: 162
1048839 ACCATCATAT
1048849 AGCACACTAGAGGATCCAATTAATTTTTCTGAGATACTTCGTATTTATCAGGTAGGAAGCCAAGA
1 AGCACACTAGAGGATCCAATTAATTTTTCTGAGATACTTCGTATTTATCAGGTAGGAAGCCAAGA
1048914 AATTTTTGTAAATTGATCAAATTCCAAAAATAAGATTCTTATAAAAAAAATGGTCAATAGCTAAC
66 AATTTTTGTAAATTGATCAAATTCCAAAAATAAGATTCTTATAAAAAAAATGGTCAATAGCTAAC
1048979 GGATTAATTAATCATTCTGAAAGAGATACATC
131 GGATTAATTAATCATTCTGAAAGAGATACATC
1049011 AGCACACTAGAGGATCCAATTAATTTTTCTGAGATACTTCGTATTTATCAGGTAGGAAGCCAAGA
1 AGCACACTAGAGGATCCAATTAATTTTTCTGAGATACTTCGTATTTATCAGGTAGGAAGCCAAGA
1049076 AATTTTTGTAAATTGATCAAATTCCAAAAATAAGATTCTTATAAAAAAAATGGTCAATAGCTAAC
66 AATTTTTGTAAATTGATCAAATTCCAAAAATAAGATTCTTATAAAAAAAATGGTCAATAGCTAAC
1049141 GGATTAATTAATCATTCTGAAAGAGATACATC
131 GGATTAATTAATCATTCTGAAAGAGATACATC
1049173 AG
1 AG
1049175 GATTATAAAC
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
162 164 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (162 bp):
AGCACACTAGAGGATCCAATTAATTTTTCTGAGATACTTCGTATTTATCAGGTAGGAAGCCAAGA
AATTTTTGTAAATTGATCAAATTCCAAAAATAAGATTCTTATAAAAAAAATGGTCAATAGCTAAC
GGATTAATTAATCATTCTGAAAGAGATACATC
Found at i:1050810 original size:49 final size:50
Alignment explanation
Indices: 1050717--1050818 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 50
1050707 GGCTCAGCTC
* * * ***
1050717 GACTGCTTGGCTTGACTCGACGGCTCAGATCGGCTCGGTGACTCGA-CTA
1 GACTGCTTGGCTAGACTCGACGACTCAGATCAGCTCGAAAACTCGATCTA
* *
1050766 GACTGCTTGGCTAGACTCGATGACTCAGCTCAGCTCGAAAACTCGATCTA
1 GACTGCTTGGCTAGACTCGACGACTCAGATCAGCTCGAAAACTCGATCTA
1050816 GAC
1 GAC
1050819 CGACCCAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
49 38 0.86
50 6 0.14
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (50 bp):
GACTGCTTGGCTAGACTCGACGACTCAGATCAGCTCGAAAACTCGATCTA
Found at i:1054999 original size:22 final size:24
Alignment explanation
Indices: 1054971--1055016 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
1054961 GTGTTTAGTA
*
1054971 GTTAGAAGTTAA-AAAGTC-AGAT
1 GTTAGAAATTAATAAAGTCTAGAT
1054993 GTTAGAAATTAATAAAGTCTAGAT
1 GTTAGAAATTAATAAAGTCTAGAT
1055017 CATAATAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 6 0.29
24 4 0.19
ACGTcount: A:0.46, C:0.04, G:0.20, T:0.30
Consensus pattern (24 bp):
GTTAGAAATTAATAAAGTCTAGAT
Done.