Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008847.1 Hibiscus syriacus cultivar Beakdansim tig00112057_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: 67956
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1128 original size:29 final size:29
Alignment explanation
Indices: 1096--1231 Score: 112
Period size: 30 Copynumber: 4.6 Consensus size: 29
1086 AGAAATCTTG
* *
1096 AAAACAGAACTTAAAGGATTAAAATGGCA
1 AAAACAAAACTTAAAGGATTAAAATAGCA
* * * * *
1125 AAAATATAAACTTAAAAGTTTAAAAACAGCG
1 AAAACA-AAACTTAAAGGATT-AAAATAGCA
* * * *
1156 AAAACATAACTTTAAGAGACT-AAATAACA
1 AAAACAAAACTTAAAG-GATTAAAATAGCA
*
1185 AAAACAGAAATTTAAAGGATTAAAATAGCA
1 AAAACA-AAACTTAAAGGATTAAAATAGCA
*
1215 AAAACAAAAATTAAAGG
1 AAAACAAAACTTAAAGG
1232 GTTGAACAAT
Statistics
Matches: 80, Mismatches: 22, Indels: 10
0.71 0.20 0.09
Matches are distributed among these distances:
29 29 0.36
30 38 0.47
31 13 0.16
ACGTcount: A:0.60, C:0.10, G:0.12, T:0.19
Consensus pattern (29 bp):
AAAACAAAACTTAAAGGATTAAAATAGCA
Found at i:3307 original size:20 final size:20
Alignment explanation
Indices: 3283--3355 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
3273 GCAGCCTTAG
* *
3283 TGCATGGATGCACAGCAGGG
1 TGCATCGATGCACAGCAGGA
*
3303 TGCATGGATGCACAGCAGGA
1 TGCATCGATGCACAGCAGGA
*
3323 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGCAGGA
3343 TGCATCGATGCAC
1 TGCATCGATGCAC
3356 TAATTGTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.33, T:0.16
Consensus pattern (20 bp):
TGCATCGATGCACAGCAGGA
Found at i:3423 original size:22 final size:23
Alignment explanation
Indices: 3390--3432 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
3380 ATGGATGCAC
3390 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
3413 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
3433 GCAAGGGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:4113 original size:85 final size:86
Alignment explanation
Indices: 3970--4164 Score: 329
Period size: 85 Copynumber: 2.3 Consensus size: 86
3960 AGGGGATGAT
* **
3970 ACTGCTCATATGTGATGAGTCTTGACCATATAAAGGTGATAACATGGTTCCTACGTGATGAGGA-
1 ACTGCTCATATGCGATGAGTCTTGACCATATAAAGGTGATAACACAGTTCCTACGTGATGAGGAC
*
4034 AGATTGTTATCAAGGGTTGAC
66 AGATGGTTATCAAGGGTTGAC
*
4055 ACTGCTCATATGCGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTACGTGATGAGGAC
1 ACTGCTCATATGCGATGAGTCTTGACCATATAAAGGTGATAACACAGTTCCTACGTGATGAGGAC
*
4120 GGATGGTTATCAAGGGTTGAC
66 AGATGGTTATCAAGGGTTGAC
4141 ACTGCTCATATGCGATGAGTCTTG
1 ACTGCTCATATGCGATGAGTCTTG
4165 GCCAGGGAAT
Statistics
Matches: 103, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 60 0.58
86 43 0.42
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (86 bp):
ACTGCTCATATGCGATGAGTCTTGACCATATAAAGGTGATAACACAGTTCCTACGTGATGAGGAC
AGATGGTTATCAAGGGTTGAC
Found at i:4116 original size:43 final size:43
Alignment explanation
Indices: 3981--4116 Score: 98
Period size: 43 Copynumber: 3.2 Consensus size: 43
3971 CTGCTCATAT
* **
3981 GTGATGAGTCTTGACCATATAAAGGTGATAACATGGTTCCTAC
1 GTGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTAC
*** *** * * * * *
4024 GTGATGAG-GAAGATTGTTATCAAGGGT--TGACACTGCTCATAT
1 GTGATGAGTCTTGA-CCATAT-AAGGGTGATAACACAGTTCCTAC
*
4066 GCGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTAC
1 GTGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTAC
4109 GTGATGAG
1 GTGATGAG
4117 GACGGATGGT
Statistics
Matches: 62, Mismatches: 26, Indels: 10
0.63 0.27 0.10
Matches are distributed among these distances:
41 6 0.10
42 21 0.34
43 30 0.48
44 5 0.08
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.29
Consensus pattern (43 bp):
GTGATGAGTCTTGACCATATAAGGGTGATAACACAGTTCCTAC
Found at i:5326 original size:14 final size:14
Alignment explanation
Indices: 5307--5338 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5297 TGCTTCATGT
5307 ATGTATGTTGATGG
1 ATGTATGTTGATGG
*
5321 ATGTATGTTGATGT
1 ATGTATGTTGATGG
5335 ATGT
1 ATGT
5339 CTTGATCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
ATGTATGTTGATGG
Found at i:9440 original size:45 final size:43
Alignment explanation
Indices: 9330--9440 Score: 145
Period size: 45 Copynumber: 2.6 Consensus size: 43
9320 TTACCACGCC
9330 TCCTCCACCACCTGTGTATTCACCTCCCCCGCCACCAACATCA
1 TCCTCCACCACCTGTGTATTCACCTCCCCCGCCACCAACATCA
* * *
9373 -CCTCCACCACCCGTGTACTCACCTCCCCCGCCGCCACCACCAT-A
1 TCCTCCACCACCTGTGTATTCACCT--CCC-CCGCCACCAACATCA
*
9417 TCCTCCACCACCTGAGTATTCACC
1 TCCTCCACCACCTGTGTATTCACC
9441 ACCTCCACCT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
42 22 0.38
44 4 0.07
45 32 0.55
ACGTcount: A:0.20, C:0.53, G:0.08, T:0.19
Consensus pattern (43 bp):
TCCTCCACCACCTGTGTATTCACCTCCCCCGCCACCAACATCA
Found at i:9455 original size:45 final size:46
Alignment explanation
Indices: 9330--9456 Score: 138
Period size: 45 Copynumber: 2.9 Consensus size: 46
9320 TTACCACGCC
*
9330 TCCTCCACCACCTGTGTATT---CACCTCCCCCGCCACCAACATCA
1 TCCTCCACCACCTGTGTATTCACCACCTCCACCGCCACCAACATCA
* * * * * *
9373 -CCTCCACCACCCGTGTACTCACCTCCCCCGCCGCCACCACCAT-A
1 TCCTCCACCACCTGTGTATTCACCACCTCCACCGCCACCAACATCA
* *
9417 TCCTCCACCACCTGAGTATTCACCACCTCCACCTCCACCA
1 TCCTCCACCACCTGTGTATTCACCACCTCCACCGCCACCA
9457 TTACCTCCTC
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
42 17 0.25
44 1 0.01
45 49 0.73
ACGTcount: A:0.20, C:0.54, G:0.07, T:0.18
Consensus pattern (46 bp):
TCCTCCACCACCTGTGTATTCACCACCTCCACCGCCACCAACATCA
Found at i:9464 original size:42 final size:42
Alignment explanation
Indices: 9331--9464 Score: 144
Period size: 42 Copynumber: 3.1 Consensus size: 42
9321 TACCACGCCT
* *
9331 CCTCCACCACCTGTGTATTCACCTCCCCCGCCACCAACATCA
1 CCTCCACCACCTGTGTATTCACCTCCCCCGCCACCACCATTA
* *
9373 CCTCCACCACCCGTGTACTCACCTCCCCCGCCGCCACCACCA-TA
1 CCTCCACCACCTGTGTATTCACCT--CCC-CCGCCACCACCATTA
* * * * *
9417 TCCTCCACCACCTGAGTATTCACCACCTCCACCTCCACCATTA
1 -CCTCCACCACCTGTGTATTCACCTCCCCCGCCACCACCATTA
9460 CCTCC
1 CCTCC
9465 TCCTCCGCCT
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
42 37 0.49
43 4 0.05
44 4 0.05
45 31 0.41
ACGTcount: A:0.20, C:0.54, G:0.07, T:0.19
Consensus pattern (42 bp):
CCTCCACCACCTGTGTATTCACCTCCCCCGCCACCACCATTA
Found at i:9701 original size:21 final size:21
Alignment explanation
Indices: 9663--9702 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9653 CACCTCCGGT
*
9663 ACATTCTCCACCACCACCACC
1 ACATTCACCACCACCACCACC
* *
9684 ACATTCACCTCCAGCACCA
1 ACATTCACCACCACCACCA
9703 ATCTATCCGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.53, G:0.03, T:0.15
Consensus pattern (21 bp):
ACATTCACCACCACCACCACC
Found at i:18920 original size:18 final size:17
Alignment explanation
Indices: 18897--18930 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18887 ATGCTATTAG
18897 TGAACCGATCGAAACCGT
1 TGAACCGATC-AAACCGT
*
18915 TGAACCGTTCAAACCG
1 TGAACCGATCAAACCG
18931 GACCGGCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (17 bp):
TGAACCGATCAAACCGT
Found at i:21061 original size:24 final size:24
Alignment explanation
Indices: 21034--21079 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
21024 GATAAAAAGT
* **
21034 ATTAATAAAATATTCATAAATATC
1 ATTAAGAAAATATAAATAAATATC
*
21058 ATTACGAAAATATAAATAAATA
1 ATTAAGAAAATATAAATAAATA
21080 AGAAAATTAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (24 bp):
ATTAAGAAAATATAAATAAATATC
Found at i:23268 original size:5 final size:5
Alignment explanation
Indices: 23258--23380 Score: 53
Period size: 5 Copynumber: 25.2 Consensus size: 5
23248 AGAAACATAA
* * *
23258 AAAAT AAAAT AAAAT AAAAT -AAAT AAAGT AAACAA AAAAT AATAA- ATAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA-AT AAAAT AA-AAT AAAAT
** * * *
23308 -AAAT -AAAT AACGT -GAAT AAAAT ATAAT -AAAC AAAAT AAAA- AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * *
23353 GAAGT AAATT AAATAT AAGAT AATAAT A
1 AAAAT AAAAT AAA-AT AAAAT AA-AAT A
23381 GTAAGAATAA
Statistics
Matches: 85, Mismatches: 23, Indels: 19
0.67 0.18 0.15
Matches are distributed among these distances:
4 20 0.24
5 54 0.64
6 11 0.13
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:23283 original size:4 final size:4
Alignment explanation
Indices: 23254--23429 Score: 63
Period size: 4 Copynumber: 40.2 Consensus size: 4
23244 ATAAAGAAAC
*
23254 ATAA A-AA ATAAA ATAAA ATAAA ATAA ATAA AGTAA ACAA A-AA AT-A
1 ATAA ATAA AT-AA AT-AA AT-AA ATAA ATAA A-TAA ATAA ATAA ATAA
* * *
23299 ATAA AT-A ATAA ATAA ATAA CGTGA ATAAA ATATA ATAA ACAAA ATAAA
1 ATAA ATAA ATAA ATAA ATAA -ATAA AT-AA ATA-A ATAA A-TAA AT-AA
* * * *
23347 AAAA ATGAA GTAA ATTAA ATATA AGATA ATAA TAGTAAGA ATAA CATAT
1 ATAA AT-AA ATAA A-TAA ATA-A ATA-A ATAA -A-T-A-A ATAA -ATAA
* *
23396 ACACA ATAA ATAA ATAA ATAA ATAA ATAG ATAA A
1 ATA-A ATAA ATAA ATAA ATAA ATAA ATAA ATAA A
23430 AAAACATCAT
Statistics
Matches: 133, Mismatches: 19, Indels: 40
0.69 0.10 0.21
Matches are distributed among these distances:
3 12 0.09
4 62 0.47
5 54 0.41
6 2 0.02
7 2 0.02
8 1 0.01
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.22
Consensus pattern (4 bp):
ATAA
Found at i:23283 original size:14 final size:14
Alignment explanation
Indices: 23258--23423 Score: 67
Period size: 14 Copynumber: 11.7 Consensus size: 14
23248 AGAAACATAA
23258 AAAATAAAATAAAAT
1 AAAAT-AAATAAAAT
*
23273 AAAATAAATAAAGT
1 AAAATAAATAAAAT
23287 AAACA-AAA-AATAAT
1 AAA-ATAAATAA-AAT
23301 AAATAATAAAT-AAAT
1 -AA-AATAAATAAAAT
** *
23316 AACGTGAATAAAAT
1 AAAATAAATAAAAT
* *
23330 ATAATAAACAAAAT
1 AAAATAAATAAAAT
* * *
23344 AAAAAAAATGAAGT
1 AAAATAAATAAAAT
*
23358 AAATTAAATATAAGAT
1 AAAATAAATA-AA-AT
*
23374 AATAAT-AGTAAGAAT
1 AA-AATAAATAA-AAT
* * * *
23389 AACATATACACAAT
1 AAAATAAATAAAAT
23403 -AAATAAAT-AAAT
1 AAAATAAATAAAAT
23415 -AAATAAATA
1 AAAATAAATA
23424 GATAAAAAAA
Statistics
Matches: 108, Mismatches: 30, Indels: 28
0.65 0.18 0.17
Matches are distributed among these distances:
12 11 0.10
13 11 0.10
14 52 0.48
15 20 0.19
16 12 0.11
17 2 0.02
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (14 bp):
AAAATAAATAAAAT
Found at i:23295 original size:34 final size:34
Alignment explanation
Indices: 23257--23360 Score: 86
Period size: 34 Copynumber: 3.0 Consensus size: 34
23247 AAGAAACATA
23257 AAAAATAAAATAAAATAAAATAAATAAAGTAAAC
1 AAAAATAAAATAAAATAAAATAAATAAAGTAAAC
* * * *
23291 AAAAA-ATAAT-AAATAATAAATAAATAACGTGAAT
1 AAAAATAAAATAAAAT-A-AAATAAATAAAGTAAAC
* * *
23325 AAAATATAATAAACAAAATAAAAAAAATGAAGTAAA
1 AAAA-AT-A-AAATAAAATAAAATAAATAAAGTAAA
23361 TTAAATATAA
Statistics
Matches: 53, Mismatches: 10, Indels: 11
0.72 0.14 0.15
Matches are distributed among these distances:
32 4 0.08
33 5 0.09
34 23 0.43
35 1 0.02
37 13 0.25
38 3 0.06
39 4 0.08
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.19
Consensus pattern (34 bp):
AAAAATAAAATAAAATAAAATAAATAAAGTAAAC
Found at i:23301 original size:19 final size:19
Alignment explanation
Indices: 23243--23303 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
23233 TAAACATGTA
23243 AATAAAG-AAACATAAAA-
1 AATAAAGTAAACATAAAAT
*
23260 AATAAAATAAA-ATAAAAT
1 AATAAAGTAAACATAAAAT
*
23278 AAATAAAGTAAACAAAAAAT
1 -AATAAAGTAAACATAAAAT
23298 AATAAA
1 AATAAA
23304 TAATAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
17 12 0.32
18 3 0.08
19 16 0.43
20 6 0.16
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.16
Consensus pattern (19 bp):
AATAAAGTAAACATAAAAT
Found at i:23578 original size:3 final size:3
Alignment explanation
Indices: 23566--23605 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
23556 TTTGTATAGG
23566 TAA T-A TAA TAA TAA TAA -AA TAA T-A TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
23606 AGACAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.18
3 24 0.73
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:23596 original size:23 final size:24
Alignment explanation
Indices: 23568--23651 Score: 91
Period size: 23 Copynumber: 3.5 Consensus size: 24
23558 TGTATAGGTA
23568 ATATAATAATAATAAA-ATAATAT
1 ATATAATAATAATAAAGATAATAT
* * *
23591 ATATAATAATAATAAAGACAAAAG
1 ATATAATAATAATAAAGATAATAT
* * *
23615 ATTTAA-AAAAATAAATATAATAT
1 ATATAATAATAATAAAGATAATAT
23638 AATATAATAATAAT
1 -ATATAATAATAAT
23652 GAATAAAAAC
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
23 28 0.60
24 14 0.30
25 5 0.11
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.31
Consensus pattern (24 bp):
ATATAATAATAATAAAGATAATAT
Found at i:23679 original size:48 final size:46
Alignment explanation
Indices: 23575--23681 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 46
23565 GTAATATAAT
* *
23575 AATAATAAA-ATAATATATATAATAATAATAAAGACAAAAGATTTA
1 AATAAAAAATATAATATATATAATAATAATAAAGACAAAAGAATTA
* * *
23620 AAAAAATAAATATAATATAATATAATAATAATGAATA-AAAACGAAATTA
1 AATAAA-AAATATAATAT-ATATAATAATAATAAAGACAAAA-G-AATTA
23669 AATAAAAAATATA
1 AATAAAAAATATA
23682 GAAAATAAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
45 4 0.08
46 3 0.06
47 11 0.22
48 24 0.47
49 9 0.18
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (46 bp):
AATAAAAAATATAATATATATAATAATAATAAAGACAAAAGAATTA
Found at i:23690 original size:20 final size:21
Alignment explanation
Indices: 23662--23702 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
23652 GAATAAAAAC
*
23662 GAAATTAAATA-AAAAATATA
1 GAAAATAAATAGAAAAATATA
*
23682 GAAAATAAATAGAAATATATA
1 GAAAATAAATAGAAAAATATA
23703 TATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (21 bp):
GAAAATAAATAGAAAAATATA
Found at i:23703 original size:2 final size:2
Alignment explanation
Indices: 23696--23847 Score: 77
Period size: 2 Copynumber: 78.5 Consensus size: 2
23686 ATAAATAGAA
*
23696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * *
23736 AT -T AT AT AA AA AT AT GT AT AT AT AT AC AT A- AGT AA AG AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
23777 AC AA AA AT A- AT AGT -T AT AA AT A- AT AT AT AT AT AT AGT A- AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * *
23817 GT TT AA AA 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 A
23848 ATAATATTAA
Statistics
Matches: 116, Mismatches: 23, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
1 8 0.07
2 104 0.90
3 4 0.03
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (2 bp):
AT
Found at i:23832 original size:26 final size:29
Alignment explanation
Indices: 23784--23837 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 29
23774 TTTACAAAAA
23784 TAATAGTTATAAATAATATATATATATAG
1 TAATAGTTATAAATAATATATATATATAG
23813 TAAT-GTT-TAAA-AATATATATATATA
1 TAATAGTTATAAATAATATATATATATA
23838 TATATATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 14 0.56
27 4 0.16
28 3 0.12
29 4 0.16
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.43
Consensus pattern (29 bp):
TAATAGTTATAAATAATATATATATATAG
Found at i:24068 original size:19 final size:19
Alignment explanation
Indices: 24041--24078 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
24031 GAATAAAAGC
*
24041 GAAATTAAATAAATATATA
1 GAAAATAAATAAATATATA
24060 GAAAATAAATAAATATATA
1 GAAAATAAATAAATATATA
24079 TATTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (19 bp):
GAAAATAAATAAATATATA
Found at i:24164 original size:378 final size:377
Alignment explanation
Indices: 23443--24137 Score: 973
Period size: 378 Copynumber: 1.8 Consensus size: 377
23433 ACATCATATT
*
23443 AATAATATATATATATACTAATATTAATATTAATAAACTCTCCTATCATTTCAACGAAATTGGAG
1 AATAATATATATATATACTAATAATAATATTAATAAACTCTCCTATCATTTCAACGAAATTGGAG
*
23508 GAGGAAACATTTAGTGAATGAAGGAAGACAAATGTGGGGCTAAGTAGGTTTGTATAGGTAATATA
66 GAGGAAAAATTTAGTGAAT--A-GAAGACAAATGTGGGGCTAAGTAGGTTTGTATAGGTAATATA
23573 ATAATAATAAAATAATATATATAATAATAATAAAGACAAAAGATTTAAAAAAATAAATATAATAT
128 ATAATAATAAAATAATATATATAATAATAATAAAGACAAAAGATTTAAAAAAAT-AATATAATAT
23638 AATATAATAATAATGAATAAAAACGAAATTAAATAAAAAATATAGAAAATAAATAGAAATATATA
192 AATATAATAATAATGAATAAAAACGAAATTAAATAAAAAATATAGAAAATAAATAGAAATATATA
* * * * ** * * * ** *
23703 TATATATATATATATATATATATATGTATATTAATTATATAAAAATATGTATATATATACATAAG
257 TATATATATATATACATATAAAAATGAATATTAACGAAAAAAAAAGAAATATAAATATACATAAG
*
23768 TAAAGATTTACAAAAATAATAGTTATAAATAATATATATATATAGTAATGTTTAAA
322 TAAAGATTTAAAAAAATAATAGTTATAAATAATATATATATATAGTAATGTTTAAA
23824 AATATATATATATATATA-TATATAATAATATTAA-ACAACTCTCCTATCATTTCAACGAAATTG
1 AATA-ATATATATATATACTA-ATAATAATATTAATA-AACTCTCCTATCATTTCAACGAAATTG
*
23887 G-GAGAGGAAAAATTTAGTGAAT-GAAGACAAATGTGGGGCTAGGTAGGTTTGTATAGGTAATAT
63 GAG-GAGGAAAAATTTAGTGAATAGAAGACAAATGTGGGGCTAAGTAGGTTTGTATAGGTAATAT
23950 AATAATAATAAAAAAATAATATATATAATAATAATAAAGACAAAAGATTT--AAAAATAATAATA
127 AATAATAAT---AAAATAATATATATAATAATAATAAAGACAAAAGATTTAAAAAAATAAT-ATA
* * *
24013 ATATACTATAATAATAATGAATAAAAGCGAAATTAAAT-AAATATATAGAAAATAAAT--AAATA
188 ATATAATATAATAATAATGAATAAAAACGAAATTAAATAAAAAATATAGAAAATAAATAGAAATA
*
24075 TATATATTATATTTATATACATGA-AAACAAT-AATGA-TAACGAAAAAAAAAGAAATAATAAAT
253 TATATA-TATATATATATACAT-ATAAA-AATGAAT-ATTAACGAAAAAAAAAGAAAT-ATAAAT
24137 A
313 A
24138 ACAATATATA
Statistics
Matches: 282, Mismatches: 19, Indels: 29
0.85 0.06 0.09
Matches are distributed among these distances:
376 11 0.04
377 29 0.10
378 80 0.28
379 45 0.16
381 46 0.16
382 71 0.25
ACGTcount: A:0.54, C:0.04, G:0.10, T:0.32
Consensus pattern (377 bp):
AATAATATATATATATACTAATAATAATATTAATAAACTCTCCTATCATTTCAACGAAATTGGAG
GAGGAAAAATTTAGTGAATAGAAGACAAATGTGGGGCTAAGTAGGTTTGTATAGGTAATATAATA
ATAATAAAATAATATATATAATAATAATAAAGACAAAAGATTTAAAAAAATAATATAATATAATA
TAATAATAATGAATAAAAACGAAATTAAATAAAAAATATAGAAAATAAATAGAAATATATATATA
TATATATATACATATAAAAATGAATATTAACGAAAAAAAAAGAAATATAAATATACATAAGTAAA
GATTTAAAAAAATAATAGTTATAAATAATATATATATATAGTAATGTTTAAA
Found at i:37478 original size:5 final size:5
Alignment explanation
Indices: 37470--37589 Score: 51
Period size: 5 Copynumber: 24.6 Consensus size: 5
37460 GATAAAAGGT
* *
37470 AAATA AAATA AACATGT AAATA AAGA-A ACATA GAAAATA AAATA AAAT-
1 AAATA AAATA AA-AT-A AAATA AA-ATA AAATA -AA-ATA AAATA AAATA
* * *
37518 AAATA AAGT- AAACA AAA-A AAATA AAA-A AAGAT- AAAT- AAATA ATAT-
1 AAATA AAATA AAATA AAATA AAATA AAATA AA-ATA AAATA AAATA AAATA
* * *
37563 GAATA AAATA TAAT- AAACA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
37590 AAATGAAGTA
Statistics
Matches: 86, Mismatches: 15, Indels: 28
0.67 0.12 0.22
Matches are distributed among these distances:
4 24 0.28
5 49 0.57
6 8 0.09
7 5 0.06
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:37488 original size:17 final size:17
Alignment explanation
Indices: 37468--37531 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
37458 AAGATAAAAG
37468 GTAAATAAAATAAACAT
1 GTAAATAAAATAAACAT
*
37485 GTAAAT-AAAGAAACAT
1 GTAAATAAAATAAACAT
*
37501 AGAAAATAAAATAAA-A-
1 -GTAAATAAAATAAACAT
*
37517 -TAAATAAAGTAAACA
1 GTAAATAAAATAAACA
37532 AAAAAAATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
14 11 0.28
15 1 0.03
16 9 0.23
17 12 0.31
18 6 0.15
ACGTcount: A:0.69, C:0.05, G:0.08, T:0.19
Consensus pattern (17 bp):
GTAAATAAAATAAACAT
Found at i:37523 original size:4 final size:4
Alignment explanation
Indices: 37504--37682 Score: 83
Period size: 4 Copynumber: 40.8 Consensus size: 4
37494 GAAACATAGA
* * *
37504 AAAT AAAAT AAAAT AAAT AAAGT AAACA AAAA AAAT AAA- AAA- AGAT
1 AAAT -AAAT -AAAT AAAT AAA-T AAA-T AAAT AAAT AAAT AAAT AAAT
* * * *
37550 AAAT AAAT AATAT GAAT AAAAT ATAAT AAACA AAAT AAAA AAAT GAAGT
1 AAAT AAAT AA-AT AAAT -AAAT A-AAT AAA-T AAAT AAAT AAAT -AAAT
* * *
37599 AAATT AAAT ATAAG ATAAT AATAGT AAGAAT AACAT ATAC ACAAT AAAT
1 AAA-T AAAT A-AAT A-AAT AA-A-T -A-AAT AA-AT AAAT A-AAT AAAT
*
37648 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AGAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
37683 AAAACATCAT
Statistics
Matches: 138, Mismatches: 21, Indels: 31
0.73 0.11 0.16
Matches are distributed among these distances:
3 5 0.04
4 78 0.57
5 50 0.36
6 2 0.01
7 2 0.01
8 1 0.01
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:37523 original size:9 final size:9
Alignment explanation
Indices: 37503--37683 Score: 90
Period size: 9 Copynumber: 19.4 Consensus size: 9
37493 AGAAACATAG
37503 AAAATAAAAT
1 AAAAT-AAAT
37513 AAAATAAAT
1 AAAATAAAT
* *
37522 AAAGTAAAC
1 AAAATAAAT
*
37531 AAAAAAAAT
1 AAAATAAAT
*
37540 AAAA-AAAG
1 AAAATAAAT
37548 ATAAATAAAT
1 A-AAATAAAT
* *
37558 AATATGAAT
1 AAAATAAAT
37567 AAAATATAAT
1 AAAATA-AAT
37577 AAACA-AAAT
1 AAA-ATAAAT
37586 AAAA-AAAT
1 AAAATAAAT
* *
37594 GAAGTAAATT
1 AAAATAAA-T
37604 AAATATAAGAT
1 AAA-ATAA-AT
*
37615 AATAAT-AGT
1 AA-AATAAAT
37624 AAGAATAACATAT
1 AA-AAT-A-A-AT
37637 ACACAATAAAT
1 A-A-AATAAAT
37648 -AAATAAAT
1 AAAATAAAT
37656 -AAATAAAT
1 AAAATAAAT
37664 -AAATAAAT
1 AAAATAAAT
*
37672 -AAATAGAT
1 AAAATAAAT
37680 AAAA
1 AAAA
37684 AAACATCATA
Statistics
Matches: 136, Mismatches: 20, Indels: 31
0.73 0.11 0.17
Matches are distributed among these distances:
8 41 0.30
9 53 0.39
10 20 0.15
11 11 0.08
12 4 0.03
13 3 0.02
14 4 0.03
ACGTcount: A:0.71, C:0.03, G:0.05, T:0.22
Consensus pattern (9 bp):
AAAATAAAT
Found at i:37539 original size:32 final size:32
Alignment explanation
Indices: 37470--37588 Score: 109
Period size: 32 Copynumber: 3.7 Consensus size: 32
37460 GATAAAAGGT
* *
37470 AAATAAAATAAACATGTAAATAAAGAAACATAGA
1 AAATAAAATAAACA--TAAATAAAGAAACAAAAA
37504 AAATAAAATAAA-ATAAATAAAGTAAACAAAAA
1 AAATAAAATAAACATAAATAAAG-AAACAAAAA
* * ** *
37536 AAATAAAA-AAAGATAAATAAATAATATGAATA
1 AAATAAAATAAACATAAATAAAGAA-ACAAAAA
*
37568 AAATATAATAAACA-AAATAAA
1 AAATAAAATAAACATAAATAAA
37589 AAAATGAAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
31 14 0.19
32 42 0.58
33 5 0.07
34 12 0.16
ACGTcount: A:0.73, C:0.03, G:0.05, T:0.18
Consensus pattern (32 bp):
AAATAAAATAAACATAAATAAAGAAACAAAAA
Found at i:37607 original size:50 final size:46
Alignment explanation
Indices: 37469--37608 Score: 113
Period size: 45 Copynumber: 2.9 Consensus size: 46
37459 AGATAAAAGG
* * * * *
37469 TAAATAAAATAAACATGTAAATAAAGAAACATAGA-AAATAAAATAAAA
1 TAAATAAAATAAACA---AAAAAAATAAAAAAAGATAAATTAAATAAAA
* *
37517 TAAATAAAGTAAACAAAAAAAATAAAAAAAGATAAA-TAAATAATA
1 TAAATAAAATAAACAAAAAAAATAAAAAAAGATAAATTAAATAAAA
* * *
37562 TGAATAAAATATAATAAACAAAATAAAAAAATGAAGTAAATTAAATA
1 TAAATAAAATA-AACAAAAAAAATAAAAAAA-G-A-TAAATTAAATA
37609 TAAGATAATA
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
45 29 0.39
46 20 0.27
47 1 0.01
48 15 0.20
49 4 0.05
50 6 0.08
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (46 bp):
TAAATAAAATAAACAAAAAAAATAAAAAAAGATAAATTAAATAAAA
Found at i:37825 original size:3 final size:3
Alignment explanation
Indices: 37813--37852 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
37803 TTTGTATAGG
37813 TAA T-A TAA TAA TAA TAA -AA TAA T-A TATA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA
37853 AGACAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
2 6 0.18
3 24 0.73
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:37843 original size:23 final size:22
Alignment explanation
Indices: 37813--37901 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 22
37803 TTTGTATAGG
37813 TAATATAATAATAATAAAATAA
1 TAATATAATAATAATAAAATAA
*
37835 TATATATAATAATAATAAAGACAA
1 TA-ATATAATAATAATAAA-ATAA
* * *
37859 AAGATTTAA-AAAAATAAAAATAA
1 TA-ATATAATAATAAT-AAAATAA
37882 TAATATAATAATGAATAAAA
1 TAATATAATAAT-AATAAAA
37902 ACGAAATTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
22 7 0.13
23 31 0.58
24 15 0.28
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (22 bp):
TAATATAATAATAATAAAATAA
Found at i:37929 original size:50 final size:47
Alignment explanation
Indices: 37828--37931 Score: 120
Period size: 47 Copynumber: 2.1 Consensus size: 47
37818 TAATAATAAT
* **
37828 AAAATAATATATATAATAATAATAAAGACAAAAGATTTAAAAAAATA
1 AAAATAATATATATAATAATAATAAAAACAAAAGAAATAAAAAAATA
**
37875 AAAATAATA-ATATAATAATGAATAAAAACGAAATTAAATAAAAAATATA
1 AAAATAATATATATAATAAT-AATAAAAAC-AAAAGAAATAAAAAA-ATA
37924 GAAAATAA
1 -AAAATAA
37932 ATAGAAATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
46 10 0.21
47 17 0.35
48 11 0.23
49 3 0.06
50 7 0.15
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (47 bp):
AAAATAATATATATAATAATAATAAAAACAAAAGAAATAAAAAAATA
Found at i:37932 original size:20 final size:21
Alignment explanation
Indices: 37904--37944 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
37894 GAATAAAAAC
*
37904 GAAATTAAATA-AAAAATATA
1 GAAAATAAATAGAAAAATATA
*
37924 GAAAATAAATAGAAATATATA
1 GAAAATAAATAGAAAAATATA
37945 TATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.24
Consensus pattern (21 bp):
GAAAATAAATAGAAAAATATA
Found at i:38032 original size:2 final size:2
Alignment explanation
Indices: 38025--38129 Score: 160
Period size: 2 Copynumber: 53.0 Consensus size: 2
38015 GTTATAAATA
* * *
38025 AT AT AT AT AT AGT A- AT GT TT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38067 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
38109 AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
38130 TAAACAACTC
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
1 2 0.02
2 91 0.96
3 2 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38231 original size:3 final size:3
Alignment explanation
Indices: 38219--38306 Score: 51
Period size: 3 Copynumber: 29.0 Consensus size: 3
38209 TTTGTATAGG
38219 TAA T-A TAA TAA TAA TAA -AA TAA T-A TATA TAA TAA TAA TAA -AGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TA-A
* * * *
38262 CAA -AA GATT TAA AAA TAA TAA TATA TATA TAA TAA TAA TGAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TA-A TA-A TAA TAA TAA T-AA TAA
38307 AAACGAAATT
Statistics
Matches: 70, Mismatches: 5, Indels: 20
0.74 0.05 0.21
Matches are distributed among these distances:
2 9 0.13
3 46 0.66
4 15 0.21
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:38470 original size:406 final size:405
Alignment explanation
Indices: 37700--38473 Score: 1088
Period size: 406 Copynumber: 1.9 Consensus size: 405
37690 CATATTAATA
37700 ATATATATATACTAATATTAATATTAATAAACTCTACTATCATTTCAACGAAATTGGAGGAGGAA
1 ATATATATATACTAATATTAATATTAATAAACTCTACTATCATTTCAACGAAATTGGAGGAGGAA
*
37765 ACATTTAGTGAATGAAGACAAATGTGGGGCTAGGTAGGTTTGTATAGGTAATATAATAATAATAA
66 AAATTTAGTGAATGAAGACAAATGTGGGGCTAGGTAGGTTTGTATAGGTAATATAATAATAATAA
37830 AATAATATATATAATAATAATAAAGACAAAAGATTTAAAAAAATAAAAATAATAATATAATAATG
131 AATAATATATATAATAATAATAAAGACAAAAGATTTAAAAAAATAAAAATAATAATATAATAATG
* * *
37895 AATAAAAACGAAATTAAATAAAAAATATAGAAAATAAATAGAAATATATATATATATATATGTAT
196 AATAAAAACGAAATTAAATAAAAAATATAGAAAATAAATAAAAATAAATAAATATATATATGTAT
* * ** ** * *
37960 ATTAATTATATAAAAATATGTATATATACATAAGTAAAGATTTACAAAAATAATAGTTATAAATA
261 ATTAATTACATAAAAATATGAATATATACATAAAAAAAGAAATACAAAAATAACAATTATAAATA
* * * *** *
38025 ATATATATATAGTAATGTTTAAATATATATATATATATATATATATATATATATATATATATATA
326 ATATAAATAAAATAAAAATTAAATAAATATATATATATATATATATATATATATATATATATATA
38090 TATATATATATATAT
391 TATATATATATATAT
* *
38105 ATATATATATA-TATATATATAATATTAA-ACAACTCTCCTATCATTTCAACGAAATTGGGGGAG
1 ATATATATATACTA-ATAT-TAATATTAATA-AACTCTACTATCATTTCAACGAAATTGGAGGAG
38168 GAAAAATTTAGTGAATGAAGACAAATGTGGGGCTAGGTAGGTTTGTATAGGTAATATAATAATAA
63 GAAAAATTTAGTGAATGAAGACAAATGTGGGGCTAGGTAGGTTTGTATAGGTAATATAATAATAA
*
38233 TAAAATAATATATATAATAATAATAAAGACAAAAGATTT--AAAAATAATAATATATATATAATA
128 TAAAATAATATATATAATAATAATAAAGACAAAAGATTTAAAAAAATAAAAATA-ATA-AT-ATA
*
38296 ATAATGAATAAAAACGAAATTAAAT-AAATATATAGAAAATAAATAAAAATAAATAAATATATAT
190 ATAATGAATAAAAACGAAATTAAATAAAAAATATAGAAAATAAATAAAAATAAATAAATATATAT
* *
38360 AT-TATATTTATATACATGAAAACA-AT-AATGATA-ACA-AAAAAAAGAAATA-ATAAATAACA
255 ATGTATATTAAT-TACAT-AAAA-ATATGAAT-ATATACATAAAAAAAGAAATACAAAAATAACA
* *
38419 A-TATATAT-ATATTAAATAAAATAAAAATTAATTGCGAAATATATATATATATATA
316 ATTATAAATAATA-TAAATAAAATAAAAATTAAAT---AAATATATATATATATATA
38474 AGGGGCTAAA
Statistics
Matches: 328, Mismatches: 27, Indels: 27
0.86 0.07 0.07
Matches are distributed among these distances:
402 3 0.01
403 20 0.06
404 22 0.07
405 36 0.11
406 209 0.64
407 37 0.11
408 1 0.00
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (405 bp):
ATATATATATACTAATATTAATATTAATAAACTCTACTATCATTTCAACGAAATTGGAGGAGGAA
AAATTTAGTGAATGAAGACAAATGTGGGGCTAGGTAGGTTTGTATAGGTAATATAATAATAATAA
AATAATATATATAATAATAATAAAGACAAAAGATTTAAAAAAATAAAAATAATAATATAATAATG
AATAAAAACGAAATTAAATAAAAAATATAGAAAATAAATAAAAATAAATAAATATATATATGTAT
ATTAATTACATAAAAATATGAATATATACATAAAAAAAGAAATACAAAAATAACAATTATAAATA
ATATAAATAAAATAAAAATTAAATAAATATATATATATATATATATATATATATATATATATATA
TATATATATATATAT
Found at i:56483 original size:3 final size:3
Alignment explanation
Indices: 56475--56571 Score: 106
Period size: 3 Copynumber: 31.7 Consensus size: 3
56465 TTCATTTAAA
* *
56475 TAT TAT TAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT TAT AAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
56523 AAT TACT AAT T-T TAT TATT TAT TAC TAA TAT TAT TAT TAAT TAT TAT
1 TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT T-AT TAT TAT
56570 TA
1 TA
56572 CAAACGGGCA
Statistics
Matches: 79, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
2 2 0.03
3 69 0.87
4 8 0.10
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:57821 original size:21 final size:21
Alignment explanation
Indices: 57795--57834 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
57785 ATAGTTATAA
57795 ATATATA-TAAT-AATTATTT
1 ATATATATTAATAAATTATTT
57814 ATATATATTAATAAATTATTT
1 ATATATATTAATAAATTATTT
57835 TGATATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATATATTAATAAATTATTT
Found at i:57832 original size:17 final size:17
Alignment explanation
Indices: 57779--57832 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
57769 AAATACTTTT
57779 ATTAT-TATAGTT-ATAA
1 ATTATATATA-TTAATAA
* *
57795 A-TATATATAATAATTA
1 ATTATATATATTAATAA
*
57811 TTTATATATATTAATAA
1 ATTATATATATTAATAA
57828 ATTAT
1 ATTAT
57833 TTTGATATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 4 0.14
16 8 0.28
17 17 0.59
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
ATTATATATATTAATAA
Found at i:60075 original size:8 final size:7
Alignment explanation
Indices: 60051--60092 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
60041 TTTTCATACA
60051 TGCA-TT
1 TGCATTT
60057 TGCATTT
1 TGCATTT
60064 TGCATCTT
1 TGCAT-TT
60072 TGCATTT
1 TGCATTT
* *
60079 TTCATTG
1 TGCATTT
60086 TGCATTT
1 TGCATTT
60093 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:60075 original size:15 final size:14
Alignment explanation
Indices: 60051--60092 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
60041 TTTTCATACA
60051 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
60064 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
60079 TTCATTGTGCATTT
1 TGCATTTTGCATTT
60093 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:60180 original size:26 final size:26
Alignment explanation
Indices: 60151--60209 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
60141 CATTCACATA
*
60151 TTTACATTTGAATTTGCATTTGCATT
1 TTTACATTTGAATTTACATTTGCATT
* * *
60177 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
60203 TTTACAT
1 TTTACAT
60210 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:64449 original size:83 final size:83
Alignment explanation
Indices: 64310--64785 Score: 749
Period size: 83 Copynumber: 5.7 Consensus size: 83
64300 CATTAACTGA
* * *
64310 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
64375 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTGG
* * * *
64393 AAGATGAATTTGTTAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGACCTGGTTTAGCAGA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
64458 ACCAATCATTGAATTGGG
66 ACCAATCATTGAATTTGG
* *
64476 AAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
64540 AACCAATCATTGAATTTAG
65 AACCAATCATTGAATTTGG
*
64559 AAGATGAATTTGTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAG
*
64623 AATCAATCATTGAATTTGG
65 AACCAATCATTGAATTTGG
*
64642 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAA
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
*
64707 ACCAATCATTGAATTTAG
66 ACCAATCATTGAATTTGG
* * *
64725 AAGATGAATTTGCTCATAGCATCTTCTGGAAGTATTCTTTGAGTTATTTGATCTGGTTTGG
1 AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
64786 TAGGAACTAC
Statistics
Matches: 370, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
82 3 0.01
83 363 0.98
84 4 0.01
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.37
Consensus pattern (83 bp):
AAGATGAATTTGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGA
ACCAATCATTGAATTTGG
Found at i:65991 original size:74 final size:74
Alignment explanation
Indices: 65839--66000 Score: 202
Period size: 74 Copynumber: 2.2 Consensus size: 74
65829 AAGCAAATAT
* * *
65839 TGGGGCATGCTGAAAACCCTTTTCAAACAGAATCAGAAATGTTGAAATATTCTGAATATTTATCA
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
65904 GCAAAATGC
66 GCAAAATGC
* * ** *
65913 TGGGGCATGCTGAAAACCCATTTCAATCAGAATCAGAACTGTTGATGCATTTTGAACACTTGTAT
1 TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACA-TT-TAT
* *
65978 TAGC-CAATG-
64 CAGCAAAATGC
65987 TGGGGCATGCTGAA
1 TGGGGCATGCTGAA
66001 GGCCTATATC
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
74 64 0.84
75 6 0.08
76 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (74 bp):
TGGGGCATGCTGAAAACCCATTTCAAACAGAATCAGAAATGTTGAAACATTCTGAACATTTATCA
GCAAAATGC
Found at i:67308 original size:22 final size:22
Alignment explanation
Indices: 67282--67336 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
67272 ATCTACACTC
*
67282 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
67304 TTCAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
67326 TTCAAAGATGA
1 TTCAAAGATGA
67337 AAACTTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Done.