Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006148.1 Hibiscus syriacus cultivar Beakdansim tig00014601_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: 98816
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:4234 original size:20 final size:18
Alignment explanation
Indices: 4197--4240 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
4187 CCCATTTCTT
4197 AATATTAAAAAATAAATA
1 AATATTAAAAAATAAATA
*
4215 AATATTAATAAAATGTAATA
1 AATATTAA-AAAAT-AAATA
4235 AATATT
1 AATATT
4241 CCTAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AATATTAAAAAATAAATA
Found at i:4266 original size:15 final size:15
Alignment explanation
Indices: 4246--4286 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
4236 ATATTCCTAA
4246 AAAAATAATTTAAAT
1 AAAAATAATTTAAAT
*
4261 AAAAATAAATTAAAT
1 AAAAATAATTTAAAT
* *
4276 ATATATAATTT
1 AAAAATAATTT
4287 TTATAATATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAAAATAATTTAAAT
Found at i:4390 original size:2 final size:2
Alignment explanation
Indices: 4383--4412 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
4373 ATTTAAACAA
*
4383 AT AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4413 TAATATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:4478 original size:23 final size:23
Alignment explanation
Indices: 4418--4479 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 23
4408 TATATTAATA
*
4418 TAATAATAATAAACAATAACTAAAG
1 TAATAATAA-AAAC-ATAACGAAAG
* ** *
4443 TAACAATTTAAACATATCGAAAG
1 TAATAATAAAAACATAACGAAAG
4466 TAATAATAAAAACA
1 TAATAATAAAAACA
4480 AAATAAAATT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
23 19 0.66
24 4 0.14
25 6 0.21
ACGTcount: A:0.61, C:0.10, G:0.05, T:0.24
Consensus pattern (23 bp):
TAATAATAAAAACATAACGAAAG
Found at i:5824 original size:12 final size:14
Alignment explanation
Indices: 5809--5864 Score: 70
Period size: 12 Copynumber: 4.4 Consensus size: 14
5799 TTCTGGCCTG
5809 TAATAATATAT-T-
1 TAATAATATATATA
5821 TAATAATATATATA
1 TAATAATATATATA
5835 TAATAATA-ATA-A
1 TAATAATATATATA
5847 TAATAATA-ATA-A
1 TAATAATATATATA
5859 TAATAA
1 TAATAA
5865 ACGTAAAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
12 30 0.71
13 4 0.10
14 8 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAATAATATATATA
Found at i:5827 original size:3 final size:3
Alignment explanation
Indices: 5821--5864 Score: 70
Period size: 3 Copynumber: 14.0 Consensus size: 3
5811 ATAATATATT
5821 TAA TAA TATA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5865 ACGTAAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 33 0.82
4 7 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:6194 original size:89 final size:89
Alignment explanation
Indices: 6038--6238 Score: 303
Period size: 89 Copynumber: 2.3 Consensus size: 89
6028 AAGGTCTTAT
* *
6038 CATCTTGCACTGTAGGTCTTACAGATGACCCAGAGGATTTAAGATCAAGAAACCTTTGAAAATCA
1 CATCATGCACTGTAGGTCTTATAGATGACCCAGAGGATTTAAGATCAAGAAACCTTTGAAAATCA
*
6103 GTTTCTTAAAATCTCATTTGAAAA
66 GTTTCTCAAAATCTCATTTGAAAA
* * * * * *
6127 CATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTTTTAAGATCATGAAACCTTTGAAAATCA
1 CATCATGCACTGTAGGTCTTATAGATGACCCAGAGGATTTAAGATCAAGAAACCTTTGAAAATCA
*
6192 GTTTCTCAAAATCTTATTTGAAAA
66 GTTTCTCAAAATCTCATTTGAAAA
*
6216 CATCATGCACTGTAGGCCTTATA
1 CATCATGCACTGTAGGTCTTATA
6239 CTATAGGTCT
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
89 100 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (89 bp):
CATCATGCACTGTAGGTCTTATAGATGACCCAGAGGATTTAAGATCAAGAAACCTTTGAAAATCA
GTTTCTCAAAATCTCATTTGAAAA
Found at i:6415 original size:75 final size:76
Alignment explanation
Indices: 6279--6472 Score: 273
Period size: 75 Copynumber: 2.6 Consensus size: 76
6269 TATCATCTTG
* ** * * *
6279 CACTCTAGGTCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCTCTCGAATGCTTTTTG
1 CACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTG
* *
6344 AAAATATCCTA
66 AAAACATCATA
* *
6355 CACTGTAGGTCTTATGGATGA-CCGAAGGTTTTGAAAATATTAAAAAGCTCCCGAAGGCTTTTTG
1 CACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTG
*
6419 AAAACATCATG
66 AAAACATCATA
*
6430 CACTGTAGGTCTTATGGATAACCCGAAGGTTTTGAAAACATCA
1 CACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCA
6473 TGAACTGAAG
Statistics
Matches: 103, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
75 66 0.64
76 37 0.36
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (76 bp):
CACTGTAGGTCTTATGGATGACCCGAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGGCTTTTTG
AAAACATCATA
Found at i:6470 original size:45 final size:45
Alignment explanation
Indices: 6404--6517 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
6394 TTAAAAAGCT
* * **
6404 CCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATAA
1 CCCGAAGG--TTTTGAAAACATCATGAACTGAAGGTCTTACAGATAA
*
6451 CCCGAAGGTTTTGAAAACATCATGAACTGAAGGTCTTACAGATGA
1 CCCGAAGGTTTTGAAAACATCATGAACTGAAGGTCTTACAGATAA
* *
6496 CCCGAAGGCTTTGAAAATATCA
1 CCCGAAGGTTTTGAAAACATCA
6518 GAAAGCTCCC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 52 0.87
47 8 0.13
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (45 bp):
CCCGAAGGTTTTGAAAACATCATGAACTGAAGGTCTTACAGATAA
Found at i:6546 original size:75 final size:74
Alignment explanation
Indices: 6451--6592 Score: 205
Period size: 75 Copynumber: 1.9 Consensus size: 74
6441 TTATGGATAA
*
6451 CCCGAAGGTTTTGAAAACATCATGAACTG-AAGGTCTTACAGATGACCCGAAGGCTTTGAAAATA
1 CCCGAAGGTTTTGAAAACATCATGAACTGTAA-GTCTTACAGATGACCCGAAGGCTTTGAAAACA
6515 TCAGAAAGCT
65 TCAGAAAGCT
* * ** *
6525 CCCGAAGGCTTTTGAAAACATCGTGCACTGTAAGTCTTATGGATGACCCGAAGGTTTTGAAAACA
1 CCCGAAGG-TTTTGAAAACATCATGAACTGTAAGTCTTACAGATGACCCGAAGGCTTTGAAAACA
6590 TCA
65 TCA
6593 TGCACTGAAG
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
74 8 0.13
75 50 0.83
76 2 0.03
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.25
Consensus pattern (74 bp):
CCCGAAGGTTTTGAAAACATCATGAACTGTAAGTCTTACAGATGACCCGAAGGCTTTGAAAACAT
CAGAAAGCT
Found at i:6552 original size:120 final size:121
Alignment explanation
Indices: 6339--6684 Score: 545
Period size: 120 Copynumber: 2.9 Consensus size: 121
6329 CTCGAATGCT
* * * ** * *
6339 TTTTGAAAATATCCT-ACACTGTAGGTCTTATGGATGA-CCGAAGGTTTTGAAAATATTAAAAAG
1 TTTTGAAAACATCATGA-ACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAG
6402 CTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATAACCCGAAGG
65 CTCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATAACCCGAAGG
*
6459 TTTTGAAAACATCATGAACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAGAAAGC
1 TTTTGAAAACATCATGAACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGC
* * *
6524 TCCCGAAGGC-TTTTGAAAACATCGTGCACTGTAAGTCTTATGGATGACCCGAAGG
66 TCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATAACCCGAAGG
*
6579 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGC
1 TTTTGAAAACATCATGAACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGC
*
6644 TCCTGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTA
66 TCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTA
6685 CAGATGACTC
Statistics
Matches: 207, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
120 144 0.70
121 63 0.30
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (121 bp):
TTTTGAAAACATCATGAACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGC
TCCCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTATGGATAACCCGAAGG
Found at i:6578 original size:46 final size:46
Alignment explanation
Indices: 6525--6637 Score: 160
Period size: 45 Copynumber: 2.5 Consensus size: 46
6515 TCAGAAAGCT
* **
6525 CCCGAAGGCTTTTGAAAACATCGTGCACTGTAA-GTCTTATGGATGA
1 CCCGAAGGCTTTTGAAAACATCATGCACTG-AAGGTCTTACAGATGA
6571 CCCGAAGG-TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGA
1 CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGA
*
6616 CCCGAAGGC-TTTGAAAATATCA
1 CCCGAAGGCTTTTGAAAACATCA
6638 AAAAGCTCCT
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
44 2 0.03
45 51 0.84
46 8 0.13
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (46 bp):
CCCGAAGGCTTTTGAAAACATCATGCACTGAAGGTCTTACAGATGA
Found at i:6671 original size:76 final size:76
Alignment explanation
Indices: 6579--6758 Score: 315
Period size: 76 Copynumber: 2.4 Consensus size: 76
6569 GACCCGAAGG
* *
6579 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCGAAGGCTTTGAAAATATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGCTTTGAAAATATCAAAAAGC
6644 TCCTGAAGGCT
66 TCCTGAAGGCT
*
6655 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACTCAAAGGCTTTGAAAATATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGCTTTGAAAATATCAAAAAGC
6720 TCCTGAAGGCT
66 TCCTGAAGGCT
* *
6731 TTTAGAAAATATCATGCACTGTAGGTCT
1 TTTTGAAAACATCATGCACTGTAGGTCT
6759 CTCATGATGT
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 99 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.28
Consensus pattern (76 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCAAAGGCTTTGAAAATATCAAAAAGC
TCCTGAAGGCT
Found at i:7251 original size:22 final size:22
Alignment explanation
Indices: 7226--7324 Score: 146
Period size: 22 Copynumber: 4.5 Consensus size: 22
7216 AATAAAGCTT
7226 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
7248 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
7270 TCATCTTT-AAAGAGATAATCTA
1 TCATCTTTGAAA-AGAGAATCTA
* *
7292 TCTTCTTTGAATAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
7314 TCATCTTTGAA
1 TCATCTTTGAA
7325 GAATATAGAT
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
21 2 0.03
22 64 0.94
23 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.36
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:10478 original size:72 final size:72
Alignment explanation
Indices: 10365--10500 Score: 202
Period size: 72 Copynumber: 1.9 Consensus size: 72
10355 GTATAACATA
*
10365 CTAGCTGAATATTATCCATAAAACCAGGGCTACTAACCAATTGCTCTAGAGGGACAACTCAAGCA
1 CTAGCTGAATATTATCCATAAAACCAGGGCGACTAACCAATTGCTCTAGAGGGACAACTCAAGCA
10430 TAACAGG
66 TAACAGG
* * * * *
10437 CTAGCTGAATATTATCCATAAAGCCAGGGCGA-TCAATCAATTGCTTTAGGGGGATAACTCAAGC
1 CTAGCTGAATATTATCCATAAAACCAGGGCGACT-AACCAATTGCTCTAGAGGGACAACTCAAGC
10501 TTTATTGTAT
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 1 0.02
72 56 0.98
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (72 bp):
CTAGCTGAATATTATCCATAAAACCAGGGCGACTAACCAATTGCTCTAGAGGGACAACTCAAGCA
TAACAGG
Found at i:11620 original size:19 final size:19
Alignment explanation
Indices: 11588--11628 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
11578 TGTTGATCAC
*
11588 ATTTTCAATTAATTCTC-A
1 ATTTTCAATAAATTCTCGA
11606 ATTTATCAATAAATTCTCGA
1 ATTT-TCAATAAATTCTCGA
11626 ATT
1 ATT
11629 CCTTCGTCGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (19 bp):
ATTTTCAATAAATTCTCGA
Found at i:12616 original size:36 final size:34
Alignment explanation
Indices: 12576--12643 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 34
12566 AAATGCGAAA
12576 AATGCATAA-ATGCAAAAATAAGAATGCAAAATGTGC
1 AATGCA-AAGATGCAAAAATAA-AATG-AAAATGTGC
*
12612 AATGCAAAGATGCAAATATAAAATGAAAATGT
1 AATGCAAAGATGCAAAAATAAAATGAAAATGT
12644 AAATGAAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 7 0.23
35 6 0.20
36 17 0.57
ACGTcount: A:0.54, C:0.09, G:0.16, T:0.21
Consensus pattern (34 bp):
AATGCAAAGATGCAAAAATAAAATGAAAATGTGC
Found at i:12649 original size:12 final size:12
Alignment explanation
Indices: 12625--12658 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
12615 GCAAAGATGC
12625 AAATATAAAATGA
1 AAATAT-AAATGA
*
12638 AAATGTAAATGA
1 AAATATAAATGA
12650 AAATATAAA
1 AAATATAAA
12659 AATGCAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (12 bp):
AAATATAAATGA
Found at i:12662 original size:20 final size:22
Alignment explanation
Indices: 12637--12690 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
12627 ATATAAAATG
* *
12637 AAAATGTAAATG-AAA-ATATA
1 AAAATGCAAATGCAAACATAAA
12657 AAAATGCAAATGCAAACATAAA
1 AAAATGCAAATGCAAACATAAA
12679 AAAATGCAAATG
1 AAAATGCAAATG
12691 TAATGAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 11 0.37
21 3 0.10
22 16 0.53
ACGTcount: A:0.63, C:0.07, G:0.11, T:0.19
Consensus pattern (22 bp):
AAAATGCAAATGCAAACATAAA
Found at i:12663 original size:47 final size:46
Alignment explanation
Indices: 12612--12721 Score: 125
Period size: 47 Copynumber: 2.3 Consensus size: 46
12602 CAAAATGTGC
* *
12612 AATGCAAAGATGCAAAT-ATAAAATGAAAATGTAAATGAAAATATAAA
1 AATGCAAA-ATGCAAATAAAAAAATGAAAATGT-AATGAAAAAATAAA
* **
12659 AATGC-AAATGCAAACATAAAAAAATGCAAATGTAATGAAAAAATATG
1 AATGCAAAATGC-AA-ATAAAAAAATGAAAATGTAATGAAAAAATAAA
12706 AATGCAAAATGCAAAT
1 AATGCAAAATGCAAAT
12722 GCAACAAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
45 4 0.07
46 6 0.11
47 25 0.46
48 19 0.35
ACGTcount: A:0.60, C:0.07, G:0.13, T:0.20
Consensus pattern (46 bp):
AATGCAAAATGCAAATAAAAAAATGAAAATGTAATGAAAAAATAAA
Found at i:15924 original size:2 final size:2
Alignment explanation
Indices: 15917--15956 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
15907 ATTTAAACAA
15917 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
15957 GACTAATATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16028 original size:23 final size:22
Alignment explanation
Indices: 15962--16029 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
15952 TATATGACTA
*
15962 ATATGAAAATAATAATAAAAA-
1 ATATGAAAGTAATAATAAAAAC
* * **
15983 ATAATTAAAGTAACAATTTAAAC
1 AT-ATGAAAGTAATAATAAAAAC
16006 ATATCGAAAGTAATAATAAAAAC
1 ATAT-GAAAGTAATAATAAAAAC
16029 A
1 A
16030 AAATAAAATT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 2 0.06
22 16 0.46
23 17 0.49
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.25
Consensus pattern (22 bp):
ATATGAAAGTAATAATAAAAAC
Found at i:17382 original size:12 final size:13
Alignment explanation
Indices: 17367--17430 Score: 75
Period size: 12 Copynumber: 5.2 Consensus size: 13
17357 TTCTGGCCTG
*
17367 TAATAATATAT-T
1 TAATAATATATAA
17379 TAATAATATATAA
1 TAATAATATATAA
17392 TAATAATA-ATAA
1 TAATAATATATAA
17404 TAATAATA-ATAA
1 TAATAATATATAA
17416 TAA-AAGTA-ATAA
1 TAATAA-TATATAA
17428 TAA
1 TAA
17431 AAGTAAAATG
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
11 2 0.04
12 39 0.80
13 8 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:17385 original size:3 final size:3
Alignment explanation
Indices: 17379--17430 Score: 79
Period size: 3 Copynumber: 17.0 Consensus size: 3
17369 ATAATATATT
17379 TAA TAA TATA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA GTAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA
17425 TAA TAA
1 TAA TAA
17431 AAGTAAAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.04
3 39 0.85
4 5 0.11
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17444 original size:12 final size:12
Alignment explanation
Indices: 17388--17436 Score: 66
Period size: 12 Copynumber: 4.1 Consensus size: 12
17378 TTAATAATAT
17388 ATAATAATAA-TA
1 ATAATAA-AAGTA
17400 ATAATAATAA-TA
1 ATAATAA-AAGTA
17412 ATAATAAAAGTA
1 ATAATAAAAGTA
17424 ATAATAAAAGTA
1 ATAATAAAAGTA
17436 A
1 A
17437 AATGAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
11 2 0.06
12 34 0.94
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
ATAATAAAAGTA
Found at i:19789 original size:14 final size:13
Alignment explanation
Indices: 19759--19806 Score: 53
Period size: 14 Copynumber: 3.7 Consensus size: 13
19749 TCAATGTAAA
19759 TAATAATATTTAG
1 TAATAATATTTAG
*
19772 TAATAATATTTTAT
1 TAATAATA-TTTAG
* *
19786 TAATAATA-ATAA
1 TAATAATATTTAG
19798 TAATAATAT
1 TAATAATAT
19807 AATAATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 10 0.33
13 8 0.27
14 12 0.40
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (13 bp):
TAATAATATTTAG
Found at i:40997 original size:17 final size:18
Alignment explanation
Indices: 40967--41000 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40957 CTTAAATTAT
*
40967 AAAAAATCTCAAATCCCA
1 AAAAAATATCAAATCCCA
40985 AAAAAATAT-AAATCCC
1 AAAAAATATCAAATCCC
41001 TTACTTGTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.24, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAAAATATCAAATCCCA
Found at i:42796 original size:17 final size:19
Alignment explanation
Indices: 42762--42798 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
42752 ATAATATTCC
*
42762 AATTATAAAAATTTATTAT
1 AATTATAAAAATTAATTAT
42781 AATTA-AAAAA-TAATTAT
1 AATTATAAAAATTAATTAT
42798 A
1 A
42799 TAATTCTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 5 0.29
19 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTATAAAAATTAATTAT
Found at i:43130 original size:29 final size:32
Alignment explanation
Indices: 43088--43157 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
43078 TCCATTATCT
*
43088 TTTTTTTAATA-TTTTTTCAC-A-TAACATTA
1 TTTTTTTAATATTTTTTTCACAATTAACATGA
* *
43117 TTTTTTTATTATTTTTTTTACAATTAACATGA
1 TTTTTTTAATATTTTTTTCACAATTAACATGA
43149 TTTTTTTAA
1 TTTTTTTAA
43158 CAACACAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 10 0.29
30 8 0.24
31 1 0.03
32 15 0.44
ACGTcount: A:0.29, C:0.07, G:0.01, T:0.63
Consensus pattern (32 bp):
TTTTTTTAATATTTTTTTCACAATTAACATGA
Found at i:43135 original size:32 final size:32
Alignment explanation
Indices: 43080--43156 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
43070 AAAAATTTTC
*
43080 CATTATCTTTTTT-TTAATATTTTTTCACA-TAA
1 CATTAT-TTTTTTATTAATATTTTTACA-ATTAA
* *
43112 CATTATTTTTTTATTATTTTTTTTACAATTAA
1 CATTATTTTTTTATTAATATTTTTACAATTAA
*
43144 CATGATTTTTTTA
1 CATTATTTTTTTA
43157 ACAACACAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 7 0.18
32 32 0.82
ACGTcount: A:0.27, C:0.09, G:0.01, T:0.62
Consensus pattern (32 bp):
CATTATTTTTTTATTAATATTTTTACAATTAA
Found at i:45543 original size:20 final size:20
Alignment explanation
Indices: 45504--45571 Score: 100
Period size: 20 Copynumber: 3.4 Consensus size: 20
45494 TCTTTTAAAC
* *
45504 AAACTTTGACCAGAAGTTTCG
1 AAACTTTCACAAG-AGTTTCG
45525 AAACTTTCACAAGAGTTTCG
1 AAACTTTCACAAGAGTTTCG
*
45545 AAACTCTCACAAGAGTTTCG
1 AAACTTTCACAAGAGTTTCG
45565 AAACTTT
1 AAACTTT
45572 ACTTGAAGTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 32 0.74
21 11 0.26
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (20 bp):
AAACTTTCACAAGAGTTTCG
Found at i:45581 original size:20 final size:19
Alignment explanation
Indices: 45504--45592 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 19
45494 TCTTTTAAAC
*
45504 AAACTTTGACCAGAAGTTTCG
1 AAACTTT-ACAAG-AGTTTCG
45525 AAACTTTCACAAGAGTTTCG
1 AAACTTT-ACAAGAGTTTCG
*
45545 AAACTCTCACAAGAGTTTCG
1 AAACT-TTACAAGAGTTTCG
**
45565 AAACTTTACTTGAAGTTTCG
1 AAACTTTACAAG-AGTTTCG
*
45585 ATACTTTA
1 AAACTTTA
45593 GGCTCCAACA
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.07
20 43 0.73
21 12 0.20
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (19 bp):
AAACTTTACAAGAGTTTCG
Found at i:48568 original size:122 final size:122
Alignment explanation
Indices: 48351--48594 Score: 434
Period size: 122 Copynumber: 2.0 Consensus size: 122
48341 AAAAAAACTT
48351 ATTAAAGGTAATATAGTAAGAGATTTGCCTAAGATAAAATTTGATCTCAATAAGATTTGTGATGT
1 ATTAAAGGTAATATAGTAAGAGATTTGCCTAAGATAAAATTTGATCTCAATAAGATTTGTGATGT
** *
48416 ATGTGCTAAGGGTAAACACAAAAGATCTTCTTTTAAACCTATTAATGTTGTATCATC
66 AAATGCTAAGGGTAAACACAAAAGATCTTCTTTTAAAACTATTAATGTTGTATCATC
* * *
48473 ATTAAAGGTAATATAGTAAGAGGTTTGCCTAAGATAAAATTTTATCTCAATAATATTTGTGATGT
1 ATTAAAGGTAATATAGTAAGAGATTTGCCTAAGATAAAATTTGATCTCAATAAGATTTGTGATGT
48538 AAATGCTAAGGGTAAACACAAAAGATCTTCTTTTAAAACTATTAATGTTGTATCATC
66 AAATGCTAAGGGTAAACACAAAAGATCTTCTTTTAAAACTATTAATGTTGTATCATC
48595 TCATAGAGTA
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
122 116 1.00
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.36
Consensus pattern (122 bp):
ATTAAAGGTAATATAGTAAGAGATTTGCCTAAGATAAAATTTGATCTCAATAAGATTTGTGATGT
AAATGCTAAGGGTAAACACAAAAGATCTTCTTTTAAAACTATTAATGTTGTATCATC
Found at i:50726 original size:12 final size:12
Alignment explanation
Indices: 50709--50738 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
50699 TGAACAGTAA
50709 TGAACAATACCG
1 TGAACAATACCG
*
50721 TGAACAATATCG
1 TGAACAATACCG
50733 TGAACA
1 TGAACA
50739 GTGCCACAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (12 bp):
TGAACAATACCG
Found at i:60246 original size:16 final size:17
Alignment explanation
Indices: 60225--60259 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
60215 GCTTATGCTT
60225 TTCTTATGTTGGAT-TA
1 TTCTTATGTTGGATATA
*
60241 TTCTTATTTTGGATATA
1 TTCTTATGTTGGATATA
60258 TT
1 TT
60260 TGGCTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.20, C:0.06, G:0.14, T:0.60
Consensus pattern (17 bp):
TTCTTATGTTGGATATA
Found at i:64828 original size:2 final size:2
Alignment explanation
Indices: 64821--64859 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
64811 GTACGAGAGT
64821 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
64860 TTAACCTCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:70234 original size:168 final size:169
Alignment explanation
Indices: 69953--70284 Score: 616
Period size: 168 Copynumber: 2.0 Consensus size: 169
69943 ATATCTTAAA
69953 AGATTCATTGAATGTCTAACTTCACATCGAATTACAAACATGCAAAAGAAAAGAAAAATACTGGA
1 AGATTCATTGAATGTCTAACTTCACATCGAATTACAAACATGCAAAAGAAAAGAAAAATACTGGA
70018 TATACCAACTAAAAAGCAAGCAACTTCAACATACAATTTTCAACTTTGGTCAGC-T-ATA-AAAA
66 TATACCAACTAAAAAGCAAGCAACTTCAACATACAATTTTCAACTTTGGTCAGCTTCATATAAAA
70080 TTAAAGGAGAAAAAAATACTGACGCCATGAAGGTAAAAG
131 TTAAAGGAGAAAAAAATACTGACGCCATGAAGGTAAAAG
70119 AGATCTCATTGAATGTCTAACTTCACCATCGAATTACAAACATGCAAAAGAAAAGAAAAATACTG
1 AGAT-TCATTGAATGTCTAACTTCA-CATCGAATTACAAACATGCAAAAGAAAAGAAAAATACTG
70184 GATATACCAACTAAAAAGCAAGCAACTTCAACATACAATTTTCAACTTTGGTCAGCTTTCATATA
64 GATATACCAACTAAAAAGCAAGCAACTTCAACATACAATTTTCAACTTTGGTCAGC-TTCATATA
70249 AAATTAAAGGAGAAAAAAATACTGACGCCATGAAGG
128 AAATTAAAGGAGAAAAAAATACTGACGCCATGAAGG
70285 ATTGGAGTGG
Statistics
Matches: 160, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
166 4 0.03
167 20 0.12
168 95 0.59
170 1 0.01
171 3 0.02
172 37 0.23
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (169 bp):
AGATTCATTGAATGTCTAACTTCACATCGAATTACAAACATGCAAAAGAAAAGAAAAATACTGGA
TATACCAACTAAAAAGCAAGCAACTTCAACATACAATTTTCAACTTTGGTCAGCTTCATATAAAA
TTAAAGGAGAAAAAAATACTGACGCCATGAAGGTAAAAG
Found at i:70622 original size:4 final size:4
Alignment explanation
Indices: 70615--70644 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
70605 AGAAAGATTG
70615 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
70645 GAAAGCAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:76959 original size:14 final size:13
Alignment explanation
Indices: 76936--76966 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
76926 ATTGTCAACA
76936 TGTTTGGTAGTTT
1 TGTTTGGTAGTTT
76949 TGTTATGGTAGTTT
1 TGTT-TGGTAGTTT
76963 TGTT
1 TGTT
76967 GCGTTCGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.10, C:0.00, G:0.29, T:0.61
Consensus pattern (13 bp):
TGTTTGGTAGTTT
Found at i:82170 original size:41 final size:41
Alignment explanation
Indices: 82124--82204 Score: 135
Period size: 41 Copynumber: 2.0 Consensus size: 41
82114 ATATAATTAG
82124 TAATTACTCATAGTCATTAAGTTGTTTTAAGCTTGTTTTTT
1 TAATTACTCATAGTCATTAAGTTGTTTTAAGCTTGTTTTTT
* * *
82165 TAATTACTCATAGTTATTAAGTTGTTTTGAGGTTGTTTTT
1 TAATTACTCATAGTCATTAAGTTGTTTTAAGCTTGTTTTT
82205 ATACTTTCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.23, C:0.07, G:0.15, T:0.54
Consensus pattern (41 bp):
TAATTACTCATAGTCATTAAGTTGTTTTAAGCTTGTTTTTT
Found at i:82222 original size:41 final size:41
Alignment explanation
Indices: 82124--82224 Score: 132
Period size: 41 Copynumber: 2.5 Consensus size: 41
82114 ATATAATTAG
* *
82124 TAATTACTCATAGTCATTAAGTTGTTTTAAGCTTGTTTTTT
1 TAATTACTCATAGTTATTAAGTTGTTTTAAGCTTGTTTTTA
* *
82165 TAATTACTCATAGTTATTAAGTTGTTTTGAGGTTGTTTTTA
1 TAATTACTCATAGTTATTAAGTTGTTTTAAGCTTGTTTTTA
* *
82206 TACTTTCTC-TAGGTTATTA
1 TAATTACTCATA-GTTATTA
82225 GTAGTAATAG
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 2 0.04
41 51 0.96
ACGTcount: A:0.24, C:0.09, G:0.14, T:0.53
Consensus pattern (41 bp):
TAATTACTCATAGTTATTAAGTTGTTTTAAGCTTGTTTTTA
Found at i:82868 original size:31 final size:29
Alignment explanation
Indices: 82796--82868 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
82786 AATTGAAGGG
*
82796 ATTGATCTTTTTGCTATTGTATTACTACAT
1 ATTGAT-TTTTTGCTAATGTATTACTACAT
82826 ATTGACTTTTTTCGCTAATGTA-TATCTACAT
1 ATTGA-TTTTTT-GCTAATGTATTA-CTACAT
82857 ATTGATATTTTT
1 ATTGAT-TTTTT
82869 TATGAAGAGA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 13 0.34
31 25 0.66
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.53
Consensus pattern (29 bp):
ATTGATTTTTTGCTAATGTATTACTACAT
Found at i:86128 original size:13 final size:14
Alignment explanation
Indices: 86110--86138 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
86100 TAAATAAGAA
86110 TATTTT-AAATTTT
1 TATTTTAAAATTTT
86123 TATTTTAAAATTTT
1 TATTTTAAAATTTT
86137 TA
1 TA
86139 AAATTTATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TATTTTAAAATTTT
Found at i:86149 original size:23 final size:22
Alignment explanation
Indices: 86112--86155 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
86102 AATAAGAATA
* *
86112 TTTTAAATTTTTATTTTAAAAT
1 TTTTAAATTTATATTTCAAAAT
86134 TTTTAAAATTTATATTTCAAAA
1 TTTT-AAATTTATATTTCAAAA
86156 ATATTTCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
TTTTAAATTTATATTTCAAAAT
Found at i:88560 original size:21 final size:21
Alignment explanation
Indices: 88530--88583 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
88520 AATTCATTCA
* *
88530 ATATGGATACTAGTTAATCTG
1 ATATGAATACCAGTTAATCTG
*
88551 ATATGAATACCAGTTCATCTG
1 ATATGAATACCAGTTAATCTG
* *
88572 GTATTAATACCA
1 ATATGAATACCA
88584 ATCATCGGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (21 bp):
ATATGAATACCAGTTAATCTG
Found at i:95339 original size:30 final size:30
Alignment explanation
Indices: 95300--95357 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
95290 AAATAAAAAA
* *
95300 TTTATAATATAACGGTAGACACCTAAAATT
1 TTTAAAATATAACAGTAGACACCTAAAATT
* *
95330 TTTAAAATATAACAGTATACATCTAAAA
1 TTTAAAATATAACAGTAGACACCTAAAA
95358 GTATAACGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.48, C:0.12, G:0.07, T:0.33
Consensus pattern (30 bp):
TTTAAAATATAACAGTAGACACCTAAAATT
Found at i:95865 original size:14 final size:13
Alignment explanation
Indices: 95837--95870 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
95827 TCATCAAAGT
95837 AAATATTTTAAAA
1 AAATATTTTAAAA
*
95850 AAATATATTTATAA
1 AAATAT-TTTAAAA
95864 AAATATT
1 AAATATT
95871 CAATAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATATTTTAAAA
Found at i:96612 original size:33 final size:34
Alignment explanation
Indices: 96569--96647 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 34
96559 TTGAAATATG
*
96569 TATATAATATAG-TTTCTAAAAACATTTT-AACTA
1 TATATTATATAGTTTTC-AAAAACATTTTAAACTA
* *
96602 TATATTATATAGTTTTCAAAAGCGTTTTAAAACTA
1 TATATTATATAGTTTTCAAAAACATTTT-AAACTA
96637 TATATTATATA
1 TATATTATATA
96648 TATTTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
33 20 0.50
34 4 0.10
35 16 0.40
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (34 bp):
TATATTATATAGTTTTCAAAAACATTTTAAACTA
Found at i:96643 original size:35 final size:35
Alignment explanation
Indices: 96597--96720 Score: 103
Period size: 36 Copynumber: 3.5 Consensus size: 35
96587 AAAACATTTT
96597 AACTATATATTATATAGTTTTCAAAAGCGTTTTAA
1 AACTATATATTATATAGTTTTCAAAAGCGTTTTAA
* * *
96632 AACTATATATTATATATATTTTTAAAATG-TTTTTAGA
1 AACTATATATTATATA-GTTTTCAAAA-GCGTTTTA-A
* * **
96669 AACTATA-AATATACGTA-TTTTC-AAACCGTTTGCA
1 AACTATATATTATA--TAGTTTTCAAAAGCGTTTTAA
96703 AACTATATATATATATAG
1 AACTATATAT-TATATAG
96721 ATATAGATAT
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
34 10 0.14
35 23 0.33
36 26 0.37
37 9 0.13
38 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (35 bp):
AACTATATATTATATAGTTTTCAAAAGCGTTTTAA
Found at i:97622 original size:165 final size:163
Alignment explanation
Indices: 97321--98463 Score: 993
Period size: 165 Copynumber: 7.0 Consensus size: 163
97311 GCTATGTTGT
* * *
97321 AAATGATGTGCCTTG-AGATGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAAATAACCCTTC
1 AAATGATGTGCCTTGAAGCTGAGCGTAGTCAAACTCGAAGGTC-TT--TTGGCAGATAACCCTTC
* * * * *
97385 TCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTAAGCGTAGTTGAACTCGAAGGT-TTT
63 TAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
* * *
97449 GGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGT
128 GGTG-CAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * * *
97486 AAATGATGTGCCCTCGAAGCTGAGTGT-GATCAAACTCGAGGGTC-TTTGGCAGATAGCCCTTCT
1 AAATGATGTG-CCTTGAAGCTGAGCGTAG-TCAAACTCGAAGGTCTTTTGGCAGATAACCCTTCT
* * *
97549 CGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAACTCGAATGTCTTTT
64 AGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTT
* * * *
97614 GGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
128 GGTG-CAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * * * * ** *
97651 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGCGGGTC-TTTGGCAGATAACCCTTCTT
1 AAATGATGTG-CCTTGAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGCAGATAACCCTTCTA
* * ** *
97715 GACTTAAGCTATGTTGCAAATGATGTGCCTTAGAGCCAAGCGTAGTCGAACTCGTAGGTCTTTGG
65 GACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
97780 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
130 -T-GCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * * *
97816 AAGTGATATGCCTTGGAA-CTGAGCCTAGTCAAACTCGAAGGTCTTTTGATCACCGAT-ACCCTT
1 AAATGATGTGCCTT-GAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTG-GCA--GATAACCCTT
* * ** * * * * *
97879 CTAGCCTTGAGCTATG-TTTAAATGAT-TACCCTTGAAGCTGAGTGTAATCGAACTCGAGGGTCT
62 CTAGACTTAAGCTATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCT
* *
97942 TT-G-GCAGATAACCC-TCATCGACTTAAGCTATGCTTC
126 TTGGTGCAGATAACCCTTC-TCGACTTAAGTTATGCTGC
* * * *
97978 AAATGA--TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAAATAACCCTTA
1 AAATGATGTGCCTTGAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG---CAGATAACCCTTC
* * * * * * * * *
98041 TAGCCTTGAG-TATGCTGTAAATGATGTGACCTCGAAGCTGAGGGTAATCGAACTTGATGGTCTT
63 TAGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
* * *
98105 T-G-GCAGACAACCCTTCTCGACTTAAGCTATGCTAC
127 TGGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * *
98140 AAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGGTCACAGATAACCCTTC
1 AAATGATGTGCCTTGAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGG---CAGATAACCCTTC
* * * * * * * * * *
98205 TAG-CTTGAGTTATGATGTAAATGATGTGCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTC
63 TAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
* * *
98269 GGT--AGATAGCCCTTCTCG-CTTAAGCTATACTGC
128 GGTGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
* * * *
98302 AAATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTAGCAGA-AA-CCTTC
1 AAATGATGTGCCTTGAAGCTGAGCGTAGTCAAACTCGAAGGTC-TT--TTGGCAGATAACCCTTC
* * * * *
98365 TCGACTTAAGTTATACTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCGAAGG-CTTT
63 TAGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
* * * * * *
98429 GTTGGTAGATAACTCTTCTAGCCTTGAGTTATGCT
128 GGT-GCAGATAACCCTTCTCGACTTAAGTTATGCT
98464 ACAATAGTTT
Statistics
Matches: 830, Mismatches: 111, Indels: 75
0.82 0.11 0.07
Matches are distributed among these distances:
159 2 0.00
160 52 0.06
161 74 0.09
162 159 0.19
163 137 0.17
164 110 0.13
165 209 0.25
166 44 0.05
167 40 0.05
168 3 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (163 bp):
AAATGATGTGCCTTGAAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGCAGATAACCCTTCTAG
ACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGT
GCAGATAACCCTTCTCGACTTAAGTTATGCTGC
Found at i:97648 original size:84 final size:83
Alignment explanation
Indices: 97286--98447 Score: 1025
Period size: 84 Copynumber: 14.2 Consensus size: 83
97276 ACAATTTTAT
* *** * * * *
97286 TGACAGATAGCCCTTCTTTCCTTGAGCTATGTTGTAAATGATGTGCCTT-GAGATGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
97350 GAACTCGAAGGTCTTTAGT
66 GAACTCGAAGGTCTTT-GG
* * * * * *
97369 TGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTAAGCGTAGTT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
97434 GAACTCGAAGGT-TTTGG
66 GAACTCGAAGGTCTTTGG
* * * * * * *
97451 TGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGT-GA
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAG-
* *
97515 TCAAACTCGAGGGTCTTT-G
64 TCGAACTCGAAGGTCTTTGG
* *
97534 -G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
97597 GAACTCGAATGTCTTTTGG
66 GAACTCGAAGGTC-TTTGG
* * * * * * * * *
97616 TGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
* **
97681 CGAACTTGCGGGTCTTT-G
65 CGAACTCGAAGGTCTTTGG
* * * **
97699 -G-CAGATAACCCTTCTTGACTTAAGCTATGTTGCAAATGATGTGCCTTAGAGCCAAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
*
97762 GAACTCGTAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * * *
97780 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAGTGATATGCCTTGGAACTGAGCCTAGT
1 -TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
* *
97845 CAAACTCGAAGGTCTTTTGA
65 CGAACTCGAAGGTC-TTTGG
* * * * * ** * * * *
97865 TCACCGAT-ACCCTTCTAGCCTTGAGCTATG-TTTAAATGAT-TACCCTTGAAGCTGAGTGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAGT
*
97927 CGAACTCGAGGGTCTTT-G
65 CGAACTCGAAGGTCTTTGG
*
97945 -G-CAGATAACCC-TCATCGACTTAAGCTATGCTTCAAATGA--TGCCTTGGAGCTGAGCGTAGT
1 TGACAGATAACCCTTC-TCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
98005 CGAACTCGAAGGTCTTTTGG
65 CGAACTCGAAGGTC-TTTGG
* * * * * * * * * * *
98025 TCACAAATAACCCTTATAGCCTTGAG-TATGCTGTAAATGATGTGACCTCGAAGCTGAGGGTAAT
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGT
* *
98089 CGAACTTGATGGTCTTT-G
65 CGAACTCGAAGGTCTTTGG
* * *
98107 -G-CAGACAACCCTTCTCGACTTAAGCTATGCTACAAATGATATGCCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *
98170 AAACTCAAAGGTCTTTTGG
66 GAACTCGAAGGTC-TTTGG
* * * * * * * * * *
98189 TCACAGATAACCCTTCTAG-CTTGAGTTATGATGTAAATGATGTGCCTCGAAGCTGAGTGTAATC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
* *
98253 GAACTCGAGGGTCTTCGG
66 GAACTCGAAGGTCTTTGG
* * *
98271 T---AGATAGCCCTTCTCG-CTTAAGCTATACTGCAAATGATGTGTCTTGGAGCTGAGCGTAGTC
1 TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
98332 GAACTCGAAGGTCTTTGG
66 GAACTCGAAGGTCTTTGG
* * * * *
98350 TTAGCAGA-AA-CCTTCTCGACTTAAGTTATACTGCAAATGATATGCCTTAGAGCTGAGCGTAGT
1 TGA-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
*
98413 CGAACTCGAAGG-CTTTGT
65 CGAACTCGAAGGTCTTTGG
** *
98431 TGGTAGATAACTCTTCT
1 TGACAGATAACCCTTCT
98448 AGCCTTGAGT
Statistics
Matches: 853, Mismatches: 187, Indels: 79
0.76 0.17 0.07
Matches are distributed among these distances:
78 35 0.04
79 85 0.10
80 104 0.12
81 128 0.15
82 158 0.19
83 140 0.16
84 175 0.21
85 28 0.03
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (83 bp):
TGACAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTC
GAACTCGAAGGTCTTTGG
Found at i:98168 original size:408 final size:404
Alignment explanation
Indices: 97321--98463 Score: 1351
Period size: 408 Copynumber: 2.8 Consensus size: 404
97311 GCTATGTTGT
* * *
97321 AAATGATGTGCCTTGAGATGAGCGTAGTCGAACTCGAAGGTCTTTAGTTGGCAAATAACCCTTCT
1 AAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
* * *
97386 CGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTAAGCGTAGTTGAACTCGAAGG--TTTT
66 CGACTTAAGTTATGCTGCAAATGATATGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTT
* * *
97449 GGTGACAGATAACCCTTCTAGACTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTG
131 GGT-AC-GAT-ACCCTTCTAG-CTTGAGCTATG-TGTAAATGATGT-CCCTTGAAGCTGAGTGTA
* *
97514 ATCAAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC
190 ATCGAACTCGAGGGTCTTTGGCAGATAACCC-TCTCGACTTAAGCTATGCTGCAAATGA--TGCC
* * * * *
97579 TTGGAGCTGAACGTAGTCGAACTCGAATGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTT
252 TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAAATAACCCTTATAGCCTTGAGTT
* * * *
97644 ATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTGCGGGTCTTTGGCAGATAACC
317 ATGCTGTAAATGATGTGACCTCGAAGCTGAGGGTAATCGAACTTGAGGGTCTTTGGCAGACAACC
* * *
97709 CTTCTTGACTTAAGCTATGTTGC
382 CTTCTCGACTTAAGCTATGCTAC
** *
97732 AAATGATGTGCCTTAGAGCCAAGCGTAGTCGAACTCGTAGGTCTTTGGTTGGCAGATAACCCTTC
1 AAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTC
* * *
97797 TCGACTTAAGTTATGCTGCAAGTGATATGCCTTGGAACTGAGCCTAGTCAAACTCGAAGGTCTTT
65 TCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTT
* *
97862 TGATCACCGATACCCTTCTAGCCTTGAGCTATGTTTAAATGAT-TACCCTTGAAGCTGAGTGTAA
130 TGGT-A-CGATACCCTTCTAG-CTTGAGCTATGTGTAAATGATGT-CCCTTGAAGCTGAGTGTAA
*
97926 TCGAACTCGAGGGTCTTTGGCAGATAACCCTCATCGACTTAAGCTATGCTTCAAATGATGCCTTG
191 TCGAACTCGAGGGTCTTTGGCAGATAACCCTC-TCGACTTAAGCTATGCTGCAAATGATGCCTTG
97991 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAAATAACCCTTATAGCCTTGAG-TATG
255 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAAATAACCCTTATAGCCTTGAGTTATG
*
98055 CTGTAAATGATGTGACCTCGAAGCTGAGGGTAATCGAACTTGATGGTCTTTGGCAGACAACCCTT
320 CTGTAAATGATGTGACCTCGAAGCTGAGGGTAATCGAACTTGAGGGTCTTTGGCAGACAACCCTT
98120 CTCGACTTAAGCTATGCTAC
385 CTCGACTTAAGCTATGCTAC
* * * **
98140 AAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCAAAGGTCTTTTGG-TCACAGATAACCCTT
1 AAATGATGTGCCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTT
* * * * * * * * *
98204 CTAG-CTTGAGTTATGATGTAAATGATGTGCC-TCGAAGCTGAGTGTAATCGAACTCGAGGGTC-
64 CTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAA-CTGAGCGTAGTCGAACTCGAAGGTCT
* * * * * ** * * *
98266 TTCGGTA-GATAGCCCTTCTCGCTTAAGCTATACTGCAAATGATGTGTCTTGGAGCTGAGCGTAG
128 TTTGGTACGATA-CCCTTCTAGCTTGAGCTAT-GTGTAAATGATGTCCCTTGAAGCTGAGTGTAA
* * * *
98330 TCGAACTCGAAGGTCTTTGGTTAGCAGA-AACCTTCTCGACTTAAGTTATACTGCAAATGATATG
191 TCGAACTCGAGGGTCTTT-G---GCAGATAACCCTCTCGACTTAAGCTATGCTGCAAATG--ATG
* * * *
98394 CCTTAGAGCTGAGCGTAGTCGAACTCGAAGG-CTTTGTTGGT---AGATAACTCTTCTAGCCTTG
250 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TT-TTGGTCACAAATAACCCTTATAGCCTTG
98455 AGTTATGCT
313 AGTTATGCT
98464 ACAATAGTTT
Statistics
Matches: 635, Mismatches: 78, Indels: 42
0.84 0.10 0.06
Matches are distributed among these distances:
403 13 0.02
404 47 0.07
405 3 0.00
406 48 0.08
407 55 0.09
408 173 0.27
409 72 0.11
410 2 0.00
411 84 0.13
412 107 0.17
413 20 0.03
414 10 0.02
415 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (404 bp):
AAATGATGTGCCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
CGACTTAAGTTATGCTGCAAATGATATGCCTTGGAACTGAGCGTAGTCGAACTCGAAGGTCTTTT
GGTACGATACCCTTCTAGCTTGAGCTATGTGTAAATGATGTCCCTTGAAGCTGAGTGTAATCGAA
CTCGAGGGTCTTTGGCAGATAACCCTCTCGACTTAAGCTATGCTGCAAATGATGCCTTGGAGCTG
AGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAAATAACCCTTATAGCCTTGAGTTATGCTGTAA
ATGATGTGACCTCGAAGCTGAGGGTAATCGAACTTGAGGGTCTTTGGCAGACAACCCTTCTCGAC
TTAAGCTATGCTAC
Done.