Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009220.1 Hibiscus syriacus cultivar Beakdansim tig00112809_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: 61580
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:6281 original size:17 final size:17
Alignment explanation
Indices: 6259--6314 Score: 112
Period size: 17 Copynumber: 3.3 Consensus size: 17
6249 AACGGTCAAC
6259 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
6276 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
6293 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
6310 GGTCA
1 GGTCA
6315 GACCGGTCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 39 1.00
ACGTcount: A:0.12, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:6328 original size:9 final size:9
Alignment explanation
Indices: 6310--6378 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
6300 GGTCGGGTCG
*
6310 GGTCAGACC
1 GGTCAAACC
6319 GGTCAAACC
1 GGTCAAACC
* *
6328 GATTCAGACC
1 G-GTCAAACC
6338 GGTCAAACC
1 GGTCAAACC
*
6347 GGTTGAAACC
1 GG-TCAAACC
6357 GGTCAAACC
1 GGTCAAACC
6366 GGTCAGAACC
1 GGTCA-AACC
6376 GGT
1 GGT
6379 TGAAAACCAG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
9 28 0.56
10 22 0.44
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:6347 original size:28 final size:27
Alignment explanation
Indices: 6310--6378 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 27
6300 GGTCGGGTCG
* * *
6310 GGTCAGACCGGTCAAACCGATTCAGACC
1 GGTCAAACCGGTCAAACCG-GTCAAACC
*
6338 GGTCAAACCGGTTGAAACCGGTCAAACC
1 GGTCAAACCGG-TCAAACCGGTCAAACC
6366 GGTCAGAACCGGT
1 GGTCA-AACCGGT
6379 TGAAAACCAG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 22 0.63
29 13 0.37
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.14
Consensus pattern (27 bp):
GGTCAAACCGGTCAAACCGGTCAAACC
Found at i:6355 original size:10 final size:10
Alignment explanation
Indices: 6316--6399 Score: 70
Period size: 9 Copynumber: 8.7 Consensus size: 10
6306 GTCGGGTCAG
6316 ACCGG-TCAA
1 ACCGGTTCAA
* *
6325 ACCGATTCAG
1 ACCGGTTCAA
6335 ACCGG-TCAA
1 ACCGGTTCAA
*
6344 ACCGGTTGAA
1 ACCGGTTCAA
6354 ACCGG-TCAA
1 ACCGGTTCAA
6363 ACCGG-TCAGA
1 ACCGGTTCA-A
*
6373 ACCGGTTGAAA
1 ACCGGTT-CAA
*
6384 ACCAGTT-AA
1 ACCGGTTCAA
6393 ACCGGTT
1 ACCGGTT
6400 TCCAGCAGCC
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
9 31 0.51
10 21 0.34
11 8 0.13
12 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:6367 original size:19 final size:19
Alignment explanation
Indices: 6316--6378 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
6306 GTCGGGTCAG
* *
6316 ACCGGTCAAACCGATTCAG
1 ACCGGTCAAACCGGTTCAA
*
6335 ACCGGTCAAACCGGTTGAA
1 ACCGGTCAAACCGGTTCAA
6354 ACCGGTCAAACCGG-TCAGA
1 ACCGGTCAAACCGGTTCA-A
6373 ACCGGT
1 ACCGGT
6379 TGAAAACCAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 2 0.05
19 37 0.95
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCAA
Found at i:8149 original size:12 final size:12
Alignment explanation
Indices: 8124--8193 Score: 61
Period size: 12 Copynumber: 5.8 Consensus size: 12
8114 ACGAAGATAT
* *
8124 CAGAAATCAAAA
1 CAGAATTCAGAA
8136 CAGAATTCAGAA
1 CAGAATTCAGAA
*
8148 CAG-ATATCATAA
1 CAGAAT-TCAGAA
* * *
8160 CAGAATCCATAT
1 CAGAATTCAGAA
*
8172 CAGAAATCAGAA
1 CAGAATTCAGAA
8184 CAGAATTCAG
1 CAGAATTCAG
8194 GTCATTTATC
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 42 0.91
13 2 0.04
ACGTcount: A:0.51, C:0.19, G:0.13, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:8191 original size:48 final size:48
Alignment explanation
Indices: 8120--8230 Score: 143
Period size: 48 Copynumber: 2.3 Consensus size: 48
8110 TTAAACGAAG
*
8120 ATATCAGAAATCAAAACAGAATTCAGAACAGATATCATAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTCAGAACAGATATCATAACAGAATCC
** ** *
8168 ATATCAGAAATCAGAACAGAATTCAGGTCATTTATCATAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTCAGAACAGATATCATAACAGAATCC
*
8216 A-AGTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
8231 TAAAATATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 54 0.98
ACGTcount: A:0.48, C:0.17, G:0.14, T:0.22
Consensus pattern (48 bp):
ATATCAGAAATCAGAACAGAATTCAGAACAGATATCATAACAGAATCC
Found at i:8228 original size:24 final size:24
Alignment explanation
Indices: 8123--8228 Score: 90
Period size: 24 Copynumber: 4.4 Consensus size: 24
8113 AACGAAGATA
*
8123 TCAGAAATCAAAACAGAATTC-AG
1 TCAGAAATCATAACAGAATTCAAG
* * *
8146 AACAGATATCATAACAGAATCCATA-
1 -TCAGAAATCATAACAGAATTCA-AG
* *
8171 TCAGAAATCAGAACAGAATTCAGG
1 TCAGAAATCATAACAGAATTCAAG
***
8195 TCATTTATCATAACAGAATTCAAG
1 TCAGAAATCATAACAGAATTCAAG
*
8219 TCGGAAATCA
1 TCAGAAATCA
8229 GATAAAATAT
Statistics
Matches: 61, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
24 60 0.98
26 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (24 bp):
TCAGAAATCATAACAGAATTCAAG
Found at i:10652 original size:13 final size:13
Alignment explanation
Indices: 10634--10673 Score: 80
Period size: 13 Copynumber: 3.1 Consensus size: 13
10624 GGGTCAACGA
10634 TCAACGGGTCGGG
1 TCAACGGGTCGGG
10647 TCAACGGGTCGGG
1 TCAACGGGTCGGG
10660 TCAACGGGTCGGG
1 TCAACGGGTCGGG
10673 T
1 T
10674 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:17533 original size:29 final size:29
Alignment explanation
Indices: 17491--17549 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
17481 ATCAACGAAG
*
17491 AAGATGAACAGCAAGAAGGGGTATGCCAA
1 AAGATGAACAGCAAGAAGGGGTATACCAA
*
17520 AAGATGAACAGCAAGGAGGGGTATACCAA
1 AAGATGAACAGCAAGAAGGGGTATACCAA
17549 A
1 A
17550 GGCAAGATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.46, C:0.14, G:0.31, T:0.10
Consensus pattern (29 bp):
AAGATGAACAGCAAGAAGGGGTATACCAA
Found at i:22506 original size:18 final size:19
Alignment explanation
Indices: 22471--22510 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
22461 ATTTAAAAAT
*
22471 TAAATTAATATGAATGAAA
1 TAAAATAATATGAATGAAA
22490 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
22508 TAA
1 TAA
22511 GCAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:22566 original size:2 final size:2
Alignment explanation
Indices: 22561--22603 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
22551 ACACACATAA
** *
22561 AT AT AT AT AT GC AT AA 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
22603 A
1 A
22604 ATAAAACATC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:22577 original size:16 final size:15
Alignment explanation
Indices: 22556--22604 Score: 66
Period size: 14 Copynumber: 3.3 Consensus size: 15
22546 ATTAAACACA
22556 CATAAATATATATAT
1 CATAAATATATATAT
22571 GCATAAATATATATAT
1 -CATAAATATATATAT
*
22587 -ATATATATATATAT
1 CATAAATATATATAT
22601 -ATAA
1 CATAA
22605 TAAAACATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
14 16 0.52
16 15 0.48
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (15 bp):
CATAAATATATATAT
Found at i:22702 original size:16 final size:16
Alignment explanation
Indices: 22683--22716 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22673 TTAAAAAACC
* *
22683 AAAGGACTAAATTATA
1 AAAGGACAAAATGATA
22699 AAAGGACAAAATGATA
1 AAAGGACAAAATGATA
22715 AA
1 AA
22717 GCATAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.62, C:0.06, G:0.15, T:0.18
Consensus pattern (16 bp):
AAAGGACAAAATGATA
Found at i:24324 original size:46 final size:42
Alignment explanation
Indices: 24200--24576 Score: 204
Period size: 46 Copynumber: 8.7 Consensus size: 42
24190 TGTCTGAGGG
* * * *
24200 TGACACTGCTCCTATGTGATGAAGAGGTCTGG-TC-GAGG-AA
1 TGACACGGCTCCTACGTGATGAAGAGG-CTGGATCTAAGGTGA
* *
24240 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAG-GCTGG--ATCT-AAGGTGA
* * *
24286 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGG-G-
1 TGACACGGCTCCTACGTGATGAAGA-GGCTGG--ATCTAAGGTGA
* * *
24329 TGACACGGCTCCTACGTGATGAAGAGGTATGG-TC-GAGG-AA
1 TGACACGGCTCCTACGTGATGAAGAGG-CTGGATCTAAGGTGA
* * *
24369 TGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAG-GCTGG--ATCT-AAGGTGA
* * * *
24415 TAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT--
1 TGACACGGCTCCTACGTGATGAAGA-GGCTGG--ATCTAAGGTGA
* * *
24458 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCT--GGGGAA
1 TGACACGGCTCCTACGTGATGAAGAG-GCTGGATCTAAGGTG-A
* **
24499 TGACACGGCTCATACGTGATGAAGAGTTATGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACGTGATGAAGAG-GCTGG--ATCT-AAGGTGA
* * *
24545 TAACACGGTTCCTACGTGATGAGGACGGCTGG
1 TGACACGGCTCCTACGTGATGAAGA-GGCTGG
24577 CCATCTTTAG
Statistics
Matches: 259, Mismatches: 49, Indels: 52
0.72 0.14 0.14
Matches are distributed among these distances:
38 2 0.01
39 3 0.01
40 59 0.23
41 30 0.12
42 3 0.01
43 54 0.21
44 4 0.02
45 14 0.05
46 84 0.32
47 6 0.02
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (42 bp):
TGACACGGCTCCTACGTGATGAAGAGGCTGGATCTAAGGTGA
Found at i:24342 original size:129 final size:129
Alignment explanation
Indices: 24164--24576 Score: 664
Period size: 129 Copynumber: 3.2 Consensus size: 129
24154 TTACGATGTT
* * * * * * * * *
24164 GTTCCTTCGTGATGAGGAAGTCAGATTGTCTGAGGGTGACACTGCTCCTATGTGATGAAGAGGTC
1 GTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGGTC
24229 TGGTCGAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
66 TGGTCGAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
*
24293 GTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGGTA
1 GTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGGTC
*
24358 TGGTCGAGGAATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
66 TGGTCGAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
* * * *
24422 GTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAGATC
1 GTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGGTC
* *
24487 TGGTCTGGGGAATGACACGGCTCATACGTGATGAAGAGTTATGGCCATCTAAAGGTGATAACACG
66 TGGTC-GAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
24552 GTTCCTACGTGATGAGGACGGCTGG
1 GTTCCTACGTGATGAGGACGGCTGG
24577 CCATCTTTAG
Statistics
Matches: 264, Mismatches: 19, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
129 183 0.69
130 81 0.31
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (129 bp):
GTTCCTACGTGATGAGGACGGCTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGAGGTC
TGGTCGAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACG
Found at i:24349 original size:43 final size:43
Alignment explanation
Indices: 24199--24524 Score: 174
Period size: 40 Copynumber: 7.6 Consensus size: 43
24189 TTGTCTGAGG
* * *
24199 GTGACACTGCTCCTATGTGATGAAGAGGTCTGG---TC-GAGGA
1 GTGACACGGCTCCTACGTGATGAAGAGG-CTGGTTATCTAAGGA
* * * ** *
24239 ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 GTGACACGGCTCCTACGTGATGAAGAG-GCTGGTTATCT-AAGGA
* * *
24284 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTAAGG-
1 G-TGACACGGCTCCTACGTGATGAAGA-GGCTGGTTATCTAAGGA
* *
24328 GTGACACGGCTCCTACGTGATGAAGAGGTATGG---TC-GAGGA
1 GTGACACGGCTCCTACGTGATGAAGAGG-CTGGTTATCTAAGGA
* * * * ** *
24368 ATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGT
1 GTGACACGGCTCCTACGTGATGAAGAG-GCTGGTTATCT-AAGGA
* * * *
24413 GATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGG-
1 G-TGACACGGCTCCTACGTGATGAAGA-GGCTGGTTATCTAAGGA
* * * **
24457 TTGACACGGCTCATACGTGATGAAGAGATCTGG---TCTGGGGA
1 GTGACACGGCTCCTACGTGATGAAGAG-GCTGGTTATCTAAGGA
* *
24498 ATGACACGGCTCATACGTGATGAAGAG
1 GTGACACGGCTCCTACGTGATGAAGAG
24525 TTATGGCCAT
Statistics
Matches: 220, Mismatches: 46, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
39 3 0.01
40 61 0.28
41 26 0.12
42 3 0.01
43 54 0.25
44 1 0.00
45 13 0.06
46 57 0.26
47 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.24
Consensus pattern (43 bp):
GTGACACGGCTCCTACGTGATGAAGAGGCTGGTTATCTAAGGA
Found at i:24578 original size:46 final size:45
Alignment explanation
Indices: 24239--24582 Score: 231
Period size: 46 Copynumber: 7.9 Consensus size: 45
24229 TGGTCGAGGA
*
24239 ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 ATGACACGGCTCATACGTGATGAAGAGTGCTGGCCATCT-AAGGTG
* * * * **
24285 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTAAGG-G
1 ATGACACGGCTCATACGTGATGAAGA-GTGCTGGCCATCTAAGGTG
* * * *
24329 -TGACACGGCTCCTACGTGATGAAGAG-GTATGG---TC-GAGG-A
1 ATGACACGGCTCATACGTGATGAAGAGTG-CTGGCCATCTAAGGTG
* *
24368 ATGACACGACTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG
1 ATGACACGGCTCATACGTGATGAAGAGTGCTGGCCATCT-AAGGTG
* * * * ** *
24414 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT-
1 ATGACACGGCTCATACGTGATGAAGA-GTGCTGGCCATCTAAGGTG
*
24458 -TGACACGGCTCATACGTGATGAAGAGAT-CTGG---TCT--GGGG
1 ATGACACGGCTCATACGTGATGAAGAG-TGCTGGCCATCTAAGGTG
**
24497 AATGACACGGCTCATACGTGATGAAGAGTTATGGCCATCTAAAGGTG
1 -ATGACACGGCTCATACGTGATGAAGAGTGCTGGCCATCT-AAGGTG
* * * *
24544 ATAACACGGTTCCTACGTGATGAGGACG-GCTGGCCATCT
1 ATGACACGGCTCATACGTGATGAAGA-GTGCTGGCCATCT
24583 TTAGGAGTTA
Statistics
Matches: 233, Mismatches: 41, Indels: 48
0.72 0.13 0.15
Matches are distributed among these distances:
38 2 0.01
39 3 0.01
40 33 0.14
41 29 0.12
42 3 0.01
43 52 0.22
44 4 0.02
45 11 0.05
46 90 0.39
47 6 0.03
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.24
Consensus pattern (45 bp):
ATGACACGGCTCATACGTGATGAAGAGTGCTGGCCATCTAAGGTG
Found at i:24635 original size:28 final size:28
Alignment explanation
Indices: 24615--24683 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
24605 AAACCAAATT
24615 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
24643 AAAGATTTGTTTCAAGAA-AAACATACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
24671 AAAGACTTTGTTT
1 AAAGA-TTTGTTT
24684 GTTTTGTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 28 0.76
29 9 0.24
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:25234 original size:27 final size:27
Alignment explanation
Indices: 25200--25256 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
25190 TAAAATTTTG
*
25200 TTTCAAAAGAAATAGACTCAAAGAT-TT
1 TTTCAAAAGAAACA-ACTCAAAGATATT
25227 TTTCAAAAGAAACAACTCAAAGATATT
1 TTTCAAAAGAAACAACTCAAAGATATT
25254 TTT
1 TTT
25257 TAATTAGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (27 bp):
TTTCAAAAGAAACAACTCAAAGATATT
Found at i:25255 original size:26 final size:27
Alignment explanation
Indices: 25200--25255 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
25190 TAAAATTTTG
* *
25200 TTTCAAAAGAAATAGACTCAAAGATTT
1 TTTCAAAAGAAACAGACTCAAAGATAT
25227 TTTCAAAAGAAACA-ACTCAAAGATAT
1 TTTCAAAAGAAACAGACTCAAAGATAT
25253 TTT
1 TTT
25256 TTAATTAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.30
Consensus pattern (27 bp):
TTTCAAAAGAAACAGACTCAAAGATAT
Found at i:25300 original size:91 final size:93
Alignment explanation
Indices: 25131--25349 Score: 252
Period size: 91 Copynumber: 2.3 Consensus size: 93
25121 TCGAGAAAAT
* * * *
25131 TTTTTTCAAAGGAAACAAACTCAAAGATTTTCTTCTCAAGAGAAATTGTCTTTAAGAGATAAAAT
1 TTTTTTCAAAAGAAACAAACTCAAAGATTTTCTTCTCAAGAGAAACTGTCTTCAAGAGAGAAAAT
25196 TTTGTTTCAAAAGAAATAGACTCAAAGA
66 TTTGTTTCAAAAGAAATAGACTCAAAGA
*
25224 TTTTTTCAAAAGAAAC-AACTCAAAGATATTT-TT-T-AATTAGAAACTGTC-TCAAGAGAGACA
1 TTTTTTCAAAAGAAACAAACTCAAAGAT-TTTCTTCTCAA-GAGAAACTGTCTTCAAGAGAGA-A
**
25284 ACA-TTTGTTTTTAAAGAAATAGACTCAAAGA
63 A-ATTTTGTTTCAAAAGAAATAGACTCAAAGA
* *
25315 TGATTTTGTTAAGAGAAACAAACTCAAAGATTTTC
1 T--TTTT-TCAAAAGAAACAAACTCAAAGATTTTC
25350 AAAATGAACA
Statistics
Matches: 108, Mismatches: 9, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
90 10 0.09
91 39 0.36
92 14 0.13
93 22 0.20
94 12 0.11
95 11 0.10
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (93 bp):
TTTTTTCAAAAGAAACAAACTCAAAGATTTTCTTCTCAAGAGAAACTGTCTTCAAGAGAGAAAAT
TTTGTTTCAAAAGAAATAGACTCAAAGA
Found at i:25451 original size:119 final size:121
Alignment explanation
Indices: 25194--25451 Score: 280
Period size: 119 Copynumber: 2.1 Consensus size: 121
25184 AAGAGATAAA
* * * *
25194 ATTTTGTTTCAAAAGAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTTTTA
1 ATTTTGTTTCAAAAGAAACAAACTCAAAGA-TTTTTCAAAAGAAACAACTCAAAGATATTCTTCA
* * * ** *
25259 ATTAGAAACTGTCTCAAGAGAGACAACATTTGTTTTTAAAGAAATAGACTCAAAGAT
65 ATGAGAAACGGTCTCAAGAGAGACAACAATTCATTTTAAAGAAACAGACTCAAAGAT
* *
25316 GATTTTG-TT-AAGAGAAACAAACTCAAAGA-TTTTCAAAATG-AACATATTCAAAGAT-TTACT
1 -ATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTCAAAA-GAAACA-ACTCAAAGATATT-CT
* *
25376 TCAA-GAGAAACGGTCTCAAGAGATACAA-AATTCATTTTAAGAGAAACAGATTCAAAGAT
62 TCAATGAGAAACGGTCTCAAGAGAGACAACAATTCATTTTAA-AGAAACAGACTCAAAGAT
25435 -TTTTGTTTCAAAAGAAA
1 ATTTTGTTTCAAAAGAAA
25452 TTATCTTAAG
Statistics
Matches: 114, Mismatches: 15, Indels: 16
0.79 0.10 0.11
Matches are distributed among these distances:
117 5 0.04
118 11 0.10
119 59 0.52
120 14 0.12
121 17 0.15
122 2 0.02
123 6 0.05
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (121 bp):
ATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTCAAAAGAAACAACTCAAAGATATTCTTCAA
TGAGAAACGGTCTCAAGAGAGACAACAATTCATTTTAAAGAAACAGACTCAAAGAT
Found at i:25463 original size:66 final size:66
Alignment explanation
Indices: 25393--25518 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 66
25383 AAACGGTCTC
* * * *
25393 AAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTAT
1 AAGAGAGACAAAATT-ATGTTTCAA-AGAAACAAACTCAAAGATTTTTATTTCAAAAGAAATTAT
25456 CTT
64 CTT
*
25459 AAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTATTTCAAAAGAAA
1 AAGAGAGACAAAATTATGTTT-CAAAGAAACAAACTCAAAGATTTTTATTTCAAAAGAAA
25519 CACTCTCAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
65 1 0.02
66 17 0.33
67 32 0.62
68 2 0.04
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.30
Consensus pattern (66 bp):
AAGAGAGACAAAATTATGTTTCAAAGAAACAAACTCAAAGATTTTTATTTCAAAAGAAATTATCT
T
Found at i:25518 original size:30 final size:30
Alignment explanation
Indices: 25472--25535 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
25462 AGAGACAAAA
* *
25472 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTATTTCAAAAGAAACAAACTCAAAGAT
**
25502 TTTTATTTCAAAAGAAACACTCTCAAAGAT
1 TTTTATTTCAAAAGAAACAAACTCAAAGAT
25532 TTTT
1 TTTT
25536 TCACAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.36
Consensus pattern (30 bp):
TTTTATTTCAAAAGAAACAAACTCAAAGAT
Found at i:25597 original size:52 final size:53
Alignment explanation
Indices: 25523--25625 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
25513 AAGAAACACT
*
25523 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAACACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
25576 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
25626 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 40 0.83
53 8 0.17
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:25682 original size:28 final size:29
Alignment explanation
Indices: 25622--25745 Score: 132
Period size: 29 Copynumber: 4.4 Consensus size: 29
25612 AAAACTTTGT
* *
25622 TTCAAAATAAATAGACTCAAAGAT-TTT-
1 TTCAAAAGAAACAGACTCAAAGATATTTA
25649 TTCAAAAGAAACA-ACTCAAAGATATTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
* * * *
25677 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
*
25706 TTCAAAAGGAACAGACTCAAAG--ATTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
*
25733 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
25746 TGTCTCCAGA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.12
27 19 0.23
28 21 0.25
29 33 0.40
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (29 bp):
TTCAAAAGAAACAGACTCAAAGATATTTA
Found at i:25705 original size:29 final size:29
Alignment explanation
Indices: 25636--25731 Score: 135
Period size: 29 Copynumber: 3.4 Consensus size: 29
25626 AAATAAATAG
*
25636 ACTCAAAGA-TTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
25662 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
25691 ACTCCAAGATTTTTATTCAAAAGGAACAG
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
25720 ACTCAAAGATTT
1 ACTCAAAGATTT
25732 ATCTCAAGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
26 9 0.15
27 3 0.05
28 11 0.18
29 38 0.62
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:25753 original size:57 final size:54
Alignment explanation
Indices: 25622--25745 Score: 133
Period size: 57 Copynumber: 2.2 Consensus size: 54
25612 AAAACTTTGT
* * * *
25622 TTCAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCCAAGATTTTTTCAAAAGAAACAACTCAAAGA-ATTTA
* *
25677 TTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAGACTCAAAG-ATTTA
1 TTCAAAAGAAACAAACTCCAAGA-TTTT-TTCAAAAGAAACA-ACTCAAAGAATTTA
*
25733 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
25746 TGTCTCCAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
55 18 0.32
56 10 0.18
57 21 0.37
58 8 0.14
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (54 bp):
TTCAAAAGAAACAAACTCCAAGATTTTTTCAAAAGAAACAACTCAAAGAATTTA
Found at i:26129 original size:36 final size:35
Alignment explanation
Indices: 26045--26148 Score: 104
Period size: 36 Copynumber: 3.0 Consensus size: 35
26035 AAAGGAAAAA
* ** *
26045 TGTCTCAAGCGAGACGAAATTTGCTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTTTTTTAGAGAAAT
* **
26079 AGTCTCAAATGAGACAAAATTTATTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTT-TTTTTAGAGAAAT
*
26115 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTT-TTTTTAGAGAAA
26149 ACGATCTCAA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
34 18 0.32
35 10 0.18
36 28 0.50
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (35 bp):
TGTCTCAAGCGAGACAAAATTTTTTTTAGAGAAAT
Found at i:26157 original size:36 final size:36
Alignment explanation
Indices: 26041--26164 Score: 94
Period size: 36 Copynumber: 3.5 Consensus size: 36
26031 TCTCAAAGGA
* * **
26041 AAAATGTCTCAAGCGAGACGAAATTT-GCTTTA-AG
1 AAAACGTCTCAAGCGAGACAAAATTTATTTTTAGAG
* **
26075 ATATA-GTCTCAAATGAGACAAAATTTATTTTTAGAG
1 A-AAACGTCTCAAGCGAGACAAAATTTATTTTTAGAG
** * *
26111 AAATTGTCTCAAGCGAGACAAAGTTTGTTTTT-GAG
1 AAAACGTCTCAAGCGAGACAAAATTTATTTTTAGAG
*
26146 AAAACGATCTCAAGTGAGA
1 AAAACG-TCTCAAGCGAGA
26165 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
34 19 0.27
35 14 0.20
36 37 0.53
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (36 bp):
AAAACGTCTCAAGCGAGACAAAATTTATTTTTAGAG
Found at i:26360 original size:36 final size:36
Alignment explanation
Indices: 26320--26401 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
26310 AAAGGAAAAA
* * *
26320 TGTCTCAAGCGAGACGAAGTTTG-TTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAA-AGAAAT
* * *
26356 TGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAAT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
26392 TGTCTCAAGC
1 TGTCTCAAGC
26402 AAAACAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
Found at i:26409 original size:36 final size:36
Alignment explanation
Indices: 26320--26414 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
26310 AAAGGAAAAA
* * * *
26320 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
* * * *
26356 TGTCTTAAGTGATACAAACTTTGTTTTTAA-AGAAAT
1 TGTCTCAAGCGAAACAAAATTTG-TTTTAAGAGAAAT
*
26392 TGTCTCAAGCAAAACAAAATTTG
1 TGTCTCAAGCGAAACAAAATTTG
26415 AGAAAACGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 41 0.87
37 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
Found at i:26459 original size:168 final size:166
Alignment explanation
Indices: 26262--26580 Score: 423
Period size: 167 Copynumber: 1.9 Consensus size: 166
26252 ACAATCTAAG
* *
26262 GTGAGATTAATTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCA
1 GTGAGATCAACTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTC-AAGGAAAAATGTCTCA
* ** * *
26327 AGCGAGAC-GAAGTTTG-TTTT-AAGAGAATTTGTCTTAAGTGATACAAACTTTGTTTTTAAAGA
65 AGCGAGACGGAA-TTTGTTTTTCAAGA-AA-TTGTCTCAAACGAGACAAAATTTGTTTTT--AGA
*
26389 AA-TTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
125 AAGCTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
* *
26430 GTGAGATCAACTTTG-TTTAATGTGAATCAAATTCGAAATTTGTATCTCAAGGAAAAATGTCTCC
1 GTGAGATCAACTTTGTTTTAA-GTGAATCAAATTCAAAATTTGTATCTCAAGGAAAAATGTCTCA
*
26494 AGTGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCT
65 AGCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCT
* *
26559 GTCTCAAGCGAGACAAAATTTG
130 GTCTCAAGCAAAACAAAATTTG
26581 CTTTGAAAGA
Statistics
Matches: 133, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
165 5 0.04
166 21 0.16
167 55 0.41
168 48 0.36
169 4 0.03
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (166 bp):
GTGAGATCAACTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTCAAGGAAAAATGTCTCAA
GCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAAAATTTGTTTTTAGAAAGCTG
TCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
Found at i:26537 original size:36 final size:35
Alignment explanation
Indices: 26504--26621 Score: 157
Period size: 36 Copynumber: 3.3 Consensus size: 35
26494 AGTGAGACGG
*
26504 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAGCGAGACAA
*
26540 AATTTGTTTTT-AGAAAGCTGTCTCAAGCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAGCGAGACAA
**
26575 AATTTGCTTTGAAAGAAATTGTCTCAAGCGAGACAAA
1 AATTTG-TTTTTAAGAAATTGTCTCAAGCGAGAC-AA
26612 AATTTGTTTT
1 AATTTGTTTT
26622 AAAATTCTCA
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
34 5 0.07
35 22 0.31
36 32 0.44
37 13 0.18
ACGTcount: A:0.36, C:0.13, G:0.17, T:0.34
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAGCGAGACAA
Found at i:27007 original size:20 final size:20
Alignment explanation
Indices: 26982--27029 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
26972 TGTAACATGC
26982 ATGTATGTGTTGATGTATGT
1 ATGTATGTGTTGATGTATGT
*
27002 ATGTATGAGTTGATGTATGT
1 ATGTATGTGTTGATGTATGT
*
27022 ATATATGT
1 ATGTATGT
27030 ATGTATGAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (20 bp):
ATGTATGTGTTGATGTATGT
Found at i:28256 original size:12 final size:11
Alignment explanation
Indices: 28228--28265 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
28218 TCCTCTTTTG
*
28228 TTCTTTGCTTT
1 TTCTTTGATTT
28239 TTCTTTGATTT
1 TTCTTTGATTT
28250 TTGCTTTGATTT
1 TT-CTTTGATTT
28262 TTCT
1 TTCT
28266 CTTTGCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.05, C:0.13, G:0.11, T:0.71
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:28967 original size:46 final size:45
Alignment explanation
Indices: 28875--28968 Score: 125
Period size: 46 Copynumber: 2.1 Consensus size: 45
28865 ATAAATGCAG
* * * *
28875 TGTTTCAAGGTGGAAAGAATGTTTCAAGGCCTTAAAGAGAGGGAA
1 TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
* *
28920 TGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAGATAGAA
1 TGTTTCAAGGT-GAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
28966 TGT
1 TGT
28969 CAAAAATTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 11 0.26
46 31 0.74
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (45 bp):
TGTTTCAAGGTGAAAAGAATATTTCAAGGCCTCAAAGAGAGAGAA
Found at i:30214 original size:31 final size:32
Alignment explanation
Indices: 30158--30219 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
30148 TGACAAAATG
30158 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
30190 ACACAAACAAAAGAGAA-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
30220 CATGTAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:31942 original size:18 final size:19
Alignment explanation
Indices: 31907--31946 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
31897 ATTTAAAAAT
*
31907 TAAATTAATATGAATGAAA
1 TAAAATAATATGAATGAAA
31926 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
31944 TAA
1 TAA
31947 GCAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:32002 original size:2 final size:2
Alignment explanation
Indices: 31997--32047 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
31987 ACACACATAA
** * *
31997 AT AT AT AT AT GC AT AA AT AT AT AT AT AC 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
32039 AT AT AT AT A
1 AT AT AT AT A
32048 ATAAAACATC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:32013 original size:16 final size:16
Alignment explanation
Indices: 31991--32039 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
31981 AATTAAACAC
31991 ACATAAATATATATAT
1 ACATAAATATATATAT
*
32007 GCATAAATATATATAT
1 ACATAAATATATATAT
*
32023 ACATATATATATATAT
1 ACATAAATATATATAT
32039 A
1 A
32040 TATATATAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (16 bp):
ACATAAATATATATAT
Found at i:32044 original size:16 final size:16
Alignment explanation
Indices: 31991--32047 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
31981 AATTAAACAC
*
31991 ACATAAATATATATAT
1 ACATATATATATATAT
* *
32007 GCATAAATATATATAT
1 ACATATATATATATAT
32023 ACATATATATATATAT
1 ACATATATATATATAT
*
32039 ATATATATA
1 ACATATATA
32048 ATAAAACATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (16 bp):
ACATATATATATATAT
Found at i:32145 original size:16 final size:16
Alignment explanation
Indices: 32126--32160 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
32116 TTTAAAAAAC
* *
32126 AAAAGGACTAAATTAT
1 AAAAGGACAAAATGAT
32142 AAAAGGACAAAATGAT
1 AAAAGGACAAAATGAT
32158 AAA
1 AAA
32161 GCATAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (16 bp):
AAAAGGACAAAATGAT
Found at i:36970 original size:12 final size:12
Alignment explanation
Indices: 36953--36990 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
36943 AAATCTAGAA
*
36953 AATGATAAATAT
1 AATGATATATAT
36965 AATGATATATAT
1 AATGATATATAT
36977 -AT-ATATATAT
1 AATGATATATAT
36987 AATG
1 AATG
36991 TCATTCATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
10 8 0.35
11 4 0.17
12 11 0.48
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (12 bp):
AATGATATATAT
Found at i:37960 original size:14 final size:14
Alignment explanation
Indices: 37941--37971 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
37931 ATTAAAATCG
*
37941 AAATAAAAAAGAGT
1 AAATAAAAAAGAAT
37955 AAATAAAAAAGAAT
1 AAATAAAAAAGAAT
37969 AAA
1 AAA
37972 GGAAAATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAATAAAAAAGAAT
Found at i:38725 original size:25 final size:25
Alignment explanation
Indices: 38696--38750 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
38686 AAAATGACAT
38696 ACTATTTCGAAAAT-AAT-AATAAAAA
1 ACTATTT-GAAAATAAATAAAT-AAAA
38721 ACTA-TTGAAAATAAATAAATAAAA
1 ACTATTTGAAAATAAATAAATAAAA
38745 ACTATT
1 ACTATT
38751 AAAAATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.22
24 13 0.48
25 8 0.30
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (25 bp):
ACTATTTGAAAATAAATAAATAAAA
Found at i:38732 original size:23 final size:24
Alignment explanation
Indices: 38704--38756 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
38694 ATACTATTTC
38704 GAAAAT-AAT-AATAAAAAACTATT
1 GAAAATAAATAAAT-AAAAACTATT
38727 GAAAATAAATAAATAAAAACTATT
1 GAAAATAAATAAATAAAAACTATT
*
38751 AAAAAT
1 GAAAAT
38757 TCAAAACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 18 0.67
25 3 0.11
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
GAAAATAAATAAATAAAAACTATT
Found at i:39016 original size:20 final size:20
Alignment explanation
Indices: 38991--39039 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
38981 TTTTATTGTG
*
38991 AGTGGAGGGAGACAAGGACT
1 AGTGGAGGCAGACAAGGACT
39011 AGTGGAGGCAGACAAGGACT
1 AGTGGAGGCAGACAAGGACT
39031 AGTGGAGGC
1 AGTGGAGGC
39040 TTGGTGGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.45, T:0.10
Consensus pattern (20 bp):
AGTGGAGGCAGACAAGGACT
Found at i:39848 original size:170 final size:170
Alignment explanation
Indices: 39660--40249 Score: 1126
Period size: 170 Copynumber: 3.5 Consensus size: 170
39650 TGCTGGTGGA
* *
39660 CACGATATCCTTCGTCGTGAAGTTAAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCATGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
*
39725 GTTGAAATTGGCTCTGAATGAAATTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
66 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
39790 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
131 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
*
39830 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTTGAGTCCAATATCCTTCGTCGTGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
39895 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
66 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
39960 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
131 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
40000 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
40065 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
66 GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
40130 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
131 ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
*
40170 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTTGTGAA
1 CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
*
40235 GTTGAAATTGACTCT
66 GTTGAAATTGGCTCT
40250 AGCTAGAACC
Statistics
Matches: 413, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 413 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (170 bp):
CACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTCGAGTCCAATATCCTTCGTCGTGAA
GTTGAAATTGGCTCTGAATGAAACTGGGAAGCCCCTTCGCTGTGGAGTTGAGCTTTGAATTGGAT
ATCCTTCGCTGTAAAGTTGAAATCCAATGTTGTTTGTGAG
Found at i:39854 original size:46 final size:44
Alignment explanation
Indices: 39787--39902 Score: 130
Period size: 44 Copynumber: 2.6 Consensus size: 44
39777 CTTTGAATTG
* *
39787 GATATCCTTCG-CTGTAAAGTTGAAATCCAAT-GTTGTTTGTGAG-CAC
1 GATATCCTTCGTC-GTGAAGTTGAAAT-C-ATGGATGTTT-TGAGTC-C
*
39833 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGTTTTGAGTCC
1 GATATCCTTCGTCGTGAAGTTGAAATCATGGATGTTTTGAGTCC
*
39877 AATATCCTTCGTCGTGAAGTTGAAAT
1 GATATCCTTCGTCGTGAAGTTGAAAT
39903 TGGCTCTGAA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
44 31 0.49
45 8 0.13
46 23 0.37
47 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (44 bp):
GATATCCTTCGTCGTGAAGTTGAAATCATGGATGTTTTGAGTCC
Found at i:47828 original size:39 final size:39
Alignment explanation
Indices: 47774--47853 Score: 117
Period size: 39 Copynumber: 2.1 Consensus size: 39
47764 TTAACAGTAG
* *
47774 ATGCAGCTTTCCCTTTGGTAGAGGATGAGTCAC-CGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTC-CTCGGGTA
*
47813 ATGCAACTTTCCCTTTAGTAGCGGATGAGTCCTCGGGTA
1 ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
47852 AT
1 AT
47854 ACTCCGGGTG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 36 0.97
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (39 bp):
ATGCAACTTTCCCTTTAGTAGAGGATGAGTCCTCGGGTA
Found at i:51432 original size:14 final size:14
Alignment explanation
Indices: 51413--51443 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
51403 ATTAAAATCG
*
51413 AAATAAAAAAGAGT
1 AAATAAAAAAGAAT
51427 AAATAAAAAAGAAT
1 AAATAAAAAAGAAT
51441 AAA
1 AAA
51444 GGAAAATTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (14 bp):
AAATAAAAAAGAAT
Found at i:52199 original size:25 final size:25
Alignment explanation
Indices: 52170--52224 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 25
52160 AAAATGACAT
52170 ACTATTTCGAAAAT-AAT-AATAAAAA
1 ACTATTT-GAAAATAAATAAAT-AAAA
52195 ACTA-TTGAAAATAAATAAATAAAA
1 ACTATTTGAAAATAAATAAATAAAA
52219 ACTATT
1 ACTATT
52225 AAAAATTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
23 6 0.22
24 13 0.48
25 8 0.30
ACGTcount: A:0.60, C:0.07, G:0.04, T:0.29
Consensus pattern (25 bp):
ACTATTTGAAAATAAATAAATAAAA
Found at i:52206 original size:23 final size:24
Alignment explanation
Indices: 52178--52230 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 24
52168 ATACTATTTC
52178 GAAAAT-AAT-AATAAAAAACTATT
1 GAAAATAAATAAAT-AAAAACTATT
52201 GAAAATAAATAAATAAAAACTATT
1 GAAAATAAATAAATAAAAACTATT
*
52225 AAAAAT
1 GAAAAT
52231 TCAAAACAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 6 0.22
24 18 0.67
25 3 0.11
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
GAAAATAAATAAATAAAAACTATT
Found at i:52486 original size:20 final size:20
Alignment explanation
Indices: 52461--52509 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
52451 TTTTATTGTG
*
52461 AGTGGAGGGAGACAAGGACT
1 AGTGGAGGCAGACAAGGACT
52481 AGTGGAGGCAGACAAGGACT
1 AGTGGAGGCAGACAAGGACT
52501 AGTGGAGGC
1 AGTGGAGGC
52510 TTGGTGGCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.45, T:0.10
Consensus pattern (20 bp):
AGTGGAGGCAGACAAGGACT
Found at i:59848 original size:26 final size:26
Alignment explanation
Indices: 59796--59848 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
59786 ATAAAACATA
* * * * *
59796 AATATGATGATGATGATGATGATAAT
1 AATATAATGATGACGACGACGACAAT
59822 AATATAATGATGACGACGACGACAAT
1 AATATAATGATGACGACGACGACAAT
59848 A
1 A
59849 TGAGAAAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (26 bp):
AATATAATGATGACGACGACGACAAT
Done.