Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008548.1 Hibiscus syriacus cultivar Beakdansim tig00111440_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: 1170587
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:254408 original size:33 final size:33
Alignment explanation
Indices: 254361--254444 Score: 141
Period size: 33 Copynumber: 2.5 Consensus size: 33
254351 GGCTCGGCTT
*
254361 GGCTCAGCTCAAACGGCTCGGCTCAGCTCAAAC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
* *
254394 GGCTCGGCTGAAACGGCTCGGCTCAGCTCAAGC
1 GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
254427 GGCTCGGCTCAAACGGCT
1 GGCTCGGCTCAAACGGCT
254445 ACTCAGGCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.20, C:0.35, G:0.30, T:0.15
Consensus pattern (33 bp):
GGCTCGGCTCAAACGGCTCGGCTCAGCTCAAAC
Found at i:258217 original size:18 final size:18
Alignment explanation
Indices: 258194--258228 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
258184 TTCCATCCGG
*
258194 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
258212 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
258229 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:259405 original size:19 final size:19
Alignment explanation
Indices: 259383--259451 Score: 102
Period size: 19 Copynumber: 3.6 Consensus size: 19
259373 CTAGGCGGCT
*
259383 CGGCTTGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
* *
259402 CGGCTCGGCTCGGCTGAAA
1 CGGCTCGGCTCAGCTCAAA
*
259421 CGGCTCGGCTCAGCTCAAG
1 CGGCTCGGCTCAGCTCAAA
259440 CGGCTCGGCTCA
1 CGGCTCGGCTCA
259452 AACGGCTACT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.16, C:0.35, G:0.32, T:0.17
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:259412 original size:14 final size:14
Alignment explanation
Indices: 259407--259458 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
259397 TCAAACGGCT
*
259407 CGGCTCGGCTGAAA
1 CGGCTCGGCTCAAA
259421 CGGCTCGGCTCAGCTCAA
1 CGGCTCGGCTCA----AA
259439 GCGGCTCGGCTCAAA
1 -CGGCTCGGCTCAAA
259454 CGGCT
1 CGGCT
259459 ACTCAGGCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 16 0.50
15 2 0.06
18 2 0.06
19 12 0.38
ACGTcount: A:0.17, C:0.35, G:0.33, T:0.15
Consensus pattern (14 bp):
CGGCTCGGCTCAAA
Found at i:261620 original size:21 final size:22
Alignment explanation
Indices: 261594--261634 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
261584 ACAAGCGTCG
261594 TAATTTTCAA-ATAAATAAACT
1 TAATTTTCAATATAAATAAACT
*
261615 TAATTTTCAATTTAAATAAA
1 TAATTTTCAATATAAATAAA
261635 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.41
Consensus pattern (22 bp):
TAATTTTCAATATAAATAAACT
Found at i:265043 original size:2 final size:2
Alignment explanation
Indices: 265036--265091 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
265026 CATGTAAACC
265036 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
265078 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
265092 TATCATAAAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:265386 original size:23 final size:23
Alignment explanation
Indices: 265360--265423 Score: 101
Period size: 23 Copynumber: 2.8 Consensus size: 23
265350 CAGCTCATAT
265360 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
265383 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
*
265406 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
265424 TATAATAATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.27, C:0.27, G:0.28, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:266409 original size:64 final size:64
Alignment explanation
Indices: 266304--266460 Score: 185
Period size: 64 Copynumber: 2.5 Consensus size: 64
266294 TAATGAAGGT
* * * ** *
266304 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGCATTCGATG-TTTATTTATTACTGGG
1 ATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGATTTATTT-TAAAAGAG
* *
266368 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTATTTATTTTAAAAGA
1 ATGCATCGATGCACTACTAATGCATCGATGCA-TAAAATGCATTCGATG-ATTTATTTTAAAAGA
266432 G
64 G
*
266433 -TGCATCGATGCACTACCAATGCATCGAT
1 ATGCATCGATGCACTACTAATGCATCGAT
266461 ACACCTTCAA
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
64 69 0.85
65 5 0.06
66 7 0.09
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTAATGCATCGATGCATAAAATGCATTCGATGATTTATTTTAAAAGAG
Found at i:270920 original size:23 final size:23
Alignment explanation
Indices: 270894--270957 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
270884 CAACTCATAT
270894 AATTGCACCGAAGTGCCACGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
270917 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCACGTAG
* *
270940 AATTGCAGCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
270958 TATAATAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.27, C:0.25, G:0.30, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCACGTAG
Found at i:274052 original size:19 final size:20
Alignment explanation
Indices: 274024--274062 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
274014 TTGTGAAAAG
274024 AAAATAATGAAAGAAAAGTA
1 AAAATAATGAAAGAAAAGTA
274044 AAAAT-ATGAAAGAAAAGTA
1 AAAATAATGAAAGAAAAGTA
274063 GAACTTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATAATGAAAGAAAAGTA
Found at i:274237 original size:14 final size:15
Alignment explanation
Indices: 274202--274230 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
274192 CCAATAGTTC
274202 TAATAAAATAAT-AA
1 TAATAAAATAATCAA
274216 TAATAAAATAATCAA
1 TAATAAAATAATCAA
274231 ACTAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 12 0.86
15 2 0.14
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (15 bp):
TAATAAAATAATCAA
Found at i:284421 original size:20 final size:20
Alignment explanation
Indices: 284398--284476 Score: 122
Period size: 20 Copynumber: 4.0 Consensus size: 20
284388 AATGCCAGTA
*
284398 TGACTATCGCAACTCGATTC
1 TGACTATCGCAACGCGATTC
*
284418 TGACTATCGCAACGAGATTC
1 TGACTATCGCAACGCGATTC
284438 TGACTATCGCAACGCGATTC
1 TGACTATCGCAACGCGATTC
* *
284458 TGACTGTCGCAATGCGATT
1 TGACTATCGCAACGCGATT
284477 TTCAAAGCGC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (20 bp):
TGACTATCGCAACGCGATTC
Found at i:284427 original size:40 final size:40
Alignment explanation
Indices: 284383--284472 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
284373 GAATATGTAA
*
284383 ATCGCAATGCCAGTATGACTATCGCAACTCGATTCTGACT
1 ATCGCAATGCCAGTATGACTATCGCAACGCGATTCTGACT
* ** * *
284423 ATCGCAACGAGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAATGCCAGTATGACTATCGCAACGCGATTCTGACT
*
284463 GTCGCAATGC
1 ATCGCAATGC
284473 GATTTTCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.26
Consensus pattern (40 bp):
ATCGCAATGCCAGTATGACTATCGCAACGCGATTCTGACT
Found at i:285134 original size:20 final size:20
Alignment explanation
Indices: 285109--285161 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
285099 TAATTTTTAT
285109 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
285129 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
285149 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
285162 TTTCATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.17, C:0.19, G:0.26, T:0.38
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:285167 original size:20 final size:20
Alignment explanation
Indices: 285129--285184 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
285119 GATAGTCAAA
* **
285129 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
285149 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
285169 TTTGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
285185 AAGTTTCAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.14, G:0.23, T:0.52
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:286932 original size:18 final size:18
Alignment explanation
Indices: 286909--286958 Score: 100
Period size: 18 Copynumber: 2.8 Consensus size: 18
286899 TTTACTCGTA
286909 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
286927 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
286945 ATTTCACTTAGATT
1 ATTTCACTTAGATT
286959 GCTTAGTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:287128 original size:20 final size:20
Alignment explanation
Indices: 287103--287170 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
287093 GTGTTTACTT
*
287103 TCGCAACGTGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
287123 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
287143 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
287163 TCGCAACG
1 TCGCAACG
287171 AAAGAATTGC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:287790 original size:18 final size:19
Alignment explanation
Indices: 287751--287792 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
287741 CTCACATGTC
287751 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
287772 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
287790 ATC
1 ATC
287793 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:289292 original size:14 final size:14
Alignment explanation
Indices: 289255--289316 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
289245 TTGCTTGTTT
*
289255 AATTGATTTATAAA
1 AATTGATTTGTAAA
289269 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
289283 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
289298 TATTGATGTGTAAA
1 AATTGATTTGTAAA
289312 TAATT
1 -AATT
289317 CTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:289520 original size:34 final size:34
Alignment explanation
Indices: 289477--289610 Score: 144
Period size: 34 Copynumber: 3.8 Consensus size: 34
289467 AGTCAATTCG
* *
289477 CGTTGCGATAGTCTAATACGCTTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
* *
289511 CGTTGCGATAGTCAAATACCCGTTGCGATAATAAAATTCG
1 CGTTGCGATAGTCAAATACGCGTTGCGAT--T----TTCT
* *
289551 CGTTGCGATAGTCAAATTCGCGTTGTGATTTTCT
1 CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
289585 CGTTGCGATAGTCAAATA-GTCGTTGC
1 CGTTGCGATAGTCAAATACG-CGTTGC
289611 TATAGTCAAA
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
33 1 0.01
34 51 0.61
36 1 0.01
38 1 0.01
40 29 0.35
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.35
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATACGCGTTGCGATTTTCT
Found at i:289568 original size:20 final size:20
Alignment explanation
Indices: 289462--289749 Score: 178
Period size: 20 Copynumber: 15.7 Consensus size: 20
289452 AAATCGCAAC
*
289462 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
289481 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
289501 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
* *
289515 GCGATAGTCAAATACCCGTT
1 GCGATAGTCAAATTCGCGTT
* *
289535 GCGATAATAAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
289555 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
289575 GTGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
*
289589 GCGATAGTCAAA-TAGTCGTT
1 GCGATAGTCAAATTCG-CGTT
*
289609 GCTATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
289629 GCGAT--T----TTTGCGTT
1 GCGATAGTCAAATTCGCGTT
* *
289643 GCGATAGTCATATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
289663 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
289683 GTGAT--T----TTTGAGTT
1 GCGATAGTCAAATTCGCGTT
* * *
289697 ACGATAATCAAATTCGTGTT
1 GCGATAGTCAAATTCGCGTT
289717 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
289737 GCGATATTCAAAT
1 GCGATAGTCAAAT
289750 GAATGTGTAA
Statistics
Matches: 204, Mismatches: 38, Indels: 53
0.69 0.13 0.18
Matches are distributed among these distances:
14 42 0.21
16 4 0.02
18 4 0.02
19 9 0.04
20 143 0.70
21 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:289589 original size:54 final size:54
Alignment explanation
Indices: 289531--289737 Score: 283
Period size: 54 Copynumber: 3.8 Consensus size: 54
289521 GTCAAATACC
*
289531 CGTTGCGATAATAAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTCT-
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTT-TG
* * * *
289585 CGTTGCGATAGTCAAA-TAGTCGTTGCTATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAATCAAATTCG-CGTTGCGATAGTCAAATTCGCGTTGTGATTTTTG
* * *
289639 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGTGATTTTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTTG
* * *
289693 AGTTACGATAATCAAATTCGTGTTGCGATAGTCAAATTCGCGTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
289738 CGATATTCAA
Statistics
Matches: 136, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
53 3 0.02
54 131 0.96
55 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.37
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTTG
Found at i:289592 original size:74 final size:74
Alignment explanation
Indices: 289471--289633 Score: 245
Period size: 74 Copynumber: 2.2 Consensus size: 74
289461 CGCGAAAGTC
* *
289471 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
289536 CGATAATAA
66 CGATAATAA
* * **
289545 AATTCGCGTTGCGATAGTCAAATTCGCGTTGTGATTTTCTCGTTGCGATAGTCAAATAGTCGTTG
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
* * *
289610 CTATAGTCA
66 CGATAATAA
289619 AATTCGCGTTGCGAT
1 AATTCGCGTTGCGAT
289634 TTTTGCGTTG
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 80 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (74 bp):
AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATTTTCTCGTTGCGATAGTCAAATACCCGTTG
CGATAATAA
Found at i:289971 original size:139 final size:140
Alignment explanation
Indices: 289720--289988 Score: 504
Period size: 139 Copynumber: 1.9 Consensus size: 140
289710 TCGTGTTGCG
*
289720 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
289785 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
289850 AATACACATA
131 AATACACATA
289860 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGT-TAATAAGTGATAACAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
*
289924 TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
289989 TACAACGTTT
Statistics
Matches: 126, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
139 90 0.71
140 36 0.29
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAAATCAAGTTACTAATACATGCCTAACTAAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:290071 original size:18 final size:18
Alignment explanation
Indices: 290048--290082 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
290038 AAGCCGGTTG
*
290048 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
290066 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
290083 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:292379 original size:24 final size:24
Alignment explanation
Indices: 292345--292398 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
292335 CTGAAACATC
292345 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
292369 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
292393 ATCAAA
1 ATCAAA
292399 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:293263 original size:84 final size:84
Alignment explanation
Indices: 293122--293285 Score: 310
Period size: 84 Copynumber: 2.0 Consensus size: 84
293112 GAGTTGCGAT
293122 TTAGGGATTTAGGTTATGAGTTGCTTCTGCTGCGTAGTTATATACCCAAAACATTTGTGTTGCGA
1 TTAGGGATTTAGGTTATGAGTTGCTTCTGCTGCGTAGTTATATACCCAAAACATTTGTGTTGCGA
293187 AACTAAAACCTGTTGTTAA
66 AACTAAAACCTGTTGTTAA
* *
293206 TTAGGGATTTAGGTTATGAGTTGCTTCTGCTGCGTAGTTATATACCGAAAACATTTGTGTTGTGA
1 TTAGGGATTTAGGTTATGAGTTGCTTCTGCTGCGTAGTTATATACCCAAAACATTTGTGTTGCGA
293271 AACTAAAACCTGTTG
66 AACTAAAACCTGTTG
293286 CAAATTTGAA
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
84 78 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (84 bp):
TTAGGGATTTAGGTTATGAGTTGCTTCTGCTGCGTAGTTATATACCCAAAACATTTGTGTTGCGA
AACTAAAACCTGTTGTTAA
Found at i:293328 original size:20 final size:20
Alignment explanation
Indices: 293303--293389 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
293293 GAAATTCAGT
293303 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
293323 GTTGCGACAGTCAGAATCGC
1 GTTGCGACAGTCAGAATCGC
* *
293343 GTTGCGACAGTCATAATCGT
1 GTTGCGACAGTCAGAATCGC
* *
293363 GTTGCGACAGTCATAATTGC
1 GTTGCGACAGTCAGAATCGC
*
293383 ATTGCGA
1 GTTGCGA
293390 TTTAGTTGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (20 bp):
GTTGCGACAGTCAGAATCGC
Found at i:293638 original size:15 final size:15
Alignment explanation
Indices: 293618--293651 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
293608 TTAAAAAAAG
293618 ATTTTAACTAGTAAC
1 ATTTTAACTAGTAAC
293633 ATTTTAACTAGTAAC
1 ATTTTAACTAGTAAC
293648 ATTT
1 ATTT
293652 CATGAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTTTAACTAGTAAC
Found at i:296096 original size:3 final size:3
Alignment explanation
Indices: 296088--296199 Score: 172
Period size: 3 Copynumber: 37.7 Consensus size: 3
296078 TTTTTATCCA
*
296088 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * *
296136 TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TTT TAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
296184 TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TA
296200 AATATATTAA
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
2 2 0.02
3 96 0.98
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:298198 original size:21 final size:21
Alignment explanation
Indices: 298174--298228 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
298164 AAATTAAAAA
* *
298174 TTTATATATTTAATTCTTTTT
1 TTTATATATTTAATTATTATT
* *
298195 TTTATTTATTTATTTATTATT
1 TTTATATATTTAATTATTATT
298216 TTTATAATATTTA
1 TTTAT-ATATTTA
298229 TATGTTATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATATATTTAATTATTATT
Found at i:308876 original size:12 final size:11
Alignment explanation
Indices: 308854--308946 Score: 84
Period size: 11 Copynumber: 8.2 Consensus size: 11
308844 TATTATGCTT
308854 AAAGAAAAGAA
1 AAAGAAAAGAA
*
308865 AGAAGAAGAGAA
1 A-AAGAAAAGAA
308877 AAAGAATAAGAAA
1 AAAGAA-AAG-AA
*
308890 ATAAGAAAAAAA
1 A-AAGAAAAGAA
308902 AAAGAAAAG-A
1 AAAGAAAAGAA
308912 AAA-AAAAGAA
1 AAAGAAAAGAA
*
308922 GAAGAAAA-AA
1 AAAGAAAAGAA
308932 AATAGAAAAAGAA
1 AA-AG-AAAAGAA
308945 AA
1 AA
308947 GGGTCAAGGT
Statistics
Matches: 67, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
9 5 0.07
10 10 0.15
11 19 0.28
12 19 0.28
13 9 0.13
14 5 0.07
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:308882 original size:14 final size:12
Alignment explanation
Indices: 308854--308947 Score: 88
Period size: 12 Copynumber: 7.8 Consensus size: 12
308844 TATTATGCTT
308854 AAAGAAAAGAAA
1 AAAGAAAAGAAA
* *
308866 GAAGAAGAG-AA
1 AAAGAAAAGAAA
308877 AAAGAATAAGAAA
1 AAAGAA-AAGAAA
308890 ATAAGAAAA-AAA
1 A-AAGAAAAGAAA
308902 AAAGAAAAGAAA
1 AAAGAAAAGAAA
308914 AAA-AAGAAGAAGA
1 AAAGAA-AAGAA-A
*
308927 AAA-AAAATAGAA
1 AAAGAAAAGA-AA
308939 AAAGAAAAG
1 AAAGAAAAG
308948 GGTCAAGGTG
Statistics
Matches: 68, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
11 16 0.24
12 31 0.46
13 16 0.24
14 5 0.07
ACGTcount: A:0.79, C:0.00, G:0.18, T:0.03
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:308931 original size:17 final size:17
Alignment explanation
Indices: 308858--308946 Score: 76
Period size: 17 Copynumber: 5.1 Consensus size: 17
308848 ATGCTTAAAG
*
308858 AAAAGAAAGAAGAAGAGA
1 AAAAAAAAGAAGAAGA-A
*
308876 AAAAGAATAAGAA-AATAA
1 AAAA-AA-AAGAAGAAGAA
308894 GAAAAAAAA-AAGAA-AA
1 -AAAAAAAAGAAGAAGAA
308910 GAAAAAAAAGAAGAAGAA
1 -AAAAAAAAGAAGAAGAA
* *
308928 AAAAAATAGAAAAAGAA
1 AAAAAAAAGAAGAAGAA
308945 AA
1 AA
308947 GGGTCAAGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
16 13 0.21
17 26 0.43
18 9 0.15
19 8 0.13
20 5 0.08
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (17 bp):
AAAAAAAAGAAGAAGAA
Found at i:309310 original size:19 final size:20
Alignment explanation
Indices: 309277--309318 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
309267 TTCAAGTTCA
*
309277 ATTTATTGGAGATTCAATTT
1 ATTTATTGGAAATTCAATTT
309297 ATTT-TTGGAAATTCAATTT
1 ATTTATTGGAAATTCAATTT
309316 ATT
1 ATT
309319 CTTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTATTGGAAATTCAATTT
Found at i:310181 original size:52 final size:52
Alignment explanation
Indices: 310099--310562 Score: 797
Period size: 52 Copynumber: 8.9 Consensus size: 52
310089 GAATGTGCTT
310099 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
* *
310151 ATAGCATCTTCTGGAAGTGTTCTTTAAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
310203 ATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* *
310255 ATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTGAACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
310307 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
310359 ATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTT-GATCAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGA-CAGAAC
*
310411 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
310463 ATAACATCTTCTGGAAGTGTTCTTTGAGTTATTTAATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
310515 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTGGACA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACA
310563 AAATCAAGTA
Statistics
Matches: 392, Mismatches: 17, Indels: 6
0.94 0.04 0.01
Matches are distributed among these distances:
51 2 0.01
52 386 0.98
53 4 0.01
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:311427 original size:118 final size:118
Alignment explanation
Indices: 311199--312541 Score: 2364
Period size: 118 Copynumber: 11.4 Consensus size: 118
311189 TCAAATCCAC
** *
311199 TTGATGGATCATTCATCCCCAGAGGAAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGAAAG
1 TTGATGGATCA-TCATTTCCAGA-GAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGG
* * * *
311260 AAGAAGAAATTCATAATGAAAAGAATTTGTTCAACCTTTTGCTTAAATTCATCAT
64 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAT
*
311315 TTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
*
311380 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAT
311433 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
311498 GAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC-AT
311551 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
*
311616 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAT
311669 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
311734 GAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAT
*
311786 TTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
*
311851 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAT
311904 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
311969 GAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC-AT
*
312022 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAATAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
*
312087 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAC
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAT
312140 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
312205 GAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC-AT
*
312258 TTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
312323 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAAT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC-AT
*
312377 TTGATGGATCATCATTTCCAAAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
1 TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
*
312442 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTTGAATTCATCAT
66 GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAT
* ** *
312495 TTGATGGAACATCATCCCCAGCAG-AA-AGTTCGTAATGAGAAGAACTC
1 TTGATGGATCATCATTTCCAG-AGAAAGAGTTCATAATGAGAAGAACTC
312542 ATCTGGAGAA
Statistics
Matches: 1185, Mismatches: 30, Indels: 23
0.96 0.02 0.02
Matches are distributed among these distances:
114 3 0.00
115 27 0.02
116 11 0.01
117 274 0.23
118 614 0.52
119 256 0.22
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (118 bp):
TTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAA
GAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAT
Found at i:312151 original size:471 final size:471
Alignment explanation
Indices: 311196--312541 Score: 2445
Period size: 471 Copynumber: 2.9 Consensus size: 471
311186 ATTTCAAATC
**
311196 CACTTGATGGATCATTCATCCCCAGAGGAAA-AGTTCATAATGAGAAGAA--C-TCATCTGAAGA
1 CACTTGATGGATCA-TCATTTCCAGA-GAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGA
* * * * *
311257 AAGAAGAAGAAATTCATAATGAAAAGAATTTGTTCAACCTTTTGCTTAAATTCATCATTTGATGG
64 AGGAAGAAG-AGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGG
311322 ATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAG
128 ATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAG
311387 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
193 TTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCC
311452 AGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAGTTCATAATGAGAA
258 AGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAGTTCATAATGAGAA
311517 GAACTTGTTCAACCTTTTGCTTGAATTCATCAATTTGATGGATCATCATTTCCAGAGAAAGAGTT
323 GAACTTGTTCAACCTTTTGCTTGAATTCATCAATTTGATGGATCATCATTTCCAGAGAAAGAGTT
311582 CATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
388 CATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
311647 ACCTTTTGCTTGAATTCAT
453 ACCTTTTGCTTGAATTCAT
311666 CACTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 CACTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
311731 GAAGAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATC
66 GAAGAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATC
311796 ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
131 ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
311861 ATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCCAGA
196 ATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCCAGA
311926 GAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAGTTCATAATGAGAAGAA
261 GAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAGTTCATAATGAGAAGAA
311991 CTTGTTCAACCTTTTGCTTGAATTCATCAATTTGATGGATCATCATTTCCAGAGAAAGAGTTCAT
326 CTTGTTCAACCTTTTGCTTGAATTCATCAATTTGATGGATCATCATTTCCAGAGAAAGAGTTCAT
*
312056 AATGAGAATAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
391 AATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
312121 TTTTGCTTGAATTCAT
456 TTTTGCTTGAATTCAT
312137 CACTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
1 CACTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
312202 GAAGAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAATTTGATGGAT
66 GAAGAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC-ATTTGATGGAT
312267 CATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTT
130 CATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTT
*
312332 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCAATTTGATGGATCATCATTTCCA
195 CATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATC-ACTTGATGGATCATCATTTCCA
*
312397 AAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
259 GAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAG-AGTTCATAATGAGAA
* * **
312462 GAACTTGTTCAATCTTTTGCTTGAATTCATC-ATTTGATGGAACATCATCCCCAGCAG-AA-AGT
323 GAACTTGTTCAACCTTTTGCTTGAATTCATCAATTTGATGGATCATCATTTCCAG-AGAAAGAGT
*
312524 TCGTAATGAGAAGAACTC
387 TCATAATGAGAAGAACTC
312542 ATCTGGAGAA
Statistics
Matches: 852, Mismatches: 16, Indels: 14
0.97 0.02 0.02
Matches are distributed among these distances:
468 4 0.00
469 27 0.03
470 14 0.02
471 513 0.60
472 156 0.18
473 91 0.11
474 47 0.06
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (471 bp):
CACTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAG
GAAGAAGAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTTGATGGATC
ATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCACTTGATGGATCATCATTTCCAGA
GAAAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAGTTCATAATGAGAAGAA
CTTGTTCAACCTTTTGCTTGAATTCATCAATTTGATGGATCATCATTTCCAGAGAAAGAGTTCAT
AATGAGAAGAACTCGTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACC
TTTTGCTTGAATTCAT
Found at i:312704 original size:3 final size:3
Alignment explanation
Indices: 312696--312819 Score: 187
Period size: 3 Copynumber: 41.7 Consensus size: 3
312686 TTTTTATCCA
* *
312696 TAT TAT TAT TAT TAA TAT TAT TAT TAT TAA TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
312744 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAA TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
312792 TTT TAT TTT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
312820 AATATATTAA
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
2 2 0.02
3 106 0.98
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:313295 original size:13 final size:13
Alignment explanation
Indices: 313273--313303 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
313263 CCACCTGCAA
313273 AGAGACAAAAAAC
1 AGAGACAAAAAAC
*
313286 AGAGAGAAAAAAC
1 AGAGACAAAAAAC
313299 AGAGA
1 AGAGA
313304 ACGGAAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.68, C:0.10, G:0.23, T:0.00
Consensus pattern (13 bp):
AGAGACAAAAAAC
Found at i:313342 original size:23 final size:24
Alignment explanation
Indices: 313295--313345 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
313285 CAGAGAGAAA
**
313295 AAACAGAGAACGGAAAGAAAAAAC
1 AAACAGAGAAAAGAAAGAAAAAAC
313319 AAACAGAGAAAAGAAA-AAAAAAC
1 AAACAGAGAAAAGAAAGAAAAAAC
313342 AAAC
1 AAAC
313346 TAATACCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.73, C:0.12, G:0.16, T:0.00
Consensus pattern (24 bp):
AAACAGAGAAAAGAAAGAAAAAAC
Found at i:317396 original size:2 final size:2
Alignment explanation
Indices: 317389--317422 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
317379 CTCTGAAGTG
317389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
317423 AGGTATCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:333257 original size:5 final size:5
Alignment explanation
Indices: 333247--333280 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
333237 AGACAGAAAG
333247 CAAAA CAAAA CAAAA CAAAA CAAAA CAAATA CAA
1 CAAAA CAAAA CAAAA CAAAA CAAAA CAAA-A CAA
333281 TGTTGTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 24 0.86
6 4 0.14
ACGTcount: A:0.76, C:0.21, G:0.00, T:0.03
Consensus pattern (5 bp):
CAAAA
Found at i:334359 original size:20 final size:20
Alignment explanation
Indices: 334336--334373 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
334326 TTTATTATTA
334336 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
334356 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
334374 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:337877 original size:15 final size:16
Alignment explanation
Indices: 337850--337892 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
337840 ATGCCTCGAA
337850 CATTTCATGCATTCTTG
1 CATTTC-TGCATTCTTG
*
337867 CATTT-TGCATTTTTG
1 CATTTCTGCATTCTTG
*
337882 CCTTTCTGCAT
1 CATTTCTGCAT
337893 CTTCATCTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 13 0.57
16 5 0.22
17 5 0.22
ACGTcount: A:0.14, C:0.23, G:0.12, T:0.51
Consensus pattern (16 bp):
CATTTCTGCATTCTTG
Found at i:338694 original size:14 final size:14
Alignment explanation
Indices: 338675--338707 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
338665 AAAGAAGAAG
338675 AATTCATCTGAAAT
1 AATTCATCTGAAAT
338689 AATTCATCTGAAAT
1 AATTCATCTGAAAT
338703 AATTC
1 AATTC
338708 TATCATGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (14 bp):
AATTCATCTGAAAT
Found at i:339052 original size:28 final size:29
Alignment explanation
Indices: 339020--339109 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 29
339010 TCCAATCAAG
* *
339020 AAAAAAAAGAAAAGAAGCAAAAGAAGA-A
1 AAAAAAAAGAAAAGAAGCAAAACAAAAGA
339048 AAAAAAAAGAAAA-AAG-AGAAACAAAAGA
1 AAAAAAAAGAAAAGAAGCA-AAACAAAAGA
*
339076 AAAAAAAAG-AAAGAA-CAAAAAAAAAAGA
1 AAAAAAAAGAAAAGAAGC-AAAACAAAAGA
*
339104 CAAAAA
1 AAAAAA
339110 GCACATGCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
26 1 0.02
27 12 0.23
28 39 0.74
29 1 0.02
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.00
Consensus pattern (29 bp):
AAAAAAAAGAAAAGAAGCAAAACAAAAGA
Found at i:339082 original size:32 final size:31
Alignment explanation
Indices: 339020--339096 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
339010 TCCAATCAAG
* * *
339020 AAAAAA-AAGAAAAGAAGCAAAAGAAGAAAA
1 AAAAAAGAAAAAAAGAAACAAAAGAAAAAAA
339050 AAAAAAGAAAAAAGAGAAACAAAAGAAAAAAA
1 AAAAAAGAAAAAA-AGAAACAAAAGAAAAAAA
*
339082 AAGAAAGAACAAAAA
1 AAAAAAGAA-AAAAA
339097 AAAAAGACAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
30 6 0.15
31 5 0.12
32 25 0.62
33 4 0.10
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (31 bp):
AAAAAAGAAAAAAAGAAACAAAAGAAAAAAA
Found at i:339109 original size:14 final size:13
Alignment explanation
Indices: 339020--339109 Score: 74
Period size: 14 Copynumber: 6.2 Consensus size: 13
339010 TCCAATCAAG
339020 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
339033 GAAGCAAAAGAAGAAAA
1 -AA--AAAA-AAGAAAA
339050 AAAAAAGAA-AAAA
1 AAAAAA-AAGAAAA
339063 GAGAAACAAAAGAAAA
1 -A-AAA-AAAAGAAAA
339079 AAAAAGAAAGAACAA
1 AAAAA-AAAGAA-AA
*
339094 AAAAAAAAGACAA
1 AAAAAAAAGAAAA
339107 AAA
1 AAA
339110 GCACATGCAA
Statistics
Matches: 66, Mismatches: 1, Indels: 19
0.77 0.01 0.22
Matches are distributed among these distances:
13 10 0.15
14 24 0.36
15 13 0.20
16 12 0.18
17 7 0.11
ACGTcount: A:0.82, C:0.04, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:339776 original size:22 final size:22
Alignment explanation
Indices: 339702--339778 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
339692 GCTACCCCAT
* * *
339702 CAAACCGTTAAGCATCAAAGGC
1 CAAACCTTTGAGCATCAAATGC
*
339724 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
339746 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
339768 CAAACCTTTGA
1 CAAACCTTTGA
339779 CCAAACATAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.39, C:0.27, G:0.14, T:0.19
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:340230 original size:18 final size:18
Alignment explanation
Indices: 340195--340230 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
340185 TCAACATCAA
**
340195 ATATTGGGGCATTTTTTG
1 ATATTGGGGCATCATTTG
340213 ATATTGGGGCATCATTTG
1 ATATTGGGGCATCATTTG
340231 GGGATTCAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.28, T:0.44
Consensus pattern (18 bp):
ATATTGGGGCATCATTTG
Found at i:341159 original size:106 final size:106
Alignment explanation
Indices: 340371--341151 Score: 1276
Period size: 106 Copynumber: 7.4 Consensus size: 106
340361 TACAGCTTTT
* *
340371 AGAGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
340436 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
*
340477 GGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
340542 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
* *
340583 AGAGCCAATTTCAACTTCACAACGAAGAATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* *
340648 TGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTT
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
*
340689 GGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
340754 CGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
*
340795 AGAGCCAATTTCAACTTCACAGCGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
*
340860 CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
* * * **
340901 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGATTCGAGACGACGCAAGTTCAACTTCAAAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
340966 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
* * * ** *
341007 GGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCGAGACAATACAAGTTCAACTTCACAA
1 AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
* * *
341072 CGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGATTCC
66 CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
*
341113 AGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC
341152 GGAACAATCC
Statistics
Matches: 630, Mismatches: 44, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
105 1 0.00
106 629 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.22
Consensus pattern (106 bp):
AGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGA
CGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTC
Found at i:342438 original size:8 final size:8
Alignment explanation
Indices: 342409--342439 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
342399 TTAGTGTTAT
*
342409 TATATATA
1 TATATTTA
342417 TATATTTA
1 TATATTTA
342425 TATATTTA
1 TATATTTA
342433 TATATTT
1 TATATTT
342440 CCTATTTTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TATATTTA
Found at i:342525 original size:20 final size:20
Alignment explanation
Indices: 342500--342537 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
342490 TTTATTATTA
342500 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
342520 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
342538 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:342529 original size:38 final size:38
Alignment explanation
Indices: 342480--342569 Score: 105
Period size: 37 Copynumber: 2.4 Consensus size: 38
342470 CTTTTGATTT
*
342480 TCTTTTTCTTTTTATTAT-TATTTTACTTATATATATA
1 TCTTTTTCTTTTTATTATATATTTTACTCATATATATA
* * *
342517 TGCTTTTAC-TTTT-TTATATATTTTACTCATTTATTTA
1 T-CTTTTTCTTTTTATTATATATTTTACTCATATATATA
342554 TCTATTTTCTTTTTAT
1 TCT-TTTTCTTTTTAT
342570 CTTTATCTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
36 6 0.14
37 26 0.60
38 10 0.23
39 1 0.02
ACGTcount: A:0.21, C:0.10, G:0.01, T:0.68
Consensus pattern (38 bp):
TCTTTTTCTTTTTATTATATATTTTACTCATATATATA
Found at i:345503 original size:21 final size:21
Alignment explanation
Indices: 345451--345503 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
345441 TAAACATGAC
345451 ATCCATAACAACAAACTTTAA
1 ATCCATAACAACAAACTTTAA
* ** *
345472 TTTGATAACAACCAACTTTAA
1 ATCCATAACAACAAACTTTAA
*
345493 ATCCATTACAA
1 ATCCATAACAA
345504 TAAATCAAAC
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (21 bp):
ATCCATAACAACAAACTTTAA
Found at i:351282 original size:42 final size:42
Alignment explanation
Indices: 351153--351332 Score: 188
Period size: 42 Copynumber: 4.3 Consensus size: 42
351143 GTTTTAAAAT
* *
351153 TTGCGGCGTTTGTTCAAAAAATGCCACTATAGATGAACCTTA
1 TTGCGACGTTTGTTGAAAAAATGCCACTATAGATGAACCTTA
** * * * * *
351195 TTATGACATTTG-T-ATAAAAATGCCGCTAAAG-T-ACAACTCA
1 TTGCGACGTTTGTTGA-AAAAATGCCACTATAGATGA-ACCTTA
*
351235 CTTGCGACGTTTGTTGAAAAAAGGCCACTATAGATGAACCTTA
1 -TTGCGACGTTTGTTGAAAAAATGCCACTATAGATGAACCTTA
*
351278 TTGCGACGTTTGTTGAAAAAATGCCACTATAGATGAACCCTA
1 TTGCGACGTTTGTTGAAAAAATGCCACTATAGATGAACCTTA
* *
351320 TTACAACGTTTGT
1 TTGCGACGTTTGT
351333 ATAAAAAGGC
Statistics
Matches: 111, Mismatches: 20, Indels: 14
0.77 0.14 0.10
Matches are distributed among these distances:
39 1 0.01
40 6 0.05
41 24 0.22
42 73 0.66
43 6 0.05
44 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (42 bp):
TTGCGACGTTTGTTGAAAAAATGCCACTATAGATGAACCTTA
Found at i:351380 original size:125 final size:124
Alignment explanation
Indices: 351153--351412 Score: 324
Period size: 125 Copynumber: 2.1 Consensus size: 124
351143 GTTTTAAAAT
* * ** *
351153 TTGCGGCGTTTGTTCAAAAAATGCCACTATAGATGAACCTTATTATGACATTTGTATAAAAATGC
1 TTGCGACGTTTGTTCAAAAAATGCCACTATAGATGAACCCTATTACAACATTTGTATAAAAAGGC
** * *
351218 CGCTAAAGTACAACTCACTTGCGACGTTTGTTGAAAAAAGGCCACTATAGATGAACCTTA
66 CGCTAAAGTACAACTCACTCACGACGTTTGTTAAAAAAACGCCACTATAGATGAACC-TA
* *
351278 TTGCGACGTTTGTTGAAAAAATGCCACTATAGATGAACCCTATTACAACGTTTGTATAAAAAGGC
1 TTGCGACGTTTGTTCAAAAAATGCCACTATAGATGAACCCTATTACAACATTTGTATAAAAAGGC
* * ** ** * *
351343 CGCTACAGTACTACTCTGTCACGGTGTTT-TTAAAAAAACGCTACTATGGATGAACCTA
66 CGCTAAAGTACAACTCACTCACGACGTTTGTTAAAAAAACGCCACTATAGATGAACCTA
*
351401 TTGCAACGTTTG
1 TTGCGACGTTTG
351413 AATAAAAAAA
Statistics
Matches: 115, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
123 13 0.11
124 23 0.20
125 79 0.69
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (124 bp):
TTGCGACGTTTGTTCAAAAAATGCCACTATAGATGAACCCTATTACAACATTTGTATAAAAAGGC
CGCTAAAGTACAACTCACTCACGACGTTTGTTAAAAAAACGCCACTATAGATGAACCTA
Found at i:351772 original size:3 final size:3
Alignment explanation
Indices: 351757--351802 Score: 58
Period size: 3 Copynumber: 14.7 Consensus size: 3
351747 AATATTGTTA
351757 TAT TAT T-T GTAT TAT TAT TAAT CTAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT -TAT TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TA
351803 ATGAACTAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
2 1 0.03
3 32 0.82
4 5 0.13
5 1 0.03
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:351775 original size:23 final size:23
Alignment explanation
Indices: 351755--351799 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
351745 AAAATATTGT
351755 TATATTATT-TGTATTATTATTAA
1 TATATTATTAT-TATTATTATTAA
*
351778 TCTATTATTATTATTATTATTA
1 TATATTATTATTATTATTATTA
351800 TTAATGAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (23 bp):
TATATTATTATTATTATTATTAA
Found at i:353319 original size:30 final size:30
Alignment explanation
Indices: 353285--353535 Score: 174
Period size: 30 Copynumber: 8.5 Consensus size: 30
353275 TGTTAATATC
**
353285 ATTTTAGTCCTTTAAATTTCTATTTTTTTT
1 ATTTTAGTCCTTTAAATTTCTATTTTTACT
* * * * *
353315 ATTTTAGTCCTTTAAATGTATGTATTTGCT
1 ATTTTAGTCCTTTAAATTTCTATTTTTACT
* * * * *
353345 A-TTTAGACCCTT-AGTTTTTGTTTTTACT
1 ATTTTAGTCCTTTAAATTTCTATTTTTACT
* *
353373 A-TTTAG-CACTTTAAGTTTCTATTTTTACC
1 ATTTTAGTC-CTTTAAATTTCTATTTTTACT
* * * * *
353402 ATTTTATTCCTTTAAATTTATGTTTGTACC
1 ATTTTAGTCCTTTAAATTTCTATTTTTACT
* *
353432 ATTTTAGTCC-TTAAAGTTT-TGGTTTTTTCT
1 ATTTTAGTCCTTTAAA-TTTCT-ATTTTTACT
* * **
353462 AGTTTAGTCCTTTAAGTTTCTATTTTTGTT
1 ATTTTAGTCCTTTAAATTTCTATTTTTACT
* *
353492 ATTTTAGTCCTTTAACTTTC-AGTTTTAGCT
1 ATTTTAGTCCTTTAAATTTCTATTTTTA-CT
353522 ATTTTAGTCCTTTA
1 ATTTTAGTCCTTTA
353536 GGTTTTTGTT
Statistics
Matches: 176, Mismatches: 36, Indels: 18
0.77 0.16 0.08
Matches are distributed among these distances:
27 1 0.01
28 20 0.11
29 34 0.19
30 115 0.65
31 6 0.03
ACGTcount: A:0.20, C:0.13, G:0.10, T:0.57
Consensus pattern (30 bp):
ATTTTAGTCCTTTAAATTTCTATTTTTACT
Found at i:353547 original size:30 final size:29
Alignment explanation
Indices: 353257--353556 Score: 157
Period size: 30 Copynumber: 10.1 Consensus size: 29
353247 ATAATTAATG
* * *
353257 TTTAGCCCTTTTAGTTTTTGTTAATA-TCAT
1 TTTAGTCCTTTAAGTTTTTGTT-TTACT-AT
* **
353287 TTTAGTCCTTTAAATTTCTAT-TTTTTTTAT
1 TTTAGTCCTTTAAGTTT-T-TGTTTTACTAT
* * * *
353317 TTTAGTCCTTTAAATGTATGTATTTGCTA-
1 TTTAGTCCTTTAAGTTTTTGT-TTTACTAT
* *
353346 TTTAGACCCTT-AGTTTTTGTTTTTACTA-
1 TTTAGTCCTTTAAGTTTTTG-TTTTACTAT
*
353374 TTTAG-CACTTTAAGTTTCTAT-TTTTACCAT
1 TTTAGTC-CTTTAAGTTT-T-TGTTTTACTAT
* * * *
353404 TTTATTCCTTTAAATTTATGTTTGTACCAT
1 TTTAGTCCTTTAAGTTTTTGTTT-TACTAT
* * * *
353434 TTTAGTCCTTAAAGTTTTGGTTTTTTCTAG
1 TTTAGTCCTTTAAGTTTTTG-TTTTACTAT
**
353464 TTTAGTCCTTTAAGTTTCTAT-TTTTGTTAT
1 TTTAGTCCTTTAAGTTT-T-TGTTTTACTAT
* **
353494 TTTAGTCCTTTAACTTTCAGTTTTAGCTAT
1 TTTAGTCCTTTAAGTTTTTGTTTTA-CTAT
* *
353524 TTTAGTCCTTTAGGTTTTTGTTTTTCCTAT
1 TTTAGTCCTTTAAGTTTTTG-TTTTACTAT
353554 TTT
1 TTT
353557 GGCCCGTGTA
Statistics
Matches: 207, Mismatches: 43, Indels: 40
0.71 0.15 0.14
Matches are distributed among these distances:
27 1 0.00
28 21 0.10
29 30 0.14
30 140 0.68
31 14 0.07
32 1 0.00
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.58
Consensus pattern (29 bp):
TTTAGTCCTTTAAGTTTTTGTTTTACTAT
Found at i:353548 original size:60 final size:60
Alignment explanation
Indices: 353285--353556 Score: 198
Period size: 60 Copynumber: 4.6 Consensus size: 60
353275 TGTTAATATC
* * ** * *
353285 ATTTTAGTCCTTTAAATTTCTATTTTTTTTATTTTAGTCCTTTAAATGT-ATGTATTT-GCT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTACTATTTTAGTCCTTTAAGTTTCA-GT-TTTAGCT
* * * * *
353345 A-TTTAGACCCTT-AGTTTTTGTTTTTACTA-TTTAG-CACTTTAAGTTTCTATTTTTA-CC
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTACTATTTTAGTC-CTTTAAGTTTC-AGTTTTAGCT
* * * * * * ** **
353402 ATTTTATTCCTTTAAATTTATGTTTGTACCATTTTAGTCCTTAAAGTTTTGGTTTTTTCT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTACTATTTTAGTCCTTTAAGTTTCAGTTTTAGCT
* * ** *
353462 AGTTTAGTCCTTTAAGTTTCTATTTTTGTTATTTTAGTCCTTTAACTTTCAGTTTTAGCT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTACTATTTTAGTCCTTTAAGTTTCAGTTTTAGCT
* * *
353522 ATTTTAGTCCTTTAGGTTTTTGTTTTTCCTATTTT
1 ATTTTAGTCCTTTAAGTTTCTGTTTTTACTATTTT
353557 GGCCCGTGTA
Statistics
Matches: 158, Mismatches: 45, Indels: 18
0.71 0.20 0.08
Matches are distributed among these distances:
56 1 0.01
57 18 0.11
58 21 0.13
59 27 0.17
60 90 0.57
61 1 0.01
ACGTcount: A:0.19, C:0.12, G:0.10, T:0.58
Consensus pattern (60 bp):
ATTTTAGTCCTTTAAGTTTCTGTTTTTACTATTTTAGTCCTTTAAGTTTCAGTTTTAGCT
Found at i:356806 original size:14 final size:14
Alignment explanation
Indices: 356787--356889 Score: 65
Period size: 15 Copynumber: 7.2 Consensus size: 14
356777 GAGAGAAGAG
356787 CAAAGAAAAAGAAA
1 CAAAGAAAAAGAAA
356801 CAAAGAAAACAAAGAAA
1 CAAAG--AA-AAAGAAA
*
356818 CAAAGAGAAAAAAAA
1 CAAAGA-AAAAGAAA
*
356833 GCAAAG-AAAA-AAT
1 -CAAAGAAAAAGAAA
*
356846 CAATGAAAAA-AGAA
1 CAAAGAAAAAGA-AA
356860 CAAAAGAAAAAG---
1 C-AAAGAAAAAGAAA
356872 CAAAGAAAAAGAAGA
1 CAAAGAAAAAGAA-A
356887 CAA
1 CAA
356890 GAAGAACACG
Statistics
Matches: 71, Mismatches: 5, Indels: 25
0.70 0.05 0.25
Matches are distributed among these distances:
11 10 0.14
12 5 0.07
13 7 0.10
14 11 0.15
15 18 0.25
16 8 0.11
17 12 0.17
ACGTcount: A:0.75, C:0.09, G:0.15, T:0.02
Consensus pattern (14 bp):
CAAAGAAAAAGAAA
Found at i:356807 original size:8 final size:8
Alignment explanation
Indices: 356794--356841 Score: 55
Period size: 8 Copynumber: 5.9 Consensus size: 8
356784 GAGCAAAGAA
356794 AAAGAAAC
1 AAAGAAAC
356802 AAAGAAAAC
1 AAAG-AAAC
356811 AAAGAAAC
1 AAAGAAAC
356819 AAAGAGAA-
1 AAAGA-AAC
356827 AAA-AAAGC
1 AAAGAAA-C
356835 AAAGAAA
1 AAAGAAA
356842 AAATCAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
6 2 0.06
7 1 0.03
8 19 0.54
9 13 0.37
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAGAAAC
Found at i:356816 original size:17 final size:16
Alignment explanation
Indices: 356792--356844 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 16
356782 AAGAGCAAAG
356792 AAAAAGAAACAAAGAA
1 AAAAAGAAACAAAGAA
356808 AACAAAGAAACAAAGAGA
1 AA-AAAGAAACAAAGA-A
*
356826 AAAAA-AAGCAAAGAA
1 AAAAAGAAACAAAGAA
356841 AAAA
1 AAAA
356845 TCAATGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 5 0.15
16 10 0.29
17 16 0.47
18 3 0.09
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAAACAAAGAA
Found at i:356879 original size:26 final size:26
Alignment explanation
Indices: 356785--356881 Score: 75
Period size: 26 Copynumber: 3.9 Consensus size: 26
356775 CAGAGAGAAG
* *
356785 AGCAAAG-AAAAAG-AAACAAAGAAA
1 AGCAAAGAAAAAAGCAAAGAAAAAAA
356809 A-CAAAGAAACAAAG---AGAAAAAAA
1 AGCAAAGAAA-AAAGCAAAGAAAAAAA
* *
356832 AGCAAAGAAAAAATCAATGAAAAAAGA
1 AGCAAAGAAAAAAGCAAAGAAAAAA-A
356859 A-CAAA-AGAAAAAGCAAAGAAAAA
1 AGCAAAGA-AAAAAGCAAAGAAAAA
356882 GAAGACAAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
23 16 0.27
24 11 0.19
25 5 0.08
26 25 0.42
27 2 0.03
ACGTcount: A:0.75, C:0.08, G:0.14, T:0.02
Consensus pattern (26 bp):
AGCAAAGAAAAAAGCAAAGAAAAAAA
Found at i:358821 original size:17 final size:17
Alignment explanation
Indices: 358784--358824 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
358774 ATGGTCGACT
* *
358784 GTTGACCGTTGAACTGT
1 GTTGACCGTTGAACGGC
*
358801 GTTGACCGTTGATCGGC
1 GTTGACCGTTGAACGGC
358818 GTTGACC
1 GTTGACC
358825 ACAGTTGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.15, C:0.22, G:0.32, T:0.32
Consensus pattern (17 bp):
GTTGACCGTTGAACGGC
Found at i:361279 original size:12 final size:12
Alignment explanation
Indices: 361259--361316 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
361249 GATACATGAC
*
361259 CTGAATTCTGTT
1 CTGATTTCTGTT
* *
361271 ATGATTTCTGAT
1 CTGATTTCTGTT
361283 CTGGA-TTCTGTT
1 CT-GATTTCTGTT
*
361295 CTGAATTCTGTT
1 CTGATTTCTGTT
*
361307 TTGATTTCTG
1 CTGATTTCTG
361317 ATATCTCCGT
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
11 2 0.05
12 33 0.89
13 2 0.05
ACGTcount: A:0.16, C:0.14, G:0.19, T:0.52
Consensus pattern (12 bp):
CTGATTTCTGTT
Found at i:361483 original size:2 final size:2
Alignment explanation
Indices: 361476--361506 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
361466 GGGATGGGGG
361476 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 T
361507 GTTTTAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:363223 original size:41 final size:41
Alignment explanation
Indices: 363166--363252 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 41
363156 TTCGCCGTTC
* * *
363166 AAAATTATGAATCGAGCTTGGTAAGTGTTTCAAAATGCCTT
1 AAAATTATGAACCGAGCTTGGTAAGTGTCTCAAAAGGCCTT
*
363207 AAAATTGTGAACCGAGCTTGGTAAGTGTCTCAAAAGGCCTT
1 AAAATTATGAACCGAGCTTGGTAAGTGTCTCAAAAGGCCTT
363248 AAAAT
1 AAAAT
363253 AATTTTTAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.30
Consensus pattern (41 bp):
AAAATTATGAACCGAGCTTGGTAAGTGTCTCAAAAGGCCTT
Found at i:363722 original size:19 final size:19
Alignment explanation
Indices: 363698--363735 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
363688 TTCGAAAAGT
363698 CATATTTTAGGTTTTTCGA
1 CATATTTTAGGTTTTTCGA
363717 CATATTTTAGGTTTTTCGA
1 CATATTTTAGGTTTTTCGA
363736 TGTCCTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.16, T:0.53
Consensus pattern (19 bp):
CATATTTTAGGTTTTTCGA
Found at i:364396 original size:30 final size:30
Alignment explanation
Indices: 364333--364425 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
364323 GAAGGACCTA
* * * *
364333 TCCAGAGGTCACAAAGA-CCCCGATAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
364362 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
364392 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
364422 TCCA
1 TCCA
364426 TATGTTCCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.27
30 43 0.73
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:364456 original size:31 final size:30
Alignment explanation
Indices: 364414--364511 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
364404 AAAGATCCTC
*
364414 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* * *
364444 GGTATACTGTCCATATGTCTCGAAAG-GCATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
*
364475 GGTAAAACTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
364507 GGTAA
1 GGTAA
364512 ACCCTCGACT
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 6 0.11
31 24 0.44
32 24 0.44
33 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:364507 original size:32 final size:32
Alignment explanation
Indices: 364417--364512 Score: 119
Period size: 32 Copynumber: 3.0 Consensus size: 32
364407 GATCCTCGGT
*
364417 AACTGTCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
*
364448 TACTGTCCATATG-TCTCG-A-AAGGCATAGGTAA
1 AACTGTCCATATGTTC-CGTAGAA--CATAGGTAA
364480 AACTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
364512 A
1 A
364513 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
29 2 0.04
30 3 0.05
31 20 0.36
32 25 0.45
33 3 0.05
34 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:365374 original size:21 final size:21
Alignment explanation
Indices: 365344--365388 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
365334 ATTCTGTCGT
* *
365344 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
365365 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
365386 TTG
1 TTG
365389 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:368462 original size:30 final size:30
Alignment explanation
Indices: 368399--368491 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
368389 GAAGGACCTA
* * * *
368399 TCCAGAGGTCACAAAGA-CCCCGATAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
368428 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
368458 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
368488 TCCA
1 TCCA
368492 TATGTTCCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.27
30 43 0.73
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:368522 original size:31 final size:30
Alignment explanation
Indices: 368480--368577 Score: 108
Period size: 31 Copynumber: 3.2 Consensus size: 30
368470 AAAGATCCTC
*
368480 GGTAACTGTCCATATGTTCCTTAGAACATA
1 GGTAACTGTCCATATGTTCCATAGAACATA
* *
368510 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTA-ACTGTCCATATGT-TCCATAGAACATA
* *
368541 GGTAAAATTGTCCATATGTTCCGTAGAACATA
1 GGT--AACTGTCCATATGTTCCATAGAACATA
368573 GGTAA
1 GGTAA
368578 ACCCTCGACT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
30 6 0.11
31 25 0.45
32 24 0.43
33 1 0.02
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (30 bp):
GGTAACTGTCCATATGTTCCATAGAACATA
Found at i:368572 original size:32 final size:32
Alignment explanation
Indices: 368483--368578 Score: 117
Period size: 32 Copynumber: 3.0 Consensus size: 32
368473 GATCCTCGGT
*
368483 AACTGTCCATATGTTCCTTAGAACATAGGT-A
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
* *
368514 TACTGTCCATATG-TCTCG-AAAGACATAGGTAA
1 AACTGTCCATATGTTC-CGTAGA-ACATAGGTAA
*
368546 AATTGTCCATATGTTCCGTAGAACATAGGTAA
1 AACTGTCCATATGTTCCGTAGAACATAGGTAA
368578 A
1 A
368579 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
30 4 0.07
31 21 0.39
32 25 0.46
33 4 0.07
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (32 bp):
AACTGTCCATATGTTCCGTAGAACATAGGTAA
Found at i:369441 original size:21 final size:21
Alignment explanation
Indices: 369411--369455 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
369401 ATTCTGTCGT
* *
369411 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
369432 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
369453 TTG
1 TTG
369456 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:370276 original size:22 final size:20
Alignment explanation
Indices: 370222--370267 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
370212 GATTTGATCT
370222 GTTTTTCAGAATTAAGCTCC
1 GTTTTTCAGAATTAAGCTCC
370242 GTTTTTCAGAATTAAGCTCC
1 GTTTTTCAGAATTAAGCTCC
370262 GTTTTT
1 GTTTTT
370268 TATGTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.46
Consensus pattern (20 bp):
GTTTTTCAGAATTAAGCTCC
Found at i:371160 original size:25 final size:25
Alignment explanation
Indices: 371132--371179 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
371122 ACTTGACCCG
371132 AAAATAATGAATCTGTAAAATGATT
1 AAAATAATGAATCTGTAAAATGATT
371157 AAAATAATGAATCTGTAAAATGA
1 AAAATAATGAATCTGTAAAATGA
371180 CCAAAATACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.04, G:0.12, T:0.29
Consensus pattern (25 bp):
AAAATAATGAATCTGTAAAATGATT
Found at i:371185 original size:25 final size:25
Alignment explanation
Indices: 371132--371187 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
371122 ACTTGACCCG
**
371132 AAAATAATGAATCTGTAAAATGATT
1 AAAATAATGAATCTGTAAAATGACC
371157 AAAATAATGAATCTGTAAAATGACC
1 AAAATAATGAATCTGTAAAATGACC
371182 AAAATA
1 AAAATA
371188 CCCCTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.55, C:0.07, G:0.11, T:0.27
Consensus pattern (25 bp):
AAAATAATGAATCTGTAAAATGACC
Found at i:372027 original size:12 final size:12
Alignment explanation
Indices: 371989--372071 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 12
371979 ATTTCCGACT
371989 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
372001 TG-ATACATGACC
1 TGAATTC-TGTTC
372013 TGAATTCTGTTC
1 TGAATTCTGTTC
* **
372025 TGATTTCTAATC
1 TGAATTCTGTTC
** *
372037 TGGGTTCTGTTA
1 TGAATTCTGTTC
372049 TGATATT-TGTTC
1 TGA-ATTCTGTTC
372061 TGAATTCTGTT
1 TGAATTCTGTT
372072 TTGATTTCTT
Statistics
Matches: 50, Mismatches: 17, Indels: 8
0.67 0.23 0.11
Matches are distributed among these distances:
11 6 0.12
12 39 0.78
13 5 0.10
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.48
Consensus pattern (12 bp):
TGAATTCTGTTC
Found at i:372293 original size:2 final size:2
Alignment explanation
Indices: 372242--372274 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
372232 GGGATGGGGG
372242 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 T
372275 GTTTTAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:373083 original size:62 final size:63
Alignment explanation
Indices: 372913--373087 Score: 214
Period size: 64 Copynumber: 2.7 Consensus size: 63
372903 CTCGAGATAG
* *
372913 TTTCTTTTGA-AAAAATCTTTGAGTCTGTTTCTTTAGAAACAAAGTTTTGTCTCTCTTAAGACAA
1 TTTCTTTTGAGAAAAATCTTTGAGTCTGTTTCTTT-GAAACAAA-ATTCGTCTCTCTTAAGACAA
* *
372977 TTTCCTTTGAGAAAAAAATCTTTGAGATC-GTTTCCATTGAAACAAAATTCGTCT-T-TTAAGAC
1 TTTCTTTTGAG--AAAAATCTTTGAG-TCTGTTT-CTTTGAAACAAAATTCGTCTCTCTTAAGAC
373039 AA
62 AA
*
373041 TTTCTTTTGAGAAAAATCCTTGAGTCTGTTTCTTTGGAAACAAAATT
1 TTTCTTTTGAGAAAAATCTTTGAGTCTGTTTCTTT-GAAACAAAATT
373088 TTCCATCTTT
Statistics
Matches: 97, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
61 5 0.05
62 27 0.28
64 28 0.29
65 1 0.01
66 6 0.06
67 25 0.26
68 5 0.05
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (63 bp):
TTTCTTTTGAGAAAAATCTTTGAGTCTGTTTCTTTGAAACAAAATTCGTCTCTCTTAAGACAA
Found at i:373205 original size:31 final size:29
Alignment explanation
Indices: 373170--373235 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
373160 GTCTTATTTG
*
373170 GAAACACAAA-ATCTTTAAGTCTGTTTCTCTT
1 GAAACA-AAACATCTTTAAGTC-ATTTC-CTT
*
373201 GAAACAAAACCATCTTTGAGTCATTTCCTT
1 GAAACAAAA-CATCTTTAAGTCATTTCCTT
373231 GAAAC
1 GAAAC
373236 GAATTTTGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 11 0.35
31 10 0.32
32 10 0.32
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (29 bp):
GAAACAAAACATCTTTAAGTCATTTCCTT
Found at i:373381 original size:40 final size:41
Alignment explanation
Indices: 373326--373511 Score: 137
Period size: 40 Copynumber: 4.4 Consensus size: 41
373316 CGGCCAGCCG
* *
373326 TCCTCATCACGTAGGAACCGTGTCATCCCCTGAT-CAGACC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCTGATACAGTCA
* *
373366 TCCTCATCACGTAGGAGCCGTGTCA-CCCTTGATAACCAGTCA
1 TCCTCATCACGTAGGAACCGTGTCATCCCCTGAT-A-CAGTCA
* * * * **
373408 TCCTCATCACGTAGGAACCATATTATCATTCCTAAAGATTGTATGTCA
1 TCCTCATCACGTAGGAACCGTGTCATC--CCCT---GA-TACA-GTCA
* * *
373456 TCCTCATCACGTAGGAACCGTGTCATCCACC-GA-CCAGGCC
1 TCCTCATCACGTAGGAACCGTGTCATCC-CCTGATACAGTCA
373496 TCCTCATCACGTAGGA
1 TCCTCATCACGTAGGA
373512 GTCGTATCAC
Statistics
Matches: 114, Mismatches: 20, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
39 7 0.06
40 42 0.37
41 1 0.01
42 25 0.22
43 3 0.03
45 2 0.02
47 3 0.03
48 30 0.26
49 1 0.01
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (41 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCTGATACAGTCA
Found at i:373617 original size:134 final size:130
Alignment explanation
Indices: 373326--373650 Score: 374
Period size: 134 Copynumber: 2.5 Consensus size: 130
373316 CGGCCAGCCG
* * *
373326 TCCTCATCACGTAGGAACCGTGTCATCC-CCTGATCAGACCTCCTCATCACGTAGGAGCCGTGTC
1 TCCTCATCACGTAGGAACCGTGTCATCCACC-GACCAGACCTCCTCATCACGTAGGAGTCGTATC
** * *
373390 ACCCTTGATAACCAGTCATCCTCATCACGTAGGAACCATATTATCATTCCTAAAGATTGTATGTC
65 ACCCTAAATAACCAGTCATCCTCATCACGTAGGAACCATATTATCATTCCTAAAGATTGTAAGAC
373455 A
130 A
*
373456 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGGCCTCCTCATCACGTAGGAGTCGTATCA
1 TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGTCGTATCA
* *
373521 CCCCTAAATAACCAGT-AGTTCTCATCACGTAGGAACGGA-ATTATCACCCTTCCTAAAGA-TG-
66 -CCCTAAATAACCAGTCA-TCCTCATCACGTAGGAAC-CATATTATCA---TTCCTAAAGATTGT
373582 ACCAGA-A
125 A--AGACA
* * * * * *
373589 CTCTTCATCACGTATGAGCCGTGTCATCCACCGACCATATCTCCTTATCACGTAGGAGTCGT
1 -TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGTCGT
373651 TCCACCTTTA
Statistics
Matches: 168, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
130 59 0.35
131 39 0.23
132 2 0.01
133 3 0.02
134 65 0.39
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.25
Consensus pattern (130 bp):
TCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCTCATCACGTAGGAGTCGTATCA
CCCTAAATAACCAGTCATCCTCATCACGTAGGAACCATATTATCATTCCTAAAGATTGTAAGACA
Found at i:373859 original size:3 final size:3
Alignment explanation
Indices: 373851--373904 Score: 51
Period size: 3 Copynumber: 17.7 Consensus size: 3
373841 CTACTAAAAA
373851 TAT TAT TA- TAT TAT T-T GTAT TAT T-T GTAT TAT TAT TAAT CTAT TAT
1 TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT T-AT -TAT TAT
373897 TAT TAT TA
1 TAT TAT TA
373905 ATTAAGTAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
2 4 0.09
3 33 0.75
4 6 0.14
5 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:374271 original size:59 final size:59
Alignment explanation
Indices: 374179--374298 Score: 213
Period size: 59 Copynumber: 2.0 Consensus size: 59
374169 TTCTAACAAA
374179 TTCACTAATTTGTTCTTTCTTTTTCAAGGATAAAGAGATAACCTTTACACTCCCTATCT
1 TTCACTAATTTGTTCTTTCTTTTTCAAGGATAAAGAGATAACCTTTACACTCCCTATCT
* **
374238 TTCACTAATTTGTTCTTTCTTTTTCACGGATAAATTGATAACCTTTACACTCCCTATCT
1 TTCACTAATTTGTTCTTTCTTTTTCAAGGATAAAGAGATAACCTTTACACTCCCTATCT
374297 TT
1 TT
374299 TCAATTAGTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (59 bp):
TTCACTAATTTGTTCTTTCTTTTTCAAGGATAAAGAGATAACCTTTACACTCCCTATCT
Found at i:374802 original size:20 final size:20
Alignment explanation
Indices: 374779--374829 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
374769 TGTTCACGAG
374779 GTATCGATACTGTAATAACA
1 GTATCGATACTGTAATAACA
374799 GTATCGATACTGTAATAACA
1 GTATCGATACTGTAATAACA
374819 GTATCGATACT
1 GTATCGATACT
374830 ACTTGTATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (20 bp):
GTATCGATACTGTAATAACA
Found at i:375518 original size:20 final size:19
Alignment explanation
Indices: 375495--375539 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
375485 AAACACATGC
375495 AAAAACA-TTAAAATTTAGGT
1 AAAAACATTTAAAATTT--GT
375515 AAAAA-ATTTAAAATTTGT
1 AAAAACATTTAAAATTTGT
375533 AAAAACA
1 AAAAACA
375540 AAGCATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 7 0.30
19 2 0.09
20 14 0.61
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (19 bp):
AAAAACATTTAAAATTTGT
Found at i:376423 original size:18 final size:18
Alignment explanation
Indices: 376400--376447 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
376390 GTTGGCTACT
376400 TCATCTTCATCATTAGAG
1 TCATCTTCATCATTAGAG
*
376418 TCATCTTCATCATTGGAG
1 TCATCTTCATCATTAGAG
376436 TCATCTTCATCA
1 TCATCTTCATCA
376448 CTCCAAGCCG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (18 bp):
TCATCTTCATCATTAGAG
Found at i:379767 original size:30 final size:28
Alignment explanation
Indices: 379666--379931 Score: 188
Period size: 30 Copynumber: 9.2 Consensus size: 28
379656 TGTTAATACC
*
379666 ATTTTAGTCCCTTAAGTTT-TTTTTAT-T
1 ATTTTAGTCCTTTAAGTTTCTTTTT-TCT
* *
379693 ATTTTAGTCCTTTAAATGTCTGTATTTTCT
1 ATTTTAGTCCTTTAAGTTTCT-T-TTTTCT
* *
379723 A-TTTAGACCCTTAAGTTTCTATTTTTACT
1 ATTTTAGTCCTTTAAGTTTCT-TTTTT-CT
* * *
379752 ATTTTAGCCCTTTAAGTTT-TATTTTGCC
1 ATTTTAGTCCTTTAAGTTTCT-TTTTTCT
* * *
379780 ATTTTATTCCTTTAAATTTATGTTTGTGTC-
1 ATTTTAGTCCTTTAAGTTTCT-TTT-T-TCT
*
379810 ATTTTAGTCCTTTAAGTTTGGTTTTTTCT
1 ATTTTAGTCCTTTAAGTTT-CTTTTTTCT
*
379839 ATTTTAGTCCATTAA--TTCTTTTTTTGCT
1 ATTTTAGTCCTTTAAGTTTC-TTTTTT-CT
*
379867 ATTTTAGTCCTTTAAATTT-TTGTTTTAGCT
1 ATTTTAGTCCTTTAAGTTTCTT-TTTT--CT
*
379897 ATTTTAGTCCTTCAAGTTTCTATTTTTCCT
1 ATTTTAGTCCTTTAAGTTTCT-TTTTT-CT
379927 ATTTT
1 ATTTT
379932 GGTCATTGCA
Statistics
Matches: 194, Mismatches: 26, Indels: 35
0.76 0.10 0.14
Matches are distributed among these distances:
27 24 0.12
28 42 0.22
29 50 0.26
30 70 0.36
31 7 0.04
32 1 0.01
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.59
Consensus pattern (28 bp):
ATTTTAGTCCTTTAAGTTTCTTTTTTCT
Found at i:379904 original size:58 final size:55
Alignment explanation
Indices: 379666--379906 Score: 191
Period size: 58 Copynumber: 4.2 Consensus size: 55
379656 TGTTAATACC
* * * * *
379666 ATTTTAGTCCCTTAAGTTTTTTTTATTATTTTAGTCCTTTAAATGTCTGTATTTTCT
1 ATTTTAGTCCCTTAATTTTTTTTTACTATTTTAGTCCTTTAAGT-TTTGT-TTTGCT
* * * *
379723 A-TTTAGACCCTTAAGTTTCTATTTTTACTATTTTAGCCCTTTAAGTTTTATTTTGCC
1 ATTTTAGTCCCTTAA-TTT-T-TTTTTACTATTTTAGTCCTTTAAGTTTTGTTTTGCT
* * * *
379780 ATTTTATTCCTTTAAATTTATGTTTGTGT-C-ATTTTAGTCCTTTAAGTTTGGTTTTTTCT
1 ATTTTAGTCCCTT-AATTT-T-TTT-T-TACTATTTTAGTCCTTTAAGTTTTG-TTTTGCT
* * *
379839 ATTTTAGTCCATTAATTCTTTTTTTGCTATTTTAGTCCTTTAAATTTTTGTTTTAGCT
1 ATTTTAGTCCCTTAATT-TTTTTTTACTATTTTAGTCCTTT-AAGTTTTGTTTT-GCT
379897 ATTTTAGTCC
1 ATTTTAGTCC
379907 TTCAAGTTTC
Statistics
Matches: 147, Mismatches: 24, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
55 1 0.01
56 14 0.10
57 28 0.19
58 60 0.41
59 43 0.29
60 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.10, T:0.58
Consensus pattern (55 bp):
ATTTTAGTCCCTTAATTTTTTTTTACTATTTTAGTCCTTTAAGTTTTGTTTTGCT
Found at i:379923 original size:87 final size:85
Alignment explanation
Indices: 379666--379931 Score: 270
Period size: 87 Copynumber: 3.1 Consensus size: 85
379656 TGTTAATACC
* * ** * * *
379666 ATTTTAGTCCCTTAAGTTTTTTTTATTATTTTAGTCCTTTAAATGTCTGTATTTTCTA-TTTAGA
1 ATTTTAGTCCATTAATTTTTTTTTGCTATTTTAGTCCTTTAAATTTATGT-TTTGCTATTTTAG-
*
379730 CCCTTAAGTTTCTATTTTTACT
64 TCCTTAAGTTTCTATTTTTACT
* * * * *
379752 ATTTTAGCCCTTTAAGTTTTATTTTGCCATTTTATTCCTTTAAATTTATGTTTGTG-TCATTTTA
1 ATTTTAGTCCATTAA-TTTTTTTTTGCTATTTTAGTCCTTTAAATTTATGTTT-TGCT-ATTTTA
*
379816 GTCCTTTAAGTTTGGT-TTTTT-CT
63 GTCC-TTAAGTTT-CTATTTTTACT
*
379839 ATTTTAGTCCATTAATTCTTTTTTTGCTATTTTAGTCCTTTAAATTTTTGTTTTAGCTATTTTAG
1 ATTTTAGTCCATTAATT-TTTTTTTGCTATTTTAGTCCTTTAAATTTATGTTTT-GCTATTTTAG
*
379904 TCCTTCAAGTTTCTATTTTTCCT
64 TCCTT-AAGTTTCTATTTTTACT
379927 ATTTT
1 ATTTT
379932 GGTCATTGCA
Statistics
Matches: 148, Mismatches: 20, Indels: 22
0.78 0.11 0.12
Matches are distributed among these distances:
86 22 0.15
87 99 0.67
88 26 0.18
89 1 0.01
ACGTcount: A:0.19, C:0.14, G:0.09, T:0.59
Consensus pattern (85 bp):
ATTTTAGTCCATTAATTTTTTTTTGCTATTTTAGTCCTTTAAATTTATGTTTTGCTATTTTAGTC
CTTAAGTTTCTATTTTTACT
Found at i:383420 original size:187 final size:188
Alignment explanation
Indices: 383105--383474 Score: 733
Period size: 187 Copynumber: 2.0 Consensus size: 188
383095 TAGAACAACG
383105 CATGTCAAATTGGCGCCGTTGTGGGAACTTCGACTAAAATTACTAATAAAGTTTTTTTTTGATTT
1 CATGTCAAATTGGCGCCGTTGTGGGAACTTCGACTAAAATTACTAATAAAGTTTTTTTTTGATTT
383170 ATGACTAAGGGAAATTTAGGATAATTAGTAGACTTTGACCCAGAAATCGAAGCTACATCAGGCGC
66 ATGACTAAGGGAAATTTAGGATAATTAGTAGACTTTGACCCAGAAATCGAAGCTACATCAGGCGC
383235 AAATTACACGCCAGAACCAATGGTACAACAAACAGTCCGCCGGTTA-CCGTGAACTGT
131 AAATTACACGCCAGAACCAATGGTACAACAAACAGTCCGCCGGTTACCCGTGAACTGT
383292 CATGTCAAATTGGCGCCGTTGTGGGAACTTCGACTAAAATTACTAATAAAGTTTTTTTTTGATTT
1 CATGTCAAATTGGCGCCGTTGTGGGAACTTCGACTAAAATTACTAATAAAGTTTTTTTTTGATTT
383357 ATGACTAAGGGAAATTTAGGATAATTAGTAGACTTTGACCCAGAAATCGAAGCTACATCAGGCGC
66 ATGACTAAGGGAAATTTAGGATAATTAGTAGACTTTGACCCAGAAATCGAAGCTACATCAGGCGC
383422 AAATTACACGCCAGAACCAATGGTACAACAAACAGTCCGCCGGTTACCCGTGA
131 AAATTACACGCCAGAACCAATGGTACAACAAACAGTCCGCCGGTTACCCGTGA
383475 CACCTGTCGT
Statistics
Matches: 182, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
187 176 0.97
188 6 0.03
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.27
Consensus pattern (188 bp):
CATGTCAAATTGGCGCCGTTGTGGGAACTTCGACTAAAATTACTAATAAAGTTTTTTTTTGATTT
ATGACTAAGGGAAATTTAGGATAATTAGTAGACTTTGACCCAGAAATCGAAGCTACATCAGGCGC
AAATTACACGCCAGAACCAATGGTACAACAAACAGTCCGCCGGTTACCCGTGAACTGT
Found at i:384607 original size:28 final size:29
Alignment explanation
Indices: 384576--384630 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
384566 AGAAAAAACT
* *
384576 ATTGACATAAACCCCCATAA-AAAAAGGG
1 ATTGACACAAACCCCCAGAAGAAAAAGGG
*
384604 ATTGACACAAATCCCCAGAAGAAAAAG
1 ATTGACACAAACCCCCAGAAGAAAAAG
384631 CACCATAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.51, C:0.22, G:0.15, T:0.13
Consensus pattern (29 bp):
ATTGACACAAACCCCCAGAAGAAAAAGGG
Found at i:389275 original size:135 final size:134
Alignment explanation
Indices: 389023--389286 Score: 336
Period size: 135 Copynumber: 2.0 Consensus size: 134
389013 CCTCCATCGT
* *
389023 AGAAGCATTCGGAATCAAATGTGCAGGAGCAAATGTATACATTGTATTTTTGTTTCCTGCCATCA
1 AGAAGCATTCAGAATCAAATGTGCAGGAGCAAATGCATACATTGTATTTTTGTTTCCTGCCATCA
* *
389088 TTGGTGCTCCGTTGATGTCTTGTCGATAACAACCCGCCATCGTAAACTCTCCATTAACAACTTGT
66 TTGGTGCTCCATTGATGTCTTGTCGATAACAACCCGCCATC-TAAACACTCCATTAACAACTTGT
389153 GAAGA
130 GAAGA
** * * *
389158 AGAAGCATTCAGAATTGAATGTGTAGGCGCAAATGCATACATTGT-TTTGTTGTTTTCTGCCATT
1 AGAAGCATTCAGAATCAAATGTGCAGGAGCAAATGCATACATTGTATTT-TTGTTTCCTGCCA-T
* * * * *
389222 GA-TGGTGCTCCATTGATTTCTTGTGGATAACAACCCTCCGT-TAGAGACACTCCATTAACAACT
64 CATTGGTGCTCCATTGATGTCTTGTCGATAACAACCCGCCATCTA-A-ACACTCCATTAACAACT
389285 TG
127 TG
389287 CGGAGAATAA
Statistics
Matches: 111, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
133 2 0.02
134 4 0.04
135 103 0.93
136 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (134 bp):
AGAAGCATTCAGAATCAAATGTGCAGGAGCAAATGCATACATTGTATTTTTGTTTCCTGCCATCA
TTGGTGCTCCATTGATGTCTTGTCGATAACAACCCGCCATCTAAACACTCCATTAACAACTTGTG
AAGA
Found at i:397421 original size:2 final size:2
Alignment explanation
Indices: 397414--397444 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
397404 CCGCCCCATA
397414 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
397445 CTACACACCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:400995 original size:2 final size:2
Alignment explanation
Indices: 400990--401027 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
400980 TTATTTATCA
400990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT
401028 CGTTACAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:402201 original size:83 final size:84
Alignment explanation
Indices: 401992--402304 Score: 217
Period size: 84 Copynumber: 3.7 Consensus size: 84
401982 GGGCTTAAAC
* * * * * *
401992 TATAAAAGTATAAAA-TATGATTGAAAAAATCAGGGACCCCAATTATAAAGGTAAAAAGTGATAT
1 TATAAAGGTA-AAAAGTAAGATTAAAAAAATTAGGGATCTCAATTATAAAGGTAAAAAGTGATAT
*
402056 TAAAAAAATAGGGTATCAAT
65 TAAAAAAATAGGGTATCAAA
* * *
402076 TTTAAAGGTAAAAAGTAAGATTAAAAAAATTAGGGGTCTCAATTATAAAGGTAAAAGGTGATATT
1 TATAAAGGTAAAAAGTAAGATTAAAAAAATTAGGGATCTCAATTATAAAGGTAAAAAGTGATATT
*
402141 GAAAAAA-AGGAGCT-T-AAA
66 AAAAAAATAGG-G-TATCAAA
* ** * * * * * *
402159 TATAAAGGT-ACAAGATGGGATTGAAAAACTTA-GGATCATCAATTATAAATGTAAAAAATTAGG
1 TATAAAGGTAAAAAG-TAAGATTAAAAAAATTAGGGATC-TCAATTATAAAGGTAAAAAGTGA-T
* ** * *
402222 ATTGAAAAAAAATTAAAGGCCTCCAT
63 ATT--AAAAAAA-T-AGGGTATCAAA
* * * *
402248 TATAAAGATAAAAAGTAGGATTACAAAAATTAGGGACCTCAATTAT-AAGGATAAAAA
1 TATAAAGGTAAAAAGTAAGATTAAAAAAATTAGGGATCTCAATTATAAAGG-TAAAAA
402305 ACTAAAATTA
Statistics
Matches: 177, Mismatches: 36, Indels: 27
0.74 0.15 0.11
Matches are distributed among these distances:
82 8 0.05
83 49 0.28
84 62 0.35
85 1 0.01
86 6 0.03
88 5 0.03
89 38 0.21
90 8 0.05
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (84 bp):
TATAAAGGTAAAAAGTAAGATTAAAAAAATTAGGGATCTCAATTATAAAGGTAAAAAGTGATATT
AAAAAAATAGGGTATCAAA
Found at i:402293 original size:43 final size:43
Alignment explanation
Indices: 401992--402304 Score: 195
Period size: 43 Copynumber: 7.3 Consensus size: 43
401982 GGGCTTAAAC
* * * *
401992 TATAAAAGTATAAAA-TATGATTGAAAAAATCAGGGACCCCAAT
1 TATAAAGGTA-AAAAGTAGGATTGAAAAAATTAGGGACCTCAAT
* *
402035 TATAAAGGTAAAAAGT--GATATTAAAAAAATAGGGTA--TCAAT
1 TATAAAGGTAAAAAGTAGGAT-TGAAAAAATTAGGG-ACCTCAAT
* * * **
402076 TTTAAAGGTAAAAAGTAAGATTAAAAAAATTAGGGGTCTCAAT
1 TATAAAGGTAAAAAGTAGGATTGAAAAAATTAGGGACCTCAAT
* * * * *
402119 TATAAAGGTAAAAGGT-GATATTGAAAAAA--A-GGAGCTTAAA
1 TATAAAGGTAAAAAGTAG-GATTGAAAAAATTAGGGACCTCAAT
* * * *
402159 TATAAAGGT-ACAAGATGGGATTGAAAAACTTA-GGATCATCAAT
1 TATAAAGGTAAAAAG-TAGGATTGAAAAAATTAGGGA-CCTCAAT
* * * *
402202 TATAAATGTAAAAAATTAGGATTGAAAAAAAATTAAAGG-CCTCCAT
1 TATAAAGGT-AAAAAGTAGGATTG--AAAAAATT-AGGGACCTCAAT
*
402248 TATAAAGATAAAAAGTAGGATT-ACAAAAATTAGGGACCTCAAT
1 TATAAAGGTAAAAAGTAGGATTGA-AAAAATTAGGGACCTCAAT
402291 TAT-AAGGATAAAAA
1 TATAAAGG-TAAAAA
402305 ACTAAAATTA
Statistics
Matches: 209, Mismatches: 39, Indels: 44
0.72 0.13 0.15
Matches are distributed among these distances:
39 3 0.01
40 25 0.12
41 24 0.11
42 38 0.18
43 75 0.36
44 7 0.03
45 15 0.07
46 19 0.09
47 1 0.00
48 2 0.01
ACGTcount: A:0.51, C:0.07, G:0.17, T:0.25
Consensus pattern (43 bp):
TATAAAGGTAAAAAGTAGGATTGAAAAAATTAGGGACCTCAAT
Found at i:402461 original size:42 final size:42
Alignment explanation
Indices: 402402--402485 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
402392 TGAACAGTTG
*
402402 CTCAAAGTGCACCACTAATATCAATATATATATATATATATA
1 CTCAAAGTGCACCACTAATAGCAATATATATATATATATATA
402444 CTCAAAGTGCACCACTAATAGCAATATATATATATATATATA
1 CTCAAAGTGCACCACTAATAGCAATATATATATATATATATA
402486 TATATATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.45, C:0.17, G:0.06, T:0.32
Consensus pattern (42 bp):
CTCAAAGTGCACCACTAATAGCAATATATATATATATATATA
Found at i:402474 original size:2 final size:2
Alignment explanation
Indices: 402467--402503 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
402457 ACTAATAGCA
*
402467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
402504 ATTTTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:404093 original size:20 final size:23
Alignment explanation
Indices: 404022--404095 Score: 64
Period size: 25 Copynumber: 3.3 Consensus size: 23
404012 GATAACAAAA
** *
404022 TAAAATAAGCAAAAAAACAGGACAT
1 TAAAATAAATAAAAATA-AGGA-AT
*
404047 TAAAATAAATAAAAATAAGGTAT
1 TAAAATAAATAAAAATAAGGAAT
*
404070 TAAAA-AATTAAAAA-AA-GAAT
1 TAAAATAAATAAAAATAAGGAAT
404090 TAAAAT
1 TAAAAT
404096 TAAGGTTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 8 0.19
21 2 0.05
22 8 0.19
23 7 0.17
24 3 0.07
25 14 0.33
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.20
Consensus pattern (23 bp):
TAAAATAAATAAAAATAAGGAAT
Found at i:405248 original size:21 final size:22
Alignment explanation
Indices: 405222--405268 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
405212 GGCCTAAAAT
405222 AATAAAAAT-AAATAAATATAA
1 AATAAAAATAAAATAAATATAA
405243 AAT-AAAATAAAATAAATATAA
1 AATAAAAATAAAATAAATATAA
*
405264 TATAA
1 AATAA
405269 TGTAACTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAAAAATAAAATAAATATAA
Found at i:405249 original size:5 final size:5
Alignment explanation
Indices: 405216--405268 Score: 56
Period size: 5 Copynumber: 10.6 Consensus size: 5
405206 CTTTTGGGCC
* *
405216 TAAAA TAATA -AAAA T-AAA TAAATA TAAAA TAAAA TAAAA TAAATA TAATA
1 TAAAA TAAAA TAAAA TAAAA TAAA-A TAAAA TAAAA TAAAA TAAA-A TAAAA
405266 TAA
1 TAA
405269 TGTAACTATA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
4 7 0.17
5 25 0.61
6 9 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
TAAAA
Found at i:405336 original size:22 final size:22
Alignment explanation
Indices: 405284--405336 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
405274 CTATAATAAT
* **
405284 AAAAACTATAATATGTTTTCAA
1 AAAAAATATAATATGTTTAAAA
**
405306 AAATTATATAATATGTTTAAAA
1 AAAAAATATAATATGTTTAAAA
405328 AAAAAATAT
1 AAAAAATAT
405337 TCTGATGTGA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.36
Consensus pattern (22 bp):
AAAAAATATAATATGTTTAAAA
Found at i:405438 original size:20 final size:18
Alignment explanation
Indices: 405413--405451 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
405403 CGATACATAA
405413 TTATAATATTAATAAATTAT
1 TTATAA-ATTAA-AAATTAT
*
405433 TTATAAATTTAAAATTAT
1 TTATAAATTAAAAATTAT
405451 T
1 T
405452 ATACCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 4 0.22
20 6 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATAAATTAAAAATTAT
Found at i:406215 original size:2 final size:2
Alignment explanation
Indices: 406203--406249 Score: 85
Period size: 2 Copynumber: 23.0 Consensus size: 2
406193 TACCTAAAAC
406203 AT AT CAT 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
406246 AT AT
1 AT AT
406250 TTTAATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 42 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:408967 original size:2 final size:2
Alignment explanation
Indices: 408962--408996 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
408952 TTAATCATTA
408962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
408997 ATTACTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:413913 original size:2 final size:2
Alignment explanation
Indices: 413906--413931 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
413896 ATATCTCCCA
413906 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
413932 CCCTCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:414464 original size:22 final size:22
Alignment explanation
Indices: 414438--414480 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
414428 TAATAAATTA
414438 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
414460 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
414481 CTGATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:414489 original size:22 final size:22
Alignment explanation
Indices: 414440--414488 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
414430 ATAAATTATT
**
414440 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATGA
414462 TAAAATAAATCAATCCATACTGA
1 TAAAATAAATCAATCCATA-TGA
414485 TAAA
1 TAAA
414489 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.53, C:0.14, G:0.02, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATGA
Found at i:414491 original size:54 final size:55
Alignment explanation
Indices: 414428--414904 Score: 340
Period size: 54 Copynumber: 8.5 Consensus size: 55
414418 ACAACTACAA
*
414428 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATACTTTTAAAATAAATCAATCAATAC
* *
414482 TGATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCATACTTTTAAAATAAATCAATCAATAC
* ** *
414536 AAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATACTTTTAAA--A--T-AAATCAATCAATAC
** * ** * *
414595 T-AT--A-T-TTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATACTTTTAAAATAAAT-CAATCAATAC
** ** *
414645 -AATCCA-TATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT-C
1 TAATAAATTA-TTTAAAATAAATCAATCCATACTTTTAAA--A--T-AAATCAATCAATAC
* * ** *
414703 T-ATACAACTA--CAATAATAAATCAATATATA-TTTTAAAATAAATCAATCTATAC
1 TAATA-AATTATTTAA-AATAAATCAATCCATACTTTTAAAATAAATCAATCAATAC
*
414756 TAATAAATTATTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAAGCAATCCATATT
1 TAATAAATTATTTAAAATAAATCAATCCATAC--------T-TTTAAAATAAATCAAT-C--A--
414821 CATAC
52 -ATAC
*
414826 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATACTTTTAAAATAAATCAATCAATAC
414880 TAATAAATTATTTAAAATAAATCAA
1 TAATAAATTATTTAAAATAAATCAA
414905 AATATACAAC
Statistics
Matches: 349, Mismatches: 33, Indels: 82
0.75 0.07 0.18
Matches are distributed among these distances:
49 2 0.01
50 11 0.03
52 12 0.03
53 7 0.02
54 186 0.53
55 9 0.03
56 1 0.00
57 8 0.02
58 27 0.08
59 6 0.02
60 27 0.08
61 1 0.00
63 1 0.00
64 15 0.04
65 1 0.00
70 35 0.10
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (55 bp):
TAATAAATTATTTAAAATAAATCAATCCATACTTTTAAAATAAATCAATCAATAC
Found at i:414498 original size:32 final size:32
Alignment explanation
Indices: 414460--414904 Score: 329
Period size: 32 Copynumber: 15.5 Consensus size: 32
414450 CAATCCATAT
*
414460 TTTAAAATAAATCAATCCATACTGATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
414492 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
414514 TTTAAAATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
414546 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
414578 TTTAAAATAAATC-A---AT-CT-AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
414600 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
414632 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
414654 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
* *
414686 TTTAAAATAAATCAATCTATAC-AACTACA--A
1 TTTAAAATAAATCAATCCATACTAA-TAAATTA
** **
414716 --T--AATAAATCAATATATA-TTTTAAA--A
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
414741 -------TAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
414766 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
414798 TTTAAAATAAAGCAATCCATATTCATACTAATAAATTA
1 TTTAAAAT--A--AAT-CA-ATCCATACTAATAAATTA
414836 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
*
414858 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
414890 TTTAAAATAAATCAA
1 TTTAAAATAAATCAA
414905 AATATACAAC
Statistics
Matches: 342, Mismatches: 13, Indels: 116
0.73 0.03 0.25
Matches are distributed among these distances:
22 74 0.22
23 12 0.04
24 4 0.01
25 5 0.01
26 28 0.08
27 4 0.01
28 14 0.04
30 5 0.01
31 10 0.03
32 149 0.44
33 2 0.01
34 4 0.01
36 4 0.01
37 2 0.01
38 25 0.07
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:414518 original size:22 final size:22
Alignment explanation
Indices: 414492--414534 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
414482 TGATAAATTA
414492 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
414514 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
414535 CAAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:414543 original size:22 final size:22
Alignment explanation
Indices: 414494--414542 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
414484 ATAAATTATT
***
414494 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATAAAA
414516 TAAAATAAATCAATCCATACAAA
1 TAAAATAAATCAATCCATA-AAA
414539 TAAA
1 TAAA
414543 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (22 bp):
TAAAATAAATCAATCCATAAAA
Done.