Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 49 of 97
Found at i:19803228 original size:17 final size:17
Alignment explanation
Indices: 19803206--19803238 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
19803196 AAACAAGGTG
*
19803206 AGGAATAGGAATTCCTA
1 AGGAATAGAAATTCCTA
19803223 AGGAATAGAAATTCCT
1 AGGAATAGAAATTCCT
19803239 CAGATTTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.24
Consensus pattern (17 bp):
AGGAATAGAAATTCCTA
Found at i:19803503 original size:33 final size:33
Alignment explanation
Indices: 19803457--19803522 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
19803447 CCCCGAAAAG
* * *
19803457 CATCTCCTCTCTCAGCCGACCTTCCCCTGTCTT
1 CATCTACTCTCTCAACCGACCTTCCCCTATCTT
* *
19803490 CATCTACTTTCTCAACCGATCTTCCCCTATCTT
1 CATCTACTCTCTCAACCGACCTTCCCCTATCTT
19803523 TCGTCCTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.14, C:0.44, G:0.06, T:0.36
Consensus pattern (33 bp):
CATCTACTCTCTCAACCGACCTTCCCCTATCTT
Found at i:19803958 original size:23 final size:23
Alignment explanation
Indices: 19803905--19803958 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
19803895 ATGAAAGTAA
*
19803905 AAATTATATAACTAATTTAATAT
1 AAATTATTTAACTAATTTAATAT
19803928 AAATTATTTAA-TAATTTAATAAT
1 AAATTATTTAACTAATTTAAT-AT
19803951 AAATTATT
1 AAATTATT
19803959 GATGTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 9 0.31
23 20 0.69
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATTATTTAACTAATTTAATAT
Found at i:19803983 original size:135 final size:137
Alignment explanation
Indices: 19803812--19804072 Score: 357
Period size: 135 Copynumber: 1.9 Consensus size: 137
19803802 ATTATATAAT
*
19803812 TAATAAATTATTAATTTTTAATGAAAATAAAAATTAAAAAGATTAAAAAATAAAAAATACAAATA
1 TAATAAATTATTAATGTTTAATGAAAATAAAAATT-AAAAGATTAAAAAATAAAAAATACAAATA
* * *
19803877 GAGAAAAAT-ACTCAAA-TAATGAAAGTAAAAATTATATAACTAATTTAAT-ATAAATTATTTAA
65 GAGAAAAATGACTCAAATTAATAAAAGTAAAAATCATAAAACTAATTTAATAATAAATTATTTAA
19803939 TAATTTAA
130 TAATTTAA
* ** * * * *
19803947 TAATAAATTATTGATGTTTAATGAAAATGTAAATTAAAAGGTTAAGACATGAAAAATACAAATAG
1 TAATAAATTATTAATGTTTAATGAAAATAAAAATTAAAAGATTAAAAAATAAAAAATACAAATAG
* ** *
19804012 AGAAAAATGATTCAAATTGTTAAAATTAAAAATCATAAAACTAATTTAATAATAAATTATT
66 AGAAAAATGACTCAAATTAATAAAAGTAAAAATCATAAAACTAATTTAATAATAAATTATT
19804073 GATATAAAAA
Statistics
Matches: 108, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 34 0.31
135 37 0.34
136 27 0.25
137 10 0.09
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (137 bp):
TAATAAATTATTAATGTTTAATGAAAATAAAAATTAAAAGATTAAAAAATAAAAAATACAAATAG
AGAAAAATGACTCAAATTAATAAAAGTAAAAATCATAAAACTAATTTAATAATAAATTATTTAAT
AATTTAA
Found at i:19806830 original size:21 final size:21
Alignment explanation
Indices: 19806800--19806847 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
19806790 TTGGACATAA
*
19806800 TCTATCGATAGATGTTTTATG
1 TCTATCGATAGATGTTCTATG
*
19806821 TCTATTGATAGATGTTCTATG
1 TCTATCGATAGATGTTCTATG
19806842 TCTATC
1 TCTATC
19806848 AATAAATGCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.48
Consensus pattern (21 bp):
TCTATCGATAGATGTTCTATG
Found at i:19809283 original size:30 final size:30
Alignment explanation
Indices: 19809247--19809331 Score: 170
Period size: 30 Copynumber: 2.8 Consensus size: 30
19809237 CTCAAAATTA
19809247 CTCTTCTTCTTTCACTAAAATTCTTTATTG
1 CTCTTCTTCTTTCACTAAAATTCTTTATTG
19809277 CTCTTCTTCTTTCACTAAAATTCTTTATTG
1 CTCTTCTTCTTTCACTAAAATTCTTTATTG
19809307 CTCTTCTTCTTTCACTAAAATTCTT
1 CTCTTCTTCTTTCACTAAAATTCTT
19809332 CTTTCATCAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.20, C:0.25, G:0.02, T:0.53
Consensus pattern (30 bp):
CTCTTCTTCTTTCACTAAAATTCTTTATTG
Found at i:19809457 original size:14 final size:14
Alignment explanation
Indices: 19809438--19809480 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
19809428 TTGACTCACC
19809438 TAAAATAACTAATT
1 TAAAATAACTAATT
* *
19809452 TAAAATAATTAAAT
1 TAAAATAACTAATT
* *
19809466 TAAACTTACTAATT
1 TAAAATAACTAATT
19809480 T
1 T
19809481 CTATGCATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAAATAACTAATT
Found at i:19809512 original size:22 final size:23
Alignment explanation
Indices: 19809487--19809533 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
19809477 ATTTCTATGC
19809487 ATTACTAT-AAGAATTAAGCT-AA
1 ATTACTATCAA-AATTAAGCTCAA
*
19809509 ATTATTATCAAAATTAAGCTCAA
1 ATTACTATCAAAATTAAGCTCAA
19809532 AT
1 AT
19809534 AACTCTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.49, C:0.11, G:0.06, T:0.34
Consensus pattern (23 bp):
ATTACTATCAAAATTAAGCTCAA
Found at i:19811642 original size:21 final size:21
Alignment explanation
Indices: 19811613--19811680 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
19811603 CTGACTTTGA
* *
19811613 ATGATGGCATCAGTCCTTGTC
1 ATGAAGGCATCAGTCTTTGTC
* *
19811634 ATGAAGGCATCTGTTTTTGTC
1 ATGAAGGCATCAGTCTTTGTC
19811655 ATGAAGGCATCAGTCTTTGTC
1 ATGAAGGCATCAGTCTTTGTC
19811676 ATGAA
1 ATGAA
19811681 TTGCATGAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (21 bp):
ATGAAGGCATCAGTCTTTGTC
Found at i:19813646 original size:37 final size:37
Alignment explanation
Indices: 19813605--19813719 Score: 178
Period size: 37 Copynumber: 3.1 Consensus size: 37
19813595 GTTGTGTGAG
*
19813605 GATGTTGAAATGTGCGAGTAGAGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAGAGAGTGCACACATGAT
* * *
19813642 GATGTT-AGAGTGTGCGAGCAGGGAGAGCACACATGAT
1 GATGTTGA-AGTGTGCGAGTAGAGAGTGCACACATGAT
19813679 GATGTTGAAGTGTGCGAGTAGAGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAGAGAGTGCACACATGAT
19813716 GATG
1 GATG
19813720 AATGCATATG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
36 1 0.01
37 67 0.97
38 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.36, T:0.23
Consensus pattern (37 bp):
GATGTTGAAGTGTGCGAGTAGAGAGTGCACACATGAT
Found at i:19824312 original size:43 final size:43
Alignment explanation
Indices: 19824200--19824315 Score: 155
Period size: 43 Copynumber: 2.7 Consensus size: 43
19824190 GGCTATATGA
**
19824200 GAGTAGGGAGTGCGCATAAGCCGAG-GATGACCAGGTTATGTGC
1 GAGTAGGGAGTGCGCATAAGCCG-GTGATGACCAGGCCATGTGC
*
19824243 GAGTAGGGAGTGCGCATAACCCGGTGATGACCCA-GCCATGTGC
1 GAGTAGGGAGTGCGCATAAGCCGGTGATGA-CCAGGCCATGTGC
* *
19824286 GAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 GAGTAGGGAGTGCGCATAAGCCGGTGATGA
19824316 TGATGATGAG
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
42 1 0.02
43 61 0.94
44 3 0.05
ACGTcount: A:0.24, C:0.18, G:0.40, T:0.18
Consensus pattern (43 bp):
GAGTAGGGAGTGCGCATAAGCCGGTGATGACCAGGCCATGTGC
Found at i:19824326 original size:20 final size:20
Alignment explanation
Indices: 19824301--19824363 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
19824291 GGGAGTGCGC
19824301 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
*
19824321 ATGAGCTGGTGATGATGATA
1 ATGAGCTGGTGATGATGATG
* *
19824341 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
19824360 ATGA
1 ATGA
19824364 TGGGTATATA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 9 0.24
20 29 0.76
ACGTcount: A:0.27, C:0.03, G:0.40, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:19827271 original size:37 final size:37
Alignment explanation
Indices: 19827230--19827307 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
19827220 GTTGTGTGAG
19827230 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
19827267 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
1 GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
19827304 GATG
1 GATG
19827308 AATGCATATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.27, C:0.10, G:0.38, T:0.24
Consensus pattern (37 bp):
GATGTTGAAGTGTGCGAGTAGGGAGTGCACACATGAT
Found at i:19830708 original size:35 final size:35
Alignment explanation
Indices: 19830660--19830734 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
19830650 TTAACTGCTG
*
19830660 ATTTTGAAGGCTGAAAGGTGCAGTTTTGGTGGCTA
1 ATTTTGAAAGCTGAAAGGTGCAGTTTTGGTGGCTA
* *
19830695 ATTTTGAAAGCTGAAAGGTGCGGTTTTGGTTGCTA
1 ATTTTGAAAGCTGAAAGGTGCAGTTTTGGTGGCTA
19830730 ATTTT
1 ATTTT
19830735 TGTAGCTTTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.23, C:0.08, G:0.31, T:0.39
Consensus pattern (35 bp):
ATTTTGAAAGCTGAAAGGTGCAGTTTTGGTGGCTA
Found at i:19830780 original size:33 final size:33
Alignment explanation
Indices: 19830742--19830822 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
19830732 TTTTGTAGCT
19830742 TTGGCTGCTGATTTTTGGAGG-GAGAAT-AGCAGC
1 TTGGCTGCTGATTTTT-GAGGAGA-AATAAGCAGC
*
19830775 TTGGCTGCT-AATTTTGAGGAGAAATAGAGCAGC
1 TTGGCTGCTGATTTTTGAGGAGAAATA-AGCAGC
19830808 TTGGCTGCTGATTTT
1 TTGGCTGCTGATTTT
19830823 GTTGTGGATA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 7 0.17
32 7 0.17
33 24 0.57
34 4 0.10
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.33
Consensus pattern (33 bp):
TTGGCTGCTGATTTTTGAGGAGAAATAAGCAGC
Found at i:19833440 original size:22 final size:22
Alignment explanation
Indices: 19833415--19833459 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
19833405 ATTTCTATAC
19833415 ATTACTA-CAAGAATTAAGCTAA
1 ATTACTATCAA-AATTAAGCTAA
* *
19833437 ATTATTATGAAAATTAAGCTAA
1 ATTACTATCAAAATTAAGCTAA
19833459 A
1 A
19833460 ATAACTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (22 bp):
ATTACTATCAAAATTAAGCTAA
Found at i:19836349 original size:14 final size:14
Alignment explanation
Indices: 19836305--19836355 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
19836295 CCAAAAACAT
19836305 CTTGTTTAGGCATC
1 CTTGTTTAGGCATC
* *
19836319 CTTAG-TCAAGCAT-
1 CTT-GTTTAGGCATC
19836332 CTTGTTTAGGCATC
1 CTTGTTTAGGCATC
*
19836346 CTTGGTTAGG
1 CTTGTTTAGG
19836356 TACCCATAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
12 1 0.03
13 9 0.31
14 18 0.62
15 1 0.03
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.39
Consensus pattern (14 bp):
CTTGTTTAGGCATC
Found at i:19843672 original size:22 final size:22
Alignment explanation
Indices: 19843630--19843670 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19843620 ACCTTTGTTT
*
19843630 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
19843652 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
19843671 TCTACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:19848240 original size:22 final size:22
Alignment explanation
Indices: 19848212--19848274 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
19848202 TTTAAAACAA
19848212 CTTT-AAACCTAAAAGCT-TTAAT
1 CTTTAAAACC-AAAAGCTCTT-AT
19848234 CTTTAAAACCAAAAGCTCTTAT
1 CTTTAAAACCAAAAGCTCTTAT
19848256 CTTTAAAACCAAAAGCTCT
1 CTTTAAAACCAAAAGCTCT
19848275 GACACCACTC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
22 32 0.82
23 7 0.18
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (22 bp):
CTTTAAAACCAAAAGCTCTTAT
Found at i:19853571 original size:21 final size:20
Alignment explanation
Indices: 19853547--19853594 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
19853537 ATCTTACCTT
*
19853547 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTGAA
*
19853568 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
19853589 TTTTTC
1 TTTTTC
19853595 TGCCTCGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:19853594 original size:22 final size:22
Alignment explanation
Indices: 19853552--19853592 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
19853542 ACCTTTTTTT
*
19853552 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
19853574 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
19853593 TCTGCCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:19855610 original size:37 final size:37
Alignment explanation
Indices: 19855471--19855609 Score: 192
Period size: 37 Copynumber: 3.8 Consensus size: 37
19855461 TGCGGTATGC
19855471 GAGTAGGGAGTGCACACATGATGATGATTGAGTGT-A
1 GAGTAGGGAGTGCACACATGATGATGATTGAGTGTGA
* *
19855507 CGAGTAGGAAATGCACACATGATGATGATTGAGTGTGA
1 -GAGTAGGGAGTGCACACATGATGATGATTGAGTGTGA
** *
19855545 GAGTAGGGAGTGCACACATGACAATGA-TGAAGTGTGT
1 GAGTAGGGAGTGCACACATGATGATGATTG-AGTGTGA
*
19855582 GAGTAGGGAGTGAACACATGATGATGAT
1 GAGTAGGGAGTGCACACATGATGATGAT
19855610 GTATGTATAT
Statistics
Matches: 89, Mismatches: 10, Indels: 5
0.86 0.10 0.05
Matches are distributed among these distances:
36 2 0.02
37 86 0.97
38 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.35, T:0.23
Consensus pattern (37 bp):
GAGTAGGGAGTGCACACATGATGATGATTGAGTGTGA
Found at i:19855888 original size:21 final size:21
Alignment explanation
Indices: 19855873--19855946 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
19855863 AATCTTGCGA
19855873 CAGCGAGAATGAATCTAGCCG
1 CAGCGAGAATGAATCTAGCCG
* *
19855894 CAGCGAAAATGAATCTCGCCG
1 CAGCGAGAATGAATCTAGCCG
19855915 CAGCGAGAATGAATCTCA-CCG
1 CAGCGAGAATGAATCT-AGCCG
*
19855936 CAACGAGAATG
1 CAGCGAGAATG
19855947 TTACTGCAGC
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.14
Consensus pattern (21 bp):
CAGCGAGAATGAATCTAGCCG
Found at i:19870245 original size:15 final size:16
Alignment explanation
Indices: 19870215--19870247 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
19870205 AAATTAGATT
19870215 TTGATTCTTTTGGATA
1 TTGATTCTTTTGGATA
*
19870231 TTGATT-TTTTTGATA
1 TTGATTCTTTTGGATA
19870246 TT
1 TT
19870248 TTTATTGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.18, C:0.03, G:0.15, T:0.64
Consensus pattern (16 bp):
TTGATTCTTTTGGATA
Found at i:19871488 original size:68 final size:68
Alignment explanation
Indices: 19871383--19871542 Score: 178
Period size: 68 Copynumber: 2.4 Consensus size: 68
19871373 TAAGATTGTA
* * * * * * *
19871383 TATATGATGTAAATTCTATATACCATATGAAGTGATTAAGTATGCATGACAAATGCCATGAGATA
1 TATATGATGTATATTCCATATACCACATGAAGCGATTAAGAAAGCATGACAAATGCCAAGAGATA
19871448 ATG
66 ATG
* * ** *
19871451 TATATGATGTATATTCCATATACTACATG-AGACGATTACGAAAGCATGATGAATGCTAAGAGAT
1 TATATGATGTATATTCCATATACCACATGAAG-CGATTAAGAAAGCATGACAAATGCCAAGAGAT
*
19871515 TATG
65 AATG
*
19871519 TATATGATGTATTTTCCATATACC
1 TATATGATGTATATTCCATATACC
19871543 TTATGAGATG
Statistics
Matches: 76, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
67 2 0.03
68 74 0.97
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.34
Consensus pattern (68 bp):
TATATGATGTATATTCCATATACCACATGAAGCGATTAAGAAAGCATGACAAATGCCAAGAGATA
ATG
Found at i:19874407 original size:15 final size:13
Alignment explanation
Indices: 19874374--19874412 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
19874364 AAAAATCAAG
19874374 TTTTTT-TTTTCC
1 TTTTTTCTTTTCC
19874386 TTTTTTCTTTTCC
1 TTTTTTCTTTTCC
19874399 TTTCCTTTCTTTTC
1 TTT--TTTCTTTTC
19874413 TTACTTCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 6 0.25
13 9 0.38
15 9 0.38
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTCTTTTCC
Found at i:19875342 original size:39 final size:39
Alignment explanation
Indices: 19875297--19875431 Score: 189
Period size: 39 Copynumber: 3.5 Consensus size: 39
19875287 GTAGTGTGTA
*** * *
19875297 GTGTGGGAGAGCACATGCCAATAATATATGCAATGTGCG
1 GTGTGGGAGAGCACATGATGATGATATATGCCATGTGCG
*
19875336 GTGTGGGAGAGCACATGATGATGATATATGCCATGTGCA
1 GTGTGGGAGAGCACATGATGATGATATATGCCATGTGCG
* *
19875375 GTATGGGAGAGCACATGATGATGATATTTGCCATGTGCG
1 GTGTGGGAGAGCACATGATGATGATATATGCCATGTGCG
*
19875414 GTGTGGGAGTGCACATGA
1 GTGTGGGAGAGCACATGA
19875432 GCTGAGTTGA
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 85 1.00
ACGTcount: A:0.27, C:0.13, G:0.34, T:0.25
Consensus pattern (39 bp):
GTGTGGGAGAGCACATGATGATGATATATGCCATGTGCG
Found at i:19877566 original size:10 final size:10
Alignment explanation
Indices: 19877553--19877577 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
19877543 GATGTTTATC
19877553 TATGTATATA
1 TATGTATATA
19877563 TATGTATATA
1 TATGTATATA
19877573 TATGT
1 TATGT
19877578 TTATGAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (10 bp):
TATGTATATA
Found at i:19877938 original size:21 final size:21
Alignment explanation
Indices: 19877878--19877939 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
19877868 TGGCCATTTG
* * *
19877878 AATCTTGCTACAGCGAGAAAG
1 AATCTCGCTGCAGCGAGAAAA
** **
19877899 AATCTCATTGCAGTAAGAAAA
1 AATCTCGCTGCAGCGAGAAAA
19877920 AATCTCGCTGCAGCGAGAAA
1 AATCTCGCTGCAGCGAGAAA
19877940 CTTTTTGTTC
Statistics
Matches: 30, Mismatches: 11, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (21 bp):
AATCTCGCTGCAGCGAGAAAA
Found at i:19882710 original size:2 final size:2
Alignment explanation
Indices: 19882703--19882734 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
19882693 TTGTATGCAA
19882703 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
19882735 GTTTTTGTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19887109 original size:20 final size:20
Alignment explanation
Indices: 19887084--19887143 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
19887074 ACATCGATGG
19887084 ATAGATGACCATATCTATCC
1 ATAGATGACCATATCTATCC
* * * * *
19887104 ATAGATAACTAGATTTATCG
1 ATAGATGACCATATCTATCC
*
19887124 ATAGATGACCCTTATCTATC
1 ATAGATGA-CCATATCTATC
19887144 GATATATAGC
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
20 22 0.76
21 7 0.24
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (20 bp):
ATAGATGACCATATCTATCC
Found at i:19888818 original size:28 final size:29
Alignment explanation
Indices: 19888777--19888836 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
19888767 GTCTATGGGC
* *
19888777 AATTTTTCAGTTTT-TGGGGCAAAAATGT
1 AATTTTTCACTTTTAGGGGGCAAAAATGT
* *
19888805 AATTTTTTACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCACTTTTA-GGGGGCAAAAATGT
19888835 AA
1 AA
19888837 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.30, C:0.08, G:0.22, T:0.40
Consensus pattern (29 bp):
AATTTTTCACTTTTAGGGGGCAAAAATGT
Found at i:19892802 original size:14 final size:14
Alignment explanation
Indices: 19892783--19892809 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19892773 CATTGCCTAG
19892783 GAGATGTTAGGGTT
1 GAGATGTTAGGGTT
19892797 GAGATGTTAGGGT
1 GAGATGTTAGGGT
19892810 GAGGATTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.33
Consensus pattern (14 bp):
GAGATGTTAGGGTT
Found at i:19897230 original size:22 final size:20
Alignment explanation
Indices: 19897205--19897248 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
19897195 GGTTTTGGCT
19897205 AAGCCTGGTAAAAGCCATTGTG
1 AAGCCTGGTAAAAG-C-TTGTG
* *
19897227 AAGCTTGGTGAAAGCTTGTG
1 AAGCCTGGTAAAAGCTTGTG
19897247 AA
1 AA
19897249 TTTCACCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 1 0.05
22 12 0.60
ACGTcount: A:0.32, C:0.14, G:0.30, T:0.25
Consensus pattern (20 bp):
AAGCCTGGTAAAAGCTTGTG
Found at i:19899470 original size:63 final size:63
Alignment explanation
Indices: 19899397--19899573 Score: 293
Period size: 63 Copynumber: 2.8 Consensus size: 63
19899387 TGATGCAACT
*
19899397 GTGCATGTGCGGAGTGGGAAGTGCAATGGCGGTTTAATGATAAAGGATGTGATAATTACGACC
1 GTGCATGTGCGGAGTGGGAAGTGCAATGCCGGTTTAATGATAAAGGATGTGATAATTACGACC
* * *
19899460 GTGCATGTGCGGAGTGGGAAGTGCAATGCCAGTTGAATGACAAA-GAGTGTGATAATTACGACC
1 GTGCATGTGCGGAGTGGGAAGTGCAATGCCGGTTTAATGATAAAGGA-TGTGATAATTACGACC
*
19899523 GTGCATGTGCGGAGTGGGAAGTGCAATGCCGGTTTAATGATAAAGGTTGTG
1 GTGCATGTGCGGAGTGGGAAGTGCAATGCCGGTTTAATGATAAAGGATGTG
19899574 GGGACGGCGA
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
62 2 0.02
63 101 0.97
64 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.36, T:0.25
Consensus pattern (63 bp):
GTGCATGTGCGGAGTGGGAAGTGCAATGCCGGTTTAATGATAAAGGATGTGATAATTACGACC
Found at i:19915193 original size:20 final size:20
Alignment explanation
Indices: 19915154--19915194 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
19915144 TAAATTTAGA
* *
19915154 TTATTTTTAGTTTTAGTTTT
1 TTATTTTTAATTTTACTTTT
*
19915174 TTATTTTTAATTTTTCTTTT
1 TTATTTTTAATTTTACTTTT
19915194 T
1 T
19915195 AATAATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.78
Consensus pattern (20 bp):
TTATTTTTAATTTTACTTTT
Found at i:19917311 original size:27 final size:28
Alignment explanation
Indices: 19917239--19917311 Score: 123
Period size: 27 Copynumber: 2.7 Consensus size: 28
19917229 CTTATTTCTA
19917239 TTGGGCCATGCCCATTTT-TCTTTCTTG
1 TTGGGCCATGCCCATTTTCTCTTTCTTG
19917266 TTGGGCCATGCCCATTTTCT-TTTCTTG
1 TTGGGCCATGCCCATTTTCTCTTTCTTG
*
19917293 TTGGGTCATGCCCATTTTC
1 TTGGGCCATGCCCATTTTC
19917312 CTTCCTTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 43 0.98
28 1 0.02
ACGTcount: A:0.08, C:0.26, G:0.19, T:0.47
Consensus pattern (28 bp):
TTGGGCCATGCCCATTTTCTCTTTCTTG
Found at i:19917692 original size:34 final size:34
Alignment explanation
Indices: 19917618--19917708 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 34
19917608 CAAAAATCTA
** **
19917618 CACTTTTTACCCTCCAAAATCAGTAGCAAAGCTG
1 CACTTTTTGGCCTCCAAAATCAGTAGCAAAAATG
*
19917652 CACTTTTTGGCCTCCAAAATTAGTAG-AAAAATAG
1 CACTTTTTGGCCTCCAAAATCAGTAGCAAAAAT-G
* ** *
19917686 CTCTTTTCAGCCTCTAAAATCAG
1 CACTTTTTGGCCTCCAAAATCAG
19917709 CCCTTAAATG
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
33 4 0.09
34 42 0.91
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (34 bp):
CACTTTTTGGCCTCCAAAATCAGTAGCAAAAATG
Found at i:19917837 original size:29 final size:30
Alignment explanation
Indices: 19917768--19917855 Score: 81
Period size: 35 Copynumber: 2.8 Consensus size: 30
19917758 TTAACTCAGC
*
19917768 TCTCTTTTCCTTTTGTTTTTCTTTCTCTCTCGG
1 TCTC-TTTCTTTTTGTTTTTC-TT-TCTCTCGG
*
19917801 CTTTCTCTTTGTTTTTGTTTTTCTTTCTCTCGG
1 ---TCTCTTTCTTTTTGTTTTTCTTTCTCTCGG
*
19917834 -CTCTTTCTTTTT-TCTTTCTTTC
1 TCTCTTTCTTTTTGTTTTTCTTTC
19917856 CTTTTTTTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
28 9 0.19
29 11 0.23
33 8 0.17
34 2 0.04
35 14 0.29
36 4 0.08
ACGTcount: A:0.00, C:0.25, G:0.08, T:0.67
Consensus pattern (30 bp):
TCTCTTTCTTTTTGTTTTTCTTTCTCTCGG
Found at i:19917873 original size:18 final size:18
Alignment explanation
Indices: 19917841--19917879 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
19917831 CGGCTCTTTC
19917841 TTTTTTCTTTCTTTC-CT
1 TTTTTTCTTTCTTTCTCT
*
19917858 TTTTTTCTTTTGTTTCTCT
1 TTTTTTC-TTTCTTTCTCT
19917877 TTT
1 TTT
19917880 GCTCTCCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 7 0.37
19 5 0.26
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (18 bp):
TTTTTTCTTTCTTTCTCT
Found at i:19917947 original size:2 final size:2
Alignment explanation
Indices: 19917940--19917974 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19917930 CTCATTCAAT
19917940 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19917975 TTTATGCCTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19930653 original size:43 final size:43
Alignment explanation
Indices: 19930600--19930724 Score: 189
Period size: 43 Copynumber: 2.9 Consensus size: 43
19930590 TCATTCATCG
* *
19930600 TCATGTGCACTCCCTACTCGCACATAGCCAGGTCATCATCGGC
1 TCATGTGCACTCCCTACTCGCACATAGCCGGGTCATCATCCGC
* *
19930643 TTATGTGCACTCCCTACTCGCACATAGTCGGGTCATCATCCGC
1 TCATGTGCACTCCCTACTCGCACATAGCCGGGTCATCATCCGC
*
19930686 TCATGTGCACTCCC-ACATCGCACATAGCTGGGTCATCAT
1 TCATGTGCACTCCCTAC-TCGCACATAGCCGGGTCATCAT
19930725 ATCACACAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
42 2 0.03
43 72 0.97
ACGTcount: A:0.21, C:0.35, G:0.18, T:0.26
Consensus pattern (43 bp):
TCATGTGCACTCCCTACTCGCACATAGCCGGGTCATCATCCGC
Found at i:19931559 original size:20 final size:20
Alignment explanation
Indices: 19931531--19931570 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
19931521 AAAAGAACAA
*
19931531 GAAGTTGCTGGAAAAATGAG
1 GAAGCTGCTGGAAAAATGAG
*
19931551 GAAGCTGCTGGAGAAATGAG
1 GAAGCTGCTGGAAAAATGAG
19931571 ATATTTATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.07, G:0.38, T:0.17
Consensus pattern (20 bp):
GAAGCTGCTGGAAAAATGAG
Found at i:19935218 original size:14 final size:15
Alignment explanation
Indices: 19935199--19935228 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
19935189 TTTGATCTAA
19935199 ATTACCTAAT-GAAG
1 ATTACCTAATAGAAG
19935213 ATTACCTAATAGAAG
1 ATTACCTAATAGAAG
19935228 A
1 A
19935229 CATACAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.47, C:0.13, G:0.13, T:0.27
Consensus pattern (15 bp):
ATTACCTAATAGAAG
Found at i:19936007 original size:57 final size:57
Alignment explanation
Indices: 19935892--19936010 Score: 168
Period size: 57 Copynumber: 2.1 Consensus size: 57
19935882 CATAATCATC
* *
19935892 CAAAGTAGTTTACATGTGATAGATTTATTTATGCAATTTAATATATGTTATGCAATG
1 CAAAGTAGTATACATGTGATAGATTTATTTATGCAATTTAATAAATGTTATGCAATG
* * **
19935949 CAAAGTAGTATGCATGTGATAGATTTATTTTGTGTGATTTAATAAATGTTATGC-ATG
1 CAAAGTAGTATACATGTGATAGATTTA-TTTATGCAATTTAATAAATGTTATGCAATG
19936006 CAAAG
1 CAAAG
19936011 ATGAGACCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
57 33 0.60
58 22 0.40
ACGTcount: A:0.34, C:0.07, G:0.18, T:0.40
Consensus pattern (57 bp):
CAAAGTAGTATACATGTGATAGATTTATTTATGCAATTTAATAAATGTTATGCAATG
Found at i:19945668 original size:6 final size:7
Alignment explanation
Indices: 19945652--19945684 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
19945642 TTTACCACAT
19945652 AAAAGGA
1 AAAAGGA
19945659 AAAAGGA
1 AAAAGGA
19945666 AAAAGGA
1 AAAAGGA
19945673 AAAAGGA
1 AAAAGGA
19945680 CAAAA
1 -AAAA
19945685 TGAGGAAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.73, C:0.03, G:0.24, T:0.00
Consensus pattern (7 bp):
AAAAGGA
Found at i:19945733 original size:16 final size:16
Alignment explanation
Indices: 19945712--19945753 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
19945702 ATTTGCCTAT
19945712 GAAAAGAAAGTAAAGA
1 GAAAAGAAAGTAAAGA
19945728 GAAAAGAAAGTAAAGA
1 GAAAAGAAAGTAAAGA
19945744 GAAAAAGAAA
1 G-AAAAGAAA
19945754 AGAAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.68
17 8 0.32
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (16 bp):
GAAAAGAAAGTAAAGA
Found at i:19945755 original size:13 final size:14
Alignment explanation
Indices: 19945712--19945768 Score: 53
Period size: 14 Copynumber: 4.0 Consensus size: 14
19945702 ATTTGCCTAT
*
19945712 GAAAAGAAAGTAAAGA
1 GAAAATAAAG-AAA-A
* *
19945728 GAAAAGAAAGTAAA
1 GAAAATAAAGAAAA
*
19945742 GAGAA-AAAGAAAA
1 GAAAATAAAGAAAA
19945755 GAAAATAAAGAAAA
1 GAAAATAAAGAAAA
19945769 AAAGATGTGA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
13 11 0.31
14 13 0.36
15 2 0.06
16 10 0.28
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (14 bp):
GAAAATAAAGAAAA
Found at i:19945755 original size:22 final size:22
Alignment explanation
Indices: 19945727--19945773 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
19945717 GAAAGTAAAG
* *
19945727 AGAAAAGAAAGTAAAGAGAAAA
1 AGAAAAGAAAATAAAGAAAAAA
19945749 AGAAAAGAAAATAAAGAAAAAA
1 AGAAAAGAAAATAAAGAAAAAA
19945771 AGA
1 AGA
19945774 TGTGACTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (22 bp):
AGAAAAGAAAATAAAGAAAAAA
Found at i:19947135 original size:28 final size:29
Alignment explanation
Indices: 19947090--19947154 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
19947080 TGGCAGCTTT
*
19947090 AACATTTTTGTCTTAATTTAGAAAAGA-A
1 AACATATTTGTCTTAATTTAGAAAAGATA
*
19947118 AACATATTTGT-TTCAATTTAGACAAGATA
1 AACATATTTGTCTT-AATTTAGAAAAGATA
19947147 AA-ATATTT
1 AACATATTT
19947155 TTTTTCTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 28 0.85
29 3 0.09
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (29 bp):
AACATATTTGTCTTAATTTAGAAAAGATA
Found at i:19947340 original size:17 final size:17
Alignment explanation
Indices: 19947318--19947350 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
19947308 ATAATAATAA
19947318 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
19947335 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
19947351 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:19953569 original size:49 final size:49
Alignment explanation
Indices: 19953512--19953610 Score: 180
Period size: 49 Copynumber: 2.0 Consensus size: 49
19953502 GAAAAATCAT
*
19953512 TAACTCTCCAGCATGCAAAAGAGTACAAGTCTAAAAACTCTCAAGGCTC
1 TAACTCTCCACCATGCAAAAGAGTACAAGTCTAAAAACTCTCAAGGCTC
*
19953561 TAACTCTCCACCATGCAAAAGAGTACGAGTCTAAAAACTCTCAAGGCTC
1 TAACTCTCCACCATGCAAAAGAGTACAAGTCTAAAAACTCTCAAGGCTC
19953610 T
1 T
19953611 CGAGTAGGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.21
Consensus pattern (49 bp):
TAACTCTCCACCATGCAAAAGAGTACAAGTCTAAAAACTCTCAAGGCTC
Found at i:19953778 original size:25 final size:25
Alignment explanation
Indices: 19953750--19953833 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
19953740 GTGGTCACAA
*
19953750 CCACGTATATCAACTTGTGGCCTAG
1 CCACGTATATCAACTCGTGGCCTAG
* * *
19953775 CCACATATATCATCTCGTGGCCTTG
1 CCACGTATATCAACTCGTGGCCTAG
*
19953800 CCATGTATAATCACAAAC-CGTGGCCTAG
1 CCACGTAT-AT--C-AACTCGTGGCCTAG
19953828 CCACGT
1 CCACGT
19953834 CTAACAGCCC
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
25 27 0.59
26 2 0.04
28 15 0.33
29 2 0.04
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (25 bp):
CCACGTATATCAACTCGTGGCCTAG
Found at i:19956443 original size:35 final size:35
Alignment explanation
Indices: 19956402--19956578 Score: 140
Period size: 35 Copynumber: 5.2 Consensus size: 35
19956392 CCAAGCTTAG
*
19956402 CCAAAACCTTTCACAATGGTTTTT-ACCGGGATCAA
1 CCAAAACCTTTCACAATGGTTTTTCA-CGGGCTCAA
* **
19956437 CAAAAACC---CA-AAGTGGTTTTTCAAAGGCTCAA
1 CCAAAACCTTTCACAA-TGGTTTTTCACGGGCTCAA
*
19956469 CCACAACCTTTCACAATGGTTTTTCACGGGCTCAA
1 CCAAAACCTTTCACAATGGTTTTTCACGGGCTCAA
**
19956504 CCAAAACC---CA-AAGTGGTTTTTCAAAGGCTCAA
1 CCAAAACCTTTCACAA-TGGTTTTTCACGGGCTCAA
* * * * *
19956536 CCACAACC-TACAATAATGGTTTTTCACGAGATCAA
1 CCAAAACCTTTC-ACAATGGTTTTTCACGGGCTCAA
19956571 CCAAAACC
1 CCAAAACC
19956579 CAACAACTAA
Statistics
Matches: 114, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
31 4 0.04
32 48 0.42
33 1 0.01
34 1 0.01
35 56 0.49
36 4 0.04
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (35 bp):
CCAAAACCTTTCACAATGGTTTTTCACGGGCTCAA
Found at i:19956514 original size:67 final size:67
Alignment explanation
Indices: 19956406--19956581 Score: 275
Period size: 67 Copynumber: 2.6 Consensus size: 67
19956396 GCTTAGCCAA
*
19956406 AACCTTTCACAATGGTTTTT-ACCGGGATCAACAAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
19956470 CAC
65 CAC
*
19956473 AACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
19956538 AC
66 AC
* * *
19956540 AACC-TACAATAATGGTTTTTCACGAGATCAACCAAAACCCAA
1 AACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACCCAA
19956582 CAACTAACTT
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
66 2 0.02
67 98 0.97
68 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:19960323 original size:21 final size:21
Alignment explanation
Indices: 19960248--19960325 Score: 88
Period size: 21 Copynumber: 3.7 Consensus size: 21
19960238 TGATTACATT
*
19960248 ATTCTTTGTCAT-ATAAGCATC
1 ATTCTTTGTCATGA-AGGCATC
*
19960269 AGTCTTTGTCATGAAGGCATC
1 ATTCTTTGTCATGAAGGCATC
*
19960290 ATTCTTTGTCATGTAGGCATC
1 ATTCTTTGTCATGAAGGCATC
*
19960311 -TATCTTTGCCATGAA
1 AT-TCTTTGTCATGAA
19960326 TTATATGAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.02
21 47 0.96
22 1 0.02
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (21 bp):
ATTCTTTGTCATGAAGGCATC
Found at i:19965309 original size:19 final size:19
Alignment explanation
Indices: 19965285--19965322 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19965275 CTGCCAAACC
*
19965285 CTCAAATTATACTCCAATA
1 CTCAAATCATACTCCAATA
19965304 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
19965323 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:19972386 original size:19 final size:19
Alignment explanation
Indices: 19972362--19972399 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
19972352 CTGCCAAACC
*
19972362 CTCAAATTATACTACAATA
1 CTCAAATCATACTACAATA
*
19972381 CTCAAATCATACTCCAATA
1 CTCAAATCATACTACAATA
19972400 AGTTAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.26, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTACAATA
Found at i:19986216 original size:2 final size:2
Alignment explanation
Indices: 19986211--19986251 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
19986201 TTTTTTTTTN
19986211 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
19986252 ATTATGTCTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:19991080 original size:2 final size:2
Alignment explanation
Indices: 19991073--19991107 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
19991063 ATTTCTTTCT
19991073 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
19991108 TTCTGGTAGG
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:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:19991559 original size:4 final size:4
Alignment explanation
Indices: 19991544--19991575 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
19991534 AATTACCACA
*
19991544 ACAT AAAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
19991576 GTCTCTGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.53, C:0.22, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:19998205 original size:17 final size:16
Alignment explanation
Indices: 19998163--19998205 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
19998153 GCATATGAAA
*
19998163 ATTTATTTAGTATTTT
1 ATTTATTTAGGATTTT
*
19998179 AGTTAGTTTAGGATTTT
1 ATTTA-TTTAGGATTTT
19998196 ATTTTATTTA
1 A-TTTATTTA
19998206 TTTAGTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (16 bp):
ATTTATTTAGGATTTT
Found at i:20001217 original size:527 final size:526
Alignment explanation
Indices: 20000211--20001263 Score: 1980
Period size: 527 Copynumber: 2.0 Consensus size: 526
20000201 AAGATCACTG
* *
20000211 GGTATTTATCTGCTGAAAATTTTGAAGCTGAAGGTGGTGAGATGGGTATTATGTATGCTTTTGTA
1 GGTATCTATCTGCTGAAAATTTTGAAGCTGAAGGTGGTGAGATGGGTATTATGTATGCTTTGGTA
* *
20000276 ACTAAGCATTTAAAAAGTGATCAGATGGGTAAATCTCCTCAATATCCAATAGAAATTCAGCAGTT
66 ACTAAGCATTTAAAAAGTGATCAGATGGGTAAATCTCCTCAATATCCAACAGAAATTCAACAGTT
*
20000341 ATTGAAGGAGTTTGGAGAATTGTTCAATGAGGATTTGCCGAAAAGTCTACCACCTTTACGAAGCA
131 ATTGAAGGAGTTTGGAGAATTGTTCAATGAGGATTTGCCGAAAAGCCTACCACCTTTACGAAGCA
* *
20000406 TCCAACATGCAATTGATTTGGTACTAGGAGCAGCATTACCAAATCTGCCAGCATATAGAATGCCA
196 TCCAACATGCAATTGATTTGGTACCAGAAGCAGCATTACCAAATCTGCCAGCATATAGAATGCCA
20000471 CCTATGCAGCGAGCTGAGGTACAAAGACAGGTTGAGGAGTTGTTGGAGAAAGGTCTAGTGCGTGA
261 CCTATGCAGCGAGCTGAGGTACAAAGACAGGTTGAGGAGTTGTTGGAGAAAGGTCTAGTGCGTGA
*
20000536 AAGTAAAAGTCCTTGTGCTTGCCCAGCTTTGTTAGCTCCTAAGAAAGATGGTTCATGGGGGATGT
326 AAGTAAAAGTCCTTGTGCTTGCCCAGCTTTGTTAGCTCCTAAGAAAGATGGTTCATGGAGGATGT
*
20000601 GTGTGGACAGCCGTGCCATAAATAAAATTACAATCAAGTATCGTTTTCCCATTTCTCGATTAGAT
391 GTGTGGACAGCCGTGCCATAAATAAAATTACAATCAAGTATCGTTTTCCCATTACTCGATTAGAT
*
20000666 GAGATGCTTGATCAATTAGTTGGTTCAAGAGTGTTTTCAAAGATCGATTTGAAGAGGGGATACCA
456 GAGATGCTTGATCAATTAGTTGGTTCAAGAGTGTTTTCAAAGATCGATTTGAAGAGCGGATACCA
20000731 TCAAAT
521 TCAAAT
*
20000737 NGGTATCTATCTGTTGAAAATTTTGAAGCTGAAGGTGGTGAGATGGGTATTATGTATGCTTTGGT
1 -GGTATCTATCTGCTGAAAATTTTGAAGCTGAAGGTGGTGAGATGGGTATTATGTATGCTTTGGT
*
20000802 AAGTAAGCATTTAAAAAGTGATCAGATGGGTAAATCTCCTCAATATCCAACAGAAATTCAACAGT
65 AACTAAGCATTTAAAAAGTGATCAGATGGGTAAATCTCCTCAATATCCAACAGAAATTCAACAGT
*
20000867 TATTGAAGGAGTTTGTAGAATTGTTCAATGAGGATTTGCCGAAAAGCCTACCACCTTTACGAAGC
130 TATTGAAGGAGTTTGGAGAATTGTTCAATGAGGATTTGCCGAAAAGCCTACCACCTTTACGAAGC
20000932 ATCCAACATGCAATTGATTTGGTACCAGAAGCAGCATTACCAAATCTGCCAGCATATAGAATGCC
195 ATCCAACATGCAATTGATTTGGTACCAGAAGCAGCATTACCAAATCTGCCAGCATATAGAATGCC
20000997 ACCTATGCAGCGAGCTGAGGTACAAAGACAGGTTGAGGAGTTGTTGGAGAAAGGTCTAGTGCGTG
260 ACCTATGCAGCGAGCTGAGGTACAAAGACAGGTTGAGGAGTTGTTGGAGAAAGGTCTAGTGCGTG
20001062 AAAGTAAAAGTCCTTGTGCTTGCCCAGCTTTGTTAGCTCCTAAGAAAGATGGTTCATGGAGGATG
325 AAAGTAAAAGTCCTTGTGCTTGCCCAGCTTTGTTAGCTCCTAAGAAAGATGGTTCATGGAGGATG
20001127 TGTGTGGACAGCCGTGCCATAAATAAAATTACAATCAAGTATCGTTTTCCCATTACTCGATTAGA
390 TGTGTGGACAGCCGTGCCATAAATAAAATTACAATCAAGTATCGTTTTCCCATTACTCGATTAGA
20001192 TGAGATGCTTGATCAATTAGTTGGTTCAAGAGTGTTTTCAAAGATCGATTTGAAGAGCGGATACC
455 TGAGATGCTTGATCAATTAGTTGGTTCAAGAGTGTTTTCAAAGATCGATTTGAAGAGCGGATACC
20001257 ATCAAAT
520 ATCAAAT
20001264 TAGAATGAGG
Statistics
Matches: 513, Mismatches: 13, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
527 513 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (526 bp):
GGTATCTATCTGCTGAAAATTTTGAAGCTGAAGGTGGTGAGATGGGTATTATGTATGCTTTGGTA
ACTAAGCATTTAAAAAGTGATCAGATGGGTAAATCTCCTCAATATCCAACAGAAATTCAACAGTT
ATTGAAGGAGTTTGGAGAATTGTTCAATGAGGATTTGCCGAAAAGCCTACCACCTTTACGAAGCA
TCCAACATGCAATTGATTTGGTACCAGAAGCAGCATTACCAAATCTGCCAGCATATAGAATGCCA
CCTATGCAGCGAGCTGAGGTACAAAGACAGGTTGAGGAGTTGTTGGAGAAAGGTCTAGTGCGTGA
AAGTAAAAGTCCTTGTGCTTGCCCAGCTTTGTTAGCTCCTAAGAAAGATGGTTCATGGAGGATGT
GTGTGGACAGCCGTGCCATAAATAAAATTACAATCAAGTATCGTTTTCCCATTACTCGATTAGAT
GAGATGCTTGATCAATTAGTTGGTTCAAGAGTGTTTTCAAAGATCGATTTGAAGAGCGGATACCA
TCAAAT
Found at i:20003777 original size:17 final size:16
Alignment explanation
Indices: 20003735--20003777 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
20003725 GCATATGGAA
*
20003735 ATTTATTTAGTATTTT
1 ATTTATTTAGGATTTT
*
20003751 AGTTAGTTTAGGATTTT
1 ATTTA-TTTAGGATTTT
20003768 ATTTTATTTA
1 A-TTTATTTA
20003778 TTTAGTTTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 3 0.14
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (16 bp):
ATTTATTTAGGATTTT
Found at i:20004728 original size:11 final size:11
Alignment explanation
Indices: 20004712--20004739 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
20004702 GATTGGTGGT
20004712 ATGACAGATCC
1 ATGACAGATCC
20004723 ATGACAGATCC
1 ATGACAGATCC
20004734 ATGACA
1 ATGACA
20004740 TTCCCTCACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (11 bp):
ATGACAGATCC
Found at i:20006960 original size:35 final size:35
Alignment explanation
Indices: 20006921--20007095 Score: 161
Period size: 35 Copynumber: 5.2 Consensus size: 35
20006911 AGGCTTAGCT
* *
20006921 AAAACCTTTCACAACGGTTTTT-ACCAGGATCAACC
1 AAAACCTTTCACAATGGTTTTTCA-CAGGCTCAACC
*
20006956 AAAACC--T-A-AAGTGGTTTTTCAAAGGCTCAACC
1 AAAACCTTTCACAA-TGGTTTTTCACAGGCTCAACC
* *
20006988 ACAACCTTTCACAATGGTTTTTCACGGGCTCAACC
1 AAAACCTTTCACAATGGTTTTTCACAGGCTCAACC
*
20007023 AAAACC---CA-AAGTGGTTTTTCAAAGGCTCAACC
1 AAAACCTTTCACAA-TGGTTTTTCACAGGCTCAACC
* * * * *
20007055 ACAACCTATAACAATGGTTTTTCACGGGATCAACC
1 AAAACCTTTCACAATGGTTTTTCACAGGCTCAACC
20007090 AAAACC
1 AAAACC
20007096 CAACAACTAA
Statistics
Matches: 114, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
31 4 0.04
32 48 0.42
33 2 0.02
34 1 0.01
35 55 0.48
36 4 0.04
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.25
Consensus pattern (35 bp):
AAAACCTTTCACAATGGTTTTTCACAGGCTCAACC
Found at i:20006996 original size:67 final size:67
Alignment explanation
Indices: 20006923--20007098 Score: 282
Period size: 67 Copynumber: 2.6 Consensus size: 67
20006913 GCTTAGCTAA
* * *
20006923 AACCTTTCACAACGGTTTTT-ACCAGGATCAACCAAAACCTAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAAC
20006987 CAC
65 CAC
*
20006990 AACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
20007055 AC
66 AC
* *
20007057 AACCTATAACAATGGTTTTTCACGGGATCAACCAAAACCCAA
1 AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAA
20007099 CAACTAACTT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
67 100 0.99
68 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (67 bp):
AACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
AC
Found at i:20007626 original size:73 final size:73
Alignment explanation
Indices: 20007486--20007667 Score: 192
Period size: 73 Copynumber: 2.5 Consensus size: 73
20007476 GACAGAATGA
* * * **
20007486 TCTTAGTCAACTAACTGCGC-TATTAGTCGACTAAGTTGTCTCTATCTTCTGAACCCAGTTTTTG
1 TCTTAGTCAACTAACTTC-CTTCTTAGTCGACTAAGTTGTCTCTATCTTCTAAACCCAGTTTCCG
20007550 GCAGT-GAGC
65 GCAGTAG-GC
* * *
20007559 TCTTAGTCAACTAACTTCCTTCTTAGTCGATTAAGTTGTTTCTATC-T-TAAAGTCCAGATTTCC
1 TCTTAGTCAACTAACTTCCTTCTTAGTCGACTAAGTTGTCTCTATCTTCTAAA-CCCAG-TTTCC
20007622 GGCAGTAGGC
64 GGCAGTAGGC
* * * *
20007632 TTTTAGTCGACTAACTTACTTCTTGGTCGACTAAGT
1 TCTTAGTCAACTAACTTCCTTCTTAGTCGACTAAGT
20007668 CTTCTCTGTC
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
71 3 0.03
72 6 0.07
73 82 0.89
74 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.38
Consensus pattern (73 bp):
TCTTAGTCAACTAACTTCCTTCTTAGTCGACTAAGTTGTCTCTATCTTCTAAACCCAGTTTCCGG
CAGTAGGC
Found at i:20011848 original size:27 final size:27
Alignment explanation
Indices: 20011797--20011848 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
20011787 ATGTCCTGGT
*
20011797 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTGACCCTGA
*
20011824 GGTGGTAAAATTACCATTTT-ACCCT
1 GGTGG-AAAATTACAATTTTGACCCT
20011849 TTTACTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTGACCCTGA
Found at i:20019245 original size:5 final size:5
Alignment explanation
Indices: 20019238--20019275 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
20019228 CTATTCAATC
* *
20019238 TAACC TAACT TAACT TAACT TAACT TATCT TAACT TAA
1 TAACT TAACT TAACT TAACT TAACT TAACT TAACT TAA
20019276 TTGGACTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (5 bp):
TAACT
Found at i:20019343 original size:15 final size:15
Alignment explanation
Indices: 20019323--20019369 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
20019313 TAAAACAACC
20019323 TTAAAATCAAAAACT
1 TTAAAATCAAAAACT
* *
20019338 TTAAAATCCAAAGCT
1 TTAAAATCAAAAACT
* *
20019353 TTAAAACCAAAATCT
1 TTAAAATCAAAAACT
20019368 TT
1 TT
20019370 GATCTTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.30
Consensus pattern (15 bp):
TTAAAATCAAAAACT
Found at i:20020781 original size:13 final size:13
Alignment explanation
Indices: 20020763--20020787 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20020753 TTTTAGAAAA
20020763 TTTATAAAATCAT
1 TTTATAAAATCAT
20020776 TTTATAAAATCA
1 TTTATAAAATCA
20020788 CAATTTCNNN
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TTTATAAAATCAT
Found at i:20025977 original size:28 final size:27
Alignment explanation
Indices: 20025932--20025984 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
20025922 ATGTCCTGAT
* *
20025932 GGTGGAAAATTATAATTTTGCCCTTGG
1 GGTGGAAAATTACAATTTTACCCTTGG
*
20025959 GGTGGCAAAATTACCATTTTACCCTT
1 GGTGG-AAAATTACAATTTTACCCTT
20025985 TTACTCCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCTTGG
Found at i:20026052 original size:20 final size:20
Alignment explanation
Indices: 20026037--20026074 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
20026027 CCTCAAATCT
20026037 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
20026057 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
20026075 GGGGTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:20026977 original size:29 final size:28
Alignment explanation
Indices: 20026932--20027073 Score: 167
Period size: 29 Copynumber: 4.9 Consensus size: 28
20026922 GGCAGCTTTG
20026932 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
20026960 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* * *
20026989 ATATGTTTGCCTTAATTAAAGACAAGAAAA
1 ACATGTTTGTCTTAATT-TAGACAAG-AAA
* * *
20027019 ATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACA-TGTTTGTCTTAATTTAGACAAGAAA
* **
20027048 ACATATTTGTCCCAATTTAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA
20027074 CAAAATATTT
Statistics
Matches: 98, Mismatches: 12, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
28 35 0.36
29 39 0.40
30 12 0.12
31 12 0.12
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.36
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:20027045 original size:59 final size:58
Alignment explanation
Indices: 20026932--20027096 Score: 199
Period size: 59 Copynumber: 2.8 Consensus size: 58
20026922 GGCAGCTTTG
* * * *
20026932 ACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTTGCCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
20026989 ATATGTTTGCCTTAATTAAAGACAAGAAAAATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATGTTTGCCTTAATT-TAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* *
20027048 ACATATTTGTCC-CAATTTAGACAAGACAAAATATTTTTTTGTCTTAATT
1 ACATGTTTG-CCTTAATTTAGACAAGA-AAAATA-TTTTTTGTCTTAATT
20027097 ACAGATAAGA
Statistics
Matches: 92, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
57 15 0.16
58 15 0.16
59 45 0.49
60 17 0.18
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (58 bp):
ACATGTTTGCCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
Found at i:20027270 original size:17 final size:17
Alignment explanation
Indices: 20027248--20027280 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20027238 ATAATAATAA
20027248 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
20027265 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
20027281 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:20028576 original size:17 final size:19
Alignment explanation
Indices: 20028542--20028584 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
20028532 GCCCCTTTCA
*
20028542 ATTTTTTTAATAATAAAATT
1 ATTTTTTT-ATAATAAAAAT
20028562 ATTTTTTT-TAA-AAAAAT
1 ATTTTTTTATAATAAAAAT
20028579 ATTTTT
1 ATTTTT
20028585 AAATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 11 0.50
18 3 0.14
20 8 0.36
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTTTATAATAAAAAT
Found at i:20032095 original size:23 final size:23
Alignment explanation
Indices: 20032048--20032096 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
20032038 ATATATATCA
* **
20032048 ATCATCATGTACACCATCCTGTC
1 ATCATCATGCACACCATCCCATC
*
20032071 ATCATCATGCACATCATCCCATC
1 ATCATCATGCACACCATCCCATC
20032094 ATC
1 ATC
20032097 CCCAACTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.29, C:0.37, G:0.06, T:0.29
Consensus pattern (23 bp):
ATCATCATGCACACCATCCCATC
Found at i:20032152 original size:43 final size:43
Alignment explanation
Indices: 20032105--20032214 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 43
20032095 TCCCCAACTC
* ** **
20032105 ATGCGCATTCCCTACTCGCACAT-GGCTAGGTCATCACCGGGTT
1 ATGCGCACTCCCTACTCGCACATAATC-AGGTCATCACCGACTT
* *
20032148 ATGCGCACTCCCTACTCGCACATAATCGGGTCATCATCGACTT
1 ATGCGCACTCCCTACTCGCACATAATCAGGTCATCACCGACTT
20032191 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCGCACATA
20032215 GCCGAGTCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
43 58 0.98
44 1 0.02
ACGTcount: A:0.22, C:0.35, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAATCAGGTCATCACCGACTT
Found at i:20033173 original size:19 final size:19
Alignment explanation
Indices: 20033151--20033188 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20033141 CCATTTGACT
*
20033151 TATTTGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
*
20033170 TATTGGGGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
20033189 GTTTAGAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.45
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:20041199 original size:19 final size:19
Alignment explanation
Indices: 20041175--20041212 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20041165 CCATTTGACT
20041175 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
20041194 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
20041213 GTTTAGAAGT
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:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:20041293 original size:28 final size:28
Alignment explanation
Indices: 20041256--20041314 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
20041246 TTTGGAGTAT
*
20041256 AGGGGTAAAA-GGATAATTTTACCACC-CC
1 AGGGGCAAAATGG-TAATTTT-CCACCACC
*
20041284 AGGGGCAAAATTGTAATTTTCCACCACC
1 AGGGGCAAAATGGTAATTTTCCACCACC
20041312 AGG
1 AGG
20041315 ACATTTTTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 5 0.19
28 21 0.78
29 1 0.04
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (28 bp):
AGGGGCAAAATGGTAATTTTCCACCACC
Found at i:20048102 original size:29 final size:28
Alignment explanation
Indices: 20048057--20048198 Score: 160
Period size: 29 Copynumber: 4.9 Consensus size: 28
20048047 GGCAGCTTTG
20048057 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
20048085 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* * *
20048114 ATATGTTTGCCTTAATTTAAGATAAGAAAA
1 ACATGTTTGTCTTAATTT-AGACAAG-AAA
* * *
20048144 ATATTTTTTGTCTTAATTTA-ATGAAGAAA
1 ACA-TGTTTGTCTTAATTTAGA-CAAGAAA
* *
20048173 ACATATTTGTCTCAATTTAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA
20048199 TAAAATATTT
Statistics
Matches: 98, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
28 35 0.36
29 40 0.41
30 10 0.10
31 13 0.13
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:20048171 original size:59 final size:58
Alignment explanation
Indices: 20048057--20048231 Score: 201
Period size: 59 Copynumber: 3.0 Consensus size: 58
20048047 GGCAGCTTTG
* * *
20048057 ACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * * *
20048114 ATATGTTTGCCTTAATTTAAGATAAGAAAAATATTTTTTGTCTTAATTTA-ATGAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATTTAGA-CAAGAAA
* * *
20048173 ACATATTTGTCTCAATTTAGACAAGATAAAATATTTTTTTGTCTTAATTACAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA-AAAATA-TTTTTTGTCTTAATT-TAGACAAGA
20048232 GTTGTCTTAA
Statistics
Matches: 97, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
57 16 0.16
58 14 0.14
59 46 0.47
60 15 0.15
61 5 0.05
62 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.39
Consensus pattern (58 bp):
ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
Found at i:20048206 original size:28 final size:28
Alignment explanation
Indices: 20048057--20048208 Score: 148
Period size: 28 Copynumber: 5.3 Consensus size: 28
20048047 GGCAGCTTTG
*
20048057 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATATTTGTCTTAATTTAGACAAGAAA
*
20048085 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATATTT-GTCTTAATTTAGACAAGAAA
* * * *
20048114 ATATGTTTGCCTTAATTTAAGATAAGAAA
1 ACATATTTGTCTTAATTT-AGACAAGAAA
*
20048143 A-ATATTTTTTGTCTTAATTTA-ATGAAGAAA
1 ACATA---TTTGTCTTAATTTAGA-CAAGAAA
*
20048173 ACATATTTGTCTCAATTTAGACAAGATAA
1 ACATATTTGTCTTAATTTAGACAAGA-AA
20048202 A-ATATTT
1 ACATATTT
20048209 TTTTGTCTTA
Statistics
Matches: 107, Mismatches: 8, Indels: 18
0.80 0.06 0.14
Matches are distributed among these distances:
28 42 0.39
29 42 0.39
30 8 0.07
31 15 0.14
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (28 bp):
ACATATTTGTCTTAATTTAGACAAGAAA
Found at i:20051096 original size:19 final size:19
Alignment explanation
Indices: 20051053--20051089 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
20051043 CCATTTAACT
*
20051053 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATTTGAG
20051072 TATTGGAGTATAATTTGA
1 TATTGGAGTATAATTTGA
20051090 AGTTTGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (19 bp):
TATTGGAGTATAATTTGAG
Found at i:20055613 original size:35 final size:35
Alignment explanation
Indices: 20055574--20055661 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 35
20055564 TTTTCAATAG
* * **
20055574 GATCAGGCGTAACCTTTATGACATACCTTTTGCAA
1 GATCAAGCGTAACCTCTACAACATACCTTTTGCAA
* * *
20055609 GATCAAGTGTAACCTCTACAACATGCCTTTTGCAG
1 GATCAAGCGTAACCTCTACAACATACCTTTTGCAA
* *
20055644 GATCGAGTGTAACCTCTA
1 GATCAAGCGTAACCTCTA
20055662 TCAAGGCACT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (35 bp):
GATCAAGCGTAACCTCTACAACATACCTTTTGCAA
Found at i:20058691 original size:17 final size:17
Alignment explanation
Indices: 20058661--20058693 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20058651 TTCTTAATAA
20058661 AATAAAACTCCTTATTG
1 AATAAAACTCCTTATTG
20058678 AATAATAACT-CTTATT
1 AATAA-AACTCCTTATT
20058694 TTATTATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.39
Consensus pattern (17 bp):
AATAAAACTCCTTATTG
Found at i:20058922 original size:29 final size:29
Alignment explanation
Indices: 20058890--20058992 Score: 124
Period size: 29 Copynumber: 3.7 Consensus size: 29
20058880 GACAAATGTG
* * *
20058890 TTTTCTTATCTAGATTAAGAAAAAATATA
1 TTTTCTTGTCTAAATTAAGAAAAAACATA
*
20058919 TTTT-TTG--TAAATTAAG-GAAAACATA
1 TTTTCTTGTCTAAATTAAGAAAAAACATA
**
20058944 TTTTCTTGTCTAAATTAAGACCAAACATA
1 TTTTCTTGTCTAAATTAAGAAAAAACATA
20058973 TTTTCTTGTCTAAATTAAGA
1 TTTTCTTGTCTAAATTAAGA
20058993 CAAACATGTT
Statistics
Matches: 64, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
25 11 0.17
26 11 0.17
28 11 0.17
29 31 0.48
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.42
Consensus pattern (29 bp):
TTTTCTTGTCTAAATTAAGAAAAAACATA
Found at i:20058948 original size:54 final size:56
Alignment explanation
Indices: 20058844--20058999 Score: 140
Period size: 54 Copynumber: 2.8 Consensus size: 56
20058834 TCTTGTCTTT
* * * ** *
20058844 AATTAAGACAAAA-ATATTTTATCTTGTTTAAATTGAGACAAATGTGTTTTCTTATCTA
1 AATTAAGAAAAAACATA-TTT-TCTTG-CTAAATTAAGACAAACATATTTTCTTATCTA
* * *
20058902 GATTAAGAAAAAATATATTTT-TTG-TAAATTAAGGA-AAACATATTTTCTTGTCTA
1 AATTAAGAAAAAACATATTTTCTTGCTAAATTAA-GACAAACATATTTTCTTATCTA
**
20058956 AATTAAGACCAAACATATTTTCTTGTCTAAATTAAGACAAACAT
1 AATTAAGAAAAAACATATTTTCTTG-CTAAATTAAGACAAACAT
20059000 GTTAAAGCTA
Statistics
Matches: 81, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
54 39 0.48
55 5 0.06
56 5 0.06
57 15 0.19
58 14 0.17
59 3 0.04
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.39
Consensus pattern (56 bp):
AATTAAGAAAAAACATATTTTCTTGCTAAATTAAGACAAACATATTTTCTTATCTA
Found at i:20058993 original size:29 final size:28
Alignment explanation
Indices: 20058834--20058999 Score: 151
Period size: 28 Copynumber: 5.9 Consensus size: 28
20058824 TTAAGACAAC
* *
20058834 TCTTGTCTTTAATTAAGACAAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAACATA-TTT
* * ** *
20058864 ATCTTGTTTAAATTGAGACAAATGTGTTT
1 -TCTTGTCTAAATTAAGACAAACATATTT
* * *
20058893 TCTTATCTAGATTAAGA-AAAAATATATT
1 TCTTGTCTAAATTAAGACAAACATAT-TT
*
20058921 T-TT-TGTAAATTAAGGA-AAACATATTT
1 TCTTGTCTAAATTAA-GACAAACATATTT
20058947 TCTTGTCTAAATTAAGACCAAACATATTT
1 TCTTGTCTAAATTAAGA-CAAACATATTT
20058976 TCTTGTCTAAATTAAGACAAACAT
1 TCTTGTCTAAATTAAGACAAACAT
20059000 GTTAAAGCTA
Statistics
Matches: 112, Mismatches: 17, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
26 11 0.10
27 20 0.18
28 32 0.29
29 30 0.27
30 13 0.12
31 6 0.05
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (28 bp):
TCTTGTCTAAATTAAGACAAACATATTT
Found at i:20070524 original size:145 final size:144
Alignment explanation
Indices: 20070257--20070543 Score: 484
Period size: 145 Copynumber: 2.0 Consensus size: 144
20070247 CTTTTATTCG
20070257 TAAGTATATGCATTAAAATCTATAATCTCCAAATTAATGCTTATATAAAAATTTAGAATTCATTT
1 TAAGTATATGCATTAAAATCTATAATCTCCAAATTAATGCTTATATAAAAATTTAGAATTCATTT
*
20070322 ACAACTTAACAAATAAAAAGCTACGACTTGACCCCTAACAGCAGAGTGACTCAGAATAAAATGCT
66 ACAACTTAACAAATAAAAAGCTACGACTTAACCCCTAACAGCAGAGTGACTCAGAATAAAATGCT
*
20070387 ATGAGATGCCTTAC
131 AAGAGATGCCTTAC
20070401 NTAAGTATATGCATTAAAATCTATAATCTCCAAATTAATGCTTATATAAAAATTTAGAATTCATT
1 -TAAGTATATGCATTAAAATCTATAATCTCCAAATTAATGCTTATATAAAAATTTAGAATTCATT
* * * * * * *
20070466 TACAACTTAATAAATAAAATGCTACGACTTAACCTCTAATAGCGGAGTGACTCGGAATAAATTGC
65 TACAACTTAACAAATAAAAAGCTACGACTTAACCCCTAACAGCAGAGTGACTCAGAATAAAATGC
20070531 TAAGAGATGCCTT
130 TAAGAGATGCCTT
20070544 TACTTATTCA
Statistics
Matches: 133, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
145 133 1.00
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (144 bp):
TAAGTATATGCATTAAAATCTATAATCTCCAAATTAATGCTTATATAAAAATTTAGAATTCATTT
ACAACTTAACAAATAAAAAGCTACGACTTAACCCCTAACAGCAGAGTGACTCAGAATAAAATGCT
AAGAGATGCCTTAC
Found at i:20099871 original size:28 final size:27
Alignment explanation
Indices: 20099835--20099887 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
20099825 ATATCCTGGT
*
20099835 GGTGGAAAATTACAATTTTGCCCCTGA
1 GGTGGAAAATTACAATTTTACCCCTGA
*
20099862 GGTGGCAAAATTACCATTTTACCCCT
1 GGTGG-AAAATTACAATTTTACCCCT
20099888 ATACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCCTGA
Found at i:20099955 original size:20 final size:20
Alignment explanation
Indices: 20099932--20099977 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
20099922 CTTCTAAACC
*
20099932 TCAAATCATACTTCAATAAG
1 TCAAATCATACTCCAATAAG
*
20099952 TCAAATTATACTCCAATAAG
1 TCAAATCATACTCCAATAAG
20099972 TCAAAT
1 TCAAAT
20099978 GGGGTCAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (20 bp):
TCAAATCATACTCCAATAAG
Found at i:20104011 original size:21 final size:21
Alignment explanation
Indices: 20103987--20104093 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 21
20103977 AGATAGGATA
*
20103987 TAAATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTATT
20104008 TAAATTTAAATTATCTATTCATTGTATT
1 TAAATTTAAA-T-T-TA---ATT-TATT
* * *
20104036 TAAATTTAAA-TAAGAATTAAT
1 TAAATTTAAATTTA-ATTTATT
* *
20104057 TACATTTAAATTTAATTTGTT
1 TAAATTTAAATTTAATTTATT
*
20104078 TAAATTTAAATATAAT
1 TAAATTTAAATTTAAT
20104094 ATCCTATCTC
Statistics
Matches: 66, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
21 40 0.61
22 5 0.08
23 1 0.02
24 3 0.05
25 1 0.02
27 3 0.05
28 13 0.20
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.50
Consensus pattern (21 bp):
TAAATTTAAATTTAATTTATT
Found at i:20105269 original size:47 final size:48
Alignment explanation
Indices: 20105165--20105290 Score: 191
Period size: 47 Copynumber: 2.6 Consensus size: 48
20105155 GTATATTTTA
* * *
20105165 TAATTATTTTACGTAATTGTTAGGTAAAATTTATAAAAATGCATGATG
1 TAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAAATGCATCATG
*
20105213 CAATTATTTTACTTATTTGTTAGGTAAAATTTAT-AAAATGCATCATG
1 TAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAAATGCATCATG
* *
20105260 TAATCATTTTACTTATTTGTTAAGTAAAATT
1 TAATTATTTTACTTATTTGTTAGGTAAAATT
20105291 ATATGCAAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
47 40 0.56
48 31 0.44
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.45
Consensus pattern (48 bp):
TAATTATTTTACTTATTTGTTAGGTAAAATTTATAAAAATGCATCATG
Found at i:20112821 original size:18 final size:19
Alignment explanation
Indices: 20112800--20112847 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
20112790 GTAATGGGTG
20112800 AAAATAATATTTTA-AAAT
1 AAAATAATATTTTATAAAT
*
20112818 AAAATAATATTTTATTAAT
1 AAAATAATATTTTATAAAT
*
20112837 AAAATATTATT
1 AAAATAATATT
20112848 AAAATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAATAATATTTTATAAAT
Found at i:20112844 original size:11 final size:11
Alignment explanation
Indices: 20112830--20112859 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
20112820 AATAATATTT
20112830 TATTAATAAAA
1 TATTAATAAAA
*
20112841 TATTATTAAAA
1 TATTAATAAAA
20112852 TATTAATA
1 TATTAATA
20112860 TTTTATTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TATTAATAAAA
Found at i:20114054 original size:61 final size:61
Alignment explanation
Indices: 20113978--20114099 Score: 183
Period size: 61 Copynumber: 2.0 Consensus size: 61
20113968 AGTTCATAGC
* *
20113978 TGTCACGACCCAAA-TTCAGGGCCATGACTGGTGCATGGGCCCAATGGACATAGTCCACTAA
1 TGTCACGACCCAAATTTC-GGGCCATGACCGGTGCATGGGCCCAATAGACATAGTCCACTAA
* * *
20114039 TGTCACGATCCAAATTTCGGGCCATGACCGGTGCATGGGCCCAATAGACGTAGTCCGCTAA
1 TGTCACGACCCAAATTTCGGGCCATGACCGGTGCATGGGCCCAATAGACATAGTCCACTAA
20114100 GCTCAAGCAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
61 52 0.95
62 3 0.05
ACGTcount: A:0.26, C:0.28, G:0.25, T:0.20
Consensus pattern (61 bp):
TGTCACGACCCAAATTTCGGGCCATGACCGGTGCATGGGCCCAATAGACATAGTCCACTAA
Found at i:20115450 original size:42 final size:43
Alignment explanation
Indices: 20115348--20115450 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
20115338 GCTCATGCAT
** * **
20115348 ACTCCCTACTCGCACATGGCTGGGTCATCATCGGGTTATGCGC
1 ACTCCCTACTCGCACATAACCGGGTCATCATCGACTTATGCGC
* *
20115391 ACTCCCTACTCGCACATAACCGGGTCATCCTCGACTTATGCTC
1 ACTCCCTACTCGCACATAACCGGGTCATCATCGACTTATGCGC
20115434 A-TCCCTACTCGCACATA
1 ACTCCCTACTCGCACATA
20115451 GTCGAGTCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 16 0.30
43 37 0.70
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.25
Consensus pattern (43 bp):
ACTCCCTACTCGCACATAACCGGGTCATCATCGACTTATGCGC
Found at i:20116030 original size:28 final size:29
Alignment explanation
Indices: 20115989--20116048 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
20115979 GTCTATGGGC
*
20115989 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
20116017 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
20116047 AA
1 AA
20116049 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:20120647 original size:60 final size:60
Alignment explanation
Indices: 20120556--20120757 Score: 289
Period size: 60 Copynumber: 3.4 Consensus size: 60
20120546 GACAAAACAA
* * * *
20120556 AAAGTTTTTCGTTGCTA-CGAGATTCAATCTCGTTGTAGCGAAATTGTAACCCAGAAACAG
1 AAAGTTTCTCGCTGC-AGCGAGATTCAATCTCGTTGCAGCGAAATTGTAACCCAGAAATAG
* * * *
20120616 AAGGTTTCTCGCTGCAGCGAGATTGAATCTCGTTGCAGCTAAATTGTAACCCAAAAATAG
1 AAAGTTTCTCGCTGCAGCGAGATTCAATCTCGTTGCAGCGAAATTGTAACCCAGAAATAG
* * *
20120676 AAAGTTTCTCGCTGCAGCGAGATTCAATATCGCTGCAACGAAATTGTAACCCAGAAATAG
1 AAAGTTTCTCGCTGCAGCGAGATTCAATCTCGTTGCAGCGAAATTGTAACCCAGAAATAG
20120736 AAAGTTTCTCGCTGCAGCGAGA
1 AAAGTTTCTCGCTGCAGCGAGA
20120758 ATAAATTTCA
Statistics
Matches: 126, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
59 1 0.01
60 125 0.99
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (60 bp):
AAAGTTTCTCGCTGCAGCGAGATTCAATCTCGTTGCAGCGAAATTGTAACCCAGAAATAG
Found at i:20120661 original size:21 final size:21
Alignment explanation
Indices: 20120622--20120661 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
20120612 ACAGAAGGTT
*
20120622 TCTCGCTGCAGCGAGATTGAA
1 TCTCGCTGCAGCGAAATTGAA
* *
20120643 TCTCGTTGCAGCTAAATTG
1 TCTCGCTGCAGCGAAATTG
20120662 TAACCCAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.23, G:0.25, T:0.30
Consensus pattern (21 bp):
TCTCGCTGCAGCGAAATTGAA
Found at i:20121195 original size:43 final size:43
Alignment explanation
Indices: 20121143--20121261 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
20121133 TCACCAGCTC
* ** * * *
20121143 ATGCACACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACAGAGTCATC-CTCGGCTT
**
20121186 ATGCGCACTCCCTACTCGCACATAACAGAGTCATCCTTTGCTT
1 ATGCGCACTCCCTACTCGCACATAACAGAGTCATCCTCGGCTT
* *
20121229 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACAGAGTCA
20121262 ATGTCATTAC
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 1 0.02
43 64 0.98
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACAGAGTCATCCTCGGCTT
Found at i:20123027 original size:29 final size:28
Alignment explanation
Indices: 20122982--20123155 Score: 177
Period size: 29 Copynumber: 5.9 Consensus size: 28
20122972 GGCAACTTTG
20122982 ACATGTTTGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAA
20123010 ACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTT-GTCTTAATTTAGACAAGAAA
* *
20123039 ATATGTTTGCCTTAATTTAAGACAAGAAAA
1 ACATGTTTGTCTTAATTT-AGACAAG-AAA
* * *
20123069 ATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACA-TGTTTGTCTTAATTTAGACAAGAAA
* * *
20123098 ACATATTTTTCTCAATTTAGACAAGATAAA
1 ACATGTTTGTCTTAATTTAGACAAG--AAA
* * *
20123128 ATATTTTTTGTCTTAATTACAGACAAGA
1 ACA-TGTTTGTCTTAATT-TAGACAAGA
20123156 GTTGTCTTAA
Statistics
Matches: 123, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
28 35 0.28
29 39 0.32
30 18 0.15
31 24 0.20
32 7 0.06
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (28 bp):
ACATGTTTGTCTTAATTTAGACAAGAAA
Found at i:20123095 original size:59 final size:58
Alignment explanation
Indices: 20122982--20123155 Score: 224
Period size: 59 Copynumber: 3.0 Consensus size: 58
20122972 GGCAACTTTG
* * *
20122982 ACATGTTTGTCTTAATTTAGACAAG-AAAACATGTTTGGTCTTAATTTAGACAAGAAA
1 ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * *
20123039 ATATGTTTGCCTTAATTTAAGACAAGAAAAATATTTTTTGTCTTAATTTAGTCAAGAAA
1 ACATGTTTGTCTTAATTT-AGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
* * * *
20123098 ACATATTTTTCTCAATTTAGACAAGATAAAATATTTTTTGTCTTAATTACAGACAAGA
1 ACATGTTTGTCTTAATTTAGACAAGA-AAAATATTTTTTGTCTTAATT-TAGACAAGA
20123156 GTTGTCTTAA
Statistics
Matches: 100, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
57 16 0.16
58 15 0.15
59 62 0.62
60 7 0.07
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (58 bp):
ACATGTTTGTCTTAATTTAGACAAGAAAAATATTTTTTGTCTTAATTTAGACAAGAAA
Found at i:20127835 original size:2 final size:2
Alignment explanation
Indices: 20127828--20127858 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20127818 TGTGGCTTAT
*
20127828 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20127859 GTATGAGTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:20129950 original size:25 final size:25
Alignment explanation
Indices: 20129916--20129971 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
20129906 ATAATCTAAA
20129916 GAATTTCGTAAGCAATGAATGTAAG
1 GAATTTCGTAAGCAATGAATGTAAG
*
20129941 GAATTTCGTAAGCAATGGATGTAAG
1 GAATTTCGTAAGCAATGAATGTAAG
*
20129966 TAATTT
1 GAATTT
20129972 TGGTAAAAAA
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:0.38, C:0.07, G:0.23, T:0.32
Consensus pattern (25 bp):
GAATTTCGTAAGCAATGAATGTAAG
Found at i:20130546 original size:61 final size:61
Alignment explanation
Indices: 20130469--20130815 Score: 577
Period size: 61 Copynumber: 5.7 Consensus size: 61
20130459 CAAATGCAAT
* *
20130469 CGTGCATGTGCGGAGTGGGCAGTGCACATGTCGGTAATGATGCTATCGTGATAATTACAAC
1 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTACAAC
* * *
20130530 TGTGCATGTGCAGAGTGGGCAGTGCACATGCCGGTAATGATGATGTCGTGATAATTACAAC
1 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTACAAC
* *
20130591 CGTGCATGTGCGGAGTGGGCAGTGCACATGTCGGTAATGATGCTATCGTGATAATTACAAC
1 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTACAAC
* * *
20130652 TGTGCATGTGTGGAGTGGGCAGTGCACATGCCGGTAATGATGTTGTCGTGATAATTACAAC
1 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTACAAC
20130713 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTACAAC
1 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTACAAC
* * *
20130774 CGTGCATGTGCTGAGTGGGCGGTGCACATGCTGGTAATGATG
1 CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATG
20130816 TACATGAGCT
Statistics
Matches: 265, Mismatches: 21, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 265 1.00
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.27
Consensus pattern (61 bp):
CGTGCATGTGCGGAGTGGGCAGTGCACATGCCGGTAATGATGCTGTCGTGATAATTACAAC
Found at i:20138345 original size:42 final size:42
Alignment explanation
Indices: 20138280--20138403 Score: 160
Period size: 42 Copynumber: 3.0 Consensus size: 42
20138270 GTTGATGTGG
* *
20138280 ACCCGGCTATGTGCGAGTAGGAGTGCACATAAGCCGTTGCTA
1 ACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTA
* *
20138322 ACCCGACTATGTGTGAGTGGGAGTGCACATAAGCCGTTGCTG
1 ACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTA
* * * *
20138364 ACCC-AGTTATATGCGAGTGGGAGTACGCATAAGCCGTTGC
1 ACCCGA-CTATGTGCGAGTGGGAGTGCACATAAGCCGTTGC
20138404 ATATGAGATG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 1 0.01
42 71 0.99
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.23
Consensus pattern (42 bp):
ACCCGACTATGTGCGAGTGGGAGTGCACATAAGCCGTTGCTA
Found at i:20142632 original size:31 final size:29
Alignment explanation
Indices: 20142561--20142700 Score: 135
Period size: 28 Copynumber: 4.8 Consensus size: 29
20142551 TTTTGACATG
*
20142561 TTTGTCTTAATTT-AGACAAGAAAATATG
1 TTTGTCTTAATTTAAGACAAGAAAATATT
* *
20142589 CTTGCCTTAATTTAAGACAAGAAAGATATTT
1 TTTGTCTTAATTTAAGACAAGAAA-ATA-TT
* * *
20142620 TTTGTCTTAATTT-AGTCAAGAAAACATA
1 TTTGTCTTAATTTAAGACAAGAAAATATT
*
20142648 TTTGTCTCAATTTAA-ACAAGATAAAATATTT
1 TTTGTCTTAATTTAAGACAAG--AAAATA-TT
20142679 TTTGTCTTAA-TTATAGACAAGA
1 TTTGTCTTAATTTA-AGACAAGA
20142701 GTTGTCTTAA
Statistics
Matches: 90, Mismatches: 13, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
28 28 0.31
29 13 0.14
30 21 0.23
31 23 0.26
32 5 0.06
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (29 bp):
TTTGTCTTAATTTAAGACAAGAAAATATT
Found at i:20142660 original size:59 final size:59
Alignment explanation
Indices: 20142561--20142700 Score: 192
Period size: 59 Copynumber: 2.4 Consensus size: 59
20142551 TTTTGACATG
* * * *
20142561 TTTGTCTTAATTTAGACAAGAAAATATGCTTGCCTTAATTTAAGACAAGA-AAGATATTT
1 TTTGTCTTAATTTAGACAAGAAAACATACTTGCCTCAATTTAA-ACAAGATAAAATATTT
* * *
20142620 TTTGTCTTAATTTAGTCAAGAAAACATATTTGTCTCAATTTAAACAAGATAAAATATTT
1 TTTGTCTTAATTTAGACAAGAAAACATACTTGCCTCAATTTAAACAAGATAAAATATTT
20142679 TTTGTCTTAATTATAGACAAGA
1 TTTGTCTTAATT-TAGACAAGA
20142701 GTTGTCTTAA
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
58 6 0.08
59 57 0.80
60 8 0.11
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.39
Consensus pattern (59 bp):
TTTGTCTTAATTTAGACAAGAAAACATACTTGCCTCAATTTAAACAAGATAAAATATTT
Found at i:20142862 original size:17 final size:17
Alignment explanation
Indices: 20142842--20142874 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20142832 ATTATAATAA
20142842 AATAA-GAGTTATTATTC
1 AATAAGGAGTT-TTATTC
20142859 AATAAGGAGTTTTATT
1 AATAAGGAGTTTTATT
20142875 TTATCAAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.39, C:0.03, G:0.15, T:0.42
Consensus pattern (17 bp):
AATAAGGAGTTTTATTC
Found at i:20151819 original size:33 final size:32
Alignment explanation
Indices: 20151781--20151844 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 32
20151771 CATGCTAGGT
*
20151781 AATTAACTTCTATAAACTTAATTA-AAATAGTTC
1 AATTAACTT-T-TAAACATAATTATAAATAGTTC
* *
20151814 AATTAAGTTTTAGACATAATTATAAATAGTT
1 AATTAACTTTTAAACATAATTATAAATAGTT
20151845 ATAATTATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 10 0.37
32 9 0.33
33 8 0.30
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (32 bp):
AATTAACTTTTAAACATAATTATAAATAGTTC
Found at i:20157877 original size:20 final size:21
Alignment explanation
Indices: 20157832--20157878 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
20157822 AGATGTCTAA
*
20157832 AATAATTATTTGAAATGAAAT
1 AATAATTATTTGAAATAAAAT
* *
20157853 TATAATTGTTTG-AATAAAAT
1 AATAATTATTTGAAATAAAAT
20157873 AATAAT
1 AATAAT
20157879 ATTCAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (21 bp):
AATAATTATTTGAAATAAAAT
Found at i:20160560 original size:43 final size:43
Alignment explanation
Indices: 20160478--20160588 Score: 120
Period size: 43 Copynumber: 2.6 Consensus size: 43
20160468 TATTGAGTCG
* * * *
20160478 GCTATGTGTGAGTAGGG-GTGTGCATAAGTCGAGGATGA-CCT
1 GCTATGTGCGAGTAGGGAGTGCGCATAACTCGAGGATGACCCA
*
20160519 GATTATGTGCGAGTAGGGAGTGCGCATAACTCG-GTGATGACCCA
1 G-CTATGTGCGAGTAGGGAGTGCGCATAACTCGAG-GATGACCCA
* *
20160563 GCCATGTGCGAGTAGAGAGTGCGCAT
1 GCTATGTGCGAGTAGGGAGTGCGCAT
20160589 GAGCTGGTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 1 0.02
42 15 0.26
43 39 0.67
44 3 0.05
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.23
Consensus pattern (43 bp):
GCTATGTGCGAGTAGGGAGTGCGCATAACTCGAGGATGACCCA
Found at i:20163139 original size:145 final size:145
Alignment explanation
Indices: 20162876--20163285 Score: 459
Period size: 145 Copynumber: 2.8 Consensus size: 145
20162866 CTAGACAGTG
**
20162876 CTGCAGCGCTGACTTCACTGCCAAACTCCAATATTACTACATTAGATAACTCTGCAACGTTGAGT
1 CTGCAGCGCTGACTTCACTGCCAAACTCCAATATTACTACATTAGATAACTCTGCAACACTGAGT
* *** * * **
20162941 TTCTGGCGCTGCAGTGTTGACTTTACTACCAAAGGCATTGTTACTACACTAGACAACGTTGCAGT
66 TTCTGACGCTGCAGCACTGACTTCACTACCAAAGGCAGTGTTACTACACTAGACAACGTTGCAAC
*
20163006 GTTGAGTTTCTAGCA
131 GTTAAGTTTCTAGCA
* * * * * *
20163021 CTGCAGC-ATCGACTTCACTGCCAAACTCCAATATTACTACATTAGA-CAGTGTTGTAGCACTGA
1 CTGCAGCGCT-GACTTCACTGCCAAACTCCAATATTACTACATTAGATAACT-CTGCAACACTGA
* * *
20163084 GTTTTTGACGCTGCAGCACTGACTTCACTACCAAAGGTAGTGTTACTACACTAGACAATGTTGCA
64 GTTTCTGACGCTGCAGCACTGACTTCACTACCAAAGGCAGTGTTACTACACTAGACAACGTTGCA
20163149 ACGTTAAGTTTCTAGCA
129 ACGTTAAGTTTCTAGCA
* * * * * * **
20163166 TTGCAGCGCTGACTTAACTGCCAAACTCCAATATTACTACAGTAAACAACGCTGCAATGCTGAGT
1 CTGCAGCGCTGACTTCACTGCCAAACTCCAATATTACTACATTAGATAACTCTGCAACACTGAGT
* ** * * *
20163231 TTCT-AGCGCTACAGTGCTGAC-TCACTGCCAAAGGCAGTGTTACTTCACTAAACAA
66 TTCTGA-CGCTGCAGCACTGACTTCACTACCAAAGGCAGTGTTACTACACTAGACAA
20163286 TATCCAAGTT
Statistics
Matches: 219, Mismatches: 41, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
144 34 0.16
145 183 0.84
146 2 0.01
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (145 bp):
CTGCAGCGCTGACTTCACTGCCAAACTCCAATATTACTACATTAGATAACTCTGCAACACTGAGT
TTCTGACGCTGCAGCACTGACTTCACTACCAAAGGCAGTGTTACTACACTAGACAACGTTGCAAC
GTTAAGTTTCTAGCA
Found at i:20163232 original size:73 final size:73
Alignment explanation
Indices: 20162876--20163262 Score: 320
Period size: 73 Copynumber: 5.3 Consensus size: 73
20162866 CTAGACAGTG
* *
20162876 CTGCAGCGCTGACTTCACTGCCAAACTCCAATATTACTACATTAGATAAC-TCTGCAACGTTGAG
1 CTGCAGCGCTGACTTCACTGCCAAACTCCAATATTACTACACTAGACAACGT-TGCAACGTTGAG
* *
20162940 TTTCTGGCG
65 TTTCTAGCA
* * * * ** * * **
20162949 CTGCAGTGTTGACTTTACTACCAAA-GGCATTGTTACTACACTAGACAACGTTGCAGTGTTGAGT
1 CTGCAGCGCTGACTTCACTGCCAAACTCCAATATTACTACACTAGACAACGTTGCAACGTTGAGT
20163013 TTCTAGCA
66 TTCTAGCA
* * ** * * **
20163021 CTGCAGC-ATCGACTTCACTGCCAAACTCCAATATTACTACATTAGACAGTGTTGTAGCACTGAG
1 CTGCAGCGCT-GACTTCACTGCCAAACTCCAATATTACTACACTAGACAACGTTGCAACGTTGAG
* *
20163085 TTT-TTGACG
65 TTTCTAG-CA
* * * * * * *
20163094 CTGCAGCACTGACTTCACTACCAAAGGT--AGTGTTACTACACTAGACAATGTTGCAACGTTAAG
1 CTGCAGCGCTGACTTCACTGCCAAA-CTCCAATATTACTACACTAGACAACGTTGCAACGTTGAG
20163157 TTTCTAGCA
65 TTTCTAGCA
* * * * * * *
20163166 TTGCAGCGCTGACTTAACTGCCAAACTCCAATATTACTACAGTAAACAACGCTGCAATGCTGAGT
1 CTGCAGCGCTGACTTCACTGCCAAACTCCAATATTACTACACTAGACAACGTTGCAACGTTGAGT
*
20163231 TTCTAGCG
66 TTCTAGCA
* *
20163239 CTACAGTGCTGAC-TCACTGCCAAA
1 CTGCAGCGCTGACTTCACTGCCAAA
20163263 GGCAGTGTTA
Statistics
Matches: 241, Mismatches: 64, Indels: 19
0.74 0.20 0.06
Matches are distributed among these distances:
71 2 0.01
72 117 0.49
73 120 0.50
74 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (73 bp):
CTGCAGCGCTGACTTCACTGCCAAACTCCAATATTACTACACTAGACAACGTTGCAACGTTGAGT
TTCTAGCA
Found at i:20174492 original size:252 final size:251
Alignment explanation
Indices: 20174040--20175139 Score: 1650
Period size: 252 Copynumber: 4.4 Consensus size: 251
20174030 NNNNNNNNNN
* *
20174040 AAATATTTAAATTTATATTCTCGGATTAAAAGTGTTTAATGTTG-TACAAATTTTAATTTTTAAA
1 AAATATTTAAATTTATATTCTCGG-TTAAAAGTGTTTAACG-AGATACAAATTTTAATTTTTAAA
* **
20174104 TAAAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTGACATGGAAAAGCCTTGATGTAAAA
64 TAAAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTAACATGGAAAAGCCTTGACATAAAA
* ** *
20174169 ATGCAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACATAAATA
129 CTATAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACGTAAATA
* *
20174234 TGTAAGAGTTAACGTAACAAGGCAATTAAGTAAAAACAATCTATATTTAATGAAAAAT
194 TGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAAT
20174292 AAATATTTAAATTTATATTCTCGAGTTAAAAGTGTTTAACGAGATACAAATTTTAATTTTTAAAT
1 AAATATTTAAATTTATATTCTCG-GTTAAAAGTGTTTAACGAGATACAAATTTTAATTTTTAAAT
*
20174357 AATA-AATAATAAGGATAAAAATAATTATAGTTCAAAGTTAACATGGAAAAGCCTTGACATAAAA
65 AA-AGAATAATAAGGATAAAAATAATTATAATTCAAAGTTAACATGGAAAAGCCTTGACATAAAA
* * * *
20174421 CTATAAGAATTGACGTAAAAACTTGTAAAGGTGGAATAATTAAATTTTAAATCTTAACGTAAGTG
129 CTATAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACGTAAATA
** * *
20174486 TGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAATGATTTAAATTTAATAAAAAAT
194 TGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAAT
*
20174544 AAATATTTAAATTTATATTCTTGGATT-AAAGTGTTTAACGATG-TACAAATTTTAATTTTTAAA
1 AAATATTTAAATTTATATTCTCGG-TTAAAAGTGTTTAACGA-GATACAAATTTTAATTTTTAAA
* * * *
20174607 TAAAGAATAATAAAGATAAAAATAATTATAATTCAAAGTTGACATGGAAAAGCCTTGACGTAAAG
64 TAAAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTAACATGGAAAAGCCTTGACATAAAA
** * *
20174672 CCGTAAGAGTTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAATGTAAATA
129 CTATAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACGTAAATA
* * * * *
20174737 TGTGACAGTTAACTTAACAATTCAATTAAGTAAAAACAATCTACATTTAATGAAAAAT
194 TGTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAAT
*
20174795 AAATATTTAAATTTATATTCTCGGGTTAAAAGTGTTTAACGATATACAAATTTTAATTTTTAAAT
1 AAATATTTAAATTTATATTCTC-GGTTAAAAGTGTTTAACGAGATACAAATTTTAATTTTTAAAT
* *
20174860 AACGAATAATAAGGATAAAAATAATTATAGTTCAAAGTTAACATGGAAAAGCCTTGACATAAAAC
65 AAAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTAACATGGAAAAGCCTTGACATAAAAC
* * * **
20174925 TATAAGAATTGATGTAAAAACTTGTAAATGTGAAATAATTAAATTTTAAATCTTAACGTAAGCAT
130 TATAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACGTAAATAT
* * *
20174990 TTAGGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATTTAAATTTAATGAAAAAT
195 GTAAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAAT
* * * *
20175047 AAATATTTAAATTTATATTCTTAGGTTAAAAGTATTTAACGATATACAAATTTTAATTTTAAAAT
1 AAATATTTAAATTTATATTC-TCGGTTAAAAGTGTTTAACGAGATACAAATTTTAATTTTTAAAT
*
20175112 AAAGAATAATAAGGATAAAAACAATTAT
65 AAAGAATAATAAGGATAAAAATAATTAT
20175140 TGAAATGCCC
Statistics
Matches: 765, Mismatches: 73, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
250 1 0.00
251 223 0.29
252 538 0.70
253 3 0.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (251 bp):
AAATATTTAAATTTATATTCTCGGTTAAAAGTGTTTAACGAGATACAAATTTTAATTTTTAAATA
AAGAATAATAAGGATAAAAATAATTATAATTCAAAGTTAACATGGAAAAGCCTTGACATAAAACT
ATAAGAATTGACGTAAAAACTTGTAAAGGTGAAATAACTAAATTTTAAATCTTAACGTAAATATG
TAAGAGTTAACGTAACAAGTCAATTAAGTAAAAACAATCTAAATTTAATGAAAAAT
Done.