Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01003599.1 Kokia drynarioides strain JFW-HI SEQ_116484, 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: 203871
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 40 characters in sequence are not A, C, G, or T
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--45 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1 TA TA TA TA 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 TA TA TA TA
43 TA T
1 TA T
46 TTAAAAAACG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:535 original size:17 final size:17
Alignment explanation
Indices: 513--554 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
503 GGAAATTATT
*
513 AATTTAAATTTAAAATA
1 AATTTAAACTTAAAATA
530 AATTTAAACTTAAAATA
1 AATTTAAACTTAAAATA
547 AATTTAAA
1 AATTTAAA
555 AAATGAGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTAAACTTAAAATA
Found at i:1097 original size:39 final size:39
Alignment explanation
Indices: 1054--1611 Score: 258
Period size: 39 Copynumber: 14.3 Consensus size: 39
1044 TCTATCGTGA
* * *
1054 GGTAAGAGATTGACTGATGGTGATCTGCCCCAAGTTCAG
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGG
* * * * * * * *
1093 GGTAAGAGATCAGA-TGACT-ATAATCTACCTCAGGTTTGA
1 GGTAAGAGAT-TGACTGA-TGGTGATCTGCCCCAGGCTCGG
* * *
1132 GGTAAGAGATTGACTGATGGTGATCTACCCTAGGCTCGA
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGG
* * * * **
1171 GGTAAAAGATTGAATGGTTGCAATCTGCCCCAGGCTCGG
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGG
** *
1210 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGG
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGG
* *** ** *
1249 GGTAAAAGATCTGA-TGACT-ACAATCTGCCTTAGGTTCGG
1 GGTAAGAGAT-TGACTGA-TGGTGATCTGCCCCAGGCTCGG
** *
1288 GGTAAGAGATCAACTGATGGTGATCTACCCCAAGGCTCGG
1 GGTAAGAGATTGACTGATGGTGATCTGCCCC-AGGCTCGG
* * * * *
1328 GGTAAAATATCAGAC-GACT-GTAATCTGCCCCAGGCTCTG
1 GGTAAGAGAT-TGACTGA-TGGTGATCTGCCCCAGGCTCGG
* * * *
1367 GGTAAGAGATTGATTCATGGTGATCTGCCCTAGGCTCGA
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGG
* * * * ** *
1406 GGTAAAAGATCAGA-TGACT-GTAATTTGCCTTAGGCTCAG
1 GGTAAGAGAT-TGACTGA-TGGTGATCTGCCCCAGGCTCGG
* * *** ** ** *
1445 GGTAAAAGATCAGAC-GGCCGCAATCTATCCCAAGCTCGG
1 GGTAAGAGAT-TGACTGATGGTGATCTGCCCCAGGCTCGG
* * * **
1484 GGTAAAAGATTGAAC-GGTCGCAATCTGCCCCAGGCTCGG
1 GGTAAGAGATTG-ACTGATGGTGATCTGCCCCAGGCTCGG
* * *
1523 GGTAAGAGATTGGCTGATGGTGATTTACCCCCAGGCTCGG
1 GGTAAGAGATTGACTGATGGTGATCT-GCCCCAGGCTCGG
* * * * *
1563 GGTAAAAGATCGGA-TGACT-GTGATCTACCCCATGATCGG
1 GGTAAGAGAT-TGACTGA-TGGTGATCTGCCCCAGGCTCGG
1602 GGTAAGAGAT
1 GGTAAGAGAT
1612 CGGAATCTTC
Statistics
Matches: 390, Mismatches: 107, Indels: 44
0.72 0.20 0.08
Matches are distributed among these distances:
38 10 0.03
39 309 0.79
40 66 0.17
41 5 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (39 bp):
GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGG
Found at i:1441 original size:78 final size:78
Alignment explanation
Indices: 1054--1611 Score: 444
Period size: 78 Copynumber: 7.1 Consensus size: 78
1044 TCTATCGTGA
* * * *
1054 GGTAAGAGATTGACTGATGGTGATCTGCCCCAAGTTC-AGGGTAAGAGATCAGATGACTATAATC
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGA-GGTAAAAGATCAGATGACTGTAATC
* * * *
1118 TACCTCAGGTTTGA
65 TGCCTCAGGCTCGG
* * * ** *
1132 GGTAAGAGATTGACTGATGGTGATCTACCCTAGGCTCGAGGTAAAAGAT-TGAATGGTTGCAATC
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAG-ATGACTGTAATC
*
1196 TGCCCCAGGCTCGG
65 TGCCTCAGGCTCGG
** * * * **
1210 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCTGATGACTACAATCT
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAGATGACTGTAATCT
* *
1275 GCCTTAGGTTCGG
66 GCCTCAGGCTCGG
** * * * *
1288 GGTAAGAGATCAACTGATGGTGATCTACCCCAAGGCTCGGGGTAAAATATCAGACGACTGTAATC
1 GGTAAGAGATTGACTGATGGTGATCTGCCCC-AGGCTCGAGGTAAAAGATCAGATGACTGTAATC
* *
1353 TGCCCCAGGCTCTG
65 TGCCTCAGGCTCGG
* * * *
1367 GGTAAGAGATTGATTCATGGTGATCTGCCCTAGGCTCGAGGTAAAAGATCAGATGACTGTAATTT
1 GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAGATGACTGTAATCT
* *
1432 GCCTTAGGCTCAG
66 GCCTCAGGCTCGG
* * *** ** ** * * * *
1445 GGTAAAAGATCAGAC-GGCCGCAATCTATCCCAAGCTCGGGGTAAAAGAT-TGA--ACGGTCGCA
1 GGTAAGAGAT-TGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAGATGAC--T-GTA
*
1506 ATCTGCCCCAGGCTCGG
62 ATCTGCCTCAGGCTCGG
* * * * * *
1523 GGTAAGAGATTGGCTGATGGTGATTTACCCCCAGGCTCGGGGTAAAAGATCGGATGACTGTGATC
1 GGTAAGAGATTGACTGATGGTGATCT-GCCCCAGGCTCGAGGTAAAAGATCAGATGACTGTAATC
* * * *
1588 TACCCCATGATCGG
65 TGCCTCAGGCTCGG
1602 GGTAAGAGAT
1 GGTAAGAGAT
1612 CGGAATCTTC
Statistics
Matches: 374, Mismatches: 93, Indels: 25
0.76 0.19 0.05
Matches are distributed among these distances:
75 2 0.01
77 6 0.02
78 249 0.67
79 112 0.30
80 3 0.01
82 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (78 bp):
GGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGAGGTAAAAGATCAGATGACTGTAATCT
GCCTCAGGCTCGG
Found at i:1479 original size:235 final size:233
Alignment explanation
Indices: 1054--1611 Score: 602
Period size: 235 Copynumber: 2.4 Consensus size: 233
1044 TCTATCGTGA
* * * * *
1054 GGTAAGAGATTGACTGATGGTGATCTGCCCCAA-GTTCAGGGTAAGAGATCAGATGACTATAATC
1 GGTAAGAGATTGACTGATGGTGATCTACCCCAAGGCTCGGGGTAAAAGATCAGATGACTGTAATC
* * * *
1118 TACCTCAGGTTTGAGGTAAGAGATTGACTGATGGTGATCTACCCTAGGCTCGAGGTAAAAGATTG
66 TACCCCAGGTCTG-GGTAAGAGATTGACTCATGGTGATCTACCCTAGGCTCGAGGTAAAAGATAG
** * * ** ** ** ** *
1183 AATGGTTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCG
130 AATGACTGCAATCTGCCCCAGGCTCAGGGTAAAAGATCAGACGACCGCAATCTACCCCAAGCTCG
** *
1248 GGGTAAAAGATCTGATGAC-T-ACAATCTGCCTTAGGTTCGG
195 GGGTAAAAGAT-TGA--ACGTCACAATCTGCCCCAGGCTCGG
** * *
1288 GGTAAGAGATCAACTGATGGTGATCTACCCCAAGGCTCGGGGTAAAATATCAGACGACTGTAATC
1 GGTAAGAGATTGACTGATGGTGATCTACCCCAAGGCTCGGGGTAAAAGATCAGATGACTGTAATC
* * *
1353 TGCCCCAGGCTCTGGGTAAGAGATTGATTCATGGTGATCTGCCCTAGGCTCGAGGTAAAAGATCA
66 TACCCCAGG-TCTGGGTAAGAGATTGACTCATGGTGATCTACCCTAGGCTCGAGGTAAAAGAT-A
* * ** * *
1418 G-ATGACTGTAATTTGCCTTAGGCTCAGGGTAAAAGATCAGACGGCCGCAATCTATCCCAAGCTC
129 GAATGACTGCAATCTGCCCCAGGCTCAGGGTAAAAGATCAGACGACCGCAATCTACCCCAAGCTC
*
1482 GGGGTAAAAGATTGAACGGTCGCAATCTGCCCCAGGCTCGG
194 GGGGTAAAAGATTGAAC-GTCACAATCTGCCCCAGGCTCGG
* * * * *
1523 GGTAAGAGATTGGCTGATGGTGATTTACCCCCAGGCTCGGGGTAAAAGATCGGATGACTGTGATC
1 GGTAAGAGATTGACTGATGGTGATCTACCCCAAGGCTCGGGGTAAAAGATCAGATGACTGTAATC
* *
1588 TACCCCATGATCGGGGTAAGAGAT
66 TACCCCA-GGTCTGGGTAAGAGAT
1612 CGGAATCTTC
Statistics
Matches: 266, Mismatches: 51, Indels: 13
0.81 0.15 0.04
Matches are distributed among these distances:
232 2 0.01
234 34 0.13
235 225 0.85
236 5 0.02
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (233 bp):
GGTAAGAGATTGACTGATGGTGATCTACCCCAAGGCTCGGGGTAAAAGATCAGATGACTGTAATC
TACCCCAGGTCTGGGTAAGAGATTGACTCATGGTGATCTACCCTAGGCTCGAGGTAAAAGATAGA
ATGACTGCAATCTGCCCCAGGCTCAGGGTAAAAGATCAGACGACCGCAATCTACCCCAAGCTCGG
GGTAAAAGATTGAACGTCACAATCTGCCCCAGGCTCGG
Found at i:1605 original size:157 final size:157
Alignment explanation
Indices: 1054--1612 Score: 552
Period size: 157 Copynumber: 3.6 Consensus size: 157
1044 TCTATCGTGA
** * * * * *
1054 GGTAAGAGATTGACTGATGGTGATCTGCCCCAAGTTCAGGGTAAGAGATCAGATGACTATAATCT
1 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCAGATGACTGTAATCT
* * * * * ** ** ** * *
1119 ACCTCAGGTTTGAGGTAAGAGATTGACTGATGGTGATCTA-CCCTAGGCTCGAGGTAAAAGATTG
66 GCCTTAGGATCGGGGTAAGAGATCAACTGACCGCAATCTACCCCAAGGCTCGGGGTAAAAGATTG
* *
1183 AATGGTTGCAATCTGCCCCAGGCTCGG
131 AACGGTCGCAATCTGCCCCAGGCTCGG
* * **
1210 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGATCTGATGACTACAATCT
1 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCAGATGACTGTAATCT
* ** ** * *
1275 GCCTTAGGTTCGGGGTAAGAGATCAACTGATGGTGATCTACCCCAAGGCTCGGGGTAAAATA-TC
66 GCCTTAGGATCGGGGTAAGAGATCAACTGACCGCAATCTACCCCAAGGCTCGGGGTAAAAGATTG
* * *
1339 AGAC-GACTGTAATCTGCCCCAGGCTCTG
131 A-ACGGTC-GCAATCTGCCCCAGGCTCGG
* * * * *
1367 GGTAAGAGATTGATTCATGGTGATCTGCCCTAGGCTCGAGGTAAAAGATCAGATGACTGTAATTT
1 GGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCAGATGACTGTAATCT
* * * * *
1432 GCCTTAGGCTCAGGGTAAAAGATCAGAC-GGCCGCAATCTATCCCAA-GCTCGGGGTAAAAGATT
66 GCCTTAGGATCGGGGTAAGAGATCA-ACTGACCGCAATCTACCCCAAGGCTCGGGGTAAAAGATT
1495 GAACGGTCGCAATCTGCCCCAGGCTCGG
130 GAACGGTCGCAATCTGCCCCAGGCTCGG
* * * * *
1523 GGTAAGAGATTGGCTGATGGTGATTTACCCCCAGGCTCGGGGTAAAAGATCGGATGACTGTGATC
1 GGTAAGAGATTGGTTGATGGTGATCT-GCCCCAGGCTCGGGGTAAAAGATCAGATGACTGTAATC
* ** *
1588 TACCCCATGATCGGGGTAAGAGATC
65 TGCCTTAGGATCGGGGTAAGAGATC
1613 GGAATCTTCA
Statistics
Matches: 334, Mismatches: 62, Indels: 13
0.82 0.15 0.03
Matches are distributed among these distances:
156 151 0.45
157 181 0.54
158 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (157 bp):
GGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATCAGATGACTGTAATCT
GCCTTAGGATCGGGGTAAGAGATCAACTGACCGCAATCTACCCCAAGGCTCGGGGTAAAAGATTG
AACGGTCGCAATCTGCCCCAGGCTCGG
Found at i:1612 original size:39 final size:40
Alignment explanation
Indices: 1511--1615 Score: 124
Period size: 40 Copynumber: 2.6 Consensus size: 40
1501 TCGCAATCTG
* * * *
1511 CCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATTTAC
1 CCCCAGGATCGGGGTAAGAGATCGGATGATGGTGATCTAC
* *
1551 CCCCAGGCTCGGGGTAAAAGATCGGATGACT-GTGATCTA-
1 CCCCAGGATCGGGGTAAGAGATCGGATGA-TGGTGATCTAC
*
1590 CCCCATGATCGGGGTAAGAGATCGGA
1 CCCCAGGATCGGGGTAAGAGATCGGA
1616 ATCTTCAATC
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
39 23 0.40
40 33 0.58
41 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.33, T:0.21
Consensus pattern (40 bp):
CCCCAGGATCGGGGTAAGAGATCGGATGATGGTGATCTAC
Found at i:3914 original size:3 final size:3
Alignment explanation
Indices: 3906--3952 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
3896 GGTCATCCCT
* * *
3906 TTC TTC TTC TTC TTC ATC ATC ATC -TC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
3953 AATATCATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (3 bp):
TTC
Found at i:12205 original size:13 final size:13
Alignment explanation
Indices: 12187--12211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12177 AAAGAGTCAA
12187 AGCAAAACACATT
1 AGCAAAACACATT
12200 AGCAAAACACAT
1 AGCAAAACACAT
12212 CAATATCAAT
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:0.56, C:0.24, G:0.08, T:0.12
Consensus pattern (13 bp):
AGCAAAACACATT
Found at i:13456 original size:29 final size:29
Alignment explanation
Indices: 13389--13461 Score: 78
Period size: 30 Copynumber: 2.5 Consensus size: 29
13379 ACTTAGGATT
13389 AAAAT-TGAACTTTTGGAAAATTTGAGGTC
1 AAAATGTG-ACTTTTGGAAAATTTGAGGTC
* *
13418 GAAAATGTGACTTTTGGAAATTTTGGGGT-
1 -AAAATGTGACTTTTGGAAAATTTGAGGTC
*
13447 AAAATGGTGATTTTT
1 AAAAT-GTGACTTTT
13462 TTCATGTTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 5 0.13
29 8 0.21
30 23 0.61
31 2 0.05
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (29 bp):
AAAATGTGACTTTTGGAAAATTTGAGGTC
Found at i:13501 original size:30 final size:29
Alignment explanation
Indices: 13467--13818 Score: 291
Period size: 30 Copynumber: 11.8 Consensus size: 29
13457 TTTTTTTCAT
** *
13467 GTTTAGGGGAAAAATGGTAATTTTGGATAA
1 GTTTAGGGTTAAAAT-GTAATTTTGGAAAA
*
13497 GTTTAGGGTTAAAATGTAATTTTAGAAAA
1 GTTTAGGGTTAAAATGTAATTTTGGAAAA
* *
13526 GTTTAAGGTTAAAATATAATTTTGGAAAA
1 GTTTAGGGTTAAAATGTAATTTTGGAAAA
* *
13555 GTTTGAGGGTCAAAATGTAATTTT-AAAAA
1 GTTT-AGGGTTAAAATGTAATTTTGGAAAA
* * *
13584 GTTTTGGGGGTCAAAATGTAATTTTAGAAAA
1 G-TTT-AGGGTTAAAATGTAATTTTGGAAAA
* * **
13615 GTTTTAAGGTCAAAATGCGATTTTAGG-AAA
1 G-TTTAGGGTTAAAATGTAATTTT-GGAAAA
* * * *
13645 GTTTTGGTGTCAAAATATGATTTTAGG-AAA
1 GTTTAGG-GTTAAAATGTAATTTT-GGAAAA
*
13675 GTTTAAGGGTCAAAATGTAATTTTAGG-AAA
1 GTTT-AGGGTTAAAATGTAATTTT-GGAAAA
* *
13705 GTTTATGGGTTAAAATGTGATTTTGGAGAA
1 GTTTA-GGGTTAAAATGTAATTTTGGAAAA
*
13735 GTTTAGGGGTTAAAGTGTAATTTT-GAAGAA
1 GTTTA-GGGTTAAAATGTAATTTTGGAA-AA
* *
13765 GTTTAGGTATTAAAATGTAATATTGGAAAA
1 GTTTAGG-GTTAAAATGTAATTTTGGAAAA
* *
13795 GTTTTAGGGTCAAAATGTGATTTT
1 G-TTTAGGGTTAAAATGTAATTTT
13819 TAAAGAAAAC
Statistics
Matches: 271, Mismatches: 39, Indels: 24
0.81 0.12 0.07
Matches are distributed among these distances:
29 58 0.21
30 192 0.71
31 21 0.08
ACGTcount: A:0.37, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
GTTTAGGGTTAAAATGTAATTTTGGAAAA
Found at i:13616 original size:60 final size:59
Alignment explanation
Indices: 13477--13818 Score: 334
Period size: 60 Copynumber: 5.7 Consensus size: 59
13467 GTTTAGGGGA
* * **
13477 AAAATGGTAATTTTGGATAAGTTTAGGGTTAAAATGTAATTTTAGAAAAG-TTTAAGGTT
1 AAAAT-GTAATTTTGGAAAAGTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTT
* *
13536 AAAATATAATTTTGGAAAAGTTTGAGGGTCAAAATGTAATTTTA-AAAAGTTTTGGGGGTC
1 AAAATGTAATTTTGGAAAAGTTT-AGGGTCAAAATGTAATTTTAGAAAAGTTTT-GGGGTT
* * ** * * *
13596 AAAATGTAATTTTAGAAAAGTTTTAAGGTCAAAATGCGATTTTAGGAAAGTTTTGGTGTC
1 AAAATGTAATTTTGGAAAAG-TTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTT
* * *
13656 AAAATATGATTTTAGG-AAAGTTTAAGGGTCAAAATGTAATTTTAGGAAAGTTTAT-GGGTT
1 AAAATGTAATTTT-GGAAAAGTTT-AGGGTCAAAATGTAATTTTAGAAAAGTTT-TGGGGTT
* * * * * **
13716 AAAATGTGATTTTGGAGAAGTTTAGGGGTTAAAGTGTAATTTT-GAAGAAGTTTAGGTATT
1 AAAATGTAATTTTGGAAAAGTTTA-GGGTCAAAATGTAATTTTAGAA-AAGTTTTGGGGTT
* *
13776 AAAATGTAATATTGGAAAAGTTTTAGGGTCAAAATGTGATTTT
1 AAAATGTAATTTTGGAAAAG-TTTAGGGTCAAAATGTAATTTT
13819 TAAAGAAAAC
Statistics
Matches: 235, Mismatches: 35, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
58 21 0.09
59 35 0.15
60 162 0.69
61 17 0.07
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (59 bp):
AAAATGTAATTTTGGAAAAGTTTAGGGTCAAAATGTAATTTTAGAAAAGTTTTGGGGTT
Found at i:13657 original size:90 final size:87
Alignment explanation
Indices: 13477--13818 Score: 328
Period size: 90 Copynumber: 3.8 Consensus size: 87
13467 GTTTAGGGGA
* * * *
13477 AAAATGGTAATTTTGGATAAGTTTA-GGGTTAAAATGTAATTTTAGAAAAGTTTAAGGTTAAAAT
1 AAAAT-GTAATTTT-AAAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTAAGGTCAAAAT
* *
13541 ATAATTTTGGAAAAG-TTTGAGGGTC
64 GTGATTTTGG-AAAGTTTTG-GGGTC
*
13566 AAAATGTAATTTTAAAAAGTTTTGGGGGTCAAAATGTAATTTTAGAAAAGTTTTAAGGTCAAAAT
1 AAAATGTAATTTTAAAAAG-TTTAGGGGTCAAAATGTAATTTTAGAAAAG-TTTAAGGTCAAAAT
* *
13631 GCGATTTTAGGAAAGTTTTGGTGTC
64 GTGATTTT-GGAAAGTTTTGGGGTC
* * * * * * *
13656 AAAATATGATTTTAGGAAAGTTTAAGGGTCAAAATGTAATTTTAGGAAAGTTTATGGGTTAAAAT
1 AAAATGTAATTTTA-AAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTA-AGGTCAAAAT
* *
13721 GTGATTTTGGAGAAGTTTAGGGGTT
64 GTGATTTTGGA-AAGTTTTGGGGTC
* * ** * * * *
13746 AAAGTGTAATTTTGAAGAAGTTTAGGTATTAAAATGTAATATTGGAAAAGTTTTAGGGTCAAAAT
1 AAAATGTAATTTT-AAAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAG-TTTAAGGTCAAAAT
13811 GTGATTTT
64 GTGATTTT
13819 TAAAGAAAAC
Statistics
Matches: 209, Mismatches: 34, Indels: 19
0.80 0.13 0.07
Matches are distributed among these distances:
87 4 0.02
88 11 0.05
89 36 0.17
90 143 0.68
91 15 0.07
ACGTcount: A:0.37, C:0.02, G:0.23, T:0.37
Consensus pattern (87 bp):
AAAATGTAATTTTAAAAAGTTTAGGGGTCAAAATGTAATTTTAGAAAAGTTTAAGGTCAAAATGT
GATTTTGGAAAGTTTTGGGGTC
Found at i:15357 original size:126 final size:126
Alignment explanation
Indices: 15221--15473 Score: 461
Period size: 126 Copynumber: 2.0 Consensus size: 126
15211 GATTTAAATT
* * **
15221 TAAAATAAATTTAAAAAATGGGTTCAATTTGGGCTCGGACAAATTGGGCTTCAACAACATAAAAT
1 TAAAATAAATTTAAAAAATGGATTCAATTTGGGCCCAAACAAATTGGGCTTCAACAACATAAAAT
*
15286 AATTCAATTTATGCATAAAAATCATACAATAAAGCACAAAATTATATATTTAATAAATTCA
66 AATTCAATTTATGCATAAAAATCATACAATAAAGCACAAAATTACATATTTAATAAATTCA
15347 TAAAATAAATTTAAAAAATGGATTCAATTTGGGCCCAAACAAATTGGGCTTCAACAACATAAAAT
1 TAAAATAAATTTAAAAAATGGATTCAATTTGGGCCCAAACAAATTGGGCTTCAACAACATAAAAT
15412 AATTCAATTTATGCATAAAAATCATACAATAAAGCACAAAATTACATATTTAATAAATTCA
66 AATTCAATTTATGCATAAAAATCATACAATAAAGCACAAAATTACATATTTAATAAATTCA
15473 T
1 T
15474 GTCTAATATA
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 122 1.00
ACGTcount: A:0.49, C:0.13, G:0.09, T:0.30
Consensus pattern (126 bp):
TAAAATAAATTTAAAAAATGGATTCAATTTGGGCCCAAACAAATTGGGCTTCAACAACATAAAAT
AATTCAATTTATGCATAAAAATCATACAATAAAGCACAAAATTACATATTTAATAAATTCA
Found at i:20211 original size:22 final size:21
Alignment explanation
Indices: 20163--20213 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
20153 CTTTGAAACT
**
20163 TTTATTTTAATTTAATTTTTA
1 TTTATTTTAAAATAATTTTTA
* *
20184 TATATTTTAAAATGATTTATTA
1 TTTATTTTAAAATAATTT-TTA
20206 TTTATTTT
1 TTTATTTT
20214 TAATATTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTATTTTAAAATAATTTTTA
Found at i:23301 original size:20 final size:20
Alignment explanation
Indices: 23276--23323 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
23266 TAATTTAAAT
23276 GTGTGTTTGTTGTGTATTTA
1 GTGTGTTTGTTGTGTATTTA
23296 GTGTGTTTGTTGTGTATTTA
1 GTGTGTTTGTTGTGTATTTA
*
23316 ATGTGTTT
1 GTGTGTTT
23324 TAAAACATGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.10, C:0.00, G:0.29, T:0.60
Consensus pattern (20 bp):
GTGTGTTTGTTGTGTATTTA
Found at i:23407 original size:32 final size:32
Alignment explanation
Indices: 23366--23453 Score: 81
Period size: 32 Copynumber: 2.8 Consensus size: 32
23356 TAAGTTTGCG
* * *
23366 TCTTCAATTATATTTTGTATTATATGTCTGCA
1 TCTTTAATTATATATTGCATTATATGTCTGCA
* * *
23398 TCTTTAATTATGTATTGCATTATGTGTTTGCA
1 TCTTTAATTATATATTGCATTATATGTCTGCA
* *
23430 -GTTTAATTATTTCA-TGCATTATAT
1 TCTTTAATTATAT-ATTGCATTATAT
23454 TTATGAATCT
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
31 19 0.41
32 27 0.59
ACGTcount: A:0.25, C:0.10, G:0.11, T:0.53
Consensus pattern (32 bp):
TCTTTAATTATATATTGCATTATATGTCTGCA
Found at i:29339 original size:9 final size:9
Alignment explanation
Indices: 29325--29349 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
29315 GATCAAGTAA
29325 AATTAAATT
1 AATTAAATT
29334 AATTAAATT
1 AATTAAATT
29343 AATTAAA
1 AATTAAA
29350 AAATATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AATTAAATT
Found at i:29805 original size:30 final size:32
Alignment explanation
Indices: 29771--29902 Score: 109
Period size: 30 Copynumber: 4.3 Consensus size: 32
29761 TTAAAATTGT
*
29771 TTTAATACTTATCTTAAT-AGTATT-TATTAA
1 TTTAATATTTATCTTAATAAGTATTATATTAA
* *
29801 TTTAATATTTATCTTATAGATAAATATTCTATTAA
1 TTTAATATTTATC-T-TA-ATAAGTATTATATTAA
* *
29836 TTTAATA--TAT-TTAAT-ATTA-AAT-TTAA
1 TTTAATATTTATCTTAATAAGTATTATATTAA
* * *
29862 TCTAATGTTTATCTTGATAAGTATTATATTAA
1 TTTAATATTTATCTTAATAAGTATTATATTAA
29894 TTTAATATT
1 TTTAATATT
29903 AAAGTGATTA
Statistics
Matches: 79, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
26 9 0.11
27 1 0.01
28 6 0.08
29 6 0.08
30 17 0.22
31 4 0.05
32 13 0.16
33 5 0.06
34 5 0.06
35 13 0.16
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.53
Consensus pattern (32 bp):
TTTAATATTTATCTTAATAAGTATTATATTAA
Found at i:35204 original size:15 final size:15
Alignment explanation
Indices: 35184--35212 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
35174 CACTATTATA
35184 TTTTTTATGTTTTTG
1 TTTTTTATGTTTTTG
35199 TTTTTTATGTTTTT
1 TTTTTTATGTTTTT
35213 CACACATAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (15 bp):
TTTTTTATGTTTTTG
Found at i:36628 original size:58 final size:56
Alignment explanation
Indices: 36447--36636 Score: 157
Period size: 58 Copynumber: 3.2 Consensus size: 56
36437 ATAAATTTAA
* * * * *
36447 TATTAAATTTAATTTAATACTTATCTTCATAATATTTTATTAAATTAATATTAAAG
1 TATTAAATTTAATCTAATATTTATATTGATAATATTTTATTAATTTAATATTAAAG
** * * * * * * *
36503 TGATTATCTTAAATTTAATAATTATCTTATAGATAAACATTTTATTAATTTATTAGATTTAA-
1 T-ATTAAATTTAATCTAAT-ATT-T-ATATTGAT-AATATTTTATTAATTTA--ATATTAAAG
*
36565 TATTAAATTTAATCTAATATTTATATTGATAAGTATTATATTAATTTAATATTAAAG
1 TATTAAATTTAATCTAATATTTATATTGATAA-TATTTTATTAATTTAATATTAAAG
36622 TAATTAAATTTAATC
1 T-ATTAAATTTAATC
36637 ATAGTTGAAC
Statistics
Matches: 102, Mismatches: 22, Indels: 18
0.72 0.15 0.13
Matches are distributed among these distances:
56 7 0.07
57 17 0.17
58 34 0.33
59 2 0.02
60 7 0.07
61 28 0.27
62 1 0.01
63 6 0.06
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (56 bp):
TATTAAATTTAATCTAATATTTATATTGATAATATTTTATTAATTTAATATTAAAG
Found at i:37363 original size:16 final size:16
Alignment explanation
Indices: 37342--37374 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
37332 ACATCACTTA
37342 CGCTCTTCACTTTACC
1 CGCTCTTCACTTTACC
37358 CGCTCTTCACTTTACC
1 CGCTCTTCACTTTACC
37374 C
1 C
37375 TTTTGTGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.45, G:0.06, T:0.36
Consensus pattern (16 bp):
CGCTCTTCACTTTACC
Found at i:37775 original size:28 final size:28
Alignment explanation
Indices: 37626--37775 Score: 165
Period size: 28 Copynumber: 5.4 Consensus size: 28
37616 CATTATTTGC
* * *
37626 CTTTCCTTTCAAAGATTTGCCACAAAGG
1 CTTTCCTTTCAGAGGTTCGCCACAAAGG
* *
37654 CTTTCCTTTTAGAGTTTCGCCACAAAGG
1 CTTTCCTTTCAGAGGTTCGCCACAAAGG
* * *
37682 CATTCCTTTCAAAGGTTCGCCATAAAGG
1 CTTTCCTTTCAGAGGTTCGCCACAAAGG
* *
37710 CTTTCTTTTCAGAGGTTCGCAACAAAGG
1 CTTTCCTTTCAGAGGTTCGCCACAAAGG
* * * *
37738 GTTTCTTTTCAGAGGTTCACCACAAGGG
1 CTTTCCTTTCAGAGGTTCGCCACAAAGG
*
37766 TTTTCCTTTC
1 CTTTCCTTTC
37776 CTAACATGTT
Statistics
Matches: 102, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 102 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (28 bp):
CTTTCCTTTCAGAGGTTCGCCACAAAGG
Found at i:42488 original size:18 final size:18
Alignment explanation
Indices: 42447--42489 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
42437 ATGAGATATA
42447 AGATTCTTATTCTTTATCT
1 AGATT-TTATTCTTTATCT
*
42466 TGATTTTATTCTATTAT-T
1 AGATTTTATTCT-TTATCT
42484 AGATTT
1 AGATTT
42490 AGACAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.60
Consensus pattern (18 bp):
AGATTTTATTCTTTATCT
Found at i:46967 original size:28 final size:29
Alignment explanation
Indices: 46934--47060 Score: 111
Period size: 28 Copynumber: 4.5 Consensus size: 29
46924 AACACGTTAG
*
46934 GAAAGGAAATCCTTTGTT-GCGAACGTTT
1 GAAAGGAAATCCTTTGTTGGCGAACCTTT
*
46962 GAAAGGAAAGCCTTT-TTGGCGAACCTTT
1 GAAAGGAAATCCTTTGTTGGCGAACCTTT
** *
46990 GAAAGG-AATGCCTTTG-TGGAAAACCTCT
1 GAAAGGAAAT-CCTTTGTTGGCGAACCTTT
* * ** *
47018 AAAAGGAAAGCCTTTG-TGGTAAACCTCT
1 GAAAGGAAATCCTTTGTTGGCGAACCTTT
*
47046 GAAAGGAAAGCCTTT
1 GAAAGGAAATCCTTT
47061 ATGGCAGACG
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
27 4 0.05
28 79 0.93
29 2 0.02
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (29 bp):
GAAAGGAAATCCTTTGTTGGCGAACCTTT
Found at i:47023 original size:56 final size:59
Alignment explanation
Indices: 46963--47098 Score: 170
Period size: 56 Copynumber: 2.3 Consensus size: 59
46953 CGAACGTTTG
* * * * *
46963 AAAGGAAAGCCTTTTTGGCGAACCTTTGAAAGGAATGCCTTTGTGG-A-A-AACCTCTA
1 AAAGGAAAGCCTTTGTGGCAAACCTCTGAAAGGAAAGCCTTTATGGCAGACAACCTCTA
*
47019 AAAGGAAAGCCTTTGTGGTAAACCTCTGAAAGGAAAGCCTTTATGGCAGACGAACCTCTA
1 AAAGGAAAGCCTTTGTGGCAAACCTCTGAAAGGAAAGCCTTTATGGCAGAC-AACCTCTA
* *
47079 TAAGGAAAGCCATTGTGGCA
1 AAAGGAAAGCCTTTGTGGCA
47099 CACTTTAAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
56 40 0.60
57 1 0.01
58 1 0.01
60 25 0.37
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (59 bp):
AAAGGAAAGCCTTTGTGGCAAACCTCTGAAAGGAAAGCCTTTATGGCAGACAACCTCTA
Found at i:47084 original size:32 final size:29
Alignment explanation
Indices: 46963--47098 Score: 122
Period size: 28 Copynumber: 4.7 Consensus size: 29
46953 CGAACGTTTG
* *
46963 AAAGGAAAGCCTTTTTGGC-G-AACCTTT
1 AAAGGAAAGCCTTTGTGGCAGAAACCTCT
*
46990 GAAAGGAATGCCTTTGTGG-A-AAACCTCT
1 -AAAGGAAAGCCTTTGTGGCAGAAACCTCT
*
47018 AAAAGGAAAGCCTTTGTGG--TAAACCTCT
1 -AAAGGAAAGCCTTTGTGGCAGAAACCTCT
*
47046 GAAAGGAAAGCCTTTATGGCAGACGAACCTCT
1 -AAAGGAAAGCCTTTGTGGCAGA--AACCTCT
*
47078 ATAAGGAAAGCCATTGTGGCA
1 A-AAGGAAAGCCTTTGTGGCA
47099 CACTTTAAGG
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
28 64 0.71
30 1 0.01
31 1 0.01
32 24 0.27
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (29 bp):
AAAGGAAAGCCTTTGTGGCAGAAACCTCT
Found at i:48913 original size:15 final size:15
Alignment explanation
Indices: 48893--48935 Score: 63
Period size: 13 Copynumber: 3.0 Consensus size: 15
48883 AATTTTCTTG
48893 AAAAATTAATTTTTA
1 AAAAATTAATTTTTA
*
48908 AAAAATTAA--TTTG
1 AAAAATTAATTTTTA
48921 AAAAATTAATTTTTA
1 AAAAATTAATTTTTA
48936 TCAAGTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 12 0.50
15 12 0.50
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
AAAAATTAATTTTTA
Found at i:55671 original size:11 final size:12
Alignment explanation
Indices: 55654--55687 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
55644 TGGACCGAAG
55654 ATGAATTAATTT
1 ATGAATTAATTT
*
55666 -TGAATTCATTT
1 ATGAATTAATTT
55677 ATGAATTAATT
1 ATGAATTAATT
55688 CACTTGTGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.38, C:0.03, G:0.09, T:0.50
Consensus pattern (12 bp):
ATGAATTAATTT
Found at i:56597 original size:37 final size:36
Alignment explanation
Indices: 56548--56623 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 36
56538 ATTCCAAAAA
56548 TAATATTATTTTAATAGT-TTAATATTAAATTTAAT-T
1 TAATATTATTTTAATAGTATT-ATATT-AATTTAATAT
*
56584 TAATAATTATTTTAATAGTATTTTATTAATTTAATAT
1 TAAT-ATTATTTTAATAGTATTATATTAATTTAATAT
56621 TAA
1 TAA
56624 AGTGATTATC
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
36 12 0.33
37 22 0.61
38 2 0.06
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (36 bp):
TAATATTATTTTAATAGTATTATATTAATTTAATAT
Found at i:56621 original size:11 final size:11
Alignment explanation
Indices: 56548--56623 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
56538 ATTCCAAAAA
*
56548 TAATATTATTT
1 TAATATTAATT
56559 TAATAGTTTAATAT
1 TAATA--TTAAT-T
56573 TAA-ATTTAATT
1 TAATA-TTAATT
*
56584 TAATAATTATTT
1 TAAT-ATTAATT
*
56596 TAATAGT-ATT
1 TAATATTAATT
56606 T--TATTAATT
1 TAATATTAATT
56615 TAATATTAA
1 TAATATTAA
56624 AGTGATTATC
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.08
10 3 0.06
11 17 0.33
12 15 0.29
13 6 0.12
14 4 0.08
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:58648 original size:50 final size:49
Alignment explanation
Indices: 58588--58730 Score: 164
Period size: 50 Copynumber: 2.9 Consensus size: 49
58578 AAGGTGGAAG
* *
58588 CAGTGGTAGTATATTTACAAATCAGTGGTGACTTGTCCACAAAAT-TATAT
1 CAGTGGTAGTATATTTGCAAAT-AGTGGTGGCTTGTCCACAAAATGT-TAT
* *
58638 TAGTGGTAGTATATCTGCATATATA-TGGTGGCTTGTCCACAAAATGTTAT
1 CAGTGGTAGTATATTTGCA-A-ATAGTGGTGGCTTGTCCACAAAATGTTAT
** *
58688 CAGTGACAGTTTATTTGCAAATAAGTGGTGGCTTGTCCACAAA
1 CAGTGGTAGTATATTTGCAAAT-AGTGGTGGCTTGTCCACAAA
58731 TGGTGTTTTG
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
48 2 0.03
49 2 0.03
50 70 0.89
51 3 0.04
52 2 0.03
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (49 bp):
CAGTGGTAGTATATTTGCAAATAGTGGTGGCTTGTCCACAAAATGTTAT
Found at i:59086 original size:29 final size:29
Alignment explanation
Indices: 59054--59115 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 29
59044 GTTTTTATGG
59054 TTATGGA-TTTATATTTCAT-TTTGGGACTT
1 TTATGGACTTTATATTT-ATATTTGGG-CTT
*
59083 TTATGGACTTTATATTTTTATTTGGGCTT
1 TTATGGACTTTATATTTATATTTGGGCTT
59112 TTAT
1 TTAT
59116 TATTTCATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.58
Consensus pattern (29 bp):
TTATGGACTTTATATTTATATTTGGGCTT
Found at i:66974 original size:25 final size:24
Alignment explanation
Indices: 66946--67025 Score: 85
Period size: 23 Copynumber: 3.4 Consensus size: 24
66936 GCTAGGCAAC
66946 AGAGAGCACACACAATGCTAATCA
1 AGAGAGCACACACAATGCTAATCA
66970 A-AGAGCACACA-AAGTGCTAATC-
1 AGAGAGCACACACAA-TGCTAATCA
* * * *
66992 AGAGAGCATACACAGTGCCAATAA
1 AGAGAGCACACACAATGCTAATCA
67016 CAGAGAGCAC
1 -AGAGAGCAC
67026 GAGACGTGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
22 3 0.07
23 33 0.72
24 2 0.04
25 8 0.17
ACGTcount: A:0.45, C:0.24, G:0.20, T:0.11
Consensus pattern (24 bp):
AGAGAGCACACACAATGCTAATCA
Found at i:66980 original size:21 final size:23
Alignment explanation
Indices: 66909--67009 Score: 82
Period size: 23 Copynumber: 4.3 Consensus size: 23
66899 CAGAGAGTAC
*
66909 CAAAGTACTAA-CAAAGAGCAC-
1 CAAAGTGCTAATCAAAGAGCACA
* * *
66930 CTAAGTGCTAGGCAACAGAGAGCACA
1 CAAAGTGCTA---ATCAAAGAGCACA
66956 CACAA-TGCTAATCAAAGAGCACA
1 CA-AAGTGCTAATCAAAGAGCACA
* *
66979 CAAAGTGCTAATCAGAGAGCATA
1 CAAAGTGCTAATCAAAGAGCACA
*
67002 CACAGTGC
1 CAAAGTGC
67010 CAATAACAGA
Statistics
Matches: 64, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
21 8 0.12
22 2 0.03
23 36 0.56
24 1 0.02
25 9 0.14
26 6 0.09
27 2 0.03
ACGTcount: A:0.44, C:0.24, G:0.20, T:0.13
Consensus pattern (23 bp):
CAAAGTGCTAATCAAAGAGCACA
Found at i:77497 original size:25 final size:24
Alignment explanation
Indices: 77450--77555 Score: 88
Period size: 25 Copynumber: 4.1 Consensus size: 24
77440 AAATTTTTAT
* *
77450 TTTTTTTAA-TTTTAAGGGTTTAAA
1 TTTTTTTAATTTTTAA-AGATTAAA
*
77474 CTTTTTTTAATTTTTATAGATTAAA
1 -TTTTTTTAATTTTTAAAGATTAAA
*
77499 TTTTTTTTATTAATTTTTAAAGATTTCAA
1 ---TTTTT-TTAATTTTTAAAGA-TTAAA
*
77528 TTTTTTTAATTTTTAAATATTTAAA
1 TTTTTTTAATTTTTAAAGA-TTAAA
77553 TTT
1 TTT
77556 ATTATTTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
25 36 0.53
26 10 0.15
27 5 0.07
28 13 0.19
29 4 0.06
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (24 bp):
TTTTTTTAATTTTTAAAGATTAAA
Found at i:77530 original size:29 final size:27
Alignment explanation
Indices: 77475--77595 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 27
77465 GGGTTTAAAC
*
77475 TTTTTTTAATTTTTATAGATTAAATTT
1 TTTTTTTAATTTTTAAAGATTAAATTT
*
77502 TTTTTATTAATTTTTAAAGATTTCAA---
1 TTTTT-TTAATTTTTAAAGA-TTAAATTT
*
77528 TTTTTTTAATTTTTAAATATTTAAATTT
1 TTTTTTTAATTTTTAAAGA-TTAAATTT
*
77556 ATTATTTTTACCAATTTTTAATAAATCTAAATTT
1 -TT-TTTTT---AATTTTTAA-AGAT-TAAATTT
77590 TTTTTT
1 TTTTTT
77596 CTATTCTACC
Statistics
Matches: 77, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
25 18 0.23
26 5 0.06
27 5 0.06
28 13 0.17
29 6 0.08
30 5 0.06
32 4 0.05
33 12 0.16
34 9 0.12
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (27 bp):
TTTTTTTAATTTTTAAAGATTAAATTT
Found at i:82000 original size:15 final size:16
Alignment explanation
Indices: 81971--82008 Score: 69
Period size: 15 Copynumber: 2.4 Consensus size: 16
81961 ATGGACAAAA
81971 TAAAGTGACATAACTT
1 TAAAGTGACATAACTT
81987 TAAAGTGA-ATAACTT
1 TAAAGTGACATAACTT
82002 TAAAGTG
1 TAAAGTG
82009 TGGACTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (16 bp):
TAAAGTGACATAACTT
Found at i:87834 original size:12 final size:12
Alignment explanation
Indices: 87816--87848 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
87806 CAACTTGTTG
87816 CTTTTATTTTAT
1 CTTTTATTTTAT
*
87828 GTTTTATTTTAT
1 CTTTTATTTTAT
87840 CTTTTATTT
1 CTTTTATTT
87849 CTTTCTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (12 bp):
CTTTTATTTTAT
Found at i:99747 original size:13 final size:14
Alignment explanation
Indices: 99717--99758 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 14
99707 AATCACTTGT
*
99717 AAAACAAAAATGAGA
1 AAAAGAAAAA-GAGA
99732 AAAAGAAAAA-AG-
1 AAAAGAAAAAGAGA
99744 AAAAGAAAAAGAGA
1 AAAAGAAAAAGAGA
99758 A
1 A
99759 TAAATTGTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 10 0.42
13 4 0.17
14 1 0.04
15 9 0.38
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAAGAGA
Found at i:101655 original size:16 final size:16
Alignment explanation
Indices: 101634--101664 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
101624 AAAGAATCAC
101634 GAGTAAGAAAACATGT
1 GAGTAAGAAAACATGT
*
101650 GAGTAAGAAATCATG
1 GAGTAAGAAAACATG
101665 AGTAGAAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.26, T:0.19
Consensus pattern (16 bp):
GAGTAAGAAAACATGT
Found at i:101773 original size:26 final size:26
Alignment explanation
Indices: 101702--101765 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
101692 AAAAAGATTA
101702 AAAAGAAAAAATCTTACTCAAGAAAC
1 AAAAGAAAAAATCTTACTCAAGAAAC
*
101728 AAAAGAAAAATTCTTACTCAAGAAAC
1 AAAAGAAAAAATCTTACTCAAGAAAC
*
101754 AAAATAAAAAAT
1 AAAAGAAAAAAT
101766 AATACTCATA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.17
Consensus pattern (26 bp):
AAAAGAAAAAATCTTACTCAAGAAAC
Found at i:106677 original size:16 final size:16
Alignment explanation
Indices: 106656--106687 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
106646 AGAAATCTAT
106656 TATGAGGTATTGGTAC
1 TATGAGGTATTGGTAC
106672 TATGAGGTATTGGTAC
1 TATGAGGTATTGGTAC
106688 CTCATACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (16 bp):
TATGAGGTATTGGTAC
Found at i:108414 original size:3 final size:3
Alignment explanation
Indices: 108406--108432 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
108396 GGACTAATGA
108406 GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG
108433 AAGAAGAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:110827 original size:482 final size:477
Alignment explanation
Indices: 109507--110939 Score: 1987
Period size: 479 Copynumber: 3.0 Consensus size: 477
109497 GGGAGAATAA
* * *
109507 ACCATAATAGAATATTGTTAAAGCTAGTACTAGAAGTTCTATTGGTTCAAAAAAGAATTTTTATT
1 ACCACAATAGAATGTTGTTAAAGCTAGTACTAGAAGTTCTATTGGTTCAAACAAGAATTTTTATT
* * * * *
109572 TGTAAAT-GTTATAGTAAGCGTCATTAAGGCAA-A-T-----A-TTAGGTGCATGGTTCAGATGA
66 TGTAAATACTT-TAGTAAGCGTCATTAGGGCAATATTAAAAAAGTAAGGTGCATGCTTTAGATGA
* * * *
109628 AGGTCTGTTGAGCATTATGTTAAAGATTGTTCACATCATTCTTTTAATGCAAGCTTTTACTCAGA
130 AGGTCTGTTGAGCATTATGTTAAAGATCGTTCACATAATTCTTTTAATGCAAGCTTTGACTCATA
* * * * * *
109693 AACGGAATTAGAGGCTGGTTTATATTGTTAGGCGTCGAGAGGATCGAGACACATCTAGAATCAAT
195 AACGGAATCAGA-ACTGGTTTATGTTGCTAGGCGTCGAGAGGATCGAGACACATCTGGCATCAAT
* * * *
109758 GAGGGTACTTTTACGATCCATTCTAATTGT-ACTTTACATTAATTGAGAATTTGTTTTCCCTAAA
259 GAAGGTACTTTTACGATCCATTCTAATTGTAAC-TTGCATTGATTGAGAATTTGTTTT-CCTTAA
*
109822 TGTTTGTTATTAATAGTGTATTTTTGAAATTGAGAATTTGGGAATGAGGAAATCGTTAGTGATAT
322 TGTTTGTTATTAATAGTGTATTTGTGAAATTGAGAATTTGGGAATGAGGAAATCGTTAGTGATAT
* * *
109887 TTATATAGATAGTCCCTTGAG--AATCCATGTATGTAACTAGGAAATCCATTGGAGATTTAAGGT
387 TTATATAGATAGTCCCTTGAGACAATCCATGTAAGTAAATA-GAAATCCATTAGAGATTTAAGGT
*
109950 GAATTATTGGAATGACATTGGAATCAT
451 GAAGTATTGGAATGACATTGGAATCAT
* * *
109977 ACCACAACAGAATGTTATTAAAGCTAGTACTAGAAGTTCTATTGGTTCAAGCAAGAATTTTTATT
1 ACCACAATAGAATGTTGTTAAAGCTAGTACTAGAAGTTCTATTGGTTCAAACAAGAATTTTTATT
* * *
110042 TGTAAATACTGTAGTAA-TGTCATTAGGGAAAATATTAGAAAAAGTAAGGTGCATGCTTTAGATG
66 TGTAAATACTTTAGTAAGCGTCATTAGGG-CAATATTA-AAAAAGTAAGGTGCATGCTTTAGATG
** * *
110106 AATTTCTGTTGAGCATTATGTTAAAGATCATTCACA-ACATTATTTTAATGCAAGCTTTGACTCA
129 AAGGTCTGTTGAGCATTATGTTAAAGATCGTTCACATA-ATTCTTTTAATGCAAGCTTTGACTCA
* * *
110170 TAAAAGAAATCAGAGACTGGTTTATGTTACTAGGCGTCGAGAGGATCGAGACACATCTGGCATCA
193 TAAACGGAATCAGA-ACTGGTTTATGTTGCTAGGCGTCGAGAGGATCGAGACACATCTGGCATCA
* * * *
110235 ATGAAGGTACTTTTACGGTCCATTCTAATTATACCTTGCATTGATTAAGAATTTGTTTTCCTTAA
257 ATGAAGGTACTTTTACGATCCATTCTAATTGTAACTTGCATTGATTGAGAATTTGTTTTCCTT-A
* *
110300 ATGTTTGTTCTTAATAGTGTATTTGTGGAATTGAGAATTTGGGAATGAGGAAATCGTTAGTGATA
321 ATGTTTGTTATTAATAGTGTATTTGTGAAATTGAGAATTTGGGAATGAGGAAATCGTTAGTGATA
*
110365 TTTATATAGATAGTCCCTTGAGACAATACATGTAAGTAAATAGAAAAATCCATTAGAGATTTAAG
386 TTTATATAGATAGTCCCTTGAGACAATCCATGTAAGTAAATAG--AAATCCATTAGAGATTTAAG
110430 GTGAAGTATTGGAATGACATTGGAATCAT
449 GTGAAGTATTGGAATGACATTGGAATCAT
*
110459 ACCACAATAAAATGTTGTTAAAGCTAGTACTAGAAGTTCTATTGGTTCAAACAAGAATTTTTATT
1 ACCACAATAGAATGTTGTTAAAGCTAGTACTAGAAGTTCTATTGGTTCAAACAAGAATTTTTATT
110524 TGTAAATACTTTAGTAAGCGTCATTAGGGCAGATATTGAAAAAAGTAAGGTGCATGCTTTAGATG
66 TGTAAATACTTTAGTAAGCGTCATTAGGGCA-ATATT-AAAAAAGTAAGGTGCATGCTTTAGATG
* * *
110589 AAGGTCTGTTGAGCATTGTGTTAAAGATCGTTCACATAATTCTTTTAATGCAAGCTTTGATTAAT
129 AAGGTCTGTTGAGCATTATGTTAAAGATCGTTCACATAATTCTTTTAATGCAAGCTTTGACTCAT
* * * * *
110654 AAACGGAATCATAATTTGGTTTATGTTGCTAGGCATCGAAACGATCGAGACACATCTGGCATCAA
194 AAACGGAATCAGAA-CTGGTTTATGTTGCTAGGCGTCGAGAGGATCGAGACACATCTGGCATCAA
* * *
110719 TGAAGATACTTTTACGATCCATTTTAATTGTAACTTGCATTGGTTGAGAATTTG-TTTCGCTTAA
258 TGAAGGTACTTTTACGATCCATTCTAATTGTAACTTGCATTGATTGAGAATTTGTTTTC-CTTAA
* * * * * *
110783 TGTTTGCTATTAATAGTGTATTTGTGAAATTAAGAATTTGGGAATAAAGAAATCATTAGTTATAT
322 TGTTTGTTATTAATAGTGTATTTGTGAAATTGAGAATTTGGGAATGAGGAAATCGTTAGTGATAT
* * * *
110848 TTATATAGATAGTCTCTTGAGACAATCCATGTAAGTAAATAGGAATCTATTTGAGATTTAAGGTG
387 TTATATAGATAGTCCCTTGAGACAATCCATGTAAGTAAATAGAAATCCATTAGAGATTTAAGGTG
*
110913 AAGTATTGGAACGACATTGGAATCAT
452 AAGTATTGGAATGACATTGGAATCAT
110939 A
1 A
110940 GTTACGCAAC
Statistics
Matches: 849, Mismatches: 90, Indels: 38
0.87 0.09 0.04
Matches are distributed among these distances:
469 9 0.01
470 74 0.09
471 2 0.00
472 1 0.00
478 4 0.00
479 263 0.31
480 48 0.06
481 15 0.02
482 229 0.27
483 202 0.24
484 2 0.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (477 bp):
ACCACAATAGAATGTTGTTAAAGCTAGTACTAGAAGTTCTATTGGTTCAAACAAGAATTTTTATT
TGTAAATACTTTAGTAAGCGTCATTAGGGCAATATTAAAAAAGTAAGGTGCATGCTTTAGATGAA
GGTCTGTTGAGCATTATGTTAAAGATCGTTCACATAATTCTTTTAATGCAAGCTTTGACTCATAA
ACGGAATCAGAACTGGTTTATGTTGCTAGGCGTCGAGAGGATCGAGACACATCTGGCATCAATGA
AGGTACTTTTACGATCCATTCTAATTGTAACTTGCATTGATTGAGAATTTGTTTTCCTTAATGTT
TGTTATTAATAGTGTATTTGTGAAATTGAGAATTTGGGAATGAGGAAATCGTTAGTGATATTTAT
ATAGATAGTCCCTTGAGACAATCCATGTAAGTAAATAGAAATCCATTAGAGATTTAAGGTGAAGT
ATTGGAATGACATTGGAATCAT
Found at i:112055 original size:24 final size:23
Alignment explanation
Indices: 112028--112073 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
112018 CCGACCAGAG
*
112028 ACCCATTGACCGAACCGTTGACCT
1 ACCCATTGACCG-ACCATTGACCT
*
112052 ACCCATTGATCGACCATTGACC
1 ACCCATTGACCGACCATTGACC
112074 CGAATCGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.26, C:0.37, G:0.15, T:0.22
Consensus pattern (23 bp):
ACCCATTGACCGACCATTGACCT
Found at i:112060 original size:12 final size:12
Alignment explanation
Indices: 112027--112073 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
112017 CCCGACCAGA
112027 GACCCATTGACC
1 GACCCATTGACC
* *
112039 GAACCGTTGACC
1 GACCCATTGACC
* *
112051 TACCCATTGATC
1 GACCCATTGACC
112063 GA-CCATTGACC
1 GACCCATTGACC
112074 CGAATCGTTG
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
11 8 0.30
12 19 0.70
ACGTcount: A:0.26, C:0.36, G:0.17, T:0.21
Consensus pattern (12 bp):
GACCCATTGACC
Found at i:112600 original size:20 final size:20
Alignment explanation
Indices: 112575--112620 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
112565 GTTCCACACC
112575 TTGTGTCACATT-ATTATGTG
1 TTGTGTCACATTAATT-TGTG
*
112595 TTGTGTCATATTAATTTGTG
1 TTGTGTCACATTAATTTGTG
112615 TTGTGT
1 TTGTGT
112621 TATCGCTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.17, C:0.07, G:0.22, T:0.54
Consensus pattern (20 bp):
TTGTGTCACATTAATTTGTG
Found at i:114782 original size:46 final size:46
Alignment explanation
Indices: 114715--114883 Score: 203
Period size: 46 Copynumber: 3.7 Consensus size: 46
114705 TATGGTAGTT
* * * *
114715 TATCTTCAAAAGTAGTGGCTTGTCCATAATATTTTAAGTGGGAGTA
1 TATCTGCAAAACTAGTGGCTTGTCCACAATATTTTAAGTGGCAGTA
* * * * * *
114761 TATCTGCAAAATTGGTGGCTTGTTCACAATTTTATTAAGTGGTAGTT
1 TATCTGCAAAACTAGTGGCTTGTCCACAATATT-TTAAGTGGCAGTA
* * *
114808 TATCTGCAAAACTGGTGGTTTGTCTACAATATTTTAAGTGGCAGTA
1 TATCTGCAAAACTAGTGGCTTGTCCACAATATTTTAAGTGGCAGTA
*
114854 TATCTGCAAAACTAGTGGCTTGTCAACAAT
1 TATCTGCAAAACTAGTGGCTTGTCCACAAT
114884 TTTATTATGT
Statistics
Matches: 104, Mismatches: 18, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
46 65 0.62
47 39 0.38
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (46 bp):
TATCTGCAAAACTAGTGGCTTGTCCACAATATTTTAAGTGGCAGTA
Found at i:114872 original size:93 final size:93
Alignment explanation
Indices: 114707--114908 Score: 273
Period size: 93 Copynumber: 2.2 Consensus size: 93
114697 GTGGAAGATA
* * * *
114707 TGGTAGTTTATCTTCAAAAGTAGTGGCTTGTCCATAATATTTTAAGTGGGAGTATATCTGCAAAA
1 TGGTAGTTTATCTGCAAAACTAGTGGCTTGTCCACAATATTTTAAGTGGCAGTATATCTGCAAAA
* *
114772 TTGGTGGCTTGTTC-ACAATTTTATTAAG
66 CTAGTGGCTTG-TCAACAATTTTATTAAG
* * *
114800 TGGTAGTTTATCTGCAAAACTGGTGGTTTGTCTACAATATTTTAAGTGGCAGTATATCTGCAAAA
1 TGGTAGTTTATCTGCAAAACTAGTGGCTTGTCCACAATATTTTAAGTGGCAGTATATCTGCAAAA
*
114865 CTAGTGGCTTGTCAACAATTTTATTATG
66 CTAGTGGCTTGTCAACAATTTTATTAAG
*
114893 TGAG-AGTTTACCTGCA
1 TG-GTAGTTTATCTGCA
114909 TTAATGTGCC
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
92 2 0.02
93 93 0.97
94 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (93 bp):
TGGTAGTTTATCTGCAAAACTAGTGGCTTGTCCACAATATTTTAAGTGGCAGTATATCTGCAAAA
CTAGTGGCTTGTCAACAATTTTATTAAG
Found at i:115503 original size:16 final size:18
Alignment explanation
Indices: 115472--115509 Score: 62
Period size: 16 Copynumber: 2.2 Consensus size: 18
115462 ATTATACATT
115472 AAATATTGATTTTTAACA
1 AAATATTGATTTTTAACA
115490 AAATA-TGA-TTTTAACA
1 AAATATTGATTTTTAACA
115506 AAAT
1 AAAT
115510 TTTGCATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.60
17 3 0.15
18 5 0.25
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (18 bp):
AAATATTGATTTTTAACA
Found at i:118935 original size:16 final size:16
Alignment explanation
Indices: 118914--118944 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
118904 ACTGTGAGAA
*
118914 TTTAGATTTTGAAAAC
1 TTTAGACTTTGAAAAC
118930 TTTAGACTTTGAAAA
1 TTTAGACTTTGAAAA
118945 TTGTACTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.42
Consensus pattern (16 bp):
TTTAGACTTTGAAAAC
Found at i:119686 original size:27 final size:26
Alignment explanation
Indices: 119623--119686 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
119613 GGGGAATGTG
*
119623 TAAAAAAACATAAATATAAATAGACA
1 TAAAAAAAAATAAATATAAATAGACA
* **
119649 TGAAAGTAAATAAATATGAAATAAGA-A
1 TAAAAAAAAATAAATAT-AAAT-AGACA
119676 TAAAAAAAAAT
1 TAAAAAAAAAT
119687 TATGCAAGTG
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
26 13 0.45
27 13 0.45
28 3 0.10
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.20
Consensus pattern (26 bp):
TAAAAAAAAATAAATATAAATAGACA
Found at i:120218 original size:19 final size:17
Alignment explanation
Indices: 120194--120234 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 17
120184 ACGGTGGTCG
120194 AAAATTTTTTTTTGAAATC
1 AAAATTTTTTTTT-AAA-C
120213 AAAATTTTTTTTTAAAC
1 AAAATTTTTTTTTAAAC
120230 AAAAT
1 AAAAT
120235 CACTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.27
18 3 0.14
19 13 0.59
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (17 bp):
AAAATTTTTTTTTAAAC
Found at i:120222 original size:18 final size:17
Alignment explanation
Indices: 120194--120234 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 17
120184 ACGGTGGTCG
120194 AAAATTTTTTTTTGAAATC
1 AAAA-TTTTTTTTGAAA-C
*
120213 AAAATTTTTTTTTAAAC
1 AAAATTTTTTTTGAAAC
120230 AAAAT
1 AAAAT
120235 CACTACTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 11 0.52
19 4 0.19
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (17 bp):
AAAATTTTTTTTGAAAC
Found at i:120284 original size:50 final size:50
Alignment explanation
Indices: 120230--120574 Score: 142
Period size: 50 Copynumber: 7.1 Consensus size: 50
120220 TTTTTTAAAC
*
120230 AAAATCACTACTTT-TCTTAAAAATCAAAACTTTTATTTCAAAATAGTTAA
1 AAAATCACTACTTTAT-TTAAAAATCTAAACTTTTATTTCAAAATAGTTAA
* * * * *
120280 AAAATCA-AACTTTGTTTAAAAAT-TAAACTTTTTTCTTTTAAAAT-GCATAA
1 AAAATCACTACTTTATTTAAAAATCTAAAC--TTTTATTTCAAAATAG-TTAA
* ** * *** *
120330 AAAAT-AGATTTTTTATTTTTAAAAATCTAAAC-TTT-CTTC-TTTTA--AAA
1 AAAATCA-CTACTTTA--TTTAAAAATCTAAACTTTTATTTCAAAATAGTTAA
*
120377 AAAATCACTACTTTATTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAA
1 AAAATCACTACTTTATTTAAAAATCTAAACTTTTATTTCAAAATAGTT-AA
* ** * * * * * *
120428 AAAATTAAAACATTATTTAAAAATTTTAA-TTTTTTCTTTAAAAT-GACT-A
1 AAAATCACTACTTTATTTAAAAATCTAAACTTTTAT-TTCAAAATAG-TTAA
*
120477 AAAAT-A-TATTTTTATTTTTAAAAATCTAAACTTTT-TTT-----T--TTAA
1 AAAATCACTA-CTTTA--TTTAAAAATCTAAACTTTTATTTCAAAATAGTTAA
* * * *
120520 AGAAATCAATACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTAA
1 A-AAATCACTACTTTATTTAAAAATCTAAACTTTTATTTCAAAATAGTTAA
120571 AAAA
1 AAAA
120575 AAAAAAAAGC
Statistics
Matches: 217, Mismatches: 43, Indels: 70
0.66 0.13 0.21
Matches are distributed among these distances:
42 1 0.00
43 19 0.09
44 8 0.04
45 19 0.09
46 5 0.02
47 16 0.07
48 11 0.05
49 25 0.12
50 52 0.24
51 47 0.22
53 9 0.04
54 5 0.02
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (50 bp):
AAAATCACTACTTTATTTAAAAATCTAAACTTTTATTTCAAAATAGTTAA
Found at i:120480 original size:147 final size:146
Alignment explanation
Indices: 120208--120728 Score: 616
Period size: 152 Copynumber: 3.5 Consensus size: 146
120198 TTTTTTTTTG
* * * *
120208 AAATCAAAATTTTTTTTTA-AACAAAATCACTACTTT-TCTTAAAAATCAAAACTTTTATTTCAA
1 AAATCTAAACTTTTTTTTTAAAAAAAATCACTACTTTATCTTAAAAATCAAAACTTTTATTTCAA
* *
120271 AATAGTT-AAAAAA-TCAAACTTTGTTTAAAAA-TTAAACTTTTTTCTTTTAAAATG-CATAAAA
66 AATAGTTAAAAAAATTAAAACATTGTTTAAAAATTTAAA-TTTTTTC-TTTAAAATGAC-T-AAA
*
120332 AATAGATTTTTTATTTTTAA
127 AATACATTTTTTATTTTTAA
*
120352 AAATCTAAACTTTCTTCTTTTAAAAAAAATCACTACTTTAT-TTAAAAATCCAAACTTTTATTTC
1 AAATCTAAACTTT-TT-TTTTAAAAAAAATCACTACTTTATCTTAAAAATCAAAACTTTTATTTC
* *
120416 AAAATAGTTAAAAAAATTAAAACATTATTTAAAAATTTTAATTTTTTCTTTAAAATGACTAAAAA
64 AAAATAGTTAAAAAAATTAAAACATTGTTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAA
*
120481 TATA-TTTTTATTTTTAA
129 TACATTTTTTATTTTTAA
* * * * *
120498 AAATCTAAACTTTTTTTTTTAAAGAAATCAATACTTTA-CTTAAAAATCCAAACTTTTATTTCGA
1 AAATCTAAACTTTTTTTTTAAAAAAAATCACTACTTTATCTTAAAAATCAAAACTTTTATTTCAA
** *
120562 AATAGTTAAAAAAAAAAAAAAGCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATGACT
66 AATAGTT-AAAAAAATTAAAA-C---A--TTGTTTAAAAATTTAAATTTTTTCTTTAAAATGACT
120627 AAAAA-ACATATTTTTATTTTTAA
124 AAAAATACAT-TTTTTATTTTTAA
* * **
120650 AAATCTAAACTTTTTTTTTAAAGAAAATCACTA-TTTTTCTTAAAAATCAAAACTTTTATTTTGA
1 AAATCTAAACTTTTTTTTTAAAAAAAATCACTACTTTATCTTAAAAATCAAAACTTTTATTTCAA
120714 AAT-GATTAAAAAAAT
66 AATAG-TTAAAAAAAT
120729 CAAACCTTTT
Statistics
Matches: 329, Mismatches: 28, Indels: 33
0.84 0.07 0.08
Matches are distributed among these distances:
144 62 0.19
145 15 0.05
146 30 0.09
147 55 0.17
148 17 0.05
149 24 0.07
150 6 0.02
151 49 0.15
152 71 0.22
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (146 bp):
AAATCTAAACTTTTTTTTTAAAAAAAATCACTACTTTATCTTAAAAATCAAAACTTTTATTTCAA
AATAGTTAAAAAAATTAAAACATTGTTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAATA
CATTTTTTATTTTTAA
Found at i:120512 original size:51 final size:50
Alignment explanation
Indices: 120294--120520 Score: 136
Period size: 51 Copynumber: 4.6 Consensus size: 50
120284 TCAAACTTTG
* *
120294 TTTAAAAAT-TAAACTTTTTTCTTTTAAAATGCATAAAAAATAGATTTTTTATT
1 TTTAAAAATCTAAACTTTTTTC-TTTAAAATAC-T-AAAAATATA-TTTTTATT
* * *
120347 TTTAAAAATCTAAACTTTCTTCTTT-TAA-A--AAAAATCACTA-CTTTA--
1 TTTAAAAATCTAAACTTTTTTCTTTAAAATACTAAAAAT-A-TATTTTTATT
* * * * ***
120392 TTTAAAAATCCAAACTTTTAT-TTCAAAATAGTTAAAAA-A-ATTAAAACATT
1 TTTAAAAATCTAAACTTTTTTCTTTAAAATA-CTAAAAATATATT--TTTATT
* *
120442 ATTTAAAAATTTTAA-TTTTTTCTTTAAAATGACTAAAAATATATTTTTATT
1 -TTTAAAAATCTAAACTTTTTTCTTTAAAAT-ACTAAAAATATATTTTTATT
*
120493 TTTAAAAATCTAAACTTTTTTTTTTAAA
1 TTTAAAAATCTAAACTTTTTTCTTTAAA
120521 GAAATCAATA
Statistics
Matches: 129, Mismatches: 26, Indels: 40
0.66 0.13 0.21
Matches are distributed among these distances:
44 2 0.02
45 21 0.16
46 1 0.01
47 11 0.09
48 2 0.02
49 6 0.05
50 17 0.13
51 39 0.30
52 4 0.03
53 15 0.12
54 11 0.09
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (50 bp):
TTTAAAAATCTAAACTTTTTTCTTTAAAATACTAAAAATATATTTTTATT
Found at i:120513 original size:24 final size:24
Alignment explanation
Indices: 120485--120534 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
120475 TAAAAATATA
120485 TTTTTATTTTT-AA-AAATCTAA-AC
1 TTTTT-TTTTTAAAGAAATC-AATAC
120508 TTTTTTTTTTAAAGAAATCAATAC
1 TTTTTTTTTTAAAGAAATCAATAC
120532 TTT
1 TTT
120535 ACTTAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 5 0.21
23 9 0.38
24 10 0.42
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTTTTTTTTAAAGAAATCAATAC
Found at i:121163 original size:3 final size:3
Alignment explanation
Indices: 121155--121212 Score: 80
Period size: 3 Copynumber: 19.3 Consensus size: 3
121145 CCCTAAAAAT
* * **
121155 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA TAA TAG TAA CGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
121203 TAA TAA TAA T
1 TAA TAA TAA T
121213 TTGGACCTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:121863 original size:48 final size:48
Alignment explanation
Indices: 121792--121887 Score: 174
Period size: 48 Copynumber: 2.0 Consensus size: 48
121782 GAAGAACGAG
*
121792 AAGAAGAAGAGAATAGTCTGCTAAGAGAGAGGAAATTGCACAAACTAT
1 AAGAAGAAGAGAATAGTCTGCTAAAAGAGAGGAAATTGCACAAACTAT
*
121840 AAGAAGAAGAGAATGGTCTGCTAAAAGAGAGGAAATTGCACAAACTAT
1 AAGAAGAAGAGAATAGTCTGCTAAAAGAGAGGAAATTGCACAAACTAT
121888 GTGGACTGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.48, C:0.10, G:0.25, T:0.17
Consensus pattern (48 bp):
AAGAAGAAGAGAATAGTCTGCTAAAAGAGAGGAAATTGCACAAACTAT
Found at i:123461 original size:23 final size:24
Alignment explanation
Indices: 123427--123476 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
123417 ATTTTCAATC
123427 AAACAAACAGACCCTA-TGTTATA
1 AAACAAACAGACCCTATTGTTATA
* *
123450 AAAC-AACGAGACTCTATTTTTATA
1 AAACAAAC-AGACCCTATTGTTATA
123474 AAA
1 AAA
123477 TTGTTTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 3 0.13
23 11 0.48
24 9 0.39
ACGTcount: A:0.48, C:0.18, G:0.08, T:0.26
Consensus pattern (24 bp):
AAACAAACAGACCCTATTGTTATA
Found at i:124723 original size:28 final size:27
Alignment explanation
Indices: 124686--124757 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 27
124676 AATTTCCATT
* *
124686 TATAATATAGTGCTGATGGACTTCCACA
1 TATAAGATAGT-CTGATAGACTTCCACA
* *
124714 TTTAAGATAGTCTTGATAGACTTCTACA
1 TATAAGATAGTC-TGATAGACTTCCACA
124742 TATAAGATAGTTCTGA
1 TATAAGATAG-TCTGA
124758 AGGGCTTTCC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.03
28 34 0.92
29 2 0.05
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (27 bp):
TATAAGATAGTCTGATAGACTTCCACA
Found at i:128742 original size:21 final size:21
Alignment explanation
Indices: 128718--128767 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
128708 CCTATAATAG
* * *
128718 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
128739 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
128760 TTCTACCG
1 TTCTACCG
128768 GTACTAAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:140858 original size:150 final size:150
Alignment explanation
Indices: 140587--140888 Score: 577
Period size: 150 Copynumber: 2.0 Consensus size: 150
140577 CACTTGGAAT
140587 CTAAGGCCTATTAAAAAACATGCTAAGATTCGAAACATCGACTATTTGTGGATCGATTGTTTTAG
1 CTAAGGCCTATTAAAAAACATGCTAAGATTCGAAACATCGACTATTTGTGGATCGATTGTTTTAG
140652 AAGTAATAGGTGTCTTGATCTTATGCTCATACTCTTTAATGACATTACAAAAGCTATTGGGAGGG
66 AAGTAATAGGTGTCTTGATCTTATGCTCATACTCTTTAATGACATTACAAAAGCTATTGGGAGGG
*
140717 GACTTAATACAAATGTCACC
131 AACTTAATACAAATGTCACC
*
140737 CTAAGGCTTATTAAAAAACATGCTAAGATTCGAAACATCGACTATTTGTGGATCGATTGTTTTAG
1 CTAAGGCCTATTAAAAAACATGCTAAGATTCGAAACATCGACTATTTGTGGATCGATTGTTTTAG
*
140802 AAGTAATAGGTGTCTTGATCTTGTGCTCATACTCTTTAATGACATTACAAAAGCTATTGGGAGGG
66 AAGTAATAGGTGTCTTGATCTTATGCTCATACTCTTTAATGACATTACAAAAGCTATTGGGAGGG
140867 AACTTAATACAAATGTCACC
131 AACTTAATACAAATGTCACC
140887 CT
1 CT
140889 TCCCCATGGC
Statistics
Matches: 149, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (150 bp):
CTAAGGCCTATTAAAAAACATGCTAAGATTCGAAACATCGACTATTTGTGGATCGATTGTTTTAG
AAGTAATAGGTGTCTTGATCTTATGCTCATACTCTTTAATGACATTACAAAAGCTATTGGGAGGG
AACTTAATACAAATGTCACC
Found at i:151268 original size:29 final size:29
Alignment explanation
Indices: 151190--151268 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 29
151180 TATATATATA
*
151190 TATATAGTTTTATTTTAATATTTAATTCTTT
1 TATATAG--TTATTTTAATATTAAATTCTTT
* *
151221 TATA-A-TTTTTTTATTTATTGAAATT-TTT
1 TATATAGTTATTTTA-ATATT-AAATTCTTT
151249 TATATAGTTATTTTAATATT
1 TATATAGTTATTTTAATATT
151269 TTTTTAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
27 7 0.18
28 11 0.28
29 9 0.23
30 8 0.21
31 4 0.10
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (29 bp):
TATATAGTTATTTTAATATTAAATTCTTT
Found at i:151669 original size:23 final size:22
Alignment explanation
Indices: 151643--151690 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
151633 AAATCCTCCA
* *
151643 TAAACCACCATTGCTAACCCCAT
1 TAAACC-CCACTGCTAACACCAT
151666 TAAAACCCCACTGCTAACACCAT
1 T-AAACCCCACTGCTAACACCAT
151689 TA
1 TA
151691 CTAAATCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 1 0.05
23 16 0.73
24 5 0.23
ACGTcount: A:0.38, C:0.38, G:0.04, T:0.21
Consensus pattern (22 bp):
TAAACCCCACTGCTAACACCAT
Found at i:152285 original size:56 final size:56
Alignment explanation
Indices: 152204--152315 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
152194 ACTTTCAGTG
152204 GCTTTGGATGATTTTGGAGGGAATAACATTTTTCCTTCTTAGTTCATCAGATTTCA
1 GCTTTGGATGATTTTGGAGGGAATAACATTTTTCCTTCTTAGTTCATCAGATTTCA
*
152260 GCTTTGGATGATTTTGGAGGGAATAACATTTTTCCTTTTTAGTTCATCAGATTTCA
1 GCTTTGGATGATTTTGGAGGGAATAACATTTTTCCTTCTTAGTTCATCAGATTTCA
152316 ACATTCTCCC
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.23, C:0.13, G:0.20, T:0.44
Consensus pattern (56 bp):
GCTTTGGATGATTTTGGAGGGAATAACATTTTTCCTTCTTAGTTCATCAGATTTCA
Found at i:154958 original size:26 final size:25
Alignment explanation
Indices: 154916--154965 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
154906 AATTAATTTG
*
154916 ATTAAAAATTTCATTTATTTTTACT
1 ATTAAAAATTTCATTTATATTTACT
154941 ATTAAAAATTAATC-TTTATATTTAC
1 ATTAAAAATT--TCATTTATATTTAC
154966 ACCAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 10 0.45
26 10 0.45
27 2 0.09
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (25 bp):
ATTAAAAATTTCATTTATATTTACT
Found at i:158888 original size:19 final size:19
Alignment explanation
Indices: 158852--158888 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
158842 ATACAAGTAT
158852 TTTATTTTTTAAATAAAAA
1 TTTATTTTTTAAATAAAAA
158871 TTTATATTTTTAAA-AAAA
1 TTTAT-TTTTTAAATAAAA
158889 GAAATGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTATTTTTTAAATAAAAA
Found at i:166195 original size:21 final size:21
Alignment explanation
Indices: 166155--166238 Score: 60
Period size: 21 Copynumber: 4.0 Consensus size: 21
166145 ATTTAGAAAT
** *
166155 AGTGTAGACTTCTATTGATACT
1 AGTG-AGACTTCTACCGATACA
* *
166177 TGTGATACTTCTACCGATACA
1 AGTGAGACTTCTACCGATACA
* *
166198 AGTGGGACTTCTACCGAAACA
1 AGTGAGACTTCTACCGATACA
* * * *
166219 AATCATACATCTACCGATAC
1 AGTGAGACTTCTACCGATAC
166239 TAAAAACTTT
Statistics
Matches: 47, Mismatches: 15, Indels: 1
0.75 0.24 0.02
Matches are distributed among these distances:
21 44 0.94
22 3 0.06
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.30
Consensus pattern (21 bp):
AGTGAGACTTCTACCGATACA
Found at i:170776 original size:43 final size:41
Alignment explanation
Indices: 170705--170803 Score: 108
Period size: 43 Copynumber: 2.4 Consensus size: 41
170695 TTGATGCATA
* **** *
170705 AATGGAAGACTCATGTCTCGGTTTGAGCATGAGAAGTTATATG
1 AATGGAAGACTCATGACTCGAAACGAGCATGAG--GATATATG
*
170748 AATGGAAGACTCATGACTCGAAACGAGCATGAGGATATATT
1 AATGGAAGACTCATGACTCGAAACGAGCATGAGGATATATG
*
170789 AAAGGAAGACTCATG
1 AATGGAAGACTCATG
170804 TCTTGGGTTG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
41 20 0.42
43 28 0.58
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.24
Consensus pattern (41 bp):
AATGGAAGACTCATGACTCGAAACGAGCATGAGGATATATG
Found at i:170839 original size:42 final size:42
Alignment explanation
Indices: 170786--170892 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
170776 ATGAGGATAT
* **
170786 ATTAAAGGAAGACTCATGTCTTGGGTTGAGAATGAAAATACA
1 ATTAAAGGAAGACTCATGTCTTAGGAAGAGAATGAAAATACA
* * ***
170828 ATTAAAGGAAGACTCATGTCTCAGGAAGAGAATGAGAATTTG
1 ATTAAAGGAAGACTCATGTCTTAGGAAGAGAATGAAAATACA
*
170870 ATTTAAGGAAGACTCATGTCTTA
1 ATTAAAGGAAGACTCATGTCTTA
170893 AAGGAGCATG
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.39, C:0.10, G:0.23, T:0.27
Consensus pattern (42 bp):
ATTAAAGGAAGACTCATGTCTTAGGAAGAGAATGAAAATACA
Found at i:171589 original size:21 final size:22
Alignment explanation
Indices: 171565--171611 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
171555 TAGTATCAAA
* *
171565 AGAAGC-ATAACTAGTTTTGGT
1 AGAAGCTATAACAAGTATTGGT
*
171586 AGAA-CTATTACAAGTATTGGT
1 AGAAGCTATAACAAGTATTGGT
171607 AGAAG
1 AGAAG
171612 TTTGCACTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.38, C:0.09, G:0.23, T:0.30
Consensus pattern (22 bp):
AGAAGCTATAACAAGTATTGGT
Found at i:193374 original size:32 final size:32
Alignment explanation
Indices: 193333--193397 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
193323 TTAAAGTAAC
193333 AAACTTGTTAGGTTAGTGTATCTTTGCTAATA
1 AAACTTGTTAGGTTAGTGTATCTTTGCTAATA
193365 AAACTTGTTAGGTTAGTGTATCTTTGCTAATA
1 AAACTTGTTAGGTTAGTGTATCTTTGCTAATA
193397 A
1 A
193398 TATGTATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.43
Consensus pattern (32 bp):
AAACTTGTTAGGTTAGTGTATCTTTGCTAATA
Done.