Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013128.1 Kokia drynarioides strain JFW-HI SEQ_128147, 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: 196367
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 274 characters in sequence are not A, C, G, or T
Found at i:8 original size:3 final size:3
Alignment explanation
Indices: 1--90 Score: 78
Period size: 3 Copynumber: 30.0 Consensus size: 3
* *
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGAA T-A TGA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* * * *
46 TAA TAA CAG TAA TGAA T-T TAT TAA TAA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
91 ATAAATAAAA
Statistics
Matches: 72, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.07
3 58 0.81
4 9 0.12
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:40 original size:30 final size:30
Alignment explanation
Indices: 6--93 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 30
1 TAATA
6 ATAATAATAATAATAATAATAATGAATATG
1 ATAATAATAATAATAATAATAATGAATATG
* * * *
36 ATAATATTAATAATAACAGTAATGAAT-TT
1 ATAATAATAATAATAATAATAATGAATATG
*
65 ATTAATAATAATAAATAAT-ATAATAAATA
1 A-TAATAATAAT-AATAATAATAATGAATA
94 AATAAAATGG
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
29 2 0.04
30 40 0.85
31 5 0.11
ACGTcount: A:0.59, C:0.01, G:0.05, T:0.35
Consensus pattern (30 bp):
ATAATAATAATAATAATAATAATGAATATG
Found at i:461 original size:11 final size:11
Alignment explanation
Indices: 437--474 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
427 TAAACTTCTA
437 AAAAAGGAAGAG
1 AAAAAGGAA-AG
*
449 AAAAATGAAAG
1 AAAAAGGAAAG
460 AAAAAGGAAAG
1 AAAAAGGAAAG
471 AAAA
1 AAAA
475 GGGGAGGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (11 bp):
AAAAAGGAAAG
Found at i:1506 original size:29 final size:29
Alignment explanation
Indices: 1223--1501 Score: 219
Period size: 29 Copynumber: 9.5 Consensus size: 29
1213 AAACTGTCCG
*
1223 AAAATTACATTTTTACCCTC-AAACTTTCA
1 AAAATTCCATTTTTACCC-CGAAACTTTCA
* *
1252 AAAATTCCATTTTTAACCCCCAAAACTTCCA
1 AAAATTCCATTTTT-A-CCCCGAAACTTTCA
* * * * *
1283 AAAATCCCATTCTTATCCCTAAATTTTCA
1 AAAATTCCATTTTTACCCCGAAACTTTCA
* *
1312 AAAATTCCATTTTTGCCACC-AAACTTCCA
1 AAAATTCCATTTTTACC-CCGAAACTTTCA
* *
1341 AAAATTCCATTTTTGCCACCG-AACTTCCAA
1 AAAATTCCATTTTTACC-CCGAAACTTTC-A
* * *
1371 AAAATCCCATTTTGACCCCG-AACTTCCA
1 AAAATTCCATTTTTACCCCGAAACTTTCA
* *
1399 AAAATTCCATTTTTAAACTCGAAAC-TTCTA
1 AAAATTCCATTTTT-ACCCCGAAACTTTC-A
* * * *
1429 AAAATTCTAGTTTTACCCCCAAAAC-TTCC
1 AAAATTCCATTTTTA-CCCCGAAACTTTCA
* *
1458 AAAATTCCATTTTGACCTCGAAACTTTCA
1 AAAATTCCATTTTTACCCCGAAACTTTCA
1487 AAAATTACCATTTTT
1 AAAATT-CCATTTTT
1502 CCTCGGGAAT
Statistics
Matches: 203, Mismatches: 35, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
28 20 0.10
29 108 0.53
30 52 0.26
31 23 0.11
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCGAAACTTTCA
Found at i:1516 original size:28 final size:29
Alignment explanation
Indices: 1485--1546 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
1475 TCGAAACTTT
* *
1485 CAAAAATTACCATTTT-TCCTCGGGAATC
1 CAAAAATTACCATTTTACCCCCGGGAATC
* *
1513 C-AAAATTACTATTTTACCCCCGGGTATC
1 CAAAAATTACCATTTTACCCCCGGGAATC
1541 CAAAAA
1 CAAAAA
1547 GTCTCATTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
27 13 0.46
28 11 0.39
29 4 0.14
ACGTcount: A:0.35, C:0.26, G:0.10, T:0.29
Consensus pattern (29 bp):
CAAAAATTACCATTTTACCCCCGGGAATC
Found at i:1521 original size:27 final size:28
Alignment explanation
Indices: 1487--1545 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
1477 GAAACTTTCA
* *
1487 AAAATTACCATTTT-TCCTCGGGAATCC
1 AAAATTACCATTTTACCCCCGGGAATCC
* *
1514 AAAATTACTATTTTACCCCCGGGTATCC
1 AAAATTACCATTTTACCCCCGGGAATCC
1542 AAAA
1 AAAA
1546 AGTCTCATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.34, C:0.25, G:0.10, T:0.31
Consensus pattern (28 bp):
AAAATTACCATTTTACCCCCGGGAATCC
Found at i:8753 original size:10 final size:10
Alignment explanation
Indices: 8738--8766 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
8728 TTCTTTAATA
8738 CATACATACT
1 CATACATACT
8748 CATACATACT
1 CATACATACT
8758 CATACATAC
1 CATACATAC
8767 CACATAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (10 bp):
CATACATACT
Found at i:13356 original size:119 final size:119
Alignment explanation
Indices: 13133--13403 Score: 443
Period size: 119 Copynumber: 2.3 Consensus size: 119
13123 ACGCGATCAT
* *
13133 CTTCCTGATGAGATACTGAGAAGAAGATCAAATCAAACCCATGCTCGATGTGAGCAAATCTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
*
13198 ACCCTAGCTTCTTGATGAGACACTAAGAAGTAGGACGAAGCAATAAGAGGTTAG
66 ACCCTAGCTTCTTGATGAGACACTAAGAAGCAGGACGAAGCAATAAGAGGTTAG
* * *
13252 CTTCTTGATGAGATATTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
* * *
13317 ACCCTAGCTTCTTGATGAGACACTGAGAAGCAGGTCGAAGTAATAAGAGGTTAG
66 ACCCTAGCTTCTTGATGAGACACTAAGAAGCAGGACGAAGCAATAAGAGGTTAG
**
13371 CTTCCTGATGAGATACTGAGAAGTGGACCAAAT
1 CTTCCTGATGAGATACTGAGAAGAAGACCAAAT
13404 TCGTCTTCCT
Statistics
Matches: 138, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
119 138 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (119 bp):
CTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGA
ACCCTAGCTTCTTGATGAGACACTAAGAAGCAGGACGAAGCAATAAGAGGTTAG
Found at i:13842 original size:206 final size:205
Alignment explanation
Indices: 13273--14060 Score: 1015
Period size: 206 Copynumber: 3.8 Consensus size: 205
13263 GATATTAAGA
* * * *
13273 AGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCTAGCTTCTTGATGAGAC
1 AGAAGACCAAATCAAACCCACGCTCGATATGAGAAAATCTTCGAACCCCAGCTTCCTGATGAGAC
* * * * * *
13338 ACTGAGAAGCAGGTCGAAGTAATAAGAGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAA
66 ACTAAGAAGCAGGTCGAAGTAATAAAATGTTAGCTTCCTGATGAAATACTGGGAAGTGAACCAAA
* * * * *
13403 TTCGTCTTCCTGATG-AGATACAGAGAAGCGAATTGAAACAAACGACGCAGTCATTTTCCTGATG
131 TTCGTCTTCCTGATGAAG-TACAGAGAAGCGGATTAAAACAAACGACGCGGTCATCTTCCTAATG
* ***
13467 AGA-TACTGAG
195 AGACAAAAAAG
* * ** * * *
13477 AAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCTTAGCTTCTTAATGAAA
1 -AGAAGACCAAATCAAACCCACGCTCGATATGAGAAAATCTTCGAACCCCAGCTTCCTGATGAGA
* * * *
13542 CACTGAGCAGCAGGTCGAAGCAATAAGAA-GTTAGCTTCCTGATGAGATACTGGGAAGTGAACCA
65 CACTAAGAAGCAGGTCGAAGTAATAA-AATGTTAGCTTCCTGATGAAATACTGGGAAGTGAACCA
*
13606 AATTCGTCTTCCTGATGAGGTACAGAGAAGCGGATTAAAACAAACGACGCGGTCATCTTCCTAAT
129 AATTCGTCTTCCTGATGAAGTACAGAGAAGCGGATTAAAACAAACGACGCGGTCATCTTCCTAAT
13671 GAGACAAAAAAG
194 GAGACAAAAAAG
* * * *
13683 AGAAGAGCAAATCAAACCCACGCTCGATATGAGAAAATCTTCGAACCCCAACTTCCTGATGCGAT
1 AGAAGACCAAATCAAACCCACGCTCGATATGAGAAAATCTTCGAACCCCAGCTTCCTGATGAGAC
* * * *
13748 ACTAAGAAGCAAGTCGAAGTATTAAAACTGTTAGCTTCCTGATGAAATACAGGGAAGTGGACCAA
66 ACTAAGAAGCAGGTCGAAGTAATAAAA-TGTTAGCTTCCTGATGAAATACTGGGAAGTGAACCAA
13813 ATTCGTCTTCCTGATGAAGTACAGAGAAGCGGATTAAAACAAACGACGCGGTCATCTTCCTAATG
130 ATTCGTCTTCCTGATGAAGTACAGAGAAGCGGATTAAAACAAACGACGCGGTCATCTTCCTAATG
13878 AGACAAAAAAG
195 AGACAAAAAAG
* * * * *
13889 AGAAAAGCAAATCAAACCCACTCTCGATATGAGAAAATCTTCGAACCCCAGCTTCCTGATGCGAT
1 AGAAGACCAAATCAAACCCACGCTCGATATGAGAAAATCTTCGAACCCCAGCTTCCTGATGAGAC
* *
13954 ACTAAGAAGCAGGTCGAAGTATTAAAACTGTTAGCTTCCTGATGAAATACGGGGAAGTGAACCAA
66 ACTAAGAAGCAGGTCGAAGTAATAAAA-TGTTAGCTTCCTGATGAAATACTGGGAAGTGAACCAA
** * * ** * * *
14019 AACCATTTTCCTGATGAAACATAGAGAAGTGGATCAAAACAA
130 ATTCGTCTTCCTGATGAAGTACAGAGAAGCGGATTAAAACAA
14061 GTGATGTAGT
Statistics
Matches: 525, Mismatches: 53, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
204 2 0.00
205 253 0.48
206 270 0.51
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (205 bp):
AGAAGACCAAATCAAACCCACGCTCGATATGAGAAAATCTTCGAACCCCAGCTTCCTGATGAGAC
ACTAAGAAGCAGGTCGAAGTAATAAAATGTTAGCTTCCTGATGAAATACTGGGAAGTGAACCAAA
TTCGTCTTCCTGATGAAGTACAGAGAAGCGGATTAAAACAAACGACGCGGTCATCTTCCTAATGA
GACAAAAAAG
Found at i:15116 original size:3 final size:3
Alignment explanation
Indices: 15110--15196 Score: 54
Period size: 3 Copynumber: 29.0 Consensus size: 3
15100 AAAAGATTCG
* * * *
15110 TAA TAA TAA TAA TAA TAA TGA TGA TGAA T-A TGA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * * *
15155 TAA CAG TAA TGAA T-T TAT TAA TAA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
15197 ATAAATAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
2 5 0.07
3 54 0.81
4 8 0.12
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:15568 original size:11 final size:11
Alignment explanation
Indices: 15544--15581 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
15534 TAAACTTCTA
15544 AAAAAGGAAGAG
1 AAAAAGGAA-AG
*
15556 AAAAATGAAAG
1 AAAAAGGAAAG
15567 AAAAAGGAAAG
1 AAAAAGGAAAG
15578 AAAA
1 AAAA
15582 GGGGAGGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (11 bp):
AAAAAGGAAAG
Found at i:16350 original size:30 final size:29
Alignment explanation
Indices: 16324--16591 Score: 330
Period size: 29 Copynumber: 9.2 Consensus size: 29
16314 CGAAAATTAT
*
16324 ATTTTTACCCCCGAACTTCCAAAAAATCCC
1 ATTTTTACCCCCGAACTTCC-AAAAATTCC
* *
16354 ATTTTTAACCTCGAAACTTCCAAAAATTCC
1 ATTTTTACCCCCG-AACTTCCAAAAATTCC
*
16384 ATTTTTACCCCCGAACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
*
16413 ATTTTTGA-CCTCGAAACTTCCAAAAATTCC
1 ATTTTT-ACCCCCG-AACTTCCAAAAATTCC
* * *
16443 ATTTTTGCCACCGAACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
* * *
16472 ATTTTTGCCGCCGAACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
*
16501 ATTTTTGA-CCTCGAACTTCCAAAAATTCC
1 ATTTTT-ACCCCCGAACTTCCAAAAATTCC
16530 A-TTTTACCCCCGAACTTCC-AAAATTCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
*
16557 ATTTTTACCCCCGAAACGTCC-AAAATTCC
1 ATTTTTACCCCCG-AACTTCCAAAAATTCC
16586 ATTTTT
1 ATTTTT
16592 TTGACCTTGA
Statistics
Matches: 211, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
27 10 0.05
28 26 0.12
29 113 0.54
30 55 0.26
31 7 0.03
ACGTcount: A:0.31, C:0.32, G:0.06, T:0.31
Consensus pattern (29 bp):
ATTTTTACCCCCGAACTTCCAAAAATTCC
Found at i:16435 original size:59 final size:59
Alignment explanation
Indices: 16324--16624 Score: 366
Period size: 59 Copynumber: 5.1 Consensus size: 59
16314 CGAAAATTAT
*
16324 ATTTTTACCCCCGAACTTCCAAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCC
1 ATTTTTACCCCCGAACTTCC-AAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCC
16384 ATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCC
1 ATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCC
* * * *
16443 ATTTTTGCCACCGAACTTCCAAAAATCCCATTTTTG-CCGCCG-AACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC-TCGAAACTTCCAAAAATTCC
* * *
16501 ATTTTTGA-CCTCGAACTTCCAAAAATTCCA-TTTT-ACCCCCG-AACTTCC-AAAATTCC
1 ATTTTT-ACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTCGAAACTTCCAAAAATTCC
* * * *
16557 ATTTTTACCCCCGAAACGTCC-AAAATTCCATTTTTTTGACCTTGAAACTTTCAAAAATTACC
1 ATTTTTACCCCCG-AACTTCCAAAAATCCCA--TTTTTGACCTCGAAACTTCCAAAAATT-CC
16619 ATTTTT
1 ATTTTT
16625 CCTTGGGAAT
Statistics
Matches: 213, Mismatches: 15, Indels: 24
0.85 0.06 0.10
Matches are distributed among these distances:
55 1 0.00
56 26 0.12
57 20 0.09
58 44 0.21
59 81 0.38
60 27 0.13
61 6 0.03
62 8 0.04
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.32
Consensus pattern (59 bp):
ATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCC
Found at i:16486 original size:88 final size:87
Alignment explanation
Indices: 16337--16624 Score: 377
Period size: 88 Copynumber: 3.3 Consensus size: 87
16327 TTTACCCCCG
* *
16337 AACTTCCAAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
1 AACTTCC-AAAAATTCCATTTTT-ACCCCG-AACTTCCAAAAATTCCATTTTTACCCCCGAACTT
16402 CCAAAAATCCCATTTTTGACCTCGA
63 CCAAAAATCCCATTTTTGACCTCGA
* * * *
16427 AACTTCCAAAAATTCCATTTTTGCCACCGAACTTCCAAAAATCCCATTTTTGCCGCCGAACTTCC
1 AACTTCCAAAAATTCCATTTTTACC-CCGAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCC
16492 AAAAATCCCATTTTTGACCTCG-
65 AAAAATCCCATTTTTGACCTCGA
*
16514 AACTTCCAAAAATTCCA-TTTTACCCCCGAACTTCC-AAAATTCCATTTTTACCCCCGAAACGTC
1 AACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCATTTTTACCCCCG-AACTTC
* *
16577 C-AAAATTCCATTTTTTTGACCTTGA
64 CAAAAATCCCA--TTTTTGACCTCGA
*
16602 AACTTTCAAAAATTACCATTTTT
1 AACTTCCAAAAATT-CCATTTTT
16625 CCTTGGGAAT
Statistics
Matches: 176, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
85 26 0.15
86 20 0.11
87 30 0.17
88 70 0.40
89 19 0.11
90 11 0.06
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCA
AAAATCCCATTTTTGACCTCGA
Found at i:25166 original size:3 final size:3
Alignment explanation
Indices: 25160--25246 Score: 54
Period size: 3 Copynumber: 29.0 Consensus size: 3
25150 AAAAGATTCG
* * * *
25160 TAA TAA TAA TAA TAA TAA TGA TGA TGAA T-A TGA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
* * * *
25205 TAA CAG TAA TGAA T-T TAT TAA TAA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
25247 ATAAATAAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
2 5 0.07
3 54 0.81
4 8 0.12
ACGTcount: A:0.56, C:0.01, G:0.07, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:25618 original size:11 final size:11
Alignment explanation
Indices: 25594--25631 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
25584 TAAACTTCTA
25594 AAAAAGGAAGAG
1 AAAAAGGAA-AG
*
25606 AAAAATGAAAG
1 AAAAAGGAAAG
25617 AAAAAGGAAAG
1 AAAAAGGAAAG
25628 AAAA
1 AAAA
25632 GGGGAGGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (11 bp):
AAAAAGGAAAG
Found at i:26400 original size:30 final size:29
Alignment explanation
Indices: 26374--26641 Score: 330
Period size: 29 Copynumber: 9.2 Consensus size: 29
26364 CGAAAATTAT
*
26374 ATTTTTACCCCCGAACTTCCAAAAAATCCC
1 ATTTTTACCCCCGAACTTCC-AAAAATTCC
* *
26404 ATTTTTAACCTCGAAACTTCCAAAAATTCC
1 ATTTTTACCCCCG-AACTTCCAAAAATTCC
*
26434 ATTTTTACCCCCGAACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
*
26463 ATTTTTGA-CCTCGAAACTTCCAAAAATTCC
1 ATTTTT-ACCCCCG-AACTTCCAAAAATTCC
* * *
26493 ATTTTTGCCACCGAACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
* * *
26522 ATTTTTGCCGCCGAACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
*
26551 ATTTTTGA-CCTCGAACTTCCAAAAATTCC
1 ATTTTT-ACCCCCGAACTTCCAAAAATTCC
26580 A-TTTTACCCCCGAACTTCC-AAAATTCC
1 ATTTTTACCCCCGAACTTCCAAAAATTCC
*
26607 ATTTTTACCCCCGAAACGTCC-AAAATTCC
1 ATTTTTACCCCCG-AACTTCCAAAAATTCC
26636 ATTTTT
1 ATTTTT
26642 TTGACCTTGA
Statistics
Matches: 211, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
27 10 0.05
28 26 0.12
29 113 0.54
30 55 0.26
31 7 0.03
ACGTcount: A:0.31, C:0.32, G:0.06, T:0.31
Consensus pattern (29 bp):
ATTTTTACCCCCGAACTTCCAAAAATTCC
Found at i:26485 original size:59 final size:59
Alignment explanation
Indices: 26374--26674 Score: 366
Period size: 59 Copynumber: 5.1 Consensus size: 59
26364 CGAAAATTAT
*
26374 ATTTTTACCCCCGAACTTCCAAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCC
1 ATTTTTACCCCCGAACTTCC-AAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCC
26434 ATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCC
1 ATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCC
* * * *
26493 ATTTTTGCCACCGAACTTCCAAAAATCCCATTTTTG-CCGCCG-AACTTCCAAAAATCCC
1 ATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC-TCGAAACTTCCAAAAATTCC
* * *
26551 ATTTTTGA-CCTCGAACTTCCAAAAATTCCA-TTTT-ACCCCCG-AACTTCC-AAAATTCC
1 ATTTTT-ACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCTCGAAACTTCCAAAAATTCC
* * * *
26607 ATTTTTACCCCCGAAACGTCC-AAAATTCCATTTTTTTGACCTTGAAACTTTCAAAAATTACC
1 ATTTTTACCCCCG-AACTTCCAAAAATCCCA--TTTTTGACCTCGAAACTTCCAAAAATT-CC
26669 ATTTTT
1 ATTTTT
26675 CCTTGGGAAT
Statistics
Matches: 213, Mismatches: 15, Indels: 24
0.85 0.06 0.10
Matches are distributed among these distances:
55 1 0.00
56 26 0.12
57 20 0.09
58 44 0.21
59 81 0.38
60 27 0.13
61 6 0.03
62 8 0.04
ACGTcount: A:0.32, C:0.31, G:0.06, T:0.32
Consensus pattern (59 bp):
ATTTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCC
Found at i:26536 original size:88 final size:87
Alignment explanation
Indices: 26387--26674 Score: 377
Period size: 88 Copynumber: 3.3 Consensus size: 87
26377 TTTACCCCCG
* *
26387 AACTTCCAAAAAATCCCATTTTTAACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTT
1 AACTTCC-AAAAATTCCATTTTT-ACCCCG-AACTTCCAAAAATTCCATTTTTACCCCCGAACTT
26452 CCAAAAATCCCATTTTTGACCTCGA
63 CCAAAAATCCCATTTTTGACCTCGA
* * * *
26477 AACTTCCAAAAATTCCATTTTTGCCACCGAACTTCCAAAAATCCCATTTTTGCCGCCGAACTTCC
1 AACTTCCAAAAATTCCATTTTTACC-CCGAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCC
26542 AAAAATCCCATTTTTGACCTCG-
65 AAAAATCCCATTTTTGACCTCGA
*
26564 AACTTCCAAAAATTCCA-TTTTACCCCCGAACTTCC-AAAATTCCATTTTTACCCCCGAAACGTC
1 AACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATTCCATTTTTACCCCCG-AACTTC
* *
26627 C-AAAATTCCATTTTTTTGACCTTGA
64 CAAAAATCCCA--TTTTTGACCTCGA
*
26652 AACTTTCAAAAATTACCATTTTT
1 AACTTCCAAAAATT-CCATTTTT
26675 CCTTGGGAAT
Statistics
Matches: 176, Mismatches: 14, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
85 26 0.15
86 20 0.11
87 30 0.17
88 70 0.40
89 19 0.11
90 11 0.06
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (87 bp):
AACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCA
AAAATCCCATTTTTGACCTCGA
Found at i:34635 original size:77 final size:77
Alignment explanation
Indices: 34508--34665 Score: 226
Period size: 77 Copynumber: 2.1 Consensus size: 77
34498 CTTCAAACCA
* * *
34508 ATTGCATCAATAAGACACTTCACTTGCTACAACGATCCTCAAGTGTACACTATAGCTCATTGCTT
1 ATTGCATCAATAAGACACTTCACTCGCTACAACAATCCTCAAGTGTACACTATAGCTCATTGCCT
* *
34573 GTAGGAGCCTTC
66 GTAGCAACCTTC
* * * * *
34585 ATTGCCTCAATAGGACACTTCACTCGCTCCAACAATCCTCAAGTGTACACTCTAGCTCGTTGCCT
1 ATTGCATCAATAAGACACTTCACTCGCTACAACAATCCTCAAGTGTACACTATAGCTCATTGCCT
34650 GTAGCAACCTTC
66 GTAGCAACCTTC
34662 ATTG
1 ATTG
34666 GTTCCAGCAG
Statistics
Matches: 71, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
77 71 1.00
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (77 bp):
ATTGCATCAATAAGACACTTCACTCGCTACAACAATCCTCAAGTGTACACTATAGCTCATTGCCT
GTAGCAACCTTC
Found at i:38357 original size:19 final size:20
Alignment explanation
Indices: 38323--38363 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
38313 ATAATAATAA
38323 AAATAAGCAAAAGTTCAAGT
1 AAATAAGCAAAAGTTCAAGT
*
38343 AAATAA-CATAAGTTCAAGT
1 AAATAAGCAAAAGTTCAAGT
38362 AA
1 AA
38364 CAACAATAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (20 bp):
AAATAAGCAAAAGTTCAAGT
Found at i:38372 original size:19 final size:19
Alignment explanation
Indices: 38333--38368 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38323 AAATAAGCAA
*
38333 AAGTTCAAGTAAATAACAT
1 AAGTTCAAGTAAACAACAT
38352 AAGTTCAAGT-AACAACA
1 AAGTTCAAGTAAACAACA
38369 ATAACACAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.22
Consensus pattern (19 bp):
AAGTTCAAGTAAACAACAT
Found at i:38470 original size:21 final size:20
Alignment explanation
Indices: 38446--38484 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
38436 ACACCATTCC
38446 AAACAACAAAATCAAAAATAA
1 AAACAACAAAA-CAAAAATAA
*
38467 AAACAACACAACAAAAAT
1 AAACAACAAAACAAAAAT
38485 CAAATAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.74, C:0.18, G:0.00, T:0.08
Consensus pattern (20 bp):
AAACAACAAAACAAAAATAA
Found at i:38494 original size:20 final size:19
Alignment explanation
Indices: 38446--38498 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
38436 ACACCATTCC
38446 AAACAACAAAATCAAAAATAA
1 AAACAAC-AAA-CAAAAATAA
38467 AAACAACACAACAAAAATCAA
1 AAACAACA-AACAAAAAT-AA
*
38488 ATA-AACAAACA
1 AAACAACAAACA
38499 GTAATAACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 4 0.14
20 12 0.41
21 13 0.45
ACGTcount: A:0.74, C:0.19, G:0.00, T:0.08
Consensus pattern (19 bp):
AAACAACAAACAAAAATAA
Found at i:38687 original size:34 final size:34
Alignment explanation
Indices: 38640--38712 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
38630 AATTGAACCG
* *
38640 AATTTTAATTTATTTAAAGTTTAAATATATTTTA
1 AATTTAAACTTATTTAAAGTTTAAATATATTTTA
** * *
38674 AATTTAAACTTATTTTGAGTTTAAATTTATTTTG
1 AATTTAAACTTATTTAAAGTTTAAATATATTTTA
38708 AATTT
1 AATTT
38713 TAATTTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.56
Consensus pattern (34 bp):
AATTTAAACTTATTTAAAGTTTAAATATATTTTA
Found at i:38718 original size:17 final size:17
Alignment explanation
Indices: 38639--38719 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 17
38629 AAATTGAACC
*
38639 GAATTTTAATTTA-TTT
1 GAATTTAAATTTATTTT
* *
38655 AAAGTTTAAATATATTTT
1 GAA-TTTAAATTTATTTT
* *
38673 AAATTTAAACTTATTTT
1 GAATTTAAATTTATTTT
*
38690 GAGTTTAAATTTATTTT
1 GAATTTAAATTTATTTT
*
38707 GAATTTTAATTTA
1 GAATTTAAATTTA
38720 AAATTTAATT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
16 2 0.04
17 45 0.85
18 6 0.11
ACGTcount: A:0.37, C:0.01, G:0.06, T:0.56
Consensus pattern (17 bp):
GAATTTAAATTTATTTT
Found at i:40465 original size:29 final size:29
Alignment explanation
Indices: 40364--40629 Score: 134
Period size: 30 Copynumber: 9.1 Consensus size: 29
40354 ATTTTGTCTA
*
40364 AAAATTACCATTTTGACCCCAAACCTTTCC
1 AAAATTACCATTTTGACCCCGAA-CTTTCC
*
40394 AAAATTACCATTTT-ACCCTCGAAC-TTCGTA
1 AAAATTACCATTTTGACCC-CGAACTTTC--C
** *
40424 AAAATTA-TGTTTTGGCCCCGAACTTTCC
1 AAAATTACCATTTTGACCCCGAACTTTCC
* * *
40452 AAAATTACCATTTT-TCCCTGAAC-ATCC
1 AAAATTACCATTTTGACCCCGAACTTTCC
* * ** * **
40479 AAAAATTATCATTTTGACTCTTAAGTTTTTT
1 -AAAATTACCATTTTGACCCCGAA-CTTTCC
* * ** * *
40510 GAAATT-GCATTTTTTCCCTCAAAC-ATCC
1 AAAATTACCATTTTGACCC-CGAACTTTCC
* *
40538 AAAAATTACCATTTTGCCCCCGAAATTTTCC
1 -AAAATTACCATTTTGACCCCG-AACTTTCC
* * *
40569 AAAATTACCATTTTGCCCCCGAACATTCA
1 AAAATTACCATTTTGACCCCGAACTTTCC
* * *
40598 AAAATTATCATGTTGCCCCCGAA-TTTCC
1 AAAATTACCATTTTGACCCCGAACTTTCC
40626 AAAA
1 AAAA
40630 ATCACATTTT
Statistics
Matches: 177, Mismatches: 44, Indels: 32
0.70 0.17 0.13
Matches are distributed among these distances:
27 3 0.02
28 38 0.21
29 63 0.36
30 69 0.39
31 4 0.02
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.34
Consensus pattern (29 bp):
AAAATTACCATTTTGACCCCGAACTTTCC
Found at i:40574 original size:59 final size:59
Alignment explanation
Indices: 40363--40629 Score: 233
Period size: 59 Copynumber: 4.6 Consensus size: 59
40353 TATTTTGTCT
* * *
40363 AAAAATTACCATTTTGACCCC-AAACCTTTCCAAAATTACCATTTTACCCTCGAACTTCGT
1 AAAAATTACCATTTTGACCCCGAAA-CTTTCCAAAATTACCATTTTTCCCTCGAACATC-C
** *
40423 AAAAATTA-TGTTTTGGCCCCG-AACTTTCCAAAATTACCATTTTTCCCT-GAACATCC
1 AAAAATTACCATTTTGACCCCGAAACTTTCCAAAATTACCATTTTTCCCTCGAACATCC
* * ** ** *** * *
40479 AAAAATTATCATTTTGACTCTTAAGTTTTTTGAAATT-GCATTTTTTCCCTCAAACATCC
1 AAAAATTACCATTTTGACCCCGAAACTTTCCAAAATTACCA-TTTTTCCCTCGAACATCC
* * * * *
40538 AAAAATTACCATTTTGCCCCCGAAATTTTCCAAAATTACCATTTTGCCCCCGAACATTC
1 AAAAATTACCATTTTGACCCCGAAACTTTCCAAAATTACCATTTTTCCCTCGAACATCC
* * *
40597 AAAAATTATCATGTTGCCCCCG-AA-TTTCCAAAA
1 AAAAATTACCATTTTGACCCCGAAACTTTCCAAAA
40630 ATCACATTTT
Statistics
Matches: 166, Mismatches: 35, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
56 8 0.05
57 24 0.14
58 44 0.27
59 80 0.48
60 10 0.06
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (59 bp):
AAAAATTACCATTTTGACCCCGAAACTTTCCAAAATTACCATTTTTCCCTCGAACATCC
Found at i:40630 original size:29 final size:30
Alignment explanation
Indices: 40363--40639 Score: 155
Period size: 29 Copynumber: 9.5 Consensus size: 30
40353 TATTTTGTCT
* *
40363 AAAAATTACCATTTTGACCCCAAACCTTTCC
1 AAAAATTACCATTTTGCCCCCGAA-CTTTCC
* * *
40394 -AAAATTACCATTTTACCCTCGAAC-TTCGT
1 AAAAATTACCATTTTGCCCCCGAACTTTC-C
** *
40423 AAAAATTA-TGTTTTGGCCCCGAACTTTCC
1 AAAAATTACCATTTTGCCCCCGAACTTTCC
* * *
40452 -AAAATTACCATTTT-TCCCTGAAC-ATCC
1 AAAAATTACCATTTTGCCCCCGAACTTTCC
* * * ** * **
40479 AAAAATTATCATTTTGACTCTTAAGTTTTT
1 AAAAATTACCATTTTGCCCCCGAACTTTCC
** * * * * *
40509 TGAAATT-GCATTTTTTCCCTCAAAC-ATCC
1 AAAAATTACCA-TTTTGCCCCCGAACTTTCC
*
40538 AAAAATTACCATTTTGCCCCCGAAATTTTCC
1 AAAAATTACCATTTTGCCCCCG-AACTTTCC
*
40569 -AAAATTACCATTTTGCCCCCGAACATT-C
1 AAAAATTACCATTTTGCCCCCGAACTTTCC
* *
40597 AAAAATTATCATGTTGCCCCCGAA-TTTCC
1 AAAAATTACCATTTTGCCCCCGAACTTTCC
*
40626 AAAAATCA-CATTTT
1 AAAAATTACCATTTT
40640 CGATTTCAAA
Statistics
Matches: 181, Mismatches: 52, Indels: 29
0.69 0.20 0.11
Matches are distributed among these distances:
27 3 0.02
28 38 0.21
29 70 0.39
30 67 0.37
31 3 0.02
ACGTcount: A:0.32, C:0.26, G:0.07, T:0.35
Consensus pattern (30 bp):
AAAAATTACCATTTTGCCCCCGAACTTTCC
Found at i:40657 original size:30 final size:28
Alignment explanation
Indices: 40621--40699 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 28
40611 TGCCCCCGAA
40621 TTTCCAAAAATCACATTTTCGATTT-CAAAT
1 TTTCCAAAAATCA-ATTTT--ATTTCCAAAT
* *
40651 TTTCCAAAAGTTTAATTTTATTTCCAAAT
1 TTTCCAAAA-ATCAATTTTATTTCCAAAT
40680 TTTCCAAAAAATTCAATTTT
1 TTTCC-AAAAA-TCAATTTT
40700 GATATTGAAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
28 4 0.10
29 10 0.24
30 25 0.61
31 2 0.05
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.44
Consensus pattern (28 bp):
TTTCCAAAAATCAATTTTATTTCCAAAT
Found at i:41994 original size:59 final size:58
Alignment explanation
Indices: 41923--42043 Score: 197
Period size: 59 Copynumber: 2.1 Consensus size: 58
41913 AAAAGGAGTT
* *
41923 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGGGTTTAAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGCTTT-AAAAATATTTGGGTTTA
* *
41982 GTTTATGAGTGTTTTTTAAGAATGAAATTATATTTGGCTTTAAAAATATTTGGGTTTA
1 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGCTTTAAAAATATTTGGGTTTA
42040 GTTT
1 GTTT
42044 GTTAATGGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 21 0.36
59 37 0.64
ACGTcount: A:0.31, C:0.01, G:0.20, T:0.48
Consensus pattern (58 bp):
GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGCTTTAAAAATATTTGGGTTTA
Found at i:42761 original size:31 final size:28
Alignment explanation
Indices: 42721--42777 Score: 78
Period size: 31 Copynumber: 1.9 Consensus size: 28
42711 AAAAAAATTA
*
42721 ATAATTTTAATCCTCAACATTTATAAAATCC
1 ATAAATTTAATCCT-AAC-TTTA-AAAATCC
42752 ATAAATTTAATCCTAACTTTAAAAAT
1 ATAAATTTAATCCTAACTTTAAAAAT
42778 TTTAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 5 0.20
29 4 0.16
30 3 0.12
31 13 0.52
ACGTcount: A:0.46, C:0.16, G:0.00, T:0.39
Consensus pattern (28 bp):
ATAAATTTAATCCTAACTTTAAAAATCC
Found at i:47728 original size:2 final size:2
Alignment explanation
Indices: 47715--47757 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
47705 TATAAAAGAC
*
47715 TA TA TC 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
47757 T
1 T
47758 TTAAAAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:49850 original size:18 final size:20
Alignment explanation
Indices: 49810--49851 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 20
49800 GAGTAGTAAT
* *
49810 TTTTTATTTTTTATATTTGG
1 TTTTTATTTTTTATAGTTCG
49830 TTTTT-TTTTTTAT-GTTCG
1 TTTTTATTTTTTATAGTTCG
49848 TTTT
1 TTTT
49852 GTAGTTCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 8 0.40
20 5 0.25
ACGTcount: A:0.10, C:0.02, G:0.10, T:0.79
Consensus pattern (20 bp):
TTTTTATTTTTTATAGTTCG
Found at i:49981 original size:46 final size:48
Alignment explanation
Indices: 49925--50014 Score: 132
Period size: 46 Copynumber: 1.9 Consensus size: 48
49915 TAATTTATGG
49925 TTTTCAATAATTTTTAT-ATTTT-TAATAACATTT-TAATAAATTATAA
1 TTTTCAATAATTTTTATAATTTTCTAATAAC-TTTATAATAAATTATAA
* *
49971 TTTTCCATAATTTTTATAATTTTCTAATAACTTTATATTAAATT
1 TTTTCAATAATTTTTATAATTTTCTAATAACTTTATAATAAATT
50015 TTATATTATT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
46 16 0.41
47 8 0.21
48 15 0.38
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (48 bp):
TTTTCAATAATTTTTATAATTTTCTAATAACTTTATAATAAATTATAA
Found at i:50005 original size:19 final size:19
Alignment explanation
Indices: 49965--50007 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
49955 TTTTAATAAA
* *
49965 TTATAATTTTCCATAATTT
1 TTATAATTTTCAATAATCT
49984 TTATAATTTTCTAATAA-CT
1 TTATAATTTTC-AATAATCT
50003 TTATA
1 TTATA
50008 TTAAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.35, C:0.09, G:0.00, T:0.56
Consensus pattern (19 bp):
TTATAATTTTCAATAATCT
Found at i:50032 original size:48 final size:47
Alignment explanation
Indices: 49925--50048 Score: 123
Period size: 48 Copynumber: 2.6 Consensus size: 47
49915 TAATTTATGG
49925 TTTTCAATAATTTTTAT-ATTTT-TAATAACATTTTAATAAATTATAA
1 TTTTC-ATAATTTTTATAATTTTCTAATAACATTTTAATAAATTATAA
* *
49971 TTTTCCATAATTTTTATAATTTTCTAATAAC-TTTATATTAAATTTTATA
1 TTTT-CATAATTTTTATAATTTTCTAATAACATTT-TAATAAATTATA-A
*
50020 TTATT-ATGATTTTCTATAAGTTTTC-AATA
1 TT-TTCATAATTTT-TATAA-TTTTCTAATA
50049 TTGTAAATAC
Statistics
Matches: 67, Mismatches: 3, Indels: 13
0.81 0.04 0.16
Matches are distributed among these distances:
46 15 0.22
47 9 0.13
48 24 0.36
49 12 0.18
50 7 0.10
ACGTcount: A:0.36, C:0.06, G:0.02, T:0.56
Consensus pattern (47 bp):
TTTTCATAATTTTTATAATTTTCTAATAACATTTTAATAAATTATAA
Found at i:50163 original size:20 final size:18
Alignment explanation
Indices: 50130--50185 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
50120 CTCTCTACAA
*
50130 ATTTTAATATTTTTTTAT
1 ATTTTAATATTTTTTTAG
*
50148 ATTTTAAATCATTTTTATAG
1 ATTTT-AAT-ATTTTTTTAG
50168 ATTTTCAATGATTTTTTT
1 ATTTT-AAT-ATTTTTTT
50186 TTTTATATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 5 0.16
19 3 0.10
20 23 0.74
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (18 bp):
ATTTTAATATTTTTTTAG
Found at i:52005 original size:39 final size:39
Alignment explanation
Indices: 51921--52010 Score: 117
Period size: 39 Copynumber: 2.3 Consensus size: 39
51911 AATGAGGTAG
* *
51921 TGAACTGCCGGTAACACTGAAAATATCGTAATGCAATAC
1 TGAACTGACGGTAACACTGAAAATACCGTAATGCAATAC
** * * *
51960 AAAACTGATGGTAACGCTGTAAATACCGTAATGCAATAC
1 TGAACTGACGGTAACACTGAAAATACCGTAATGCAATAC
51999 TGAACTGACGGT
1 TGAACTGACGGT
52011 GATACTATAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (39 bp):
TGAACTGACGGTAACACTGAAAATACCGTAATGCAATAC
Found at i:58304 original size:67 final size:67
Alignment explanation
Indices: 58196--58334 Score: 224
Period size: 67 Copynumber: 2.1 Consensus size: 67
58186 GTCTAGGCTA
* * ** * *
58196 TGTGCCTTATAAAAGAGAAATAGTGAGTTACACGATCTGGACACATGGGCGTGGGCCAAACTGTG
1 TGTGCCTTATAAAAGAGAAACAGTGAGTTACACGATCTGGACACACGAACGTAGGCCAAACCGTG
58261 TG
66 TG
58263 TGTGCCTTATAAAAGAGAAACAGTGAGTTACACGATCTGGACACACGAACGTAGGCCAAACCGTG
1 TGTGCCTTATAAAAGAGAAACAGTGAGTTACACGATCTGGACACACGAACGTAGGCCAAACCGTG
58328 TG
66 TG
58330 TGTGC
1 TGTGC
58335 TTGTTTCACG
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (67 bp):
TGTGCCTTATAAAAGAGAAACAGTGAGTTACACGATCTGGACACACGAACGTAGGCCAAACCGTG
TG
Found at i:58718 original size:39 final size:39
Alignment explanation
Indices: 58675--58774 Score: 119
Period size: 39 Copynumber: 2.6 Consensus size: 39
58665 TTGCAATGAG
*
58675 ATACTGAACTGACGGTAACACTGAAAATACCGTAATGCA
1 ATACTGAACTGACGGTAACACTGAAAATACCGTAACGCA
** * * *
58714 ATACTGATTTGACGGTAACATTGTAAATACCGTAACGTA
1 ATACTGAACTGACGGTAACACTGAAAATACCGTAACGCA
* * *
58753 ATGCTGAACTAACGGTGACACT
1 ATACTGAACTGACGGTAACACT
58775 ATAAACACTA
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
39 49 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (39 bp):
ATACTGAACTGACGGTAACACTGAAAATACCGTAACGCA
Found at i:59713 original size:5 final size:5
Alignment explanation
Indices: 59705--59732 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
59695 AGTGTATAAT
59705 ATATG ATATG ATATG ATATG ATATG ATA
1 ATATG ATATG ATATG ATATG ATATG ATA
59733 CGTGGTTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.18, T:0.39
Consensus pattern (5 bp):
ATATG
Found at i:61689 original size:23 final size:23
Alignment explanation
Indices: 61663--61732 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
61653 TTCATTTAAC
61663 TTAATTGAACATGTTCACGAACA
1 TTAATTGAACATGTTCACGAACA
** * *
61686 TTAAACGGACATGTTCATGAACA
1 TTAATTGAACATGTTCACGAACA
* *
61709 TATAATTAAACATGTTCACAAACA
1 T-TAATTGAACATGTTCACGAACA
61733 ATGTTAATGA
Statistics
Matches: 36, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
23 20 0.56
24 16 0.44
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (23 bp):
TTAATTGAACATGTTCACGAACA
Found at i:62216 original size:16 final size:16
Alignment explanation
Indices: 62197--62276 Score: 51
Period size: 15 Copynumber: 5.2 Consensus size: 16
62187 ATTTTTATTA
62197 AATTATATTTAATAAT
1 AATTATATTTAATAAT
*
62213 AATTATATTGAA-ATAT
1 AATTATATTTAATA-AT
* * * *
62229 GATTA-AATTATTTAT
1 AATTATATTTAATAAT
* * *
62244 TATTAT-TTTTATTA-
1 AATTATATTTAATAAT
62258 AATTATATTTAATAAT
1 AATTATATTTAATAAT
62274 AAT
1 AAT
62277 CTTATTAAAA
Statistics
Matches: 46, Mismatches: 13, Indels: 10
0.67 0.19 0.14
Matches are distributed among these distances:
14 5 0.11
15 21 0.46
16 20 0.43
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
AATTATATTTAATAAT
Found at i:62236 original size:61 final size:61
Alignment explanation
Indices: 62148--62286 Score: 210
Period size: 61 Copynumber: 2.3 Consensus size: 61
62138 TTAATATAAA
*
62148 AATAATTATATTAAAAATGTTATTAAATTATATATTTTTATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAAAATG-TATTAAATTATATATTATTATTTTTATTAAATTATATTTAAT
* *
62210 AATAATTATATTGAAATATG-ATTAAATTATTTATTATTATTTTTATTAAATTATATTTAAT
1 AATAATTATATT-AAAAATGTATTAAATTATATATTATTATTTTTATTAAATTATATTTAAT
62271 AATAATCT-TATTAAAA
1 AATAAT-TATATTAAAA
62287 TTTAATAACA
Statistics
Matches: 71, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
60 3 0.04
61 49 0.69
62 13 0.18
63 6 0.08
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.53
Consensus pattern (61 bp):
AATAATTATATTAAAAATGTATTAAATTATATATTATTATTTTTATTAAATTATATTTAAT
Found at i:93804 original size:21 final size:21
Alignment explanation
Indices: 93765--93804 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
93755 TTTTTTATAA
**
93765 TTTAATTAATCATGTTTTAGT
1 TTTAATTAATCATAATTTAGT
*
93786 TTTAATTAATCTTAATTTA
1 TTTAATTAATCATAATTTA
93805 CTTAACTAAG
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:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (21 bp):
TTTAATTAATCATAATTTAGT
Found at i:102257 original size:29 final size:29
Alignment explanation
Indices: 102202--102279 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
102192 AAAAGTATTT
* * *
102202 AAATATTCAGATAAAAATTAAACATTTTA
1 AAATATTCAAATAAAAGTTAAACATTTCA
*
102231 AAATATTCATATAAAAGTT-AACAATTTCA
1 AAATATTCAAATAAAAGTTAAAC-ATTTCA
*
102260 AAAGTATTTAAATAAAAGTT
1 AAA-TATTCAAATAAAAGTT
102280 TTTTAAATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 3 0.07
29 25 0.60
30 14 0.33
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (29 bp):
AAATATTCAAATAAAAGTTAAACATTTCA
Found at i:108594 original size:17 final size:20
Alignment explanation
Indices: 108555--108595 Score: 61
Period size: 17 Copynumber: 2.2 Consensus size: 20
108545 AAATGTAATA
108555 AAAAAACATAATAAATCTTC
1 AAAAAACATAATAAATCTTC
108575 AAAAAA-AT-ATAAAT-TTC
1 AAAAAACATAATAAATCTTC
108592 AAAA
1 AAAA
108596 TCCCTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 6 0.29
19 2 0.10
20 6 0.29
ACGTcount: A:0.66, C:0.10, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAAAACATAATAAATCTTC
Found at i:109950 original size:25 final size:26
Alignment explanation
Indices: 109922--109980 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
109912 GCTTAAAGGT
*
109922 TTTTAAAGGGTTTATAA-GG-TTTGGG
1 TTTTAAAGGG-TAATAAGGGTTTTGGG
109947 TTTTAAATGGGTAATAAGGGTTTTGGG
1 TTTTAAA-GGGTAATAAGGGTTTTGGG
109974 -TTTAAAG
1 TTTTAAAG
109981 TTTGGGTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
25 13 0.43
26 11 0.37
27 6 0.20
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (26 bp):
TTTTAAAGGGTAATAAGGGTTTTGGG
Found at i:116922 original size:14 final size:14
Alignment explanation
Indices: 116905--116995 Score: 92
Period size: 14 Copynumber: 6.5 Consensus size: 14
116895 CAAAGTCAAA
*
116905 GTCAACAATCAATG
1 GTCAACAATCAACG
*
116919 GTCAACAATTAACG
1 GTCAACAATCAACG
**
116933 GTCAACTGTCAACG
1 GTCAACAATCAACG
** *
116947 GTCAACTGTCAAAG
1 GTCAACAATCAACG
*
116961 GTCAACTATCAACG
1 GTCAACAATCAACG
**
116975 GTCAATGATCAACG
1 GTCAACAATCAACG
116989 GTCAACA
1 GTCAACA
116996 GTCGGTCAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 65 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (14 bp):
GTCAACAATCAACG
Found at i:117009 original size:7 final size:7
Alignment explanation
Indices: 116929--116994 Score: 69
Period size: 7 Copynumber: 9.4 Consensus size: 7
116919 GTCAACAATT
116929 AACGGTC
1 AACGGTC
*
116936 AACTGTC
1 AACGGTC
116943 AACGGTC
1 AACGGTC
*
116950 AACTGTC
1 AACGGTC
*
116957 AAAGGTC
1 AACGGTC
**
116964 AACTATC
1 AACGGTC
116971 AACGGTC
1 AACGGTC
* *
116978 AATGATC
1 AACGGTC
116985 AACGGTC
1 AACGGTC
116992 AAC
1 AAC
116995 AGTCGGTCAA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
7 45 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (7 bp):
AACGGTC
Found at i:117051 original size:15 final size:16
Alignment explanation
Indices: 117031--117065 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
117021 GGGTTTGAAC
117031 TTGGTTCA-ATTGGGT
1 TTGGTTCACATTGGGT
*
117046 TTGGTTCACTTTGGGT
1 TTGGTTCACATTGGGT
117062 TTGG
1 TTGG
117066 GTTATTAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.09, C:0.09, G:0.34, T:0.49
Consensus pattern (16 bp):
TTGGTTCACATTGGGT
Found at i:118467 original size:16 final size:17
Alignment explanation
Indices: 118428--118460 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
118418 AATTAAGATA
*
118428 AATATATAAAAAATTTC
1 AATAAATAAAAAATTTC
118445 AATAAATAAAAAATTT
1 AATAAATAAAAAATTT
118461 ATAAAATTAT
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:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAATAAAAAATTTC
Found at i:121163 original size:123 final size:124
Alignment explanation
Indices: 121010--121261 Score: 335
Period size: 126 Copynumber: 2.0 Consensus size: 124
121000 TTGGGCTTAA
* ** **
121010 TTCGATCCAATATGCTTTCAAG-TTTTTTTTTTTATGCTATTTTTGTTCGTTTTACGGTTTATGT
1 TTCGACCCAATATGCTTTCAAGTTTTTTTTTTTTATGCTATTCCTGTTCGTTTTACGGTCCATGT
* ** * * * * *
121074 TCGGGATGCATGGTTATCCTTTCTAACAATGTTGTCTCCAAAATTCGAACTTAGGTCCT
66 TCAGGATGCATGACTATCCATCCTAACAATGTTATCTCCAAAATTCGAACTTAAGTCAT
121133 TTCGACCCAATATGCTTTCAAGTTTTTTTTTTTTTTATGCTATTCCTGTTCGTTTTACGGTCCAT
1 TTCGACCCAATATGCTTTCAAG--TTTTTTTTTTTTATGCTATTCCTGTTCGTTTTACGGTCCAT
* * *
121198 GTTCAGGATGCGTGACTGTCCATCCTAACAATGTTATCTCCAAAGTTCGAACTTAAGTCAT
64 GTTCAGGATGCATGACTATCCATCCTAACAATGTTATCTCCAAAATTCGAACTTAAGTCAT
121259 TTC
1 TTC
121262 CTTAGGAGTG
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
123 21 0.19
126 89 0.81
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.45
Consensus pattern (124 bp):
TTCGACCCAATATGCTTTCAAGTTTTTTTTTTTTATGCTATTCCTGTTCGTTTTACGGTCCATGT
TCAGGATGCATGACTATCCATCCTAACAATGTTATCTCCAAAATTCGAACTTAAGTCAT
Found at i:123756 original size:28 final size:24
Alignment explanation
Indices: 123695--123749 Score: 92
Period size: 24 Copynumber: 2.3 Consensus size: 24
123685 AATCTTTTAG
* *
123695 TTAAACTCTATTTATTTGTTTCAA
1 TTAAACTCTGTTTATTTGTTCCAA
123719 TTAAACTCTGTTTATTTGTTCCAA
1 TTAAACTCTGTTTATTTGTTCCAA
123743 TTAAACT
1 TTAAACT
123750 ATGTCTGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (24 bp):
TTAAACTCTGTTTATTTGTTCCAA
Found at i:125928 original size:15 final size:16
Alignment explanation
Indices: 125908--125941 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
125898 CTTAATTATT
*
125908 TATAATTATA-ATTTA
1 TATAATAATATATTTA
125923 TATAATAATATATTTA
1 TATAATAATATATTTA
125939 TAT
1 TAT
125942 GAAAATGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TATAATAATATATTTA
Found at i:126389 original size:70 final size:71
Alignment explanation
Indices: 126315--126472 Score: 205
Period size: 70 Copynumber: 2.3 Consensus size: 71
126305 TAATTTTCAC
* * *
126315 TAAAAAAATTAATTTTAATCTCATATTGATTAGAGAATACT-TTCATAGCTAATTTCTTCACTAT
1 TAAAAAAATTAATTTTAATCCCACATTGATTAGAGAATACTCATCATAGCTAATTTCTTCACTAT
126379 TTTAAT
66 TTTAAT
* * * * * *
126385 TAAAATAATTAATTTTAATCCCACATTGATTTGAGAATACTCATGATTGCTCATTTTTTCACTAT
1 TAAAAAAATTAATTTTAATCCCACATTGATTAGAGAATACTCATCATAGCTAATTTCTTCACTAT
*
126450 TTTCAT
66 TTTAAT
126456 T-AAAAAA-TAATTTTAAT
1 TAAAAAAATTAATTTTAAT
126473 TAACTAGAGA
Statistics
Matches: 76, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
69 10 0.13
70 42 0.55
71 24 0.32
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (71 bp):
TAAAAAAATTAATTTTAATCCCACATTGATTAGAGAATACTCATCATAGCTAATTTCTTCACTAT
TTTAAT
Found at i:126665 original size:30 final size:28
Alignment explanation
Indices: 126620--126682 Score: 72
Period size: 30 Copynumber: 2.2 Consensus size: 28
126610 AATAAGTGTC
*
126620 AATTTGTTCAATATTTTCATTAAAAAAGTT
1 AATTTCTTCAATATTTT-ATTAAAAAA-TT
* * *
126650 AATTTCTTCATTATTTTATTTAAATATT
1 AATTTCTTCAATATTTTATTAAAAAATT
126678 AATTT
1 AATTT
126683 TAATCCCACG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 7 0.24
29 7 0.24
30 15 0.52
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (28 bp):
AATTTCTTCAATATTTTATTAAAAAATT
Found at i:127882 original size:19 final size:19
Alignment explanation
Indices: 127860--127921 Score: 63
Period size: 19 Copynumber: 3.1 Consensus size: 19
127850 ATTTTAGAAA
127860 TTTTTTAAAATTTATAATT
1 TTTTTTAAAATTTATAATT
*
127879 TTTTTAAAAATTAAATATAATT
1 TTTTTTAAAATT---TATAATT
*
127901 TTTTATAAATATTT-TAATT
1 TTTTTTAAA-ATTTATAATT
127920 TT
1 TT
127922 AATTTTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 18 0.50
20 1 0.03
22 14 0.39
23 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTTTAAAATTTATAATT
Found at i:127892 original size:25 final size:24
Alignment explanation
Indices: 127867--127930 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 24
127857 AAATTTTTTA
127867 AAATTTATAATTTTTTTAAAAATT
1 AAATTTATAATTTTTTTAAAAATT
*
127891 AAA--TATAATTTTTTATAAATATTT
1 AAATTTATAATTTTTT-TAAA-AATT
*
127915 TAATTT-TAATTTTTTT
1 AAATTTATAATTTTTTT
127931 TTTTTTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
22 11 0.32
23 4 0.12
24 9 0.26
25 9 0.26
26 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
AAATTTATAATTTTTTTAAAAATT
Found at i:128670 original size:5 final size:5
Alignment explanation
Indices: 128650--128691 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
128640 AGTTTTAAGC
* *
128650 ATATT ATATA CATATA TTATA ATATA ATATA ATATA ATATA A
1 ATATA ATATA -ATATA ATATA ATATA ATATA ATATA ATATA A
128692 GCTGTCAGTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (5 bp):
ATATA
Found at i:132832 original size:21 final size:22
Alignment explanation
Indices: 132792--132833 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
132782 CTCAAACAAC
132792 AACAAAAAAAAACCCTCGAAAA
1 AACAAAAAAAAACCCTCGAAAA
*
132814 AACAATAAAAAACCC-CGAAA
1 AACAAAAAAAAACCCTCGAAA
132834 TTTAGAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.67, C:0.24, G:0.05, T:0.05
Consensus pattern (22 bp):
AACAAAAAAAAACCCTCGAAAA
Found at i:134308 original size:96 final size:96
Alignment explanation
Indices: 134144--134428 Score: 448
Period size: 96 Copynumber: 3.0 Consensus size: 96
134134 ATCTTCCACG
134144 AGCTTCCTTTCTTGCCTTTTA-ATACGTTAACAAGCCAAAGATTGTTAAATTCAATGATGATCCT
1 AGCTTCCTTTCTTGCCTTTTAGA-ACGTTAACAAGCCAAAGATTGTTAAATTCAATGATGATCCT
*
134208 CGACTAGTCATTCATTTTGACAAGTGAA-TTC
65 CGACTAGTCATTCCTTTTGACAAGTGAACTTC
* * *
134239 TAGCTTCCTTTCTTGCCTTTCAGAATGTTAACAAGCCAAAGATTGTTAAATTCAATGATAATCCT
1 -AGCTTCCTTTCTTGCCTTTTAGAACGTTAACAAGCCAAAGATTGTTAAATTCAATGATGATCCT
*
134304 CGACTAGTCATTCCTTTAGACAAGTGAACTTC
65 CGACTAGTCATTCCTTTTGACAAGTGAACTTC
* * * * *
134336 AACTTCCTTTCTTGCCTTTTAGTACGTTAACAAGTCAAAGGTTGTTAAATTCAATGATGATCCTG
1 AGCTTCCTTTCTTGCCTTTTAGAACGTTAACAAGCCAAAGATTGTTAAATTCAATGATGATCCTC
134401 GACTAGTCATTCCTTTTGACAAGTGAAC
66 GACTAGTCATTCCTTTTGACAAGTGAAC
134429 ACCTTAAATG
Statistics
Matches: 173, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
96 169 0.98
97 4 0.02
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.36
Consensus pattern (96 bp):
AGCTTCCTTTCTTGCCTTTTAGAACGTTAACAAGCCAAAGATTGTTAAATTCAATGATGATCCTC
GACTAGTCATTCCTTTTGACAAGTGAACTTC
Found at i:160767 original size:3 final size:3
Alignment explanation
Indices: 160759--160789 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
160749 TAAATATCTT
160759 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
160790 ATAATAAAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:162670 original size:32 final size:32
Alignment explanation
Indices: 162620--162682 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
162610 CTAGTGACTT
162620 AAATAAAAACTTTTGAATAGTTCAATGACTGA
1 AAATAAAAACTTTTGAATAGTTCAATGACTGA
*
162652 AAATGAAAA-TTTTCGAATAGTTCAATGACTG
1 AAATAAAAACTTTT-GAATAGTTCAATGACTG
162683 TTTTGTAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 4 0.14
32 25 0.86
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.32
Consensus pattern (32 bp):
AAATAAAAACTTTTGAATAGTTCAATGACTGA
Found at i:163630 original size:52 final size:53
Alignment explanation
Indices: 163567--163667 Score: 134
Period size: 52 Copynumber: 1.9 Consensus size: 53
163557 AGAGGTGATG
* * *
163567 AAATTGTAAATTAATCTTTGATAAAAGT-TATTT-AATCCCTTCAAAAATAATA
1 AAATTATAAATTAATATATGATAAAAGTATATTTGAATCCCTT-AAAAATAATA
* *
163619 AAATTATAAATTAATATATGATAAAATTATATTTGAATCTCTTAAAAAT
1 AAATTATAAATTAATATATGATAAAAGTATATTTGAATCCCTTAAAAAT
163668 TTTATAATTC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
52 24 0.57
53 11 0.26
54 7 0.17
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (53 bp):
AAATTATAAATTAATATATGATAAAAGTATATTTGAATCCCTTAAAAATAATA
Found at i:165209 original size:47 final size:47
Alignment explanation
Indices: 165155--165246 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
165145 TCCTTTTGCA
*
165155 TATTCCCAAGCATTCTTTTATTGCTTAGATGGTCATTCTCAATAGGC
1 TATTCCCAAGCATTCTTTTATTGCTTAGATGGTCATTCACAATAGGC
165202 TATTCCCAAGCATTCTTTTATTGCTTAGATGGTCATTCACAATAG
1 TATTCCCAAGCATTCTTTTATTGCTTAGATGGTCATTCACAATAG
165247 ACTTCCTATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.40
Consensus pattern (47 bp):
TATTCCCAAGCATTCTTTTATTGCTTAGATGGTCATTCACAATAGGC
Found at i:168056 original size:30 final size:31
Alignment explanation
Indices: 168020--168090 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
168010 CATTTAACAT
168020 AACAGTCACTCAAC-TT-T-AAAAATGTGACAA
1 AACAGTCACT-AACGTTATCAAAAA-GTGACAA
*
168050 AACAGTCACTAACGTTATCGAAAAGTGACAA
1 AACAGTCACTAACGTTATCAAAAAGTGACAA
*
168081 AACAATCACT
1 AACAGTCACT
168091 GATTAACAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.33
31 17 0.47
32 4 0.11
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.21
Consensus pattern (31 bp):
AACAGTCACTAACGTTATCAAAAAGTGACAA
Found at i:168169 original size:14 final size:14
Alignment explanation
Indices: 168131--168174 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
168121 GAATGATGAC
168131 GTTAACCAAAATAACT
1 GTTAACCAAAAT-A-T
* *
168147 CTAAACCAAAATAT
1 GTTAACCAAAATAT
168161 GTTAACCAAAATAT
1 GTTAACCAAAATAT
168175 ATGAATAACA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 13 0.54
15 1 0.04
16 10 0.42
ACGTcount: A:0.52, C:0.18, G:0.05, T:0.25
Consensus pattern (14 bp):
GTTAACCAAAATAT
Found at i:168254 original size:49 final size:47
Alignment explanation
Indices: 168201--168316 Score: 128
Period size: 47 Copynumber: 2.4 Consensus size: 47
168191 ACTAAAATTT
* **
168201 AAATAACCTTAAATCCCAAACAAGAGCAATCAGAATCC-AATCAAAATCG
1 AAATAACCCTAAAT--CAAA-AAGAAAAATCAGAATCCAAATCAAAATCG
* *
168250 AAATAACCCTAAATCAAAAATAAAAATCAGAATCCAAATCAAAATTG
1 AAATAACCCTAAATCAAAAAGAAAAATCAGAATCCAAATCAAAATCG
*
168297 -AATAAGTCCTAAATCAAAAA
1 AAATAA-CCCTAAATCAAAAA
168317 TCACAATCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
46 19 0.32
47 27 0.46
49 13 0.22
ACGTcount: A:0.56, C:0.20, G:0.06, T:0.18
Consensus pattern (47 bp):
AAATAACCCTAAATCAAAAAGAAAAATCAGAATCCAAATCAAAATCG
Found at i:168339 original size:47 final size:47
Alignment explanation
Indices: 168228--168317 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 47
168218 AAACAAGAGC
168228 AATCAGAATCC-AATCAAAATCGAAATAACCCTAAATCAAAAATAAA
1 AATCAGAATCCAAATCAAAATCGAAATAACCCTAAATCAAAAATAAA
* *
168274 AATCAGAATCCAAATCAAAATTG-AATAAGTCCTAAATCAAAAAT
1 AATCAGAATCCAAATCAAAATCGAAATAA-CCCTAAATCAAAAAT
168318 CACAATCAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
46 16 0.40
47 24 0.60
ACGTcount: A:0.57, C:0.18, G:0.06, T:0.20
Consensus pattern (47 bp):
AATCAGAATCCAAATCAAAATCGAAATAACCCTAAATCAAAAATAAA
Found at i:168348 original size:47 final size:46
Alignment explanation
Indices: 168228--168348 Score: 124
Period size: 47 Copynumber: 2.6 Consensus size: 46
168218 AAACAAGAGC
*
168228 AATCAGAATCC-AATCAAAATCGAAATAACCCTAAATCAAAAATAAA
1 AATCAGAATCCAAATCAAATTC-AAATAACCCTAAATCAAAAATAAA
* * * *
168274 AATCAGAATCCAAATCAAAATT-GAATAAGTCCTAAATCAAAAATCAC
1 AATCAGAATCCAAATC-AAATTCAAATAA-CCCTAAATCAAAAATAAA
168321 AATCA-ATAT-CAACATCAAATTCAAATAA
1 AATCAGA-ATCCAA-ATCAAATTCAAATAA
168349 ACACAAAATA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
46 25 0.40
47 34 0.54
48 4 0.06
ACGTcount: A:0.56, C:0.19, G:0.04, T:0.21
Consensus pattern (46 bp):
AATCAGAATCCAAATCAAATTCAAATAACCCTAAATCAAAAATAAA
Found at i:176546 original size:2 final size:2
Alignment explanation
Indices: 176539--176563 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
176529 TATCCAATAC
176539 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
176564 AGTGTTTCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:178138 original size:83 final size:80
Alignment explanation
Indices: 177973--178185 Score: 243
Period size: 83 Copynumber: 2.6 Consensus size: 80
177963 AAAATTGGAA
* * * * * *
177973 AATAATCTGTTTCGGGATTTATT-CCGCTGTTCAACAAATTTGATTCTATTTTAATTTATTTCAA
1 AATAATCTGTTTCAGGATTTATTCCCACCGTTTAACAGATTTTATTCTATTTTAATTTATTTCAA
178037 AACAAGAATTAAGTG
66 AACAAGAATTAAGTG
* *
178052 AATAATTCTGTTTC-GGATTTATTTCCCACCGTTTAACAGATTTTAATCTATTTTAATTTTTTTT
1 AATAA-TCTGTTTCAGGATTTA-TTCCCACCGTTTAACAGATTTTATTCTATTTTAA-TTTATTT
*
178116 CCAAACCAAGAA-TAAGTTG
63 -CAAAACAAGAATTAAG-TG
* * *
178135 AATAAATCTATTTCAGGATTTATTCCCACCGATTAACAGATTATATTCTAT
1 AAT-AATCTGTTTCAGGATTTATTCCCACCGTTTAACAGATTTTATTCTAT
178186 ATTTGGATTT
Statistics
Matches: 114, Mismatches: 12, Indels: 12
0.83 0.09 0.09
Matches are distributed among these distances:
79 12 0.11
80 10 0.09
81 25 0.22
82 10 0.09
83 48 0.42
84 9 0.08
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.42
Consensus pattern (80 bp):
AATAATCTGTTTCAGGATTTATTCCCACCGTTTAACAGATTTTATTCTATTTTAATTTATTTCAA
AACAAGAATTAAGTG
Found at i:179776 original size:19 final size:20
Alignment explanation
Indices: 179752--179789 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
179742 AAGGAAGTGT
179752 CTGATATAGAC-TTATGTGC
1 CTGATATAGACTTTATGTGC
*
179771 CTGATATAGGCTTTATGTG
1 CTGATATAGACTTTATGTG
179790 GGAAAGGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.39
Consensus pattern (20 bp):
CTGATATAGACTTTATGTGC
Found at i:180489 original size:29 final size:29
Alignment explanation
Indices: 180455--180544 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
180445 TAGAAAATCA
* * *
180455 TCCTACAATCACTTGGAAATATGGGTGTG
1 TCCTACAACCACTTGGAAATGTGGGGGTG
* * * *
180484 TCCTACAGCTACATAGAAATGTGGGGGTG
1 TCCTACAACCACTTGGAAATGTGGGGGTG
*
180513 TCCTACAACCACTTGAAAATGTGGGGGGTG
1 TCCTACAACCACTTGGAAATGT-GGGGGTG
180543 TC
1 TC
180545 TTGCTAACGT
Statistics
Matches: 48, Mismatches: 12, Indels: 1
0.79 0.20 0.02
Matches are distributed among these distances:
29 39 0.81
30 9 0.19
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.27
Consensus pattern (29 bp):
TCCTACAACCACTTGGAAATGTGGGGGTG
Found at i:181643 original size:13 final size:13
Alignment explanation
Indices: 181611--181644 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
181601 AGAAGTCAAT
*
181611 GTATGAAAATAAG
1 GTATGAGAATAAG
181624 GTATGAGAATAAG
1 GTATGAGAATAAG
181637 GTATGAGA
1 GTATGAGA
181645 TTCTCTACTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (13 bp):
GTATGAGAATAAG
Found at i:189806 original size:14 final size:15
Alignment explanation
Indices: 189771--189808 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
189761 GTCATTTATT
189771 ACAATAAATGGCATTA
1 ACAAT-AATGGCATTA
189787 ACAATAATGG-ATTA
1 ACAATAATGGCATTA
*
189801 ATAATAAT
1 ACAATAAT
189809 ATCTATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 11 0.52
15 5 0.24
16 5 0.24
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.29
Consensus pattern (15 bp):
ACAATAATGGCATTA
Found at i:189854 original size:19 final size:18
Alignment explanation
Indices: 189813--189857 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
189803 AATAATATCT
*
189813 ATAATAATATCAATGGTA
1 ATAATAATAACAATGGTA
* *
189831 TTAATAATAAACAGTGGTA
1 ATAATAAT-AACAATGGTA
189850 ATAATAAT
1 ATAATAAT
189858 GATATATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.51, C:0.04, G:0.11, T:0.33
Consensus pattern (18 bp):
ATAATAATAACAATGGTA
Found at i:190950 original size:29 final size:29
Alignment explanation
Indices: 190904--191242 Score: 261
Period size: 29 Copynumber: 11.6 Consensus size: 29
190894 TTCCTAAACT
190904 TTCCAAAAATTCCA-TTTTTACCCTCGAAC
1 TTCCAAAAA-TCCATTTTTTACCCTCGAAC
* *
190933 TTCTAAAAATCCATTTTTTACCC-CAAAAC
1 TTCCAAAAATCCATTTTTTACCCTC-GAAC
* * *
190962 TTCTAAAAATTC-TATTTTTA-CCTCAAAC
1 TTCCAAAAATCCAT-TTTTTACCCTCGAAC
* *
190990 TTCCAAAAATCCCATTTTTGACCC-CAAAAC
1 TTCCAAAAAT-CCATTTTTTACCCTC-GAAC
*
191020 TTCCAAAATTTCCA-TTTTTACCCTCGAAC
1 TTCCAAAA-ATCCATTTTTTACCCTCGAAC
* *
191049 TTCTAAAAATCCCATTTTTGA-CCTCGAAAC
1 TTCCAAAAAT-CCATTTTTTACCCTCG-AAC
*
191079 TTCCAAAAATTCCA-TTTTTACTCTCGAAC
1 TTCCAAAAA-TCCATTTTTTACCCTCGAAC
* *
191108 TTCCAAAAATCCCATTTTTGACCC-CAAAAC
1 TTCCAAAAAT-CCATTTTTTACCCTC-GAAC
*
191138 TTCCAAAAATTCCA--TTTTACCCCCGAAC
1 TTCCAAAAA-TCCATTTTTTACCCTCGAAC
* * *
191166 TTTCAAAAATGCCATTTTTGA-CCTCAAAAC
1 TTCCAAAAAT-CCATTTTTTACCCTC-GAAC
* * * *
191196 TGCTAAAAATTCATTTTTTGCCCTCGAAC
1 TTCCAAAAATCCATTTTTTACCCTCGAAC
*
191225 TTCCAAAATCTCCATTTT
1 TTCCAAAA-ATCCATTTT
191243 GGACTTCAAA
Statistics
Matches: 249, Mismatches: 35, Indels: 51
0.74 0.10 0.15
Matches are distributed among these distances:
27 1 0.00
28 44 0.18
29 112 0.45
30 89 0.36
31 3 0.01
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.35
Consensus pattern (29 bp):
TTCCAAAAATCCATTTTTTACCCTCGAAC
Found at i:191005 original size:58 final size:59
Alignment explanation
Indices: 190899--191265 Score: 476
Period size: 59 Copynumber: 6.3 Consensus size: 59
190889 TGGAGTTCCT
* *
190899 AAACTTTCCAAAAATTCCATTTTTACCCTCGAACTTCTAAAAAT-CCATTTTTTACCCCA
1 AAAC-TTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
190958 AAACTTCTAAAAATTCTATTTTTA-CCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * *
191016 AAACTTCCAAAATTTCCATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
*
191075 AAACTTCCAAAAATTCCATTTTTACTCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * *
191134 AAACTTCCAAAAATTCCA-TTTTACCCCCGAACTTTCAAAAATGCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * * * **
191192 AAACTGCTAAAAATT-CATTTTTTGCCCTCGAACTTCC-AAAATCTCCATTTTGGACTTCA
1 AAACTTCCAAAAATTCCA-TTTTTACCCTCGAACTTCCAAAAATC-CCATTTTTGACCCCA
191251 AAAC-TCTCAAAAATT
1 AAACTTC-CAAAAATT
191266 ACCCTCTTAC
Statistics
Matches: 270, Mismatches: 32, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
57 18 0.07
58 107 0.40
59 145 0.54
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (59 bp):
AAACTTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:191174 original size:117 final size:116
Alignment explanation
Indices: 190899--191302 Score: 507
Period size: 117 Copynumber: 3.4 Consensus size: 116
190889 TGGAGTTCCT
* * *
190899 AAACTTTCCAAAAATTCCATTTTTACCCTCGAACTTCTAAAAATCCATTTTTTACCCCAAAACTT
1 AAAC-TTCCAAAAATTCCATTTTTACCCCCGAACTTCTAAAAATCCATTTTTGACCTCAAAACTT
* *
190964 CTAAAAATTCTATTTTTACCTCAAACTTCCAAAAATCCCATTTTTGACCCCA
65 CTAAAAATTCCATTTTTACCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
* * *
191016 AAACTTCCAAAATTTCCATTTTTACCCTCGAACTTCTAAAAATCCCATTTTTGACCTCGAAACTT
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCTAAAAAT-CCATTTTTGACCTCAAAACTT
*
191081 CCAAAAATTCCATTTTTACTCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
65 CTAAAAATTCCATTTTTAC-CTCGAACTTCCAAAAATCCCATTTTTGACCCCA
191134 AAACTTCCAAAAATTCCA-TTTTACCCCCGAACTT-TCAAAAATGCCATTTTTGACCTCAAAACT
1 AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCT-AAAAAT-CCATTTTTGACCTCAAAACT
* * * **
191197 GCTAAAAATT-CATTTTTTGCCCTCGAACTTCC-AAAATCTCCATTTTGGACTTCA
64 TCTAAAAATTCCA-TTTTT-ACCTCGAACTTCCAAAAATC-CCATTTTTGACCCCA
* *
191251 AAAC-TCTCAAAAATTACC-CTCTTACCCCCGAA-TATCTAAAAATTCCATTTTT
1 AAACTTC-CAAAAATT-CCATTTTTACCCCCGAACT-TCTAAAAA-TCCATTTTT
191303 AAACCTTAAA
Statistics
Matches: 257, Mismatches: 18, Indels: 23
0.86 0.06 0.08
Matches are distributed among these distances:
116 49 0.19
117 128 0.50
118 78 0.30
119 2 0.01
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (116 bp):
AAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCTAAAAATCCATTTTTGACCTCAAAACTTC
TAAAAATTCCATTTTTACCTCGAACTTCCAAAAATCCCATTTTTGACCCCA
Found at i:191549 original size:14 final size:14
Alignment explanation
Indices: 191530--191559 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
191520 CACATGCTTG
191530 TTTTCAAAAAAAAT
1 TTTTCAAAAAAAAT
*
191544 TTTTCATAAAAAAT
1 TTTTCAAAAAAAAT
191558 TT
1 TT
191560 AAAATCAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTTCAAAAAAAAT
Found at i:192692 original size:20 final size:19
Alignment explanation
Indices: 192666--192713 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
192656 GTTGAAACTA
*
192666 TTGAAATGA-AATATATCTT
1 TTGAAATGATAATAAAT-TT
192685 TGTGAAAT-ATAATAAATTT
1 T-TGAAATGATAATAAATTT
192704 TTGAAATGAT
1 TTGAAATGAT
192714 TTCGATGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.24
19 7 0.28
20 12 0.48
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (19 bp):
TTGAAATGATAATAAATTT
Found at i:193183 original size:13 final size:13
Alignment explanation
Indices: 193165--193205 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
193155 GTTAACACTT
193165 TGAAATGTCTATA
1 TGAAATGTCTATA
193178 TGAAATGGT-TATA
1 TGAAAT-GTCTATA
*
193191 TGAAATGGCTATA
1 TGAAATGTCTATA
193204 TG
1 TG
193206 GATTGGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.88
14 2 0.08
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (13 bp):
TGAAATGTCTATA
Found at i:193195 original size:26 final size:26
Alignment explanation
Indices: 193165--193242 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 26
193155 GTTAACACTT
193165 TGAAATGTCTATATGAAATGGTTATA
1 TGAAATGTCTATATGAAATGGTTATA
* * *
193191 TGAAATGGCTATATGGATTGGTTATA
1 TGAAATGTCTATATGAAATGGTTATA
* *
193217 TGGAAATAATC-ATATGAAATGTTTAT
1 T-GAAAT-GTCTATATGAAATGGTTAT
193243 GTGGATAGAT
Statistics
Matches: 42, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
26 24 0.57
27 17 0.40
28 1 0.02
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (26 bp):
TGAAATGTCTATATGAAATGGTTATA
Found at i:193216 original size:13 final size:13
Alignment explanation
Indices: 193174--193221 Score: 60
Period size: 13 Copynumber: 3.7 Consensus size: 13
193164 TTGAAATGTC
*
193174 TATATGAAATGGT
1 TATATGGAATGGT
* *
193187 TATATGAAATGGC
1 TATATGGAATGGT
*
193200 TATATGGATTGGT
1 TATATGGAATGGT
193213 TATATGGAA
1 TATATGGAA
193222 ATAATCATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.35, C:0.02, G:0.25, T:0.38
Consensus pattern (13 bp):
TATATGGAATGGT
Found at i:195800 original size:100 final size:100
Alignment explanation
Indices: 195624--195822 Score: 371
Period size: 100 Copynumber: 2.0 Consensus size: 100
195614 ACTACTCAGT
*
195624 GCTCATGATAATAGCCAAGGTGATAACGATGATGTTGAAGATCTTCAGGTATATTTCACTATGAT
1 GCTCATGATAATAGCCAAGGTGATAACGATGATGTTAAAGATCTTCAGGTATATTTCACTATGAT
195689 TTATTTATTATATCATGTTTATTAGAATTTGGGAA
66 TTATTTATTATATCATGTTTATTAGAATTTGGGAA
195724 GCTCATGATAATAGCCAAGGTGATAACGATGATGTTAAAGATCTTCAGGTATATTTCACTATGAT
1 GCTCATGATAATAGCCAAGGTGATAACGATGATGTTAAAGATCTTCAGGTATATTTCACTATGAT
* *
195789 TTATTTGTTATATCATGTTTATTATAATTTGGGA
66 TTATTTATTATATCATGTTTATTAGAATTTGGGA
195823 CTAATCATGG
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.40
Consensus pattern (100 bp):
GCTCATGATAATAGCCAAGGTGATAACGATGATGTTAAAGATCTTCAGGTATATTTCACTATGAT
TTATTTATTATATCATGTTTATTAGAATTTGGGAA
Done.