Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012574.1 Kokia drynarioides strain JFW-HI SEQ_127583, 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: 120554
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Warning! 125 characters in sequence are not A, C, G, or T
Found at i:1830 original size:19 final size:21
Alignment explanation
Indices: 1788--1832 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
1778 GAAAACATAG
*
1788 ACATA-TATATAGCAATATCA
1 ACATATTATATAGCAATAGCA
1808 ACATATTAT-TAGCAA-AGCA
1 ACATATTATATAGCAATAGCA
1827 ACATAT
1 ACATAT
1833 AAAAAACAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 11 0.48
21 3 0.13
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.29
Consensus pattern (21 bp):
ACATATTATATAGCAATAGCA
Found at i:2667 original size:22 final size:21
Alignment explanation
Indices: 2617--2697 Score: 60
Period size: 22 Copynumber: 3.7 Consensus size: 21
2607 ATTATAATGG
*
2617 TAAAATAA-TAAAAATACATGAA
1 TAAAATAATTAAATA-ACAT-AA
*
2639 TATAAATAATTAAATGAAGATAA
1 TA-AAATAATTAAAT-AACATAA
*
2662 TCAAATGCAATT-AATAACATAA
1 TAAAAT--AATTAAATAACATAA
2684 TAAAATAA-TAAATA
1 TAAAATAATTAAATA
2698 GGAGTAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
19 1 0.02
20 6 0.12
22 17 0.35
23 12 0.25
24 11 0.23
25 1 0.02
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
TAAAATAATTAAATAACATAA
Found at i:3114 original size:16 final size:15
Alignment explanation
Indices: 3077--3115 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3067 AAATGACATG
*
3077 AAAATAAATAACAAC
1 AAAATAAATAACAAA
*
3092 AAGATAAATAAACAAA
1 AAAATAAAT-AACAAA
3108 AAAATAAA
1 AAAATAAA
3116 AATAAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.77, C:0.08, G:0.03, T:0.13
Consensus pattern (15 bp):
AAAATAAATAACAAA
Found at i:3217 original size:20 final size:21
Alignment explanation
Indices: 3192--3250 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 21
3182 AAAATAAATG
3192 AAAAATAAATAAATAAA-CAA
1 AAAAATAAATAAATAAACCAA
*
3212 AAAAATCAATAAATTAAATCCAA
1 AAAAATAAATAAA-TAAA-CCAA
*
3235 AATAAATAATTAAATA
1 AA-AAATAAATAAATA
3251 TAAATAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 12 0.38
21 4 0.12
23 7 0.22
24 9 0.28
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAATAAATAAATAAACCAA
Found at i:3257 original size:4 final size:4
Alignment explanation
Indices: 3183--3250 Score: 50
Period size: 4 Copynumber: 17.2 Consensus size: 4
3173 TTAGGCATGA
* * * *
3183 AAAT AAAT GAA- AAAT AAAT AAAT AAAC AAAA AAAT CAAT AAATT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAAT
** *
3231 CCA- AAAT AAAT AATT AAAT A
1 AAAT AAAT AAAT AAAT AAAT A
3251 TAAATAATAA
Statistics
Matches: 48, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
3 3 0.06
4 41 0.85
5 4 0.08
ACGTcount: A:0.71, C:0.06, G:0.01, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5254 original size:63 final size:63
Alignment explanation
Indices: 5129--5255 Score: 182
Period size: 63 Copynumber: 2.0 Consensus size: 63
5119 ACCCACTTGA
** * *
5129 CATATTTTGATTTTTGGCTACTATTTTCAGGATCGCGATACCAAGCCTTGGACGTCGCGATAC
1 CATATTTTGATGCTTGGCTACTATCTTCAGGATCGCGATACCAAGCCTTGGACATCGCGATAC
* * * *
5192 CATATTTTGATGCTTGGCTACTGTCTTCGGGATCGCGATACCAAGCCTTGGATATCGTGATAC
1 CATATTTTGATGCTTGGCTACTATCTTCAGGATCGCGATACCAAGCCTTGGACATCGCGATAC
5255 C
1 C
5256 CTCTTCTTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.21, C:0.23, G:0.22, T:0.34
Consensus pattern (63 bp):
CATATTTTGATGCTTGGCTACTATCTTCAGGATCGCGATACCAAGCCTTGGACATCGCGATAC
Found at i:6583 original size:30 final size:31
Alignment explanation
Indices: 6548--6623 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 31
6538 TTTTTTTATT
*
6548 TAATTTGGTACTTAAACTTGAC-ATTTTTCC
1 TAATTTGGTACCTAAACTTGACTATTTTTCC
*
6578 TAATTTGGTACCTAAACTTGACTTTTTTTCC
1 TAATTTGGTACCTAAACTTGACTATTTTTCC
*
6609 TAATTTAGTACCTAA
1 TAATTTGGTACCTAA
6624 TCTTTTTTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 21 0.50
31 21 0.50
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (31 bp):
TAATTTGGTACCTAAACTTGACTATTTTTCC
Found at i:6942 original size:60 final size:59
Alignment explanation
Indices: 6775--6962 Score: 159
Period size: 57 Copynumber: 3.1 Consensus size: 59
6765 ATAAATTTCG
* * * *
6775 GTATCAAATTGAATCTAAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAAATGTTAAGTTCAA
1 GTATCAAA-TGAAT-TAAAAAAAGTTTAGGTA-CAAAATAAG-AAAAAAAATGTCAAGTTCAA
* * ** ** * * *
6838 GTACCGAATTGGGTCCAAAAAAGTATAGGTACCAAATTAGAAAAAAAATGTCAAGTTCAA
1 GTATC-AAATGAATTAAAAAAAGTTTAGGTACAAAATAAGAAAAAAAATGTCAAGTTCAA
*
6898 GTATCAAAT-AATTAAAAAAAGTTTAGGTGCTAAAATAAG--AAAAAATGTCAAGTTCATA
1 GTATCAAATGAATTAAAAAAAGTTTAGGTAC-AAAATAAGAAAAAAAATGTCAAGTTCA-A
6956 -TATCAAA
1 GTATCAAA
6963 AGTTATATAT
Statistics
Matches: 99, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
57 24 0.24
58 16 0.16
59 9 0.09
60 23 0.23
61 5 0.05
62 13 0.13
63 7 0.07
64 2 0.02
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (59 bp):
GTATCAAATGAATTAAAAAAAGTTTAGGTACAAAATAAGAAAAAAAATGTCAAGTTCAA
Found at i:7280 original size:22 final size:24
Alignment explanation
Indices: 7240--7283 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
7230 TGATAATATG
7240 TTTTGATATAACAAATTAAAGTAT
1 TTTTGATATAACAAATTAAAGTAT
7264 TTTTGA-ATAA-AAATTAAAGT
1 TTTTGATATAACAAATTAAAGT
7284 TAAATAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 10 0.50
23 4 0.20
24 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (24 bp):
TTTTGATATAACAAATTAAAGTAT
Found at i:9211 original size:30 final size:29
Alignment explanation
Indices: 9138--9437 Score: 208
Period size: 30 Copynumber: 10.1 Consensus size: 29
9128 TTTTATCTAG
* * * *
9138 AAATTTTGTTTTGACCCTTAAGTTGTCCAA
1 AAATTTAGATTTGACCCTAAACTT-TCCAA
** * *
9168 AAATCAAGTTTTGACTCCTAAATTTTCCAA
1 AAATTTAGATTTGAC-CCTAAACTTTCCAA
* *
9198 AAATTTAGATTTGACCGTCAAACTTCCCAA
1 AAATTTAGATTTGACCCT-AAACTTTCCAA
* ** *
9228 AAATTCATTTTTAACCCTTAAACTTTCCAA
1 AAATTTAGATTTGACCC-TAAACTTTCCAA
* * *
9258 AAA-TTAAATTTAGACCCCTATACTTTCCAT
1 AAATTTAGATTT-GA-CCCTAAACTTTCCAA
* *
9288 AAATTCATATTTGACCCTCAAACTTTCCAA
1 AAATTTAGATTTGACCCT-AAACTTTCCAA
* * ** *
9318 AAAATTAGATTTGACCATGTACTTCCCAA
1 AAATTTAGATTTGACCCTAAACTTTCCAA
* * * *
9347 AAATTCAAATTTAACCCCTAAATTTTCCAA
1 AAATTTAGATTTGA-CCCTAAACTTTCCAA
*
9377 AAATTTGGATTTGACCCCTAAACTTTCCAA
1 AAATTTAGATTTGA-CCCTAAACTTTCCAA
* * *
9407 AAA-TTATGTTTTGGCCCTAAACTTTCTAA
1 AAATTTA-GATTTGACCCTAAACTTTCCAA
9436 AA
1 AA
9438 TTTCATTTTT
Statistics
Matches: 209, Mismatches: 52, Indels: 19
0.75 0.19 0.07
Matches are distributed among these distances:
29 47 0.22
30 145 0.69
31 17 0.08
ACGTcount: A:0.36, C:0.22, G:0.07, T:0.36
Consensus pattern (29 bp):
AAATTTAGATTTGACCCTAAACTTTCCAA
Found at i:9374 original size:59 final size:59
Alignment explanation
Indices: 9184--9437 Score: 226
Period size: 59 Copynumber: 4.3 Consensus size: 59
9174 AGTTTTGACT
* * * * *
9184 CCTAAATTTTCCAAAAATTTAGATTTGACCGTCAAACTTCCCAAAAATTCATTTTTAACC
1 CCTAAACTTTCCAAAAAATTAGATTTGACCAT-ATACTTCCCAAAAATTCATATTTAACC
* * * * * *
9244 CTTAAACTTTCC-AAAAATTAAATTTAGACCCCTATACTTTCCATAAATTCATATTTGA-C
1 CCTAAACTTTCCAAAAAATTAGATTT-GA-CCATATACTTCCCAAAAATTCATATTTAACC
* *
9303 CCTCAAACTTTCCAAAAAATTAGATTTGACCATGTACTTCCCAAAAATTCAAATTTAACC
1 CCT-AAACTTTCCAAAAAATTAGATTTGACCATATACTTCCCAAAAATTCATATTTAACC
* * * * * * * ***
9363 CCTAAATTTTCCAAAAATTTGGATTTGACCCCTAAACTTTCCAAAAATT-ATGTTTTGGC
1 CCTAAACTTTCCAAAAAATTAGATTTGA-CCATATACTTCCCAAAAATTCATATTTAACC
*
9422 CCTAAACTTTCTAAAA
1 CCTAAACTTTCCAAAA
9438 TTTCATTTTT
Statistics
Matches: 156, Mismatches: 32, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
59 78 0.50
60 63 0.40
61 15 0.10
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.35
Consensus pattern (59 bp):
CCTAAACTTTCCAAAAAATTAGATTTGACCATATACTTCCCAAAAATTCATATTTAACC
Found at i:9393 original size:119 final size:119
Alignment explanation
Indices: 9163--9437 Score: 322
Period size: 119 Copynumber: 2.3 Consensus size: 119
9153 CCTTAAGTTG
* * * * * *
9163 TCCAAAAATCAAGTTTTGACTCCTAAATTTTCCAAAAATTTAGATTTGACCGTCAAACTTCCCAA
1 TCCAAAAATTATGATTTGAC-CCTAAACTTTCCAAAAAATTAGATTTGACCATCAAACTTCCCAA
** * *
9228 AAATTCATTTTTAACCCTTAAACTTTCCAAAAATTAAATTTAGACCCCTATACTT
65 AAATTCAAATTTAACCCCTAAACTTTCCAAAAATTAAATTTAGACCCCTAAACTT
* **
9283 TCCATAAATTCAT-ATTTGACCCTCAAACTTTCCAAAAAATTAGATTTGACCAT-GTACTTCCCA
1 TCCAAAAATT-ATGATTTGACCCT-AAACTTTCCAAAAAATTAGATTTGACCATCAAACTTCCCA
* **
9346 AAAATTCAAATTTAACCCCTAAATTTTCCAAAAATTTGGATTT-GACCCCTAAACTT
64 AAAATTCAAATTTAACCCCTAAACTTTCCAAAAA-TTAAATTTAGACCCCTAAACTT
* * *
9402 TCCAAAAATTATGTTTTGGCCCTAAACTTTCTAAAA
1 TCCAAAAATTATGATTTGACCCTAAACTTTCCAAAA
9438 TTTCATTTTT
Statistics
Matches: 131, Mismatches: 20, Indels: 10
0.81 0.12 0.06
Matches are distributed among these distances:
118 14 0.11
119 70 0.53
120 46 0.35
121 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.06, T:0.35
Consensus pattern (119 bp):
TCCAAAAATTATGATTTGACCCTAAACTTTCCAAAAAATTAGATTTGACCATCAAACTTCCCAAA
AATTCAAATTTAACCCCTAAACTTTCCAAAAATTAAATTTAGACCCCTAAACTT
Found at i:9449 original size:89 final size:89
Alignment explanation
Indices: 9138--9451 Score: 305
Period size: 89 Copynumber: 3.5 Consensus size: 89
9128 TTTTATCTAG
* * * * * *
9138 AAATTTTGTTTTGACCCTTAAGTTGTCCAAAAA-TCAAGTTTTGACTCCTAAATTTTCCAAAAAT
1 AAATTATGTTTTGACCCTAAACTT-TCCAAAAATTCAA-ATTTAACCCCTAAATTTTCCAAAAAT
* *
9202 TTAGATTTGACCGTCAAACTTCCCAA
64 TTAGATTTGACCCTCAAACTTTCCAA
* * * *
9228 AAATTCAT-TTTTAACCCTTAAACTTTCCAAAAATT-AAATTTAGACCCCTATACTTTCCATAAA
1 AAATT-ATGTTTTGACCC-TAAACTTTCCAAAAATTCAAATTTA-ACCCCTAAATTTTCCAAAAA
* *
9291 TTCATATTTGACCCTCAAACTTTCCAAA
63 TTTAGATTTGACCCTCAAACTTTCC-AA
* * ** *
9319 AAATTA-GATTTGACCATGTACTTCCCAAAAATTCAAATTTAACCCCTAAATTTTCCAAAAATTT
1 AAATTATGTTTTGACCCTAAACTTTCCAAAAATTCAAATTTAACCCCTAAATTTTCCAAAAATTT
*
9383 GGATTTGACCC-CTAAACTTTCCAA
66 AGATTTGACCCTC-AAACTTTCCAA
* * * **
9407 AAATTATGTTTTGGCCCTAAACTTTCTAAAATTTCATTTTTAACC
1 AAATTATGTTTTGACCCTAAACTTTCCAAAAATTCAAATTTAACC
9452 TAGTTTTTCC
Statistics
Matches: 179, Mismatches: 36, Indels: 19
0.76 0.15 0.08
Matches are distributed among these distances:
88 9 0.05
89 82 0.46
90 74 0.41
91 14 0.08
ACGTcount: A:0.35, C:0.22, G:0.06, T:0.37
Consensus pattern (89 bp):
AAATTATGTTTTGACCCTAAACTTTCCAAAAATTCAAATTTAACCCCTAAATTTTCCAAAAATTT
AGATTTGACCCTCAAACTTTCCAA
Found at i:9600 original size:6 final size:6
Alignment explanation
Indices: 9589--9617 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
9579 GCGTATTTTG
9589 TTTATT TTTATT TTTATT TTTATT TTTAT
1 TTTATT TTTATT TTTATT TTTATT TTTAT
9618 ATAGTTGTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTATT
Found at i:10855 original size:21 final size:21
Alignment explanation
Indices: 10829--10870 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
10819 ATCTGTACCT
10829 ATGTTTTCGTGAAGTTTTCAC
1 ATGTTTTCGTGAAGTTTTCAC
10850 ATGTTTTCGTGAAGTTTTCAC
1 ATGTTTTCGTGAAGTTTTCAC
10871 TTCCGTGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.14, G:0.19, T:0.48
Consensus pattern (21 bp):
ATGTTTTCGTGAAGTTTTCAC
Found at i:14024 original size:59 final size:58
Alignment explanation
Indices: 13896--14031 Score: 139
Period size: 58 Copynumber: 2.3 Consensus size: 58
13886 TCTCGGGTGC
* * * ** *
13896 AAAATGGTAATTTTGGGAAAATTCGCGATTTAAAATGAAATTTTAGACATCCGAGAGT
1 AAAATGGTAATTTTGAGAAAAATCGAGATAAAAAACGAAATTTTAGACATCCGAGAGT
* * * * *
13954 AAAACGATAATTGTT-AGAAAAATCGAGATAAAAAACGAAATTTATTGACATTCGAGGGT
1 AAAATGGTAATT-TTGAGAAAAATCGAGATAAAAAACGAAATTT-TAGACATCCGAGAGT
14013 AAAATGGTAATTTTTGAGA
1 AAAATGGTAA-TTTTGAGA
14032 GTTTCGGGGT
Statistics
Matches: 61, Mismatches: 13, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
58 32 0.52
59 24 0.39
60 5 0.08
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.29
Consensus pattern (58 bp):
AAAATGGTAATTTTGAGAAAAATCGAGATAAAAAACGAAATTTTAGACATCCGAGAGT
Found at i:14041 original size:29 final size:29
Alignment explanation
Indices: 14004--14235 Score: 145
Period size: 30 Copynumber: 7.8 Consensus size: 29
13994 TTTATTGACA
14004 TTCGAGGGT-AAAATGGTAATTTTTGAGAGT
1 TTCG-GGGTAAAAAT-GTAATTTTTGAGAGT
* * *
14034 TTCGGGGTCAAAAATGCAGTTTTTGA-ACAT
1 TTCGGGGT-AAAAATGTAATTTTTGAGA-GT
* * * *
14064 TT-GAGGGTTAAAATGCATTTTTTGAAAGT
1 TTCG-GGGTAAAAATGTAATTTTTGAGAGT
* *
14093 TTTGGGGTTAAAAATGGAATTTTT-AGAGGT
1 TTCGGGG-TAAAAATGTAATTTTTGAGA-GT
*
14123 TTGGGGGTAAAAATGTAATTTTT-AGAAGT
1 TTCGGGGTAAAAATGTAATTTTTGAG-AGT
** *
14152 TTCAAGGTCAAAAATGGAATTTTTTGA-AGT
1 TTCGGGGT-AAAAATGTAA-TTTTTGAGAGT
* *
14182 TTAGGGGTAAAAATGTAATTTTT-ACATGT
1 TTCGGGGTAAAAATGTAATTTTTGAGA-GT
* * *
14211 TTCGAGATCAAAAATGAAATTTTTG
1 TTCGGGGT-AAAAATGTAATTTTTG
14236 GATAGTTTGG
Statistics
Matches: 162, Mismatches: 24, Indels: 31
0.75 0.11 0.14
Matches are distributed among these distances:
27 1 0.01
28 6 0.04
29 69 0.43
30 75 0.46
31 10 0.06
32 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (29 bp):
TTCGGGGTAAAAATGTAATTTTTGAGAGT
Found at i:14047 original size:59 final size:59
Alignment explanation
Indices: 13984--14235 Score: 138
Period size: 59 Copynumber: 4.3 Consensus size: 59
13974 AATCGAGATA
* *
13984 AAAAACGAAATTTATTG-ACATTCGAGGG-TAAAATGGTAATTTTTGAGAGTTTCGGGGTC
1 AAAAACGAAATTT-TTGAACATTCGAGGGTTAAAAT-GCAATTTTTGAAAGTTTCGGGGTC
* * * * * * *
14043 AAAAATGCAGTTTTTGAACATTTGAGGGTTAAAATGCATTTTTTGAAAGTTTTGGGGTT
1 AAAAACGAAATTTTTGAACATTCGAGGGTTAAAATGCAATTTTTGAAAGTTTCGGGGTC
* * ** * * * * **
14102 AAAAATGGAATTTTT-AGAGGTTTGGGGGTAAAAATGTAATTTTT-AGAAGTTTCAAGGTC
1 AAAAACGAAATTTTTGA-ACATTCGAGGGTTAAAATGCAATTTTTGA-AAGTTTCGGGGTC
* * ** * * * * * *
14161 AAAAATGGAATTTTTTGAAGTTTAG-GGGTAAAAATGTAATTTTT-ACATGTTTCGAGATC
1 AAAAA-CGAAATTTTTGAACATTCGAGGGTTAAAATGCAATTTTTGA-AAGTTTCGGGGTC
*
14220 AAAAATGAAATTTTTG
1 AAAAACGAAATTTTTG
14236 GATAGTTTGG
Statistics
Matches: 155, Mismatches: 32, Indels: 13
0.77 0.16 0.06
Matches are distributed among these distances:
58 14 0.09
59 122 0.79
60 18 0.12
61 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.37
Consensus pattern (59 bp):
AAAAACGAAATTTTTGAACATTCGAGGGTTAAAATGCAATTTTTGAAAGTTTCGGGGTC
Found at i:15353 original size:3 final size:3
Alignment explanation
Indices: 15345--15413 Score: 66
Period size: 3 Copynumber: 22.0 Consensus size: 3
15335 TCCTTTTTTG
* * * *
15345 TTA TTA TTA TTA TTA TTA CTA TTA TTAA TTA ATA TCA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
*
15391 TCCTA TTA TTA ATA TTA TTA TTA
1 T--TA TTA TTA TTA TTA TTA TTA
15414 AGACTATTTA
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
3 47 0.89
4 3 0.06
5 3 0.06
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:16107 original size:6 final size:6
Alignment explanation
Indices: 16096--16166 Score: 76
Period size: 6 Copynumber: 12.3 Consensus size: 6
16086 AAATTTGAAC
* * * *
16096 TAAATT TAAATT TAAA-A CAAATT TAAATT TAAA-A TGAATT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
16142 TAAATT TAAA-G TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
16167 GAAATAAATC
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
5 10 0.19
6 42 0.81
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (6 bp):
TAAATT
Found at i:16122 original size:23 final size:23
Alignment explanation
Indices: 16096--16151 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
16086 AAATTTGAAC
* *
16096 TAAATTTAAATTTAAAACAAATT
1 TAAATTTAAAATGAAAACAAATT
***
16119 TAAATTTAAAATGAATTTAAATT
1 TAAATTTAAAATGAAAACAAATT
16142 TAAATTTAAA
1 TAAATTTAAA
16152 GTAAATTTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
TAAATTTAAAATGAAAACAAATT
Found at i:16135 original size:11 final size:11
Alignment explanation
Indices: 16119--16162 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
16109 AAAACAAATT
16119 TAAATTTAAAA
1 TAAATTTAAAA
* *
16130 TGAATTTAAATT
1 TAAATTTAAA-A
*
16142 TAAATTTAAAG
1 TAAATTTAAAA
16153 TAAATTTAAA
1 TAAATTTAAA
16163 TTTAGAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:16158 original size:23 final size:23
Alignment explanation
Indices: 16114--16166 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
16104 AATTTAAAAC
*
16114 AAATTTAAATTTAAAATGAATTT
1 AAATTTAAATTTAAAATAAATTT
*
16137 AAATTTAAATTTAAAGTAAATTT
1 AAATTTAAATTTAAAATAAATTT
16160 AAATTTA
1 AAATTTA
16167 GAAATAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
AAATTTAAATTTAAAATAAATTT
Found at i:16180 original size:18 final size:17
Alignment explanation
Indices: 16066--16145 Score: 90
Period size: 17 Copynumber: 4.7 Consensus size: 17
16056 ATTTTAAAGT
* *
16066 TTTAACTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
* *
16082 TTTCAAATTTGAACTAAA
1 TTT-AAATTTAAAATAAA
*
16100 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAATAAA
*
16117 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATAAA
16134 TTTAAATTTAAA
1 TTTAAATTTAAA
16146 TTTAAAGTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
16 3 0.06
17 46 0.87
18 4 0.08
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:17033 original size:201 final size:200
Alignment explanation
Indices: 16551--17584 Score: 1304
Period size: 201 Copynumber: 5.1 Consensus size: 200
16541 TGACTTGGCC
** * *** ** * * *
16551 TTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTGTTTTGATCCACTTCTCTGTGTTTC
1 TTCTTCTTTGTATCTCATCAGGAAGATGACTGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
* * * * * * *
16616 ATTAGGAAGATGAATTTGGTTCACTTCTTAGTATTTCAACAGGAAGCTAACCA-TTTATTGCTTC
66 ATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * * *
16680 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACACCAAGCGTGGGT
131 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTGAG-
* *
16745 TTGATT
195 TTGGTA
* * * ** *
16751 TGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGTATTGCTTGTTTCAATCTGCTTCTCTGT
1 T--TCTTCTT-T--GTATCTCATCAGGAAGATGACTGCATCACTTGTTTCAATCCGCTTCTCTGT
*
16816 ATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATT
61 ATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATT
* * *
16881 GCTTCGACATGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTTACATCGAGCC
126 GCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAG-C
16946 CTGAGTTGGTA
190 CTGAGTTGGTA
* *
16957 TTCTTCTTTGTATCTCATTAGGAAGATGA-TCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCT
1 TTCTTCTTTGTATCTCATCAGGAAGATGACT-GCATCACTTGTTTCAATCCGCTTCTCTGTATCT
* *
17021 CATCAAGAAGACGAATTTGGTCAACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTT
65 CATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTT
* * * * *
17086 CG-CCTTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTGCTCGCATTGAGCGTGG
130 CGACC-TGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTGA
* *
17150 GTTCGATT
194 GTT-GGTA
* * *
17158 TGGTCTTCTTCTCAGTATCTCATCAGAAAGGTGACTGCATCGCTTGTTTCAATCCGCTTCTCTGT
1 T--TCTTCTT-T--GTATCTCATCAGGAAGATGACTGCATCACTTGTTTCAATCCGCTTCTCTGT
* *
17223 ATCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAACTAACCATTTTATT
61 ATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATT
* *
17288 GCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCC
126 GCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCC
*
17353 TCAAGTTGGTA
191 T-GAGTTGGTA
* * * *
17364 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTTACTTGTTTCAATCCGCTTCTCTGTACCTC
1 TTCTTCTTTGTATCTCATCAGGAAGATGACTGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
17429 ATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTC
66 ATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
* * * * *
17493 GCCCTGCTTCTTAGTATCTCATCAGGAAGTTGGGATTCGAAGATTTGCTCACATCAAGCCTTGAG
131 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCC-TGAG
17558 TTGGTA
195 TTGGTA
*
17564 TACTTCTCTT-TATCTCATCAG
1 TTCTTCT-TTGTATCTCATCAG
17585 TAAGCTAACC
Statistics
Matches: 731, Mismatches: 83, Indels: 40
0.86 0.10 0.05
Matches are distributed among these distances:
200 98 0.13
201 264 0.36
202 6 0.01
203 9 0.01
204 14 0.02
205 92 0.13
206 238 0.33
207 10 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (200 bp):
TTCTTCTTTGTATCTCATCAGGAAGATGACTGCATCACTTGTTTCAATCCGCTTCTCTGTATCTC
ATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTC
GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAGCCTGAGT
TGGTA
Found at i:17305 original size:407 final size:403
Alignment explanation
Indices: 16551--17551 Score: 1466
Period size: 407 Copynumber: 2.5 Consensus size: 403
16541 TGACTTGGCC
* * **** ** * * *
16551 TTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTGTTTTGATCCACTTCTCTGTGTTTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTC
* * * * * * *
16616 ATTAGGAAGATGAATTTGGTTCACTTCTTAGTATTTCAACAGGAAGCTAACCATTTATTGCTTCG
66 ATCAAGAAGACGAATTTGG-TCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
16681 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACACCAAGCGTGGGTT
130 -CCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGCTCACACCAAGCGTGGGTT
* * * * *
16746 TGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGTATTGCTTGTTTCAATCTGCTTC
193 CGATTTGGTCTTCTTCTCAATATCTCATCAGAAAGATGACCGCATCGCTTGTTTCAATCCGCTTC
* *
16811 TCTGTATCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATT
258 TCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCATT
* *
16876 TTATTGCTTCGACATGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGCTTACATC
323 TTATTGCTTCGACATGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATC
*
16941 GAGCC-CTGAGTTGGTA
388 GAGCCTC-AAGTTGGTA
* *
16957 TTCTTCTTTGTATCTCATTAGGAAGATGA-TCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACT-GCCTCACTTGTTTCAATCCGCTTCTCTGTATCT
17021 CATCAAGAAGACGAATTTGGTCAACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTT
65 CATCAAGAAGACGAATTTGGTC-ACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTT
* ***
17086 CGCCTTGCTTCTCAGTATCTCATCAGGAAGCTGGAGTTCGAAGATTTGCTCGCATTGAGCGTGGG
128 CGCC-TGCTTCTCAGTATCTCATCAGGAAGCTGG-GTTCGAAGATTTGCTCACACCAAGCGTGGG
* * *
17151 TTCGATTTGGTCTTCTTCTCAGTATCTCATCAGAAAGGTGACTGCATCGCTTGTTTCAATCCGCT
191 TTCGATTTGGTCTTCTTCTCAATATCTCATCAGAAAGATGACCGCATCGCTTGTTTCAATCCGCT
*
17216 TCTCTGTATCTCATCAAGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAACTAACCA
256 TCTCTGTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCA
* *
17281 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCA
321 TTTTATTGCTTCGACATGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
*
17346 TTGAGCCTCAAGTTGGTA
386 TCGAGCCTCAAGTTGGTA
* *
17364 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTTACTTGTTTCAATCCGCTTCTCTGTACCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTC
17429 ATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
66 ATCAAGAAGACGAATTTGGT-CACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
* * *
17494 CCCTGCTTCTTAGTATCTCATCAGGAAGTTGGGATTCGAAGATTTGCTCACATCAAGC
130 -CCTGCTTCTCAGTATCTCATCAGGAAGCTGGG-TTCGAAGATTTGCTCACACCAAGC
17552 CTTGAGTTGG
Statistics
Matches: 535, Mismatches: 50, Indels: 20
0.88 0.08 0.03
Matches are distributed among these distances:
405 3 0.01
406 159 0.30
407 370 0.69
408 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (403 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTC
ATCAAGAAGACGAATTTGGTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGC
CTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCACACCAAGCGTGGGTTCGA
TTTGGTCTTCTTCTCAATATCTCATCAGAAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCT
GTATCTCATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAACTAACCATTTTA
TTGCTTCGACATGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGAG
CCTCAAGTTGGTA
Found at i:17668 original size:115 final size:114
Alignment explanation
Indices: 17451--17657 Score: 308
Period size: 115 Copynumber: 1.8 Consensus size: 114
17441 AATTTGGTCC
* *
17451 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTTAGTATCTCATC
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTTAGTATCTCATC
* *
17516 AGGAAGTTGGGATTCGAAGATTTGCTCACATCAAGCCTTGAGTTGGTAT
66 AAGAAGCTGGGATTCGAAGATTTGCTCACATCAAGCCTTGAGTTGGTAT
** * * *
17565 ACTTCTCTTTATCTCATCAGTAAGCTAACCATTTTATTACTTCGACCTTCTTCTTAGTATCTCGT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTACTTCGACCTGCTTCTTAGTATCTCAT
17630 CAAGAAGCTGTGG-TTCGAAGATTTGCTC
65 CAAGAAGCTG-GGATTCGAAGATTTGCTC
17658 GCTTTGAGCC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
114 27 0.33
115 53 0.65
116 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.17, T:0.37
Consensus pattern (114 bp):
ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTTAGTATCTCATC
AAGAAGCTGGGATTCGAAGATTTGCTCACATCAAGCCTTGAGTTGGTAT
Found at i:29259 original size:96 final size:96
Alignment explanation
Indices: 29082--29263 Score: 253
Period size: 96 Copynumber: 1.9 Consensus size: 96
29072 GAAAAGGATG
* **
29082 TTCGATTATCTCGATTTGATGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTCAGAATCGA
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAAATTTTCAGAATCGA
*
29147 AGATAATGAAACATTGCCTCGATTAAGGGTA
66 AGATAAAGAAACATTGCCTCGATTAAGGGTA
* *
29178 TTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAGATTTTC-GAAACTC
1 TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAAATTTTCAG-AA-TC
*
29242 GAA-ATAAA-AGAATATTGCCTCG
64 GAAGATAAAGA-AACATTGCCTCG
29264 CTTTTAAAGT
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
95 2 0.03
96 69 0.91
97 5 0.07
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (96 bp):
TTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGTAAATTTTCAGAATCGA
AGATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:29541 original size:28 final size:27
Alignment explanation
Indices: 29482--29542 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
29472 AAATGAGACT
*
29482 TTTTGGATACTTGGGGCAAAATAGTAA
1 TTTTGGATACTTGAGGCAAAATAGTAA
* *
29509 TTTTGGATTCTTAGAGGCAAAATGGTAA
1 TTTTGGATACTT-GAGGCAAAATAGTAA
29537 TTTTGG
1 TTTTGG
29543 GAAAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 11 0.37
28 19 0.63
ACGTcount: A:0.30, C:0.07, G:0.26, T:0.38
Consensus pattern (27 bp):
TTTTGGATACTTGAGGCAAAATAGTAA
Found at i:29644 original size:30 final size:29
Alignment explanation
Indices: 29612--29921 Score: 246
Period size: 29 Copynumber: 10.6 Consensus size: 29
29602 AATCGAGATA
*
29612 AAAAATGGAATTTTTGGATA-TTCGGGGGT
1 AAAAATGGAATTTTTGGA-AGTTCGAGGGT
* *
29641 -AAAATGGTAATTTTT-TAGAGTTTTG-GGGT
1 AAAAATGG-AATTTTTGGA-AG-TTCGAGGGT
* *
29670 CAAAAATAGAGTTTTTGGACA-TTCGAGGGT
1 -AAAAATGGAATTTTTGGA-AGTTCGAGGGT
* **
29700 -AAAATGTAATTTTTGGAAGTTTTAGGGT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGT
* * * *
29728 AAAAATTGGATTTTTTAGAGGTT-TAGGGGT
1 AAAAA-TGGAATTTTTGGAAGTTCGA-GGGT
* *
29758 AAAAATGTAATTTTTTGAAGTTTCG-GGGT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGGT
*
29787 AAAAAAT-GAAATTTTGGAAGTTCGAGGGT
1 -AAAAATGGAATTTTTGGAAGTTCGAGGGT
*
29816 AAAAATGTAATTTTTGGAAGTTTC-AGGGTT
1 AAAAATGGAATTTTTGGAAG-TTCGAGGG-T
29846 AAAAATGGAATTTTTGGAAGTTCGAGGGT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGT
** *
29875 AAAAATATAATTTTTGAAAGTATCGA-GGT
1 AAAAATGGAATTTTTGGAAGT-TCGAGGGT
*
29904 CAAAATGGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
29922 CACTTTAAGG
Statistics
Matches: 226, Mismatches: 35, Indels: 40
0.75 0.12 0.13
Matches are distributed among these distances:
27 1 0.00
28 40 0.18
29 103 0.46
30 74 0.33
31 8 0.04
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGT
Found at i:29675 original size:59 final size:59
Alignment explanation
Indices: 29612--29921 Score: 291
Period size: 59 Copynumber: 5.3 Consensus size: 59
29602 AATCGAGATA
* *
29612 AAAAATGGAATTTTTGGATATTCGGGGGT-AAAATGGTAATTTTTTAG-AGTTTTGGGGTC
1 AAAAATGGAATTTTTGGA-ATTCGAGGGTAAAAAT-GTAATTTTTTAGAAGTTTCGGGGTC
* * * **
29671 AAAAATAGAGTTTTTGGACATTCGAGGGT-AAAATGTAA-TTTTTGGAAGTTTTAGGGT-
1 AAAAATGGAATTTTTGGA-ATTCGAGGGTAAAAATGTAATTTTTTAGAAGTTTCGGGGTC
* * * * *
29728 AAAAATTGGATTTTTTAGAGGTT-TAGGGGTAAAAATGTAATTTTTT-GAAGTTTCGGGGTA
1 AAAAA-TGGAATTTTTGGA-ATTCGA-GGGTAAAAATGTAATTTTTTAGAAGTTTCGGGGTC
* * * *
29788 AAAAAT-GAAATTTTGGAAGTTCGAGGGTAAAAATGTAA-TTTTTGGAAGTTTCAGGGTT
1 AAAAATGGAATTTTTGGAA-TTCGAGGGTAAAAATGTAATTTTTTAGAAGTTTCGGGGTC
* * * *
29846 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGA-AAGTATCGAGGTC
1 AAAAATGGAATTTTTGGAA-TTCGAGGGTAAAAATGTAATTTTTTAGAAGTTTCGGGGTC
29905 -AAAATGGAATTTTTGGA
1 AAAAATGGAATTTTTGGA
29922 CACTTTAAGG
Statistics
Matches: 211, Mismatches: 29, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
57 17 0.08
58 89 0.42
59 91 0.43
60 14 0.07
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGAATTCGAGGGTAAAAATGTAATTTTTTAGAAGTTTCGGGGTC
Found at i:29919 original size:88 final size:87
Alignment explanation
Indices: 29620--29921 Score: 287
Period size: 88 Copynumber: 3.4 Consensus size: 87
29610 TAAAAAATGG
* * * * * *
29620 AATTTTTGGATA-TTCGGGGGT-AAAATGGTAATTTTT-TAGAGTTTTGGGGTCAAAAATAGAGT
1 AATTTTTGGA-AGTTCGAGGGTAAAAATGG-AATTTTTGGA-AG-TTTAGGGTTAAAAATGGAAT
*
29682 TTTTGGACA-TTCGAGGGT-AAAATGT
62 TTTTGGA-AGTTCGAGGGTAAAAATAT
** * * * * *
29707 AATTTTTGGAAGTTTTAGGGTAAAAATTGGATTTTTTAGAGGTTTAGGGGTAAAAATGTAATTTT
1 AATTTTTGGAAGTTCGAGGGTAAAAA-TGGAATTTTTGGAAGTTTAGGGTTAAAAATGGAATTTT
*
29772 TTGAAGTTTCG-GGGTAAAAA-AT
65 TGGAAG-TTCGAGGGTAAAAATAT
* *
29794 GAAATTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCAGGGTTAAAAATGGAATTT
1 -AATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTT-AGGGTTAAAAATGGAATTT
29859 TTGGAAGTTCGAGGGTAAAAATAT
64 TTGGAAGTTCGAGGGTAAAAATAT
* *
29883 AATTTTTGAAAGTATCGA-GGTCAAAATGGAATTTTTGGA
1 AATTTTTGGAAGT-TCGAGGGTAAAAATGGAATTTTTGGA
29922 CACTTTAAGG
Statistics
Matches: 175, Mismatches: 28, Indels: 23
0.77 0.12 0.10
Matches are distributed among these distances:
86 2 0.01
87 59 0.34
88 104 0.59
89 10 0.06
ACGTcount: A:0.33, C:0.03, G:0.26, T:0.37
Consensus pattern (87 bp):
AATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTAGGGTTAAAAATGGAATTTTT
GGAAGTTCGAGGGTAAAAATAT
Found at i:29919 original size:117 final size:114
Alignment explanation
Indices: 29612--29923 Score: 346
Period size: 117 Copynumber: 2.7 Consensus size: 114
29602 AATCGAGATA
* * * *
29612 AAAAATGGAATTTTTGGATA-TTCGGGGGT-AAAATGGTAATTTTTTAGAGTTTTGGGGTCAAAA
1 AAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAAT-GTAATTTTTGAAAGTTTCGGGGTC-AAA
* *
29675 ATAGAGTTTTTGGACATTCGAGGGTAAAATGTAATTTTTGGAAGTTTTAGGGT
63 AT-GAATTTTTGGACATTCGAGGGTAAAATGTAATTTTTGGAAGTTTCAGGGT
* * * * *
29728 AAAAATTGGATTTTTTAGAGGTT-TAGGGGTAAAAATGTAATTTTTTG-AAGTTTCGGGGTAAAA
1 AAAAA-TGGAATTTTTGGAAGTTCGA-GGGTAAAAATGTAA-TTTTTGAAAGTTTCGGGGT-CAA
*
29791 AATGAAATTTTGGA-AGTTCGAGGGTAAAAATGTAATTTTTGGAAGTTTCAGGGTT
62 AATGAATTTTTGGACA-TTCGAGGGT-AAAATGTAATTTTTGGAAGTTTCAGGG-T
* * *
29846 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATAATTTTTGAAAGTATCGAGGTCAAAATG
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAAT-
29911 GAATTTTTGGACA
65 GAATTTTTGGACA
29924 CTTTAAGGAC
Statistics
Matches: 162, Mismatches: 21, Indels: 24
0.78 0.10 0.12
Matches are distributed among these distances:
115 1 0.01
116 34 0.21
117 109 0.67
118 18 0.11
ACGTcount: A:0.34, C:0.04, G:0.26, T:0.36
Consensus pattern (114 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTTCGGGGTCAAAATG
AATTTTTGGACATTCGAGGGTAAAATGTAATTTTTGGAAGTTTCAGGGT
Found at i:31818 original size:6 final size:6
Alignment explanation
Indices: 31752--31804 Score: 81
Period size: 6 Copynumber: 8.8 Consensus size: 6
31742 GTTCAAAATT
*
31752 ATTTCAA ATTTAA A-GTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
31800 ATTTA
1 ATTTA
31805 GAAATAAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
5 4 0.09
6 35 0.81
7 4 0.09
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:32825 original size:17 final size:16
Alignment explanation
Indices: 32799--32833 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
32789 GAAACCCAAG
32799 AAAAAAAAGAAAGAAA
1 AAAAAAAAGAAAGAAA
*
32815 AAAAGAAAAGAAGGAAA
1 AAAA-AAAAGAAAGAAA
32832 AA
1 AA
32834 GTCAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAGAAA
Found at i:34408 original size:99 final size:97
Alignment explanation
Indices: 34282--34811 Score: 464
Period size: 99 Copynumber: 5.4 Consensus size: 97
34272 AGTTGAAAAT
* * * *
34282 AACCCTATACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGCAACGACAAATTTGGTACCATAA
1 AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGTAACGACGAATCTGGTACCATAA
** * *
34347 AGATATGAAAGGAAAGGTTGAGGTTGCAATGGTG
66 A-ATAT-AAAGGAAAGGTTGAGGCCGCAACGGCG
* ** * * * * * * *
34381 AACCCTGTACCTTATAAGACATGATGGGAAAGATCGAGGCCGTAACGACGGATCTAGCACCATGG
1 AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGTAACGACGAATCTGGTACCAT-A
* * *** *
34446 AAATA-AAGGGAAAGGTTGAGGTCGCAGTTGCA
65 AAATATAAAGGAAAGGTTGAGGCCGCAACGGCG
* * ** **
34478 AACCCTGTACCTTAAAAGATGTGATGAGAAGGATTGAGGCCATAACGGTGAATCTGGTACCATGA
1 AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGTAACGACGAATCTGGTACCAT-A
* *
34543 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGCG
65 AAATAT-AAAGGAAAGGTTGAGGCCGCAACGGCG
** * * * * *
34577 AACCCCATACCTTAGAAGATGTAATGGGAAGGATTGAGGCTGTAATGGCGAATCCGGTATCATAG
1 AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGTAACGACGAATCTGGTACCATA-
34642 AAATATAAAGGGAAAGGTTGAGGCCGCAACGGCG
65 AAATATAAA-GGAAAGGTTGAGGCCGCAACGGCG
** * * *
34676 AA-CCTGATATCC-TAGAA-ACATGATGGGAAAGATTGAGGCTGCAAC-AGCGAATCTAGTACCA
1 AACCCTG-TA-CCTTAGAAGATGTGATGGGAAGGATTGAGGCTGTAACGA-CGAATCTGGTACCA
*
34737 TGAAAATATAAATGGAAAGGTTGAGGCCACAACGGCG
63 T-AAAATATAAA-GGAAAGGTTGAGGCCGCAACGGCG
*
34774 AA-CCTGGTACCTTAGAA-ACGTGATGGGAAAGG-TTGAGG
1 AACCCT-GTACCTTAGAAGATGTGATGGG-AAGGATTGAGG
34812 TCGCAACGGT
Statistics
Matches: 351, Mismatches: 68, Indels: 25
0.79 0.15 0.06
Matches are distributed among these distances:
97 79 0.23
98 98 0.28
99 170 0.48
100 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (97 bp):
AACCCTGTACCTTAGAAGATGTGATGGGAAGGATTGAGGCTGTAACGACGAATCTGGTACCATAA
AATATAAAGGAAAGGTTGAGGCCGCAACGGCG
Found at i:34565 original size:49 final size:49
Alignment explanation
Indices: 34336--34968 Score: 268
Period size: 49 Copynumber: 12.9 Consensus size: 49
34326 ACGACAAATT
* ** * *
34336 TGGTACCATA-AAGATATGAAAGGAAAGGTTGAGGTTGCAATGGTGAACCC
1 TGGTACCATAGAA-ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAA-CC
* * * * * * * * * *
34386 T-GTACCTTATAAGACATGATGGGAAAGATCGAGGCCGTAACGACGGATC
1 TGGTACCATAGAA-ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * *** *
34435 TAGCACCATGGAAATA--AAGGGAAAGGTTGAGGTCGCAGTTGCAAACCC
1 TGGTACCATAGAAATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAA-CC
* * * * * ** * *
34483 T-GTACCTTAAAAGATGTGATGAG-AAGGATTGAGGCCATAACGGTGAATC
1 TGGTACCATAGAA-ATATGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACC
34532 TGGTACCAT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
1 TGGTACCATAGAA-ATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
*** * * * * *
34581 CCATACCTTAG-AAGATGTAATGGG-AAGGATTGAGGCTGTAATGGCGAATCC
1 TGGTACCATAGAAATATG-AA-GGGAAAGG-TTGAGGCCGCAACGGCGAA-CC
* *
34632 -GGTATCATAGAAATATAAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
1 TGGTACCATAGAAATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * * * *
34680 TGATATCC-TAGAAACATGATGGGAAAGATTGAGGCTGCAACAGCGAATC
1 TGGTA-CCATAGAAATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * *
34729 TAGTACCAT-GAAAATATAAATGGAAAGGTTGAGGCCACAACGGCGAACC
1 TGGTACCATAG-AAATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* ** * * * *
34778 TGGTACCTTAGAAACGTGATGGGAAAGGTTGAGGTCGCAACGGTGGACC
1 TGGTACCATAGAAATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * * * * ** * *
34827 TTGTCCCTTAGAAGATGTGACGGG-AAGGATCGAGGCCACAACTACAAATC
1 TGGTACCATAGAA-ATATGAAGGGAAAGG-TTGAGGCCGCAACGGCGAACC
* * * * * *
34877 TAGTACCAT-GAAAATATAAAGGGAAAGATTAAGGCCACAACGGCAAACC
1 TGGTACCATAG-AAATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* * * * * * *
34926 TAGTACCTTAGAAACATGATGGGAAAGATTGAAGCCACAACGG
1 TGGTACCATAGAAATATGAAGGGAAAGGTTGAGGCCGCAACGG
34969 TAAATCTTAT
Statistics
Matches: 422, Mismatches: 135, Indels: 53
0.69 0.22 0.09
Matches are distributed among these distances:
47 25 0.06
48 13 0.03
49 255 0.60
50 123 0.29
51 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.19
Consensus pattern (49 bp):
TGGTACCATAGAAATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
Found at i:35264 original size:114 final size:114
Alignment explanation
Indices: 35051--35333 Score: 354
Period size: 114 Copynumber: 2.5 Consensus size: 114
35041 AGCAAAATGG
* * * *
35051 AGTGAAACTTCAAATCCCATCTTCCTCGTGAGGTATAGAGAAGTGGGTCAAAACAGTATGTTAAA
1 AGTGAGACTTCAAATCCCATCTTCCTAGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGCTAAA
* *
35116 TCAAAACAACGAAGCTGAGCTCAACGTCCCTGAGGATA-AAGTGGAGTGG
66 TCAAAACAACGAAGCTGAGCTCAACGTCCCTGAGGATACAA-TAGAGTGA
* * * * * * * *
35165 GGTGAGACTTCAAATCTCATCTTCCTAATGAGGTACAGAAAAGTGGGTTAAGATAGTATGCTGAA
1 AGTGAGACTTCAAATCCCATCTTCCTAGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGCTAAA
* * * * *
35230 TCAAAACAGCGAAGTTGATCTCAATGTCCTTGAGGATACAATAGAGTGA
66 TCAAAACAACGAAGCTGAGCTCAACGTCCCTGAGGATACAATAGAGTGA
*
35279 AGTGAGACTTCGAATCCCATCTTCCTAGTGAGGTACAGAGAAGTGGGAT-AAAACA
1 AGTGAGACTTCAAATCCCATCTTCCTAGTGAGGTACAGAGAAGTGGG-TCAAAACA
35334 AATAGCGAAT
Statistics
Matches: 141, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
114 138 0.98
115 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.24, T:0.24
Consensus pattern (114 bp):
AGTGAGACTTCAAATCCCATCTTCCTAGTGAGGTACAGAGAAGTGGGTCAAAACAGTATGCTAAA
TCAAAACAACGAAGCTGAGCTCAACGTCCCTGAGGATACAATAGAGTGA
Found at i:37180 original size:30 final size:29
Alignment explanation
Indices: 37132--37377 Score: 133
Period size: 30 Copynumber: 8.2 Consensus size: 29
37122 CCCCAAATTA
*
37132 TCCAAAAATTAAGTTTTGACCCTTAAACTT
1 TCCAAAAATT-AGATTTGACCCTTAAACTT
* **
37162 TCCAAAAATATTGATTTGACCCTCGAAC-T
1 TCCAAAAAT-TAGATTTGACCCTTAAACTT
* * * *
37191 TCTTATAAATTCAGATTTAACCGC-CAAACTT
1 TC-CAAAAATT-AGATTTGACC-CTTAAACTT
* * **
37222 TCCAAAAATTAAATTTAAACCCTTGTACTT
1 TCCAAAAATTAGATTT-GACCCTTAAACTT
* * *
37252 TCCATAAATTCGTATTTGACCTTTAAACTT
1 TCCAAAAATTAG-ATTTGACCCTTAAACTT
* * *
37282 TCTAAAAATTCGGATTTGACTCCCGT--ACTT
1 TCCAAAAATT-AGATTTGA--CCCTTAAACTT
* * *
37312 TCCAAAAATTCAAATTTCACCCTCAAACTT
1 TCCAAAAATT-AGATTTGACCCTTAAACTT
* * *
37342 CCCAAAAATTTGGATTTAACCC-TAAACTT
1 TCCAAAAA-TTAGATTTGACCCTTAAACTT
37371 TCCAAAA
1 TCCAAAA
37378 TTTTGTTTTT
Statistics
Matches: 163, Mismatches: 39, Indels: 29
0.71 0.17 0.13
Matches are distributed among these distances:
28 3 0.02
29 22 0.13
30 123 0.75
31 12 0.07
32 3 0.02
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTAGATTTGACCCTTAAACTT
Found at i:37281 original size:90 final size:90
Alignment explanation
Indices: 37123--37377 Score: 225
Period size: 90 Copynumber: 2.8 Consensus size: 90
37113 CTTTTTGACC
* ** * *
37123 CCCAAA-TTATCCAAAAATTAAGTTTTGACCCTTAAACTTTCCAAAAATATTGATTTGACCCTCG
1 CCCAAACTT-TCCAAAAATTAAATTTAAACCCTTAAACTTTCCAAAAATATCGATTTGACCCTCA
*
37187 AAC-TTCTTATAAATTCAGATTTAAC-
65 AACTTTC-TAAAAATTCAGATTTAACT
** * * *
37212 CGCCAAACTTTCCAAAAATTAAATTTAAACCCTTGTACTTTCCATAAAT-TCGTATTTGACCTTT
1 C-CCAAACTTTCCAAAAATTAAATTTAAACCCTTAAACTTTCCAAAAATATCG-ATTTGACCCTC
* *
37276 AAACTTTCTAAAAATTCGGATTTGACT
64 AAACTTTCTAAAAATTCAGATTTAACT
** * * * * * *
37303 CCCGTACTTTCCAAAAATTCAAATTT-CACCCTCAAACTTCCCAAAAATTTGGATTTAACCCT-A
1 CCCAAACTTTCCAAAAATT-AAATTTAAACCCTTAAACTTTCCAAAAATATCGATTTGACCCTCA
*
37366 AACTTTCCAAAA
65 AACTTTCTAAAA
37378 TTTTGTTTTT
Statistics
Matches: 134, Mismatches: 25, Indels: 14
0.77 0.14 0.08
Matches are distributed among these distances:
89 15 0.11
90 105 0.78
91 14 0.10
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (90 bp):
CCCAAACTTTCCAAAAATTAAATTTAAACCCTTAAACTTTCCAAAAATATCGATTTGACCCTCAA
ACTTTCTAAAAATTCAGATTTAACT
Found at i:37382 original size:29 final size:30
Alignment explanation
Indices: 37325--37382 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
37315 AAAAATTCAA
*
37325 ATTTCACCCTCAAACTTCCCAAAAATTTGG
1 ATTTAACCCTCAAACTTCCCAAAAATTTGG
* *
37355 ATTTAACCCT-AAACTTTCCAAAATTTTG
1 ATTTAACCCTCAAACTTCCCAAAAATTTG
37383 TTTTTGACCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.34
Consensus pattern (30 bp):
ATTTAACCCTCAAACTTCCCAAAAATTTGG
Found at i:43736 original size:507 final size:507
Alignment explanation
Indices: 42783--43743 Score: 1744
Period size: 507 Copynumber: 1.9 Consensus size: 507
42773 AACAACTTTA
*
42783 GTTTTGAATAGTTGTTTTTAAGAACAACTGTTGTTCGAGAATAGCTTTGCTCGGAATTGGACTTT
1 GTTTTGAATAGTTGTTTTTAAGAACAACTATTGTTCGAGAATAGCTTTGCTCGGAATTGGACTTT
*
42848 AATTAGAAATGTTGTTATCCAGTGTAGTTATTTGAAAACAACTTATATTGATAATAGCTAAAGTT
66 AATTAGAAATGTTGTCATCCAGTGTAGTTATTTGAAAACAACTTATATTGATAATAGCTAAAGTT
* ** *
42913 CGGAATTACTCATGTTTAGAATAACGATATTTCAAGAATAACTATGTTTAGAGCAATCATTGTTT
131 CGAAACGACTCATGTTTAGAATAACGATATTTCAAGAATAACTATGTTTAAAGCAATCATTGTTT
42978 GTAACAACTTGTATTTAGAACAATTGTATTTTTCTAGAAGAGCTATTATTCAGAATAAGCTTTAC
196 GTAACAACTTGTATTTAGAACAATTGTATTTTTCTAGAAGAGCTATTATTCAGAATAAGCTTTAC
43043 CAAAAAAAGCATCATCATAAAAGAACTCTAATTCAAAACAACCTCTACATTAAGAACAACTATGT
261 CAAAAAAAGCATCATCATAAAAGAACTCTAATTCAAAACAACCTCTACATTAAGAACAACTATGT
43108 TGAAAACAACTAATCTTTGGAGCAAGTCAAAATAAATTTTATTTAGGAACAACTCTCATCCAAGA
326 TGAAAACAACTAATCTTTGGAGCAAGTCAAAATAAATTTTATTTAGGAACAACTCTCATCCAAGA
* * * *
43173 GCAACCATCGTTTTATGTTTCAAGAGATGTTTCGCGAAAGATGTTTAACATGGTACTGCTTCACA
391 ACAACCATCGTTTTATGTTTCAAGAGATGTTTCACGAAAGATGTTCAACATGGTACTACTTCACA
43238 ACTAATCTTTGGAGCAAGTCAAAATAACTTTTATTTAGGAACAACTAATCTT
456 ACTAATCTTTGGAGCAAGTCAAAATAACTTTTATTTAGGAACAACTAATCTT
* *
43290 GTTTTGAATAGTTGTTTTTAAGAACAACTATTGTTCGAGAATAGCTTTGTTTGGAATTGGACTTT
1 GTTTTGAATAGTTGTTTTTAAGAACAACTATTGTTCGAGAATAGCTTTGCTCGGAATTGGACTTT
* *
43355 AGTTAGAAATGTTGTCATCCTA-TGTAGTTATTTGAAAACAACTTATGTTGATAATAGCTAAAGT
66 AATTAGAAATGTTGTCATCC-AGTGTAGTTATTTGAAAACAACTTATATTGATAATAGCTAAAGT
*
43419 TCGAAACGACTCCTGTTTAGAATAACGATATTTCAAGAATAACTATGTTTAAAGCAATCATTGTT
130 TCGAAACGACTCATGTTTAGAATAACGATATTTCAAGAATAACTATGTTTAAAGCAATCATTGTT
43484 TGTAACAACTTGTATTTAGAACAATTGTATTTTTCTAGAAGAGCTATTATTCAGAATAAGCTTTA
195 TGTAACAACTTGTATTTAGAACAATTGTATTTTTCTAGAAGAGCTATTATTCAGAATAAGCTTTA
*
43549 CCAAAAAAAGCATCATTATAAAAGAACTCTAATTCAAAACAACCTCTACATTAAGAACAACTATG
260 CCAAAAAAAGCATCATCATAAAAGAACTCTAATTCAAAACAACCTCTACATTAAGAACAACTATG
* *
43614 TTGAAAACAACTAATCTTTGGAGCAAGTCATAATAACTTTTATTTAGGAACAACTCTCATCCAAG
325 TTGAAAACAACTAATCTTTGGAGCAAGTCAAAATAAATTTTATTTAGGAACAACTCTCATCCAAG
43679 AACAACCATCGTTTTATGTTTCAAGAGATGTTTCACGAAAGATGTTCAACATGGTACTACTTCAC
390 AACAACCATCGTTTTATGTTTCAAGAGATGTTTCACGAAAGATGTTCAACATGGTACTACTTCAC
43744 CAAAGTAAAG
Statistics
Matches: 435, Mismatches: 18, Indels: 2
0.96 0.04 0.00
Matches are distributed among these distances:
507 434 1.00
508 1 0.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (507 bp):
GTTTTGAATAGTTGTTTTTAAGAACAACTATTGTTCGAGAATAGCTTTGCTCGGAATTGGACTTT
AATTAGAAATGTTGTCATCCAGTGTAGTTATTTGAAAACAACTTATATTGATAATAGCTAAAGTT
CGAAACGACTCATGTTTAGAATAACGATATTTCAAGAATAACTATGTTTAAAGCAATCATTGTTT
GTAACAACTTGTATTTAGAACAATTGTATTTTTCTAGAAGAGCTATTATTCAGAATAAGCTTTAC
CAAAAAAAGCATCATCATAAAAGAACTCTAATTCAAAACAACCTCTACATTAAGAACAACTATGT
TGAAAACAACTAATCTTTGGAGCAAGTCAAAATAAATTTTATTTAGGAACAACTCTCATCCAAGA
ACAACCATCGTTTTATGTTTCAAGAGATGTTTCACGAAAGATGTTCAACATGGTACTACTTCACA
ACTAATCTTTGGAGCAAGTCAAAATAACTTTTATTTAGGAACAACTAATCTT
Found at i:60618 original size:116 final size:116
Alignment explanation
Indices: 60414--60645 Score: 421
Period size: 116 Copynumber: 2.0 Consensus size: 116
60404 AGCTAAAGAA
*
60414 TCTCTTAAACATATCTCTATGCCAATTCAACTGACTAATTAACAATCATAAGCATGTAAAGAATC
1 TCTCTTAAACATATCTCTATGCCAATTCAACCGACTAATTAACAATCATAAGCATGTAAAGAATC
*
60479 AAGTGAAGTAACAATCATATCTCTATGTTGAAACAATTTAATCACAAAAAT
66 AAGTGAAGTAACAATCATATCTCTATATTGAAACAATTTAATCACAAAAAT
*
60530 TCTCTTAAACATATCTCTATGTCAATTCAACCGACTAATTAACAATCATAAGCATGTAAATG-AT
1 TCTCTTAAACATATCTCTATGCCAATTCAACCGACTAATTAACAATCATAAGCATGTAAA-GAAT
60594 CAAGTGAAGTAACAATCATATCTCTATATTGAAACAATTTAATCACAAAAAT
65 CAAGTGAAGTAACAATCATATCTCTATATTGAAACAATTTAATCACAAAAAT
60646 CCTACAAGTT
Statistics
Matches: 112, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
116 111 0.99
117 1 0.01
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (116 bp):
TCTCTTAAACATATCTCTATGCCAATTCAACCGACTAATTAACAATCATAAGCATGTAAAGAATC
AAGTGAAGTAACAATCATATCTCTATATTGAAACAATTTAATCACAAAAAT
Found at i:61043 original size:17 final size:17
Alignment explanation
Indices: 61023--61108 Score: 127
Period size: 17 Copynumber: 5.1 Consensus size: 17
61013 ATCAAGCCCA
*
61023 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
61040 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
61057 ATTATAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
61074 ATATTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
*
61091 ATTTTAAATTTGAATTT
1 ATTTTAAATTTAAATTT
61108 A
1 A
61109 ATTAAAAATG
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 61 1.00
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:61051 original size:6 final size:6
Alignment explanation
Indices: 61025--61109 Score: 72
Period size: 6 Copynumber: 14.8 Consensus size: 6
61015 CAAGCCCAAT
* * *
61025 TTTAAA TTTTAA TTT-AT TTTAAG TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
* * *
61071 TTTATA -TTAAA TTTAAA TTT-AT TTTAAA TTTGAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
61110 TTAAAAATGT
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
4 3 0.05
5 13 0.21
6 44 0.70
7 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:61096 original size:11 final size:11
Alignment explanation
Indices: 61025--61109 Score: 75
Period size: 11 Copynumber: 7.5 Consensus size: 11
61015 CAAGCCCAAT
61025 TTTAAATTTTAA
1 TTTAAA-TTTAA
*
61037 TTT-ATTTTAA
1 TTTAAATTTAA
61047 GTTTAAATTT-A
1 -TTTAAATTTAA
61058 TTATAAATTTAAA
1 TT-TAAATTT-AA
* *
61071 TTTATATTAAA
1 TTTAAATTTAA
*
61082 TTTAAATTTAT
1 TTTAAATTTAA
61093 TTTAAATTTGAA
1 TTTAAATTT-AA
61105 TTTAA
1 TTTAA
61110 TTAAAAATGT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
10 7 0.12
11 31 0.53
12 18 0.31
13 3 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:62670 original size:59 final size:59
Alignment explanation
Indices: 62585--62722 Score: 174
Period size: 59 Copynumber: 2.4 Consensus size: 59
62575 GTACGCGTTA
* * * ** *
62585 GACCCCTAAAATTTTTCAAAATTATATTTTAAC-CCTTAAACTTTTTTAAAATTATATTTT
1 GACCCCTAAACTTTCTCAAAATTATATTTTAACACCTT-AACTTCTCAAAAATTACA-TTT
62645 GACCCCTAAACTTTCT-AAAATTATATTTTAACACCTTAACTTCTCAAAAATTACATTT
1 GACCCCTAAACTTTCTCAAAATTATATTTTAACACCTTAACTTCTCAAAAATTACATTT
*
62703 GACCCCTTAAC-TTCTCAAAA
1 GACCCCTAAACTTTCTCAAAA
62723 AATGCATTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
57 4 0.06
58 17 0.25
59 30 0.43
60 18 0.26
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.40
Consensus pattern (59 bp):
GACCCCTAAACTTTCTCAAAATTATATTTTAACACCTTAACTTCTCAAAAATTACATTT
Found at i:62673 original size:29 final size:29
Alignment explanation
Indices: 62598--62871 Score: 171
Period size: 29 Copynumber: 9.3 Consensus size: 29
62588 CCCTAAAATT
* *
62598 TTTC-AAAATTATATTTTAACCCTTAAAC
1 TTTCAAAAATTATATTTTGACCCCTAAAC
**
62626 TTTTTTAAAATTATATTTTGACCCCTAAAC
1 -TTTCAAAAATTATATTTTGACCCCTAAAC
* * * *
62656 TTTCTAAAATTATATTTTAACACCTTAAC
1 TTTCAAAAATTATATTTTGACCCCTAAAC
* *
62685 TTCTCAAAAATTACA-TTTGACCCCTTAAC
1 TT-TCAAAAATTATATTTTGACCCCTAAAC
* **
62714 TTCTCAAAAAATGCATTTTGACCCCTAAAC
1 TT-TCAAAAATTATATTTTGACCCCTAAAC
* *
62744 TTCCAAAAATTATATTTT-AACCCTCAAAC
1 TTTCAAAAATTATATTTTGACCCCT-AAAC
* * * * *
62773 ATTTCAAACACTACATTTTTACCCCCAAAC
1 -TTTCAAAAATTATATTTTGACCCCTAAAC
* * * * * *
62803 ATCCAAAAATCAATTTTTTTAACCCC-GAAC
1 TTTCAAAAAT-TA-TATTTTGACCCCTAAAC
* * *
62833 ATCCAAAAATTATAATTTTG-CCCCCAAAC
1 TTTCAAAAATTAT-ATTTTGACCCCTAAAC
*
62862 TTCCAAAAAT
1 TTTCAAAAAT
62872 CACATTTTTT
Statistics
Matches: 196, Mismatches: 39, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
28 10 0.05
29 94 0.48
30 79 0.40
31 13 0.07
ACGTcount: A:0.38, C:0.24, G:0.02, T:0.35
Consensus pattern (29 bp):
TTTCAAAAATTATATTTTGACCCCTAAAC
Found at i:62751 original size:58 final size:58
Alignment explanation
Indices: 62610--62791 Score: 161
Period size: 59 Copynumber: 3.1 Consensus size: 58
62600 TCAAAATTAT
* ** * * *
62610 ATTTTAAC-CCTTAAACTTTTTTAAAATTATATTTTGACCCCTAAACTTTCTAAAATTAT
1 ATTTTAACACC-TAAACTTCTCAAAAATTATA-TTTGACCCCTAAACTTTCAAAAAATAC
* * * *
62669 ATTTTAACACCTTAACTTCTCAAAAATTACATTTGACCCCTTAACTTCTCAAAAAATGC
1 ATTTTAACACCTAAACTTCTCAAAAATTATATTTGACCCCTAAACTT-TCAAAAAATAC
* * * * * *
62728 ATTTTGACCCCTAAACTTC-CAAAAATTATATTTTAACCCTCAAACATTTCAAACACTAC
1 ATTTTAACACCTAAACTTCTCAAAAATTATATTTGACCCCT-AAAC-TTTCAAAAAATAC
62787 ATTTT
1 ATTTT
62792 TACCCCCAAA
Statistics
Matches: 99, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
58 33 0.33
59 62 0.63
60 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (58 bp):
ATTTTAACACCTAAACTTCTCAAAAATTATATTTGACCCCTAAACTTTCAAAAAATAC
Found at i:62797 original size:59 final size:57
Alignment explanation
Indices: 62598--62812 Score: 155
Period size: 59 Copynumber: 3.7 Consensus size: 57
62588 CCCTAAAATT
* * * *** *
62598 TTTCAAAATTATATTTTAACCCTTAAACTTTTTTAAAATTATATTTTGACCC-CTAAAC
1 TTTCAAAAATACATTTTAACCCCTAAAC-TTCCAAAAATTATATTTTAACCCTC-AAAC
* * * * * * * *
62656 TTTCTAAAATTATATTTTAACACCTTAACTTCTCAAAAATTACATTTGACCCCT-TAAC
1 TTTC-AAAAATACATTTTAACCCCTAAACTTC-CAAAAATTATATTTTAACCCTCAAAC
* *
62714 TTCTCAAAAAATGCATTTTGACCCCTAAACTTCCAAAAATTATATTTTAACCCTCAAAC
1 TT-TC-AAAAATACATTTTAACCCCTAAACTTCCAAAAATTATATTTTAACCCTCAAAC
* * * *
62773 ATTTCAAACACTACATTTTTACCCCCAAACATCCAAAAAT
1 -TTTCAAA-AATACATTTTAACCCCTAAACTTCCAAAAAT
62813 CAATTTTTTT
Statistics
Matches: 123, Mismatches: 27, Indels: 13
0.75 0.17 0.08
Matches are distributed among these distances:
58 32 0.26
59 89 0.72
60 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (57 bp):
TTTCAAAAATACATTTTAACCCCTAAACTTCCAAAAATTATATTTTAACCCTCAAAC
Found at i:62880 original size:29 final size:29
Alignment explanation
Indices: 62682--62910 Score: 124
Period size: 30 Copynumber: 7.7 Consensus size: 29
62672 TTAACACCTT
* * **
62682 AACTTCTCAAAAATTACA-TTTGACCCCTT
1 AACTTC-CAAAAATCACATTTTTACCCCCA
* * *
62711 AACTTCTCAAAAAAT-GCATTTTGACCCCTA
1 AACTTC-C-AAAAATCACATTTTTACCCCCA
* * * *
62741 AACTTCCAAAAATTATATTTTAACCCTCA
1 AACTTCCAAAAATCACATTTTTACCCCCA
* *
62770 AACATTTCAAACA-CTACATTTTTACCCCCA
1 AAC-TTCCAAAAATC-ACATTTTTACCCCCA
* * *
62800 AACATCCAAAAATCA-ATTTTTTTAACCCCG
1 AACTTCCAAAAATCACA--TTTTTACCCCCA
* * * * *
62830 AACATCCAAAAATTATAATTTTGCCCCCA
1 AACTTCCAAAAATCACATTTTTACCCCCA
* *
62859 AACTTCCAAAAATCACATTTTTTACCCTCG
1 AACTTCCAAAAATCACA-TTTTTACCCCCA
* *
62889 AACATCCAAAAATTACCATTTT
1 AACTTCCAAAAATCA-CATTTT
62911 AATCCTGAAC
Statistics
Matches: 157, Mismatches: 32, Indels: 21
0.75 0.15 0.10
Matches are distributed among these distances:
28 7 0.04
29 53 0.34
30 94 0.60
31 3 0.02
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATCACATTTTTACCCCCA
Found at i:62910 original size:59 final size:58
Alignment explanation
Indices: 62727--62997 Score: 203
Period size: 59 Copynumber: 4.6 Consensus size: 58
62717 TCAAAAAATG
* * * * * * * *
62727 CATTTTGACCCCTAAACTTCCAAAAATTATA-TTTTAACCCTCAAACATTTCAAACACTA-
1 CATTTTG-CCCCCAAACTTCCAAAAATCACATTTTTTACCC-CGAACA-TCCAAAAATTAC
* * *
62786 CATTTTTACCCCCAAACATCCAAAAATCA-ATTTTTTTAACCCCGAACATCCAAAAATTAT
1 CA-TTTTGCCCCCAAACTTCCAAAAATCACA-TTTTTT-ACCCCGAACATCCAAAAATTAC
*
62846 AATTTTGCCCCCAAACTTCCAAAAATCACATTTTTTACCCTCGAACATCCAAAAATTAC
1 CATTTTGCCCCCAAACTTCCAAAAATCACATTTTTTACCC-CGAACATCCAAAAATTAC
*** ** * *
62905 CATTTTAATCCTGAACTTTTTCC-AAAATTACCA-TTTTT-CCCCGAGCATCCAAAAATTAC
1 CATTTTGCCCCCAAAC---TTCCAAAAATCA-CATTTTTTACCCCGAACATCCAAAAATTAC
* * *
62964 CATTTTGCCCTCAAATTTCCAAAAGTCACATTTT
1 CATTTTGCCCCCAAACTTCCAAAAATCACATTTT
62998 CAACTTCAAA
Statistics
Matches: 169, Mismatches: 30, Indels: 28
0.74 0.13 0.12
Matches are distributed among these distances:
56 6 0.04
57 8 0.05
58 5 0.03
59 111 0.66
60 18 0.11
61 15 0.09
62 6 0.04
ACGTcount: A:0.36, C:0.28, G:0.03, T:0.32
Consensus pattern (58 bp):
CATTTTGCCCCCAAACTTCCAAAAATCACATTTTTTACCCCGAACATCCAAAAATTAC
Found at i:62911 original size:29 final size:29
Alignment explanation
Indices: 62819--62975 Score: 108
Period size: 30 Copynumber: 5.3 Consensus size: 29
62809 AAATCAATTT
**
62819 TTTTAACCC-CGAACATCCAAAAATTATAA
1 TTTT-ACCCTCGAACATCCAAAAATTACCA
* * * * *
62848 TTTTGCCCCCAAACTTCCAAAAATCA-CA
1 TTTTACCCTCGAACATCCAAAAATTACCA
62876 TTTTTTACCCTCGAACATCCAAAAATTACCA
1 --TTTTACCCTCGAACATCCAAAAATTACCA
* *
62907 TTTTAATCCT-GAACTTTTTCC-AAAATTACCA
1 TTTT-ACCCTCGAAC---ATCCAAAAATTACCA
* *
62938 TTTTTCCC-CGAGCATCCAAAAATTACCA
1 TTTTACCCTCGAACATCCAAAAATTACCA
*
62966 TTTTGCCCTC
1 TTTTACCCTC
62976 AAATTTCCAA
Statistics
Matches: 100, Mismatches: 17, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
27 3 0.03
28 21 0.21
29 27 0.27
30 30 0.30
31 16 0.16
32 3 0.03
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
TTTTACCCTCGAACATCCAAAAATTACCA
Found at i:62987 original size:28 final size:27
Alignment explanation
Indices: 62923--62987 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
62913 TCCTGAACTT
* * *
62923 TTTCCAAAATTACCATTTTTCCCCGAG
1 TTTCCAAAATTACCATTTTGCCCCAAA
**
62950 CATCCAAAAATTACCATTTTGCCCTCAAA
1 TTTCC-AAAATTACCATTTTGCCC-CAAA
62979 TTTCCAAAA
1 TTTCCAAAA
62988 GTCACATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (27 bp):
TTTCCAAAATTACCATTTTGCCCCAAA
Found at i:63015 original size:118 final size:115
Alignment explanation
Indices: 62825--63046 Score: 266
Period size: 118 Copynumber: 1.9 Consensus size: 115
62815 ATTTTTTTAA
* * * *
62825 CCCCGAACATCCAAAAATTATAATTTTGCCCCCAAACTTCCAAAAATCACATTTTTTACCCTCGA
1 CCCCGAACATCCAAAAATTACAATTTTGCCCCCAAACTTCCAAAAATCACATTTTTCAACCTCAA
* *
62890 ACATCCAAAAATTACCATTTTAATCCTGAACTTTTTCCAAAATTACCATTTTT
66 ACATCCAAAAATT-CAATTTTAATCCCGAA--TTTTCCAAAATTACCATTTTT
* * * * * *
62943 CCCCGAGCATCCAAAAATTACCATTTTGCCCTCAAATTTCCAAAAGTCACA-TTTTCAACTTCAA
1 CCCCGAACATCCAAAAATTACAATTTTGCCCCCAAACTTCCAAAAATCACATTTTTCAACCTCAA
** *
63007 ATTTTCCAAAAGTTCAATTTTAATCCCGAATTTTCCAAAA
66 A-CATCCAAAAATTCAATTTTAATCCCGAATTTTCCAAAA
63047 ATTATGTTTC
Statistics
Matches: 88, Mismatches: 15, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
115 10 0.11
117 24 0.27
118 54 0.61
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (115 bp):
CCCCGAACATCCAAAAATTACAATTTTGCCCCCAAACTTCCAAAAATCACATTTTTCAACCTCAA
ACATCCAAAAATTCAATTTTAATCCCGAATTTTCCAAAATTACCATTTTT
Found at i:67280 original size:3 final size:3
Alignment explanation
Indices: 67272--67298 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
67262 CTCGACGTGT
67272 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
67299 ATAAAAAAAG
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:68221 original size:12 final size:13
Alignment explanation
Indices: 68204--68233 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
68194 TTTAATGAAG
68204 AAAAATA-AATAA
1 AAAAATATAATAA
68216 AAAAATATAATAA
1 AAAAATATAATAA
68229 AAAAA
1 AAAAA
68234 GAGAAGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.41
13 10 0.59
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (13 bp):
AAAAATATAATAA
Found at i:68261 original size:12 final size:12
Alignment explanation
Indices: 68245--68279 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
68235 AGAAGAAAAA
68245 AAAAAACAAGAAC
1 AAAAAA-AAGAAC
*
68258 AAAAATAAGAAC
1 AAAAAAAAGAAC
68270 AAAAAAAAGA
1 AAAAAAAAGA
68280 GGAAAAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.80, C:0.09, G:0.09, T:0.03
Consensus pattern (12 bp):
AAAAAAAAGAAC
Found at i:68270 original size:18 final size:15
Alignment explanation
Indices: 68227--68277 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
68217 AAAATATAAT
* *
68227 AAAAAAAGAGAAGAA
1 AAAAAAAAACAAGAA
68242 AAAAAAAAACAAGAA
1 AAAAAAAAACAAGAA
68257 CAAAAATAAGAACAA-AA
1 -AAAAA-AA-AACAAGAA
68274 AAAA
1 AAAA
68278 GAGGAAAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
15 13 0.42
16 9 0.29
17 4 0.13
18 5 0.16
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (15 bp):
AAAAAAAAACAAGAA
Found at i:69263 original size:49 final size:48
Alignment explanation
Indices: 69207--69335 Score: 143
Period size: 48 Copynumber: 2.6 Consensus size: 48
69197 TGAGTCGCGG
* * * * *
69207 TACCATGAATATTTGAAAGGAAAAGTTGAGGTCGTAATGACAAACCCTA
1 TACCATGAAGATTTG-AAGGAAAAGTTGAGGCCGCAACGACAAACCCAA
* * *
69256 TACCATGAAGATTTG-AGAAAAAGTTTGAGGCCGCAACGGCGAACCCAA
1 TACCATGAAGATTTGAAGGAAAAG-TTGAGGCCGCAACGACAAACCCAA
*
69304 TACCATGAAGAGTTGAAGGAAAAGGTTGAGGC
1 TACCATGAAGATTTGAAGGAAAA-GTTGAGGC
69336 TACAAAGACG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
47 7 0.10
48 32 0.48
49 27 0.40
50 1 0.01
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.20
Consensus pattern (48 bp):
TACCATGAAGATTTGAAGGAAAAGTTGAGGCCGCAACGACAAACCCAA
Found at i:69348 original size:49 final size:48
Alignment explanation
Indices: 69207--69349 Score: 130
Period size: 49 Copynumber: 2.9 Consensus size: 48
69197 TGAGTCGCGG
* * * *
69207 TACCATGAATATTTGAAAGGAAAA-GTTGAGG-TCGTAATGACAAACCCTA
1 TACCATGAAGATTTG-AAGGAAAAGGTTGAGGCTC--AAAGACGAACCCAA
* * * * *
69256 TACCATGAAGATTTG-AGAAAAAGTTTGAGGCCGCAACGGCGAACCCAA
1 TACCATGAAGATTTGAAGGAAAAGGTTGAGG-CTCAAAGACGAACCCAA
*
69304 TACCATGAAGAGTTGAAGGAAAAGGTTGAGGCTACAAAGACGAACC
1 TACCATGAAGATTTGAAGGAAAAGGTTGAGGCT-CAAAGACGAACC
69350 TAGTACCTTA
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
47 6 0.08
48 31 0.41
49 37 0.49
50 1 0.01
ACGTcount: A:0.40, C:0.17, G:0.24, T:0.19
Consensus pattern (48 bp):
TACCATGAAGATTTGAAGGAAAAGGTTGAGGCTCAAAGACGAACCCAA
Found at i:69607 original size:24 final size:24
Alignment explanation
Indices: 69575--69623 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
69565 ACAAGAAGGG
**
69575 CAAATTGAAGATTCTGATCTCTTA
1 CAAATTGAAGATTCCAATCTCTTA
69599 CAAATTGAAGATTCCAATCTCTTA
1 CAAATTGAAGATTCCAATCTCTTA
69623 C
1 C
69624 CCCGATCATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.20, G:0.10, T:0.35
Consensus pattern (24 bp):
CAAATTGAAGATTCCAATCTCTTA
Found at i:69741 original size:78 final size:78
Alignment explanation
Indices: 69612--69879 Score: 369
Period size: 78 Copynumber: 3.4 Consensus size: 78
69602 ATTGAAGATT
* * ** *
69612 CCAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCATCCGATCTTTTACCCTGAGCTTGGGGC
1 CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTTTTACCCCAAGCATGGGGC
69677 AAATCACCATCAG
66 AAATCACCATCAG
* * * * *
69690 CCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCATCTGAACTTTTACCCCAAGCCTGAGGC
1 CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTTTTACCCCAAGCATGGGGC
69755 AAATCACCATCAG
66 AAATCACCATCAG
* *
69768 CCAATCTCTTACCCCGAGCCA-GGGGCAGATTGCAACCATCCGATCTTTTACCCCAACCATAGGG
1 CCAATCTCTTACCCCGAG-CATGGGGCAGATTGCAACCATCCGATCTTTTACCCCAAGCATGGGG
* *
69832 CAAATCA-CAGCCAT
65 CAAATCACCA-TCAG
*
69846 CCAATCTCTTACCCCGATCATGGGGCAGATTGCA
1 CCAATCTCTTACCCCGAGCATGGGGCAGATTGCA
69880 GTTATCCAAA
Statistics
Matches: 168, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
77 4 0.02
78 163 0.97
79 1 0.01
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.22
Consensus pattern (78 bp):
CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAACCATCCGATCTTTTACCCCAAGCATGGGGC
AAATCACCATCAG
Found at i:69888 original size:39 final size:39
Alignment explanation
Indices: 69611--69880 Score: 196
Period size: 39 Copynumber: 6.9 Consensus size: 39
69601 AATTGAAGAT
*
69611 TCCAATCTCTTACCCCGATCATGGGGCAGATTGCAGCCA
1 TCCAATCTCTTACCCCGAGCATGGGGCAGATTGCAGCCA
* * * * *
69650 TCCGATCTTTTACCCTGAGCTTGGGGCA-AAT-CA-CCA
1 TCCAATCTCTTACCCCGAGCATGGGGCAGATTGCAGCCA
* *
69686 TCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAACCA
1 T---CCAATCTCTTACCCCGAGCATGGGGCAGATTGCAGCCA
* * * * * *
69728 TCTGAA-CTTTTACCCCAAGCCTGAGGCA-AAT-CA-CCA
1 TC-CAATCTCTTACCCCGAGCATGGGGCAGATTGCAGCCA
*
69764 TCAGCCAATCTCTTACCCCGAGCCA-GGGGCAGATTGCAACCA
1 T---CCAATCTCTTACCCCGAG-CATGGGGCAGATTGCAGCCA
* * * * * * **
69806 TCCGATCTTTTACCCCAACCATAGGGCAAATCACAGCCA
1 TCCAATCTCTTACCCCGAGCATGGGGCAGATTGCAGCCA
*
69845 TCCAATCTCTTACCCCGATCATGGGGCAGATTGCAG
1 TCCAATCTCTTACCCCGAGCATGGGGCAGATTGCAG
69881 TTATCCAAAA
Statistics
Matches: 176, Mismatches: 39, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
36 8 0.05
37 4 0.02
38 8 0.05
39 137 0.78
40 7 0.04
41 4 0.02
42 8 0.05
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (39 bp):
TCCAATCTCTTACCCCGAGCATGGGGCAGATTGCAGCCA
Found at i:70265 original size:209 final size:209
Alignment explanation
Indices: 69890--70908 Score: 1344
Period size: 209 Copynumber: 4.9 Consensus size: 209
69880 GTTATCCAAA
* * *
69890 AAAACAA-TGAGGCGATCATCTTCCTGATGAGATACTGAGAAGTATACCAAATCAATGAAACAAG
1 AAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAA
* * * * * *
69954 GCTCAATATGATCGAAACTTCAAACCCCAGCTTCCTAATGAGATATTGAGAAGCAGGTCGAAGAA
66 GCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * * * *
70019 AAAAAATGGTCATCTTTCTAATGAGATACTGAGAAGTGGACCAAATCTATCTTCCTGATGAGATA
131 ATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATGAGATA
* *
70084 CAAAGAAGTGGATT
196 CAGAGAAGCGGATT
* ** * * * * *
70098 AAAACAGGTGATACGGTCATCTTTCTAATGAAATACAGAGAAGTATACCGAATCAATGAAACAAG
1 AAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAA
* * ** * * *
70163 GCTTAATATGAGCGAAACTTCGAACCTTAACTTTCTGATGAGATACTGAGAAACAGGTCGAAGCA
66 GCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * * *
70228 ATAAAATGGTCAACTTCTTGATGAGATATAGAGAAGTGGACCAAAT-TCGTCTTCTTGATGAGAT
131 ATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCT-GTCTTCCTGATGAGAT
*
70292 ACAGAGAAGTGGA-T
195 ACAGAGAAGCGGATT
* * * * *
70306 AGAAACAAGTGAGGCAGTCATCTTCTTGATAAAATACGGAGAAGTATACCAAATCAATGAAACAA
1 A-AAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAA
* * * *
70371 AGCTCAATGTGAACGAAACTTCGAACCCCAACTTCCTGATGAGACACTAAGAAGCAGGTCGAAGC
65 AGCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGC
* * * ** *
70436 AATAAAATGATCAGCTTCCTAATGAGATACAGAGAAGTTAACCAAATTTGTCTTCCTGATGAGAT
130 AATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATGAGAT
70501 ACAGAGAAGCGGATT
195 ACAGAGAAGCGGATT
* *
70516 GAAACAAGTGAGGCGGTCATCTTCCCGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAA
1 AAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAA
* * * * * *
70581 GCTCAATGTGAGCGAAACTTCAAACCCCAGCTTCCTAATAAGGTACTAAGAAGTAGGTCGAAGCA
66 GCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * * * *
70646 ATAAAATTGTCGTGTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTAATGAGATA
131 ATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATGAGATA
70711 CAGAGAAGCGGATT
196 CAGAGAAGCGGATT
*
70725 AAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAATTATACCAAATCAATGAAACAAA
1 AAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAA
* * *
70790 GCTCAATGTGAGCGAAACTTCGAACCCCAGCTTTCTGATGAGATACAGAGAAGTAGGTCGAAGCA
66 GCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
* * *
70855 ATAAAGTGGTCATCTTCCTGACGAGATACAGAGAAGTGAACCAAAT-TCGTCTTC
131 ATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCT-GTCTTC
70909 TTAGTGAAAT
Statistics
Matches: 703, Mismatches: 102, Indels: 11
0.86 0.12 0.01
Matches are distributed among these distances:
208 9 0.01
209 692 0.98
210 2 0.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (209 bp):
AAAACAAGTGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGTATACCAAATCAATGAAACAAA
GCTCAATGTGAGCGAAACTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCA
ATAAAATGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTCCTGATGAGATA
CAGAGAAGCGGATT
Found at i:71263 original size:17 final size:17
Alignment explanation
Indices: 71243--71311 Score: 84
Period size: 17 Copynumber: 4.1 Consensus size: 17
71233 ATCAAGCCCA
*
71243 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
*
71260 ATTTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
* * *
71277 ATTTTGAGTTTAAATTA
1 ATTTTAAATTTAAATTT
*
71294 ATTTTAAATTTGAATTT
1 ATTTTAAATTTAAATTT
71311 A
1 A
71312 ATTAAAAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 44 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:71294 original size:22 final size:22
Alignment explanation
Indices: 71246--71317 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 22
71236 AAGCCCAATT
* *
71246 TTAAATTTTAATTT-ATTTTAA
1 TTAAATTTAAATTTGAATTTAA
* *
71267 GTTTAAATTT-ATTTTGAGTTTAAA
1 --TTAAATTTAAATTTGAATTT-AA
*
71291 TTAATTTTAAATTTGAATTTAA
1 TTAAATTTAAATTTGAATTTAA
71313 TTAAA
1 TTAAA
71318 AATGTCCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
22 17 0.43
23 21 0.52
24 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.56
Consensus pattern (22 bp):
TTAAATTTAAATTTGAATTTAA
Found at i:72877 original size:30 final size:30
Alignment explanation
Indices: 72807--73138 Score: 201
Period size: 30 Copynumber: 11.2 Consensus size: 30
72797 AATTTTTTAG
* * *
72807 AATTACATTTT-AACCTCTAAACTTTTCCAA
1 AATTACATTTTGACCCT-TAAACTTCTCAAA
* * *
72837 AATTTCTATTTTGACCCATAAACTTCCCAAA
1 AATTAC-ATTTTGACCCTTAAACTTCTCAAA
* * * *
72868 AACTATATTTTAACCCCCT-AACTTCTCAAA
1 AATTACATTTTGA-CCCTTAAACTTCTCAAA
72898 AATTACATTTTGACCCCTTAAA-TTCTCAAA
1 AATTACATTTTGA-CCCTTAAACTTCTCAAA
72928 AATTACATTTTGACACC-TAAACTT-TCCAAA
1 AATTACATTTTGAC-CCTTAAACTTCT-CAAA
* *
72958 AATTATATTTTAACCCTTAAACTTCTCAAA
1 AATTACATTTTGACCCTTAAACTTCTCAAA
* *
72988 AATTACATTTTTG--CATCTAAACATC-CAAA
1 AATTACA-TTTTGACCCT-TAAACTTCTCAAA
* * **
73017 AATCACATTTTTTACCCCCAAACATT-T-AAA
1 AATTACA-TTTTGACCCTTAAAC-TTCTCAAA
**
73047 AATTATCATTTTG-CCCCCAAACTTC-CAAA
1 AATTA-CATTTTGACCCTTAAACTTCTCAAA
* * *
73076 AATCACATTTTTTACCCTTAAAC--GTCAAA
1 AATTACA-TTTTGACCCTTAAACTTCTCAAA
* * *
73105 AA-TACCATTTTGACCC-AAAACTTTTCCAA
1 AATTA-CATTTTGACCCTTAAACTTCTCAAA
73134 AATTA
1 AATTA
73139 TTATTTTGCC
Statistics
Matches: 237, Mismatches: 40, Indels: 50
0.72 0.12 0.15
Matches are distributed among these distances:
27 4 0.02
28 13 0.05
29 59 0.25
30 125 0.53
31 33 0.14
32 3 0.01
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
AATTACATTTTGACCCTTAAACTTCTCAAA
Found at i:72928 original size:60 final size:59
Alignment explanation
Indices: 72807--73098 Score: 225
Period size: 60 Copynumber: 4.9 Consensus size: 59
72797 AATTTTTTAG
* * * * *
72807 AATTACATTTTAACCTCTAAACTTTTCCAAAATTTCTATTTTGACCCATAAACTTCCCAAA
1 AATTACATTTTAACCCCTAAAC-TTTCAAAAATTAC-ATTTTGACCCTTAAACTTCTCAAA
* *
72868 AACTATATTTTAACCCCCT-AACTTCTCAAAAATTACATTTTGACCCCTTAAA-TTCTCAAA
1 AATTACATTTTAA-CCCCTAAACTT-TCAAAAATTACATTTTGA-CCCTTAAACTTCTCAAA
* * * *
72928 AATTACATTTTGACACCTAAACTTTCCAAAAATTATATTTTAACCCTTAAACTTCTCAAA
1 AATTACATTTTAACCCCTAAACTTT-CAAAAATTACATTTTGACCCTTAAACTTCTCAAA
** ** * * * * **
72988 AATTACATTTTTGCATCTAAACATCCAAAAATCACATTTTTTACCCCCAAACATT-T-AAA
1 AATTACATTTTAACCCCTAAACTTTCAAAAATTACA-TTTTGACCCTTAAAC-TTCTCAAA
* * * * *
73047 AATTATCATTTT-GCCCCCAAACTTCCAAAAATCACATTTTTTACCCTTAAAC
1 AATTA-CATTTTAACCCCTAAACTTTCAAAAATTACA-TTTTGACCCTTAAAC
73099 GTCAAAAATA
Statistics
Matches: 193, Mismatches: 29, Indels: 20
0.80 0.12 0.08
Matches are distributed among these distances:
59 64 0.33
60 93 0.48
61 32 0.17
62 4 0.02
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.36
Consensus pattern (59 bp):
AATTACATTTTAACCCCTAAACTTTCAAAAATTACATTTTGACCCTTAAACTTCTCAAA
Found at i:73027 original size:59 final size:59
Alignment explanation
Indices: 72887--73098 Score: 225
Period size: 59 Copynumber: 3.6 Consensus size: 59
72877 TTAACCCCCT
* * *
72887 AACTTCTCAAAAATTACATTTTGACCCCTTAAA-TTCTCAAAAATTACATTTTGACACCTA
1 AACTTC-CAAAAATCACATTTTTAACCCTTAAACTTCTCAAAAATTACATTTTG-CACCTA
* * *
72947 AACTTTCCAAAAATTATA-TTTTAACCCTTAAACTTCTCAAAAATTACATTTTTGCATCTA
1 AAC-TTCCAAAAATCACATTTTTAACCCTTAAACTTCTCAAAAATTACA-TTTTGCACCTA
* * ** * *
73007 AACATCCAAAAATCACATTTTTTACCCCCAAACATT-T-AAAAATTATCATTTTGCCCCCA
1 AACTTCCAAAAATCACATTTTTAACCCTTAAAC-TTCTCAAAAATTA-CATTTTGCACCTA
*
73066 AACTTCCAAAAATCACATTTTTTACCCTTAAAC
1 AACTTCCAAAAATCACATTTTTAACCCTTAAAC
73099 GTCAAAAATA
Statistics
Matches: 130, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
59 69 0.53
60 51 0.39
61 10 0.08
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.35
Consensus pattern (59 bp):
AACTTCCAAAAATCACATTTTTAACCCTTAAACTTCTCAAAAATTACATTTTGCACCTA
Found at i:73135 original size:59 final size:59
Alignment explanation
Indices: 72923--73127 Score: 161
Period size: 59 Copynumber: 3.5 Consensus size: 59
72913 CCTTAAATTC
* * * * ** **
72923 TCAAAAATTA-CATTTTGACACCTAAACTTTCCAAAAATTATA-TTTTAACCCTTAAACTTC
1 TCAAAAATTACCATTTTGAC-CCAAAAC-TTCCAAAAATCACATTTTTTACCCCCAAAC-AG
* * * *
72983 TCAAAAATTA-CATTTTTG-CATCTAAACATCCAAAAATCACATTTTTTACCCCCAAACAT
1 TCAAAAATTACCA-TTTTGAC-CCAAAACTTCCAAAAATCACATTTTTTACCCCCAAACAG
* * * * **
73042 TTAAAAATTATCATTTTGCCCCCAAACTTCCAAAAATCACATTTTTTACCCTTAAAC-G
1 TCAAAAATTACCATTTTGACCCAAAACTTCCAAAAATCACATTTTTTACCCCCAAACAG
73100 TCAAAAA-TACCATTTTGACCCAAAACTT
1 TCAAAAATTACCATTTTGACCCAAAACTT
73128 TTCCAAAATT
Statistics
Matches: 121, Mismatches: 20, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
57 18 0.15
58 6 0.05
59 57 0.47
60 35 0.29
61 5 0.04
ACGTcount: A:0.40, C:0.24, G:0.02, T:0.34
Consensus pattern (59 bp):
TCAAAAATTACCATTTTGACCCAAAACTTCCAAAAATCACATTTTTTACCCCCAAACAG
Found at i:73165 original size:28 final size:28
Alignment explanation
Indices: 73132--73204 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
73122 AAACTTTTCC
** *
73132 AAAATTATTATTTTGCCCCTAGCATCAA
1 AAAATTACCATTTTGCCCCCAGCATCAA
* *
73160 AAAATTACCATTTTACCCCCAGCATCCA
1 AAAATTACCATTTTGCCCCCAGCATCAA
73188 AAAATTACCATTTTGCC
1 AAAATTACCATTTTGCC
73205 TTCAAATTTC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATTACCATTTTGCCCCCAGCATCAA
Found at i:83940 original size:14 final size:14
Alignment explanation
Indices: 83921--83953 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
83911 AAGTCTTCCC
83921 CTCAATTGTAATCA
1 CTCAATTGTAATCA
83935 CTCAATTGTAATCA
1 CTCAATTGTAATCA
*
83949 TTCAA
1 CTCAA
83954 AGTAATAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.36
Consensus pattern (14 bp):
CTCAATTGTAATCA
Found at i:88852 original size:24 final size:24
Alignment explanation
Indices: 88824--88871 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
88814 GTTCACGAAC
*
88824 AAGCTTATTTATTGACTCATTTAT
1 AAGCTCATTTATTGACTCATTTAT
* *
88848 AAGCTCGTTTATTGACTCGTTTAT
1 AAGCTCATTTATTGACTCATTTAT
88872 TTATAAATGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.48
Consensus pattern (24 bp):
AAGCTCATTTATTGACTCATTTAT
Found at i:90247 original size:21 final size:21
Alignment explanation
Indices: 90169--90260 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 21
90159 TTACTTATAA
* *
90169 TTTTTAAAAATATTTTTTTAT
1 TTTTTAAAAATATTTTATGAT
**
90190 TTTTTAAAAATAGATTATGAT
1 TTTTTAAAAATATTTTATGAT
* *
90211 GTTTTAAAGACT-TTTTAATGAT
1 TTTTTAAA-AATATTTT-ATGAT
*
90233 TTTTTAAAAA-ATTTTATGAA
1 TTTTTAAAAATATTTTATGAT
*
90253 TTTCTAAA
1 TTTTTAAA
90261 TTTCAAGTGA
Statistics
Matches: 56, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 11 0.20
21 31 0.55
22 14 0.25
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTTTAAAAATATTTTATGAT
Found at i:104616 original size:21 final size:21
Alignment explanation
Indices: 104578--104619 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
104568 TTGATCGATG
*
104578 GCTTAGCATGCAGCATGAAGA
1 GCTTACCATGCAGCATGAAGA
104599 GCTTACCA-GCAGCAATGAAGA
1 GCTTACCATGCAGC-ATGAAGA
104620 ATCAGATGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (21 bp):
GCTTACCATGCAGCATGAAGA
Done.