Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01001492.1 Kokia drynarioides strain JFW-HI SEQ_113029, 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: 48478
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 18 characters in sequence are not A, C, G, or T
Found at i:1681 original size:29 final size:28
Alignment explanation
Indices: 1592--2055 Score: 233
Period size: 29 Copynumber: 15.9 Consensus size: 28
1582 GCAAGGGGCC
* *
1592 AAATGGTAATTTTGGGAAAGTTTAAGGTTTA
1 AAAT-GTAATTTT-GGAAAGTTT-AGGGTAA
* * * *
1623 AAATGGAATTTTTAGACA-TTCGAGGGT-A
1 AAATGTAA-TTTTGGAAAGTT-TAGGGTAA
1651 AAATAGTAATTTTGGAAAGTTTAGGGATAA
1 AAAT-GTAATTTTGGAAAGTTTAGGG-TAA
* ***
1681 AAATGTAATTTT-TAAAAAATAGGGTTCAA
1 AAATGTAATTTTGGAAAGTTTAGGG-T-AA
* *
1710 AAATGAAATTTTAGAAAGTTTAGGGGT-A
1 AAATGTAATTTTGGAAAGTTTA-GGGTAA
* **
1738 AAATGGTAATTTTAGAAAAATTAGGGTTAA
1 AAAT-GTAATTTTGGAAAGTTTAGGG-TAA
*
1768 AAATAG-AATTTTGGAAAGTTCGAGGGTAA
1 AAAT-GTAATTTTGGAAAGTT-TAGGGTAA
* * * *
1797 AAATGTAATTTTTGGAAAAATTAAAGTTAA
1 AAATGTAA-TTTTGG-AAAGTTTAGGGTAA
*
1827 AAATGGAATTTTGGAAAGTTTAAGGGTAA
1 AAATGTAATTTTGGAAAGTTT-AGGGTAA
* * **
1856 AAATGTAATTTTTTGTAAA-CTCGGGGTAA
1 AAATGTAA--TTTTGGAAAGTTTAGGGTAA
* * * *
1885 AAATGGAGTTTTGGAAAGTTTGGGGGCAA
1 AAATGTAATTTTGGAAAGTTT-AGGGTAA
* *
1914 AAATGTAATTTTGGGAAAATTGA-GGTCAA
1 AAATGTAATTTT-GGAAAGTTTAGGGT-AA
* *
1943 AAATGGAATTTTGGAAAGTTTGGGGGT-A
1 AAATGTAATTTTGGAAAGTTT-AGGGTAA
* * ** **
1971 AAATGTAATTTTTTGAAAAATCGAGATTAA
1 AAATGTAA--TTTTGGAAAGTTTAGGGTAA
* ***
2001 AAATGAAATTTTGGAAAGTACGGAGGTAA
1 AAATGTAATTTTGGAAAGTTTAG-GGTAA
*
2030 AAATGTAATTTTTGGATAGTTTAGGG
1 AAATGTAA-TTTTGGAAAGTTTAGGG
2056 ACCTTCAGGG
Statistics
Matches: 325, Mismatches: 78, Indels: 62
0.70 0.17 0.13
Matches are distributed among these distances:
27 8 0.02
28 67 0.21
29 142 0.44
30 84 0.26
31 24 0.07
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (28 bp):
AAATGTAATTTTGGAAAGTTTAGGGTAA
Found at i:1685 original size:58 final size:57
Alignment explanation
Indices: 1592--2042 Score: 260
Period size: 58 Copynumber: 7.7 Consensus size: 57
1582 GCAAGGGGCC
* * * *
1592 AAATGGTAATTTTGGGAAAGTTTAAGGTTTAAAATGGAATTTTTAGACATTCGAGGG-T-A
1 AAATAGTAATTTT-GGAAAGTTT-AGGGTAAAAATGGAATTTTTAGAAATT--AGGGTTAA
* * *
1651 AAATAGTAATTTTGGAAAGTTTAGGGATAAAAATGTAATTTTTAAAAAATAGGGTTCAA
1 AAATAGTAATTTTGGAAAGTTTAGGG-TAAAAATGGAATTTTTAGAAATTAGGGTT-AA
* *
1710 AAAT-GAAATTTTAGAAAGTTTAGGGGT-AAAATGGTAA-TTTTAGAAAAATTAGGGTTAA
1 AAATAGTAATTTTGGAAAGTTTA-GGGTAAAAATGG-AATTTTTAG--AAATTAGGGTTAA
* * * **
1768 AAATAG-AATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATTAAAGTTAA
1 AAATAGTAATTTTGGAAAGTT-TAGGGTAAAAATGGAATTTTT--AGAAATTAGGGTTAA
* * * * * *
1827 AAAT-GGAATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTTGTAAACTCGGGGTAA
1 AAATAGTAATTTTGGAAAGTTT-AGGGTAAAAATGGAATTTTTAG-AAATTAGGGTTAA
* * * * * ** *
1885 AAAT-GGAGTTTTGGAAAGTTTGGGGGCAAAAATGTAATTTTGGGAAAATT-GAGGTCAA
1 AAATAGTAATTTTGGAAAGTTT-AGGGTAAAAATGGAATTTTTAG-AAATTAG-GGTTAA
* * * * * * *
1943 AAAT-GGAATTTTGGAAAGTTTGGGGGT-AAAATGTAATTTTTTGAAAAATCGAGATTAA
1 AAATAGTAATTTTGGAAAGTTT-AGGGTAAAAATGGAATTTTTAG-AAATTAG-GGTTAA
* *** *
2001 AAAT-GAAATTTTGGAAAGTACGGAGGTAAAAATGTAATTTTT
1 AAATAGTAATTTTGGAAAGTTTAG-GGTAAAAATGGAATTTTT
2043 GGATAGTTTA
Statistics
Matches: 325, Mismatches: 46, Indels: 42
0.79 0.11 0.10
Matches are distributed among these distances:
56 4 0.01
57 37 0.11
58 178 0.55
59 105 0.32
61 1 0.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (57 bp):
AAATAGTAATTTTGGAAAGTTTAGGGTAAAAATGGAATTTTTAGAAATTAGGGTTAA
Found at i:1815 original size:59 final size:59
Alignment explanation
Indices: 1658--2045 Score: 395
Period size: 58 Copynumber: 6.7 Consensus size: 59
1648 GTAAAATAGT
* *
1658 AATTTTGGAAAGTTT-AGGGATAAAAATGTAATTTTT--AAAAAATAGGGTTCAAAAATGA
1 AATTTTGGAAAGTTTGAGGG-TAAAAATGTAATTTTTGGAAAAATTAGGGTT-AAAAATGG
* * *
1716 AATTTTAGAAAGTTT-AGGGGT-AAAATGGTAA-TTTTAGAAAAATTAGGGTTAAAAATAG
1 AATTTTGGAAAGTTTGA-GGGTAAAAAT-GTAATTTTTGGAAAAATTAGGGTTAAAAATGG
* **
1774 AATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATTAAAGTTAAAAATGG
1 AATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAAAATTAGGGTTAAAAATGG
* * * * * *
1833 AATTTTGGAAAGTTTAAGGGTAAAAATGTAATTTTTTG-TAAACTCGGGGTAAAAATGG
1 AATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAAAATTAGGGTTAAAAATGG
* * * * *
1891 AGTTTTGGAAAGTTTGGGGGCAAAAATGTAA-TTTTGGGAAAATT-GAGGTCAAAAATGG
1 AATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAAAATTAG-GGTTAAAAATGG
* * * * *
1949 AATTTTGGAAAGTTTGGGGGT-AAAATGTAATTTTTTGAAAAA-TCGAGATTAAAAATGA
1 AATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAAAATTAG-GGTTAAAAATGG
**
2007 AATTTTGGAAAGTACG-GAGGTAAAAATGTAATTTTTGGA
1 AATTTTGGAAAGTTTGAG-GGTAAAAATGTAATTTTTGGA
2046 TAGTTTAGGG
Statistics
Matches: 279, Mismatches: 38, Indels: 25
0.82 0.11 0.07
Matches are distributed among these distances:
57 26 0.09
58 158 0.57
59 95 0.34
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (59 bp):
AATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTGGAAAAATTAGGGTTAAAAATGG
Found at i:3215 original size:3 final size:3
Alignment explanation
Indices: 3207--3285 Score: 106
Period size: 3 Copynumber: 26.0 Consensus size: 3
3197 TTACTATCAT
3207 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
3254 TATA TTA TAA ATA ATA TTA TTAA TTA TTA TTA
1 T-TA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
3286 ATGCCTTTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
2 1 0.01
3 64 0.93
4 4 0.06
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:4021 original size:17 final size:16
Alignment explanation
Indices: 3992--4072 Score: 63
Period size: 17 Copynumber: 4.8 Consensus size: 16
3982 GGAAATTAAT
3992 TTTAAAGTTTAAAATTA
1 TTTAAA-TTTAAAATTA
* *
4009 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAAT-TA
**
4027 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAA-TTA
**
4044 TTTAAATTTAAAACAAA
1 TTTAAATTTAAAA-TTA
4061 TTTAAATTTAAA
1 TTTAAATTTAAA
4073 TTTAAAGTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
17 50 0.88
18 7 0.12
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (16 bp):
TTTAAATTTAAAATTA
Found at i:4029 original size:11 final size:12
Alignment explanation
Indices: 3987--4087 Score: 70
Period size: 11 Copynumber: 8.8 Consensus size: 12
3977 GACTTGGAAA
*
3987 TTAATTTTAAAGT
1 TTAAATTTAAA-T
*
4000 TTAAAATT--AT
1 TTAAATTTAAAT
4010 TTCAAATTTAAA-
1 TT-AAATTTAAAT
*
4022 CTAAATTTAAAT
1 TTAAATTTAAAT
**
4034 TTAAA-ACAAAT
1 TTAAATTTAAAT
4045 TTAAATTTAAA-
1 TTAAATTTAAAT
**
4056 ACAAATTTAAAT
1 TTAAATTTAAAT
4068 TTAAATTTAAA-
1 TTAAATTTAAAT
*
4079 GTAAATTTA
1 TTAAATTTA
4088 TTTAGAAATA
Statistics
Matches: 68, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
10 3 0.04
11 41 0.60
12 17 0.25
13 7 0.10
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:4034 original size:6 final size:6
Alignment explanation
Indices: 3987--4087 Score: 70
Period size: 6 Copynumber: 17.5 Consensus size: 6
3977 GACTTGGAAA
* * *
3987 TTAATT TTAAAGT TTAAAA TT--AT TTCAAAT TTAAA- CTAAAT TTAAAT
1 TTAAAT TTAAA-T TTAAAT TTAAAT TT-AAAT TTAAAT TTAAAT TTAAAT
** **
4034 TTAAA- ACAAAT TTAAAT TTAAA- ACAAAT TTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
4079 GTAAAT TTA
1 TTAAAT TTA
4088 TTTAGAAATA
Statistics
Matches: 72, Mismatches: 15, Indels: 16
0.70 0.15 0.16
Matches are distributed among these distances:
4 3 0.04
5 14 0.19
6 45 0.62
7 10 0.14
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:4049 original size:23 final size:23
Alignment explanation
Indices: 4041--4087 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
4031 AATTTAAAAC
4041 AAATTTAAATTTAAAACAAATTT
1 AAATTTAAATTTAAAACAAATTT
**
4064 AAATTTAAATTTAAAGTAAATTT
1 AAATTTAAATTTAAAACAAATTT
4087 A
1 A
4088 TTTAGAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
AAATTTAAATTTAAAACAAATTT
Found at i:4087 original size:17 final size:17
Alignment explanation
Indices: 4008--4072 Score: 105
Period size: 17 Copynumber: 3.8 Consensus size: 17
3998 GTTTAAAATT
4008 ATTTCAAATTT-AAACTAA
1 ATTT-AAATTTAAAAC-AA
4026 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
4043 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAACAA
4060 ATTTAAATTTAAA
1 ATTTAAATTTAAA
4073 TTTAAAGTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
17 38 0.83
18 8 0.17
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAACAA
Found at i:4813 original size:98 final size:98
Alignment explanation
Indices: 4572--4966 Score: 429
Period size: 98 Copynumber: 4.0 Consensus size: 98
4562 CCTTTTCTAC
* * * *
4572 TTCTGAGGTA-TAAGGTTCGCCATTACGACTTAAACCTTCCCCTTGTGTATTTGCGGTATTAGAT
1 TTCTGAGGTACT-AGGTTCGCCATTACGACTTAAACCTTTCCCTTGTGTCTTCGCGGTACTAGAT
*
4636 CCGCCGTTGCGGCTTAGATCTTTCCCTTCATG-T
65 CCGCCGTTGCAGCTTAGATCTTTCCCTTCATGTT
* * * * * **
4669 CTCTGAGGTACTAGGTTCACCATTGCCACTTAAACCTTTCCTTTGTGTCTTCGTAGTACTAGATC
1 TTCTGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCCTTGTGTCTTCGCGGTACTAGATC
* *
4734 CACCGTTGCGGCTTAGATCTTTCCCTTCATGTT
66 CGCCGTTGCAGCTTAGATCTTTCCCTTCATGTT
* * * *
4767 TTCTGAGGTACTAGGTTCTCCATTGCGACTTAAATCTTTCCCTTGTGTCTTCATTGCGGTACTGG
1 TTCTGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCCTTGTGTCTTC---GCGGTACTAG
* * *
4832 ATTCGCCGTTGTAGATTAGATCTTTCCCTTCATGTCT
63 ATCCGCCGTTGCAGCTTAGATCTTTCCCTTCATGT-T
* ** * ** * *
4869 TT-TAAGGTACTAGGTTCGCCATTACGACTT-AACCTTTCCCTCCATATCTTCTTGGCACTGGAT
1 TTCTGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCCT-TGTGTCTTCGCGGTACTAGAT
* *
4932 TCGCCGTTGCAGCTTAAATCTTTCCCTTCATGTT
65 CCGCCGTTGCAGCTTAGATCTTTCCCTTCATGTT
4966 T
1 T
4967 CACGGTACTG
Statistics
Matches: 253, Mismatches: 38, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
97 84 0.33
98 88 0.35
100 10 0.04
101 68 0.27
102 3 0.01
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.39
Consensus pattern (98 bp):
TTCTGAGGTACTAGGTTCGCCATTACGACTTAAACCTTTCCCTTGTGTCTTCGCGGTACTAGATC
CGCCGTTGCAGCTTAGATCTTTCCCTTCATGTT
Found at i:4955 original size:49 final size:49
Alignment explanation
Indices: 4827--4958 Score: 119
Period size: 49 Copynumber: 2.7 Consensus size: 49
4817 TCATTGCGGT
* * * * * *
4827 ACTGGATTCGCCGTTGTAGATTAGATCTTTCCCTTCATGTCTTTTAAGGT
1 ACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTCCATATCTTTT-AGGC
* * *
4877 ACTAGG-TTCGCCATTAC-GACTT-AACCTTTCCCTCCATATCTTCTT-GGC
1 ACT-GGATTCGCCGTTGCAG-CTTAAATCTTTCCCTCCATATCTT-TTAGGC
4925 ACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCT
1 ACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCT
4959 TCATGTTTCA
Statistics
Matches: 64, Mismatches: 12, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
47 2 0.03
48 17 0.27
49 28 0.44
50 15 0.23
51 2 0.03
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (49 bp):
ACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTCCATATCTTTTAGGC
Found at i:6821 original size:52 final size:52
Alignment explanation
Indices: 6743--6846 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
6733 CTTCTTCTAG
6743 GATTTTCTTAGCCTTGATTGCATCAATACATCTTAGCAACACCTGATCCTTT
1 GATTTTCTTAGCCTTGATTGCATCAATACATCTTAGCAACACCTGATCCTTT
6795 GATTTTCTTAGCCTTGATTGCATCAATACATCTTAGCAACACCTGATCCTTT
1 GATTTTCTTAGCCTTGATTGCATCAATACATCTTAGCAACACCTGATCCTTT
6847 CTCCTTTTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (52 bp):
GATTTTCTTAGCCTTGATTGCATCAATACATCTTAGCAACACCTGATCCTTT
Found at i:9746 original size:18 final size:18
Alignment explanation
Indices: 9705--9747 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
9695 CCAATAGTGT
9705 TTTTCTCATCTCTCGCTTC
1 TTTTC-CATCTCTCGCTTC
* **
9724 CTTTCCATCTCTTTCTTC
1 TTTTCCATCTCTCGCTTC
9742 TTTTCC
1 TTTTCC
9748 TTCACATCTG
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.05, C:0.37, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTCCATCTCTCGCTTC
Found at i:11794 original size:15 final size:15
Alignment explanation
Indices: 11753--11802 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
11743 TCGGGTCCCC
*
11753 TTTATTATTACTA-A
1 TTTATTATTATTATA
*
11767 TATTATTAATATTATA
1 T-TTATTATTATTATA
11783 TTTATTATTATTATA
1 TTTATTATTATTATA
11798 TTTAT
1 TTTAT
11803 GAAGTATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 1 0.03
15 28 0.90
16 2 0.06
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTATTATTATA
Found at i:12531 original size:23 final size:22
Alignment explanation
Indices: 12499--12545 Score: 85
Period size: 23 Copynumber: 2.1 Consensus size: 22
12489 GGACATTATT
12499 AATTTAAATAAATTTAAACTTA
1 AATTTAAATAAATTTAAACTTA
12521 AATTTCAAATAAATTTAAACTTA
1 AATTT-AAATAAATTTAAACTTA
12544 AA
1 AA
12546 ATAATTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.38
Consensus pattern (22 bp):
AATTTAAATAAATTTAAACTTA
Found at i:12535 original size:11 final size:10
Alignment explanation
Indices: 12499--12539 Score: 55
Period size: 10 Copynumber: 3.8 Consensus size: 10
12489 GGACATTATT
12499 AATTTAAATA
1 AATTTAAATA
12509 AATTTAAACTTA
1 AATTTAAA--TA
12521 AATTTCAAATA
1 AATTT-AAATA
12532 AATTTAAA
1 AATTTAAA
12540 CTTAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 11 0.39
11 7 0.25
12 7 0.25
13 3 0.11
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (10 bp):
AATTTAAATA
Found at i:12538 original size:17 final size:17
Alignment explanation
Indices: 12513--12574 Score: 81
Period size: 17 Copynumber: 3.7 Consensus size: 17
12503 TAAATAAATT
* *
12513 TAAACTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
12530 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
12547 T-AATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
12563 TAAATTTAAATT
1 TAAATTTAAATT
12575 CTGTTGGGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.37
17 24 0.63
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:12538 original size:33 final size:31
Alignment explanation
Indices: 12499--12573 Score: 78
Period size: 33 Copynumber: 2.3 Consensus size: 31
12489 GGACATTATT
* *
12499 AATTTAAATAAATTTAAACTTAAATTTCAAATA
1 AATTTAAATAAA-AT-AACTTAAATTTAAAATA
* *
12532 AATTTAAACTTAAAATAATTTAATTTTAAAATA
1 AATTTAAA--TAAAATAACTTAAATTTAAAATA
12565 AATTTAAAT
1 AATTTAAAT
12574 TCTGTTGGGC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
31 1 0.03
33 30 0.83
34 1 0.03
35 4 0.11
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (31 bp):
AATTTAAATAAAATAACTTAAATTTAAAATA
Found at i:13401 original size:209 final size:209
Alignment explanation
Indices: 13039--13483 Score: 624
Period size: 209 Copynumber: 2.1 Consensus size: 209
13029 TGATTCGGTC
* * * *
13039 TACTTCTCTGTATCTCATCAGGGAGATGACCGCCTCACTTGTTTTAATTCACTTCCCTGTTTCTC
1 TACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCCCTGTATCTC
** * * *
13104 ATCAGGAAGATGGACTTGGTCCACTTCTCTGTATCTCATCAGCAAGACGACCATTTTATTGCTTC
66 ATCAGGAAGACAGACTTGGTCAACTTCTCTGTATCTCATCAGCAAGACAACCACTTTATTGCTTC
* *
13169 GACCTACTTCTCAGTACCTCATCAAGAAGCTGGGGTTCAAAGTTTCGAC-CGCATTAAGCTTTGT
131 GACCTACTTCTCAGTACCTCATCAAGAAGCTAGGGTTCAAAGTTTCG-CTCACATTAAGCTTTGT
* *
13233 TTCATTGATTTGGCA
195 GTCATTGATTTCGCA
* * *
13248 TACTTCTTTGTATCTCATCAGGAAGATGACTGCATCACTTGTTTTAATCCACTTCTCTGTATCTC
1 TACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCCCTGTATCTC
* *
13313 ATCAGGAAGACAGATTTGGTCAACTTCTCTGTATCTCATCAAG-AAGACAACCGCTTTATTGCTT
66 ATCAGGAAGACAGACTTGGTCAACTTCTCTGTATCTCATC-AGCAAGACAACCACTTTATTGCTT
* * * * * *
13377 CGACCTGCTTCTTATTATCTCATCAAGAAGCTAGGGTTCGAAGTTTCGCTCACATTGAGCTTTGT
130 CGACCTACTTCTCAGTACCTCATCAAGAAGCTAGGGTTCAAAGTTTCGCTCACATTAAGCTTTGT
*
13442 GTCATTGATTTCGTA
195 GTCATTGATTTCGCA
*
13457 TACTTCTCTGTATCTCATGAGGAAGAT
1 TACTTCTCTGTATCTCATCAGGAAGAT
13484 AGATTTGGTC
Statistics
Matches: 207, Mismatches: 27, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
208 1 0.00
209 204 0.99
210 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (209 bp):
TACTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCACTTCCCTGTATCTC
ATCAGGAAGACAGACTTGGTCAACTTCTCTGTATCTCATCAGCAAGACAACCACTTTATTGCTTC
GACCTACTTCTCAGTACCTCATCAAGAAGCTAGGGTTCAAAGTTTCGCTCACATTAAGCTTTGTG
TCATTGATTTCGCA
Found at i:13482 original size:160 final size:160
Alignment explanation
Indices: 13298--13814 Score: 642
Period size: 160 Copynumber: 3.2 Consensus size: 160
13288 GTTTTAATCC
* *
13298 ACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTCAACTTCTCTGTATCTCATCAAGAAGACAA
1 ACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTCAACTTCTCTGTATCTCATCAGGAAGACGA
* * * *
13363 CCGCTTTATTGCTTCGACCTGCTTCTTATTATCTCATCAAGAAGCTAGGGTTCGAAGTTTCGCTC
66 CCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTC
* * *
13428 ACATTGAGCTTTGTGTCATTGATTTCGTAT
131 ATATTGAGCTTTGTTTCATTGATTTGGTAT
* * *
13458 ACTTCTCTGTATCTCATGAGGAAGATAGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACGA
1 ACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTCAACTTCTCTGTATCTCATCAGGAAGACGA
* * *
13523 TCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTTGAAGTTTCGCTC
66 CCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTC
13588 ATATTGAGCTTTGTTTCATTGATTTGGTAT
131 ATATTGAGCTTTGTTTCATTGATTTGGTAT
* ** * *
13618 ACTTCTCTGTA-CATCATCAGGAAGATGACCGCATCACTTATTTTAATCCGCTTCTCTATATCTC
1 ACTTCTCTGTATC-TCATCAGG-A-A-GACAG-AT---TT-GGTCAA----CTTCTCTGTATCTC
** * * *
13682 ATCAGGAAGACGACCATTTTATTACTTCGACCTGCTCCTCAGTACCTCATCAGGAAGC-CGAGGT
53 ATCAGGAAGACGACCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAG-GGT
*
13746 TCAAAGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTAT
117 TCGAAGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTAT
* *
13790 ACTTCTCTATATCTCATCAAGAAGA
1 ACTTCTCTGTATCTCATCAGGAAGA
13815 TTACCGCATC
Statistics
Matches: 309, Mismatches: 33, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
159 1 0.00
160 163 0.53
161 1 0.00
162 1 0.00
163 3 0.01
164 2 0.01
167 2 0.01
168 2 0.01
169 2 0.01
170 1 0.00
171 2 0.01
172 128 0.41
173 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (160 bp):
ACTTCTCTGTATCTCATCAGGAAGACAGATTTGGTCAACTTCTCTGTATCTCATCAGGAAGACGA
CCGCTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTCGCTC
ATATTGAGCTTTGTTTCATTGATTTGGTAT
Found at i:13782 original size:172 final size:172
Alignment explanation
Indices: 13492--13863 Score: 584
Period size: 172 Copynumber: 2.2 Consensus size: 172
13482 ATAGATTTGG
* * * * *
13492 TCCACTTCTCTGTATCTCATCAGGAAGACGATCGCTTTATTACTTCGACCTGCTTCTCAGTATCT
1 TCCACTTCTCTATATCTCATCAGGAAGACGACCACTTTATTACTTCGACCTGCTCCTCAGTACCT
* * **
13557 CATCAGGAAGCTGGGGTTTGAAGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTATACTT
66 CATCAGGAAGCCGAGGTTCAAAGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTATACTT
* *
13622 CTCTGTA-CATCATCAGGAAGATGACCGCATCACTTATTTTAA
131 CTCTATATC-TCATCAAGAAGATGACCGCATCACTTATTTTAA
* *
13664 TCCGCTTCTCTATATCTCATCAGGAAGACGACCATTTTATTACTTCGACCTGCTCCTCAGTACCT
1 TCCACTTCTCTATATCTCATCAGGAAGACGACCACTTTATTACTTCGACCTGCTCCTCAGTACCT
13729 CATCAGGAAGCCGAGGTTCAAAGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTATACTT
66 CATCAGGAAGCCGAGGTTCAAAGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTATACTT
* *
13794 CTCTATATCTCATCAAGAAGATTACCGCATCACTTGTTTTAA
131 CTCTATATCTCATCAAGAAGATGACCGCATCACTTATTTTAA
*
13836 TCCACTTCTCTATATCTCATTAGGAAGA
1 TCCACTTCTCTATATCTCATCAGGAAGA
13864 TGGATTTTGT
Statistics
Matches: 182, Mismatches: 17, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
172 181 0.99
173 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.37
Consensus pattern (172 bp):
TCCACTTCTCTATATCTCATCAGGAAGACGACCACTTTATTACTTCGACCTGCTCCTCAGTACCT
CATCAGGAAGCCGAGGTTCAAAGTTTCGCTCATATTGAGCTTTGTTTCATTGATTTGGTATACTT
CTCTATATCTCATCAAGAAGATGACCGCATCACTTATTTTAA
Found at i:14030 original size:42 final size:37
Alignment explanation
Indices: 13943--14036 Score: 98
Period size: 37 Copynumber: 2.4 Consensus size: 37
13933 TGCCCCATGA
* * *
13943 TCGGGGTAAGAGATTGGATGGTTGTGATCTACCTATG
1 TCGGGGTAAGAGATCGGATGGTTGTGATCTACCCAAG
*
13980 TCGGGGTAAGAGATCGGGTGGCTGATGATGATCTACCCAAG
1 TCGGGGTAAGAGATCGGATGG-T--TG-TGATCTACCCAAG
*
14021 CTCGGGGTAAAAGATC
1 -TCGGGGTAAGAGATC
14037 AAATGACTGA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
37 19 0.40
38 1 0.02
40 2 0.04
41 11 0.23
42 14 0.30
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.26
Consensus pattern (37 bp):
TCGGGGTAAGAGATCGGATGGTTGTGATCTACCCAAG
Found at i:14169 original size:39 final size:39
Alignment explanation
Indices: 13930--14347 Score: 131
Period size: 39 Copynumber: 10.7 Consensus size: 39
13920 GATAACTGCA
* * * *
13930 ATCTGCCCCATGATCGGGGTAAGAGATTGGATGGTTG-TG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCT-GATGATG
* * *
13969 ATCT-ACCTATG-TCGGGGTAAGAGATCGGGTGGCTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT----TGGCTGATGATG
* * * **** *
14010 ATCT-ACCCAAGCTCGGGGTAAAAGATCAAATGACTGA-A
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGA-TGATG
* * * *
14048 ATCTGCCCTAGCCTCGGGGTAAAAGATTGGCTAATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* ** * * * * * ** *
14087 ATTTGCCTTAGGCTAGAGGTAAAATATCGAATG--GCAGTA
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATG-A-TG
* *
14126 ATCTGCCCCAGGCTTGGGGTAAGAGATTGGTTGATGATG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
** * * * *
14165 ATCTGCCTTAGGCTTGAGGTAAAAGA-T--CTGATGGCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGAT-GATG
* * * ** * *
14202 CAATCTGTCTCAAGCTCGGGGTAAGAGATTTACTGGTGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * * * * * *
14243 ATTTGCCACAAGCTCGAGGTAAGAGATCGGATG--GCTG
1 ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
*
14280 CAATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGGTG
1 --ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
* * *
14321 ATTTGCCCCGGGCTCGGGGTAAAAGAT
1 ATCTGCCCCAGGCTCGGGGTAAGAGAT
14348 CGGAATCTTC
Statistics
Matches: 279, Mismatches: 77, Indels: 46
0.69 0.19 0.11
Matches are distributed among these distances:
36 4 0.01
37 21 0.08
38 17 0.06
39 193 0.69
40 5 0.02
41 22 0.08
42 17 0.06
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.26
Consensus pattern (39 bp):
ATCTGCCCCAGGCTCGGGGTAAGAGATTGGCTGATGATG
Found at i:14336 original size:78 final size:78
Alignment explanation
Indices: 13980--14351 Score: 359
Period size: 78 Copynumber: 4.7 Consensus size: 78
13970 TCTACCTATG
* * * * ** *
13980 TCGGGGTAAGAGATCGGGTGGCTGATGATGATCTACC-CAAGCTCGGGGTAAAAGATCAAATGAC
1 TCGGGGTAAGAGAT----TGGCTGATGATGATTTGCCTCAGGCTCGAGGTAAAAGATCGGATGGC
* * *
14044 TGAAATCTGCCCTAGCC
62 TGCAATCTGCCCCAGGC
* * * * * * * *
14061 TCGGGGTAAAAGATTGGCTAATGATGATTTGCCTTAGGCTAGAGGTAAAATATCGAATGGCAGTA
1 TCGGGGTAAGAGATTGGCTGATGATGATTTGCCTCAGGCTCGAGGTAAAAGATCGGATGGCTGCA
14126 ATCTGCCCCAGGC
66 ATCTGCCCCAGGC
* * * * * *
14139 TTGGGGTAAGAGATTGGTTGATGATGATCTGCCTTAGGCTTGAGGTAAAAGATCTGATGGCTGCA
1 TCGGGGTAAGAGATTGGCTGATGATGATTTGCCTCAGGCTCGAGGTAAAAGATCGGATGGCTGCA
* * *
14204 ATCTGTCTCAAGC
66 ATCTGCCCCAGGC
** * * * * *
14217 TCGGGGTAAGAGATTTACTGGTGGTGATTTGCCACAAGCTCGAGGTAAGAGATCGGATGGCTGCA
1 TCGGGGTAAGAGATTGGCTGATGATGATTTGCCTCAGGCTCGAGGTAAAAGATCGGATGGCTGCA
14282 ATCTGCCCCAGGC
66 ATCTGCCCCAGGC
* * * *
14295 TCGGGGTAAGAGATTGGCTGATGGTGATTTGCCCCGGGCTCGGGGTAAAAGATCGGA
1 TCGGGGTAAGAGATTGGCTGATGATGATTTGCCTCAGGCTCGAGGTAAAAGATCGGA
14352 ATCTTCATTC
Statistics
Matches: 237, Mismatches: 53, Indels: 5
0.80 0.18 0.02
Matches are distributed among these distances:
77 16 0.07
78 208 0.88
81 13 0.05
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.25
Consensus pattern (78 bp):
TCGGGGTAAGAGATTGGCTGATGATGATTTGCCTCAGGCTCGAGGTAAAAGATCGGATGGCTGCA
ATCTGCCCCAGGC
Found at i:14668 original size:99 final size:99
Alignment explanation
Indices: 14560--14884 Score: 454
Period size: 99 Copynumber: 3.3 Consensus size: 99
14550 TAAGATATCG
* * * * * *
14560 GGTTCGCCATTGCAGCCTCAACTTTTCCCTTCATATCTTTTAAGGTTCCAGGTTTGTCGTTGCGG
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACCAGGTTCGCCGTTGCGG
* *
14625 CCCCAACCTTTCCCTTAAAATCTTCATGGTACCGG
66 CCACAACCTTTCCCTTAAAATCTTCATGGTACC-A
*
14660 GGTT-GCCATTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACTAGGTTCGCCGTTGCGG
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACCAGGTTCGCCGTTGCGG
* *
14724 CCTCAACCTTTCCTTTAAAATCTTCATGGTACCA
66 CCACAACCTTTCCCTTAAAATCTTCATGGTACCA
* * * * * * *
14758 GGTTCACCATTGCGACCTCAATCTTTCCCTTCAAATCTTCTAAGGTACCAGGTTCGCCATTACGA
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACCAGGTTCGCCGTTGCGG
*
14823 CCACAGCCTTTCCCTTAAAATCTTCATGGTACCA
66 CCACAACCTTTCCCTTAAAATCTTCATGGTACCA
*
14857 GGTTCGCCATTACGGCCTCAACCTTTCC
1 GGTTCGCCATTGCGGCCTCAACCTTTCC
14885 TATCACATTT
Statistics
Matches: 199, Mismatches: 25, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
98 4 0.02
99 191 0.96
100 4 0.02
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.33
Consensus pattern (99 bp):
GGTTCGCCATTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACCAGGTTCGCCGTTGCGG
CCACAACCTTTCCCTTAAAATCTTCATGGTACCA
Found at i:14681 original size:49 final size:49
Alignment explanation
Indices: 14560--14884 Score: 355
Period size: 49 Copynumber: 6.6 Consensus size: 49
14550 TAAGATATCG
* * * * * *
14560 GGTTCGCCATTGCAGCCTCAACTTTTCCCTTCATATCTTTTAAGGTTCCA
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTAAAATC-TTCAAGGTACCA
* * * * * *
14610 GGTTTGTCGTTGCGGCCCCAACCTTTCCCTTAAAATCTTCATGGTACCGG
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTAAAATCTTCAAGGTACC-A
* * *
14660 GGTT-GCCATTGCGGCCTCAACCTTTCCCTTCATATCTTCTAAGGTACTA
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTAAAATCTTC-AAGGTACCA
* * *
14709 GGTTCGCCGTTGCGGCCTCAACCTTTCCTTTAAAATCTTCATGGTACCA
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTAAAATCTTCAAGGTACCA
* * * *
14758 GGTTCACCATTGCGACCTCAATCTTTCCCTTCAAATCTTCTAAGGTACCA
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTAAAATCTTC-AAGGTACCA
* * * * *
14808 GGTTCGCCATTACGACCACAGCCTTTCCCTTAAAATCTTCATGGTACCA
1 GGTTCGCCATTGCGGCCTCAACCTTTCCCTTAAAATCTTCAAGGTACCA
*
14857 GGTTCGCCATTACGGCCTCAACCTTTCC
1 GGTTCGCCATTGCGGCCTCAACCTTTCC
14885 TATCACATTT
Statistics
Matches: 228, Mismatches: 43, Indels: 9
0.81 0.15 0.03
Matches are distributed among these distances:
49 116 0.51
50 112 0.49
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.33
Consensus pattern (49 bp):
GGTTCGCCATTGCGGCCTCAACCTTTCCCTTAAAATCTTCAAGGTACCA
Found at i:15025 original size:50 final size:50
Alignment explanation
Indices: 14921--15025 Score: 113
Period size: 50 Copynumber: 2.1 Consensus size: 50
14911 CCATTACGAC
* * * ** * *
14921 CTCAATCTTTCCAATCACATCTTCTGAGGTACCGGGTTCGTCGTTGCCGC
1 CTCAACCTTTCCAATCACATCTTCTAAGGTACCGGATTCACCGTCGCCGA
**
14971 CTCAACCTTTCCTGTCACATCTTCTAAGGTACCGGATTCACCGTCG-CGAA
1 CTCAACCTTTCCAATCACATCTTCTAAGGTACCGGATTCACCGTCGCCG-A
15021 CTCAA
1 CTCAA
15026 TCATTCCCTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
49 2 0.04
50 43 0.96
ACGTcount: A:0.20, C:0.33, G:0.17, T:0.30
Consensus pattern (50 bp):
CTCAACCTTTCCAATCACATCTTCTAAGGTACCGGATTCACCGTCGCCGA
Found at i:15963 original size:7 final size:6
Alignment explanation
Indices: 15951--16043 Score: 54
Period size: 6 Copynumber: 15.3 Consensus size: 6
15941 TGACCTCTCC
* * *
15951 TTTTCT ATTTTCT TTTTCT TTTT-T TATT-T TTTCCT TTTT-T TCTTTTT
1 TTTTCT -TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT T-TTTCT
15998 TTTTC- TTTTCT TTCTT-T TGTATTCT TTTTCT TTCTT-T CTTTTCT TT
1 TTTTCT TTTTCT TT-TTCT T-T-TTCT TTTTCT TT-TTCT -TTTTCT TT
16044 CTTTTTTATT
Statistics
Matches: 70, Mismatches: 6, Indels: 21
0.72 0.06 0.22
Matches are distributed among these distances:
5 14 0.20
6 35 0.50
7 19 0.27
8 2 0.03
ACGTcount: A:0.03, C:0.15, G:0.01, T:0.81
Consensus pattern (6 bp):
TTTTCT
Found at i:15986 original size:34 final size:35
Alignment explanation
Indices: 15948--16050 Score: 92
Period size: 34 Copynumber: 3.0 Consensus size: 35
15938 CCTTGACCTC
15948 TCCTTTTCTAT-TTTCTTTTTCTTTT-TTTATTTTT
1 TCCTTTT-TATCTTTCTTTTTCTTTTCTTTATTTTT
* * *
15982 TCCTTTTTTTCTTTTTTTTTCTTTTCTTTCTTTTGT
1 TCCTTTTTATCTTTCTTTTTCTTTTCTTTATTTT-T
* *
16018 ATTC-TTTT-TCTTTC--TTTCTTTTCTTTCTTTTT
1 -TCCTTTTTATCTTTCTTTTTCTTTTCTTTATTTTT
16050 T
1 T
16051 ATTTATTTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 11
0.79 0.07 0.14
Matches are distributed among these distances:
31 1 0.02
32 1 0.02
33 19 0.32
34 20 0.33
35 12 0.20
36 5 0.08
37 2 0.03
ACGTcount: A:0.03, C:0.17, G:0.01, T:0.80
Consensus pattern (35 bp):
TCCTTTTTATCTTTCTTTTTCTTTTCTTTATTTTT
Found at i:15987 original size:16 final size:15
Alignment explanation
Indices: 15963--16066 Score: 64
Period size: 16 Copynumber: 6.4 Consensus size: 15
15953 TTCTATTTTC
15963 TTTTTCTTTTTTTAT
1 TTTTTCTTTTTTTAT
*
15978 TTTTTCCTTTTTTTCTTTT
1 TTTTT-C--TTTTT-TTAT
*
15997 TTTTTCTTTTCTTTCT
1 TTTTTCTTTT-TTTAT
* * *
16013 TTTGTATTCTTTTTCT
1 TTTTTCTT-TTTTTAT
*
16029 TTCTTTCTTTTCTTTCT
1 TT-TTTCTTTT-TTTAT
* *
16046 TTTTTATTTATTTAT
1 TTTTTCTTTTTTTAT
16061 TTTTTC
1 TTTTTC
16067 ATTGAATCCA
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
15 14 0.20
16 29 0.41
17 14 0.20
18 6 0.08
19 8 0.11
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (15 bp):
TTTTTCTTTTTTTAT
Found at i:15990 original size:10 final size:9
Alignment explanation
Indices: 15958--16049 Score: 76
Period size: 10 Copynumber: 9.4 Consensus size: 9
15948 TCCTTTTCTA
15958 TTTTCTTTTT
1 TTTTC-TTTT
*
15968 CTTTTTTTATT
1 -TTTTCTT-TT
*
15979 TTTTCCTTT
1 TTTTCTTTT
15988 TTTTCTTTTT
1 TTTTC-TTTT
15998 TTTTCTTTT
1 TTTTCTTTT
*
16007 CTTTCTTTT
1 TTTTCTTTT
*
16016 GTATTCTTTT
1 -TTTTCTTTT
*
16026 TCTTTCTTTC
1 T-TTTCTTTT
16036 TTTTCTTTCT
1 TTTTCTTT-T
16046 TTTT
1 TTTT
16050 TATTTATTTA
Statistics
Matches: 66, Mismatches: 10, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
9 27 0.41
10 33 0.50
11 6 0.09
ACGTcount: A:0.02, C:0.15, G:0.01, T:0.82
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:16011 original size:4 final size:4
Alignment explanation
Indices: 15965--16047 Score: 50
Period size: 4 Copynumber: 20.8 Consensus size: 4
15955 CTATTTTCTT
* * *
15965 TTTC TTTT TTTA TTT- TTTCC TTTT TTTC TTT- TTT- TTTC TTTTC TTTC
1 TTTC TTTC TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC -TTTC TTTC
*
16012 TTTTG TATTC -TT- TTTC TTTC TTTC TTTTC TTTC TTT
1 -TTTC T-TTC TTTC TTTC TTTC TTTC -TTTC TTTC TTT
16048 TTTATTTATT
Statistics
Matches: 64, Mismatches: 6, Indels: 18
0.73 0.07 0.20
Matches are distributed among these distances:
3 13 0.20
4 35 0.55
5 16 0.25
ACGTcount: A:0.02, C:0.16, G:0.01, T:0.81
Consensus pattern (4 bp):
TTTC
Found at i:16011 original size:19 final size:19
Alignment explanation
Indices: 15958--16047 Score: 87
Period size: 19 Copynumber: 4.7 Consensus size: 19
15948 TCCTTTTCTA
*
15958 TTTTCTTTTTCTTTTTTTATT
1 TTTTC-TTTTCTTTCTTT-TT
15979 TTTTCCTTTT-TTTCTTTTT
1 TTTT-CTTTTCTTTCTTTTT
*
15998 TTTTCTTTTCTTTCTTTTG
1 TTTTCTTTTCTTTCTTTTT
* *
16017 TATTCTTTTTCTTTC-TTTC
1 TTTTC-TTTTCTTTCTTTTT
16036 TTTTC-TTTCTTT
1 TTTTCTTTTCTTT
16048 TTTATTTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.11
18 5 0.08
19 25 0.41
20 15 0.25
21 8 0.13
22 1 0.02
ACGTcount: A:0.02, C:0.16, G:0.01, T:0.81
Consensus pattern (19 bp):
TTTTCTTTTCTTTCTTTTT
Found at i:16063 original size:24 final size:24
Alignment explanation
Indices: 15959--16063 Score: 83
Period size: 24 Copynumber: 4.3 Consensus size: 24
15949 CCTTTTCTAT
*
15959 TTTCTTTTTCTTT-TTTTATTTTTTCC
1 TTTC-TTTTCTTTCTTTT-TTATTT-C
*
15985 TTT-TTTTCTTT-TTTTTTCTTTTC
1 TTTCTTTTCTTTCTTTTTT-ATTTC
* *
16008 TTTCTTTTGTATTC-TTTTTCTTTC
1 TTTCTTTTCT-TTCTTTTTTATTTC
*
16032 TTTCTTTTCTTTCTTTTTTATTTA
1 TTTCTTTTCTTTCTTTTTTATTTC
*
16056 TTTATTTT
1 TTTCTTTT
16064 TTCATTGAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
23 9 0.13
24 49 0.72
25 7 0.10
26 3 0.04
ACGTcount: A:0.05, C:0.13, G:0.01, T:0.81
Consensus pattern (24 bp):
TTTCTTTTCTTTCTTTTTTATTTC
Found at i:20723 original size:97 final size:97
Alignment explanation
Indices: 20557--20750 Score: 298
Period size: 97 Copynumber: 2.0 Consensus size: 97
20547 AAACCTTAGA
* *
20557 AAAGGGTATTCGATTATCCCGATTTGAAGAAAAGTCACGCCTAGTAAGTAAAGGCACAAATGTTC
1 AAAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACACCTAGTAAGTAAAGGCACAAATGTTC
20622 AAAACCAGAGATAAAGAAACATTACCTCGATT
66 AAAACCAGAGATAAAGAAACATTACCTCGATT
* * * *
20654 AAAGGGTATTTGATTATCCCGGTTTGAAGAAAAATCACACCTAGTAAGTTAAGGCACAAATTTTC
1 AAAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACACCTAGTAAGTAAAGGCACAAATGTTC
* * * *
20719 AAAACCCGAGATAAAGGAATATTGCCTCGATT
66 AAAACCAGAGATAAAGAAACATTACCTCGATT
20751 TTAAATATTT
Statistics
Matches: 87, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
97 87 1.00
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.25
Consensus pattern (97 bp):
AAAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACACCTAGTAAGTAAAGGCACAAATGTTC
AAAACCAGAGATAAAGAAACATTACCTCGATT
Found at i:21179 original size:29 final size:29
Alignment explanation
Indices: 21128--21339 Score: 190
Period size: 29 Copynumber: 7.5 Consensus size: 29
21118 ATTCGAGGGC
21128 AAAATGGTAA-TTTTGGATGTTCAGGAGT
1 AAAATGGTAATTTTTGGATGTTCAGGAGT
* * *
21156 AAGATGGTAATTTTTGGATATTCA-GAGGG
1 AAAATGGTAATTTTTGGATGTTCAGGA-GT
*
21185 AAAATGGTGATTTTTGGATGTTCGAGGA-T
1 AAAATGGTAATTTTTGGATGTTC-AGGAGT
* * * *
21214 AAAATGGTGATTTTTGGATGTTTAGGGGC
1 AAAATGGTAATTTTTGGATGTTCAGGAGT
21243 AAAATGGTAA-TTTTGGATGTTC-GG-GT
1 AAAATGGTAATTTTTGGATGTTCAGGAGT
* * ** *
21269 AAAATGGTAATTTTTAGAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGATGTTCAGGAGT
* *
21298 AAAAT-GTAATTTTTGAGAAGTTTAGG-GT
1 AAAATGGTAATTTTTG-GATGTTCAGGAGT
*
21326 AAAAT-GTGATTTTT
1 AAAATGGTAATTTTT
21340 AAAAGTTTGA
Statistics
Matches: 156, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
26 11 0.07
27 11 0.07
28 51 0.33
29 80 0.51
30 1 0.01
31 2 0.01
ACGTcount: A:0.30, C:0.02, G:0.29, T:0.38
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGATGTTCAGGAGT
Found at i:21184 original size:58 final size:58
Alignment explanation
Indices: 21104--21283 Score: 237
Period size: 58 Copynumber: 3.2 Consensus size: 58
21094 AGTCGAAAGT
* *
21104 GTAATTTTTTGGAAATTC-GAGGGCAAAATGGTAATTTTGGATGTTCAGGAGTAAGATG
1 GTAA-TTTTTGGATATTCAGAGGGCAAAATGGTAATTTTGGATGTTCAGGAGTAAAATG
*
21162 GTAATTTTTGGATATTCAGAGGG-AAAATGGTGATTTTTGGATGTTCGAGGA-TAAAATG
1 GTAATTTTTGGATATTCAGAGGGCAAAATGGT-AATTTTGGATGTTC-AGGAGTAAAATG
* * *
21220 GTGATTTTTGGATGTTTAG-GGGCAAAATGGTAATTTTGGATGTTC-GG-GTAAAATG
1 GTAATTTTTGGATATTCAGAGGGCAAAATGGTAATTTTGGATGTTCAGGAGTAAAATG
21275 GTAATTTTT
1 GTAATTTTT
21284 AGAAGTTTGG
Statistics
Matches: 109, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
55 17 0.16
57 36 0.33
58 52 0.48
59 4 0.04
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.38
Consensus pattern (58 bp):
GTAATTTTTGGATATTCAGAGGGCAAAATGGTAATTTTGGATGTTCAGGAGTAAAATG
Found at i:21321 original size:84 final size:87
Alignment explanation
Indices: 21104--21324 Score: 218
Period size: 84 Copynumber: 2.6 Consensus size: 87
21094 AGTCGAAAGT
* * ** * * * * *
21104 GTAATTTTTTGGAAATTCGAGGGCAAAATGGTAA-TTTTGGATGTTCAGGAGTAAGATGGTAATT
1 GTAA-TTTTTAGAAGTTCGAGGATAAAATGGTAATTTTTGGAAGTTTAGGGGCAAAATGGTAATT
21168 TTTGGATATTCAGAGGGAAAATG
65 TTTGGATATTCAGAGGGAAAATG
* * * * *
21191 GTGATTTTTGGATGTTCGAGGATAAAATGGTGATTTTTGGATGTTTAGGGGCAAAATGGTAA-TT
1 GTAATTTTTAGAAGTTCGAGGATAAAATGGTAATTTTTGGAAGTTTAGGGGCAAAATGGTAATTT
* *
21255 TTGGATGTTC-G-GGTAAAATG
66 TTGGATATTCAGAGGGAAAATG
* * *
21275 GTAATTTTTAGAAGTTTGGGGGTAAAAT-GTAATTTTTGAGAAGTTTAGGG
1 GTAATTTTTAGAAGTTCGAGGATAAAATGGTAATTTTTG-GAAGTTTAGGG
21325 TAAAATGTGA
Statistics
Matches: 112, Mismatches: 20, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
83 9 0.08
84 40 0.36
85 1 0.01
86 35 0.31
87 27 0.24
ACGTcount: A:0.29, C:0.03, G:0.30, T:0.37
Consensus pattern (87 bp):
GTAATTTTTAGAAGTTCGAGGATAAAATGGTAATTTTTGGAAGTTTAGGGGCAAAATGGTAATTT
TTGGATATTCAGAGGGAAAATG
Found at i:21398 original size:29 final size:29
Alignment explanation
Indices: 21366--21464 Score: 130
Period size: 29 Copynumber: 3.4 Consensus size: 29
21356 AATGTAACAA
*
21366 TTGAAAGGTTAGGGGT-AAGAATGTATTTT
1 TTGAAAGTTTAGGGGTCAA-AATGTATTTT
*
21395 TTGAAAGTTTA-GGGTCAAAATGTAATTT
1 TTGAAAGTTTAGGGGTCAAAATGTATTTT
21423 TTGAGAAGTTTAGGGGTCAAAATGTAATTTT
1 TTGA-AAGTTTAGGGGTCAAAATGT-ATTTT
*
21454 TGGAAAGTTTA
1 TTGAAAGTTTA
21465 AGTGTTAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 7
0.85 0.05 0.10
Matches are distributed among these distances:
28 17 0.27
29 19 0.31
30 19 0.31
31 7 0.11
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
TTGAAAGTTTAGGGGTCAAAATGTATTTT
Found at i:21442 original size:30 final size:29
Alignment explanation
Indices: 21213--21485 Score: 212
Period size: 28 Copynumber: 9.6 Consensus size: 29
21203 TGTTCGAGGA
* *
21213 TAAAATGGTGATTTTTG-GATGTTTAGGGG
1 TAAAAT-GTAATTTTTGAGAAGTTTAGGGG
* * *
21242 CAAAATGGTAA-TTTTG-GATG-TT-CGGG
1 TAAAAT-GTAATTTTTGAGAAGTTTAGGGG
*
21268 TAAAATGGTAATTTTT-AGAAGTTTGGGGG
1 TAAAAT-GTAATTTTTGAGAAGTTTAGGGG
21297 TAAAATGTAATTTTTGAGAAGTTTA-GGG
1 TAAAATGTAATTTTTGAGAAGTTTAGGGG
* * *
21325 TAAAATGTGATTTTT-AAAAGTTT-GAGTG
1 TAAAATGTAATTTTTGAGAAGTTTAG-GGG
* *** *
21353 AAAAATGTAACAATTGA-AAGGTTAGGGG
1 TAAAATGTAATTTTTGAGAAGTTTAGGGG
*
21381 TAAGAATGTATTTTTTGA-AAGTTTA-GGG
1 TAA-AATGTAATTTTTGAGAAGTTTAGGGG
21409 TCAAAATGTAATTTTTGAGAAGTTTAGGGG
1 T-AAAATGTAATTTTTGAGAAGTTTAGGGG
* *
21439 TCAAAATGTAATTTTTG-GAAAGTTTAAGTGT
1 T-AAAATGTAATTTTTGAG-AAGTTT-AGGGG
*
21470 TAAAATATAATTTTTG
1 TAAAATGTAATTTTTG
21486 GATAATTTAG
Statistics
Matches: 202, Mismatches: 27, Indels: 29
0.78 0.10 0.11
Matches are distributed among these distances:
26 13 0.06
27 16 0.08
28 75 0.37
29 54 0.27
30 40 0.20
31 4 0.02
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (29 bp):
TAAAATGTAATTTTTGAGAAGTTTAGGGG
Found at i:21496 original size:60 final size:58
Alignment explanation
Indices: 21294--21497 Score: 154
Period size: 60 Copynumber: 3.6 Consensus size: 58
21284 AGAAGTTTGG
* * *
21294 GGGT-AAAATGTAATTTTTGAGAAGTTTA-GGGTAA-AATGTGATTTTT-AAAAGTTT-
1 GGGTCAAAATATAATTTTTGAGAAATTTAGGGGTAAGAATGT-ATTTTTGGAAAGTTTA
* * * *** ** *
21348 GAGTGAAAAATGTAACAATTGA-AAGGTTAGGGGTAAGAATGTATTTTTTGAAAGTTTA
1 GGGT-CAAAATATAATTTTTGAGAAATTTAGGGGTAAGAATGTATTTTTGGAAAGTTTA
* *
21406 GGGTCAAAATGTAATTTTTGAGAAGTTTAGGGGTCAA-AATGTAATTTTTGGAAAGTTTAA
1 GGGTCAAAATATAATTTTTGAGAAATTTAGGGGT-AAGAATGT-ATTTTTGGAAAGTTT-A
* *
21466 GTGTTAAAATATAATTTTTG-GATAATTTAGGG
1 GGGTCAAAATATAATTTTTGAGA-AATTTAGGG
21498 ACCTTTTGGG
Statistics
Matches: 122, Mismatches: 17, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
54 3 0.02
55 6 0.05
56 25 0.20
57 25 0.20
58 19 0.16
59 18 0.15
60 26 0.21
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (58 bp):
GGGTCAAAATATAATTTTTGAGAAATTTAGGGGTAAGAATGTATTTTTGGAAAGTTTA
Found at i:22186 original size:19 final size:18
Alignment explanation
Indices: 22145--22192 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
22135 AGGTAAAAAG
* *
22145 CTTTTTTTTTTGTTTTTC
1 CTTTTTTTTTCGTTATTC
*
22163 ATTTTCTTTTTCGTTATTC
1 CTTTT-TTTTTCGTTATTC
22182 CTTTTTTTTTC
1 CTTTTTTTTTC
22193 AATTTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 15 0.60
ACGTcount: A:0.04, C:0.15, G:0.04, T:0.77
Consensus pattern (18 bp):
CTTTTTTTTTCGTTATTC
Found at i:22355 original size:23 final size:25
Alignment explanation
Indices: 22311--22356 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
22301 ATTTTTTTTA
22311 AAAATCCTATTTTATTATTCCATGC
1 AAAATCCTATTTTATTATTCCATGC
*
22336 AAAAT-CTGTTTT-TTATTCCAT
1 AAAATCCTATTTTATTATTCCAT
22357 TTTTTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.48
Consensus pattern (25 bp):
AAAATCCTATTTTATTATTCCATGC
Found at i:22620 original size:15 final size:15
Alignment explanation
Indices: 22579--22628 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
22569 TTTCGAGTCC
*
22579 TTTATTATTACTA-A
1 TTTATTATTATTATA
*
22593 TATTATTACTATTATA
1 T-TTATTATTATTATA
22609 TTTATTATTATTATA
1 TTTATTATTATTATA
22624 TTTAT
1 TTTAT
22629 GAAGTATTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 1 0.03
15 28 0.90
16 2 0.06
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTATTATTATTATA
Found at i:23363 original size:11 final size:10
Alignment explanation
Indices: 23327--23384 Score: 59
Period size: 10 Copynumber: 5.8 Consensus size: 10
23317 GGACATTATT
23327 AATTTAAATA
1 AATTTAAATA
23337 AATTTAAACTTA
1 AATTTAAA--TA
23349 AATTTATAATA
1 AATTTA-AATA
23360 AATTTAAAT-
1 AATTTAAATA
*
23369 --TTCAAATA
1 AATTTAAATA
23377 AATTTAAA
1 AATTTAAA
23385 CTTAAAATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
7 6 0.15
10 16 0.40
11 8 0.20
12 8 0.20
13 2 0.05
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
AATTTAAATA
Found at i:23366 original size:17 final size:17
Alignment explanation
Indices: 23341--23412 Score: 99
Period size: 17 Copynumber: 4.2 Consensus size: 17
23331 TAAATAAATT
* *
23341 TAAACTTAAATTTATAA
1 TAAATTTAAATTTAAAA
*
23358 TAAATTTAAATTTCAAA
1 TAAATTTAAATTTAAAA
*
23375 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
23392 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
23409 TAAA
1 TAAA
23413 GTCTGTTGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 48 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:23367 original size:6 final size:6
Alignment explanation
Indices: 23327--23407 Score: 59
Period size: 6 Copynumber: 14.3 Consensus size: 6
23317 GGACATTATT
*
23327 AATTTA AA--TA AATTTA AACTTA AATTTA TAA--TA AATTTA AATTTCA
1 AATTTA AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTT-A
* * *
23373 AA--TA AATTTA AACTTA AA-ATA AATTTA ATTTTA AA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AA
23408 ATAAAGTCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
4 9 0.15
5 7 0.12
6 38 0.64
7 5 0.08
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (6 bp):
AATTTA
Found at i:23854 original size:11 final size:11
Alignment explanation
Indices: 23838--23863 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
23828 ATCAAAAAAA
23838 AGAAAGAAGAG
1 AGAAAGAAGAG
23849 AGAAAGAAGAG
1 AGAAAGAAGAG
23860 AGAA
1 AGAA
23864 CAGAGGATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (11 bp):
AGAAAGAAGAG
Found at i:24243 original size:30 final size:30
Alignment explanation
Indices: 24205--24442 Score: 151
Period size: 29 Copynumber: 8.1 Consensus size: 30
24195 CTCATGAGGT
*
24205 CCCT-AAACTTTCTATAAATTATATTTTGA
1 CCCTCAAACTTTCTAAAAATTATATTTTGA
* *
24234 CCCTCAAACTTGC-AAAAATT-TAGATTTGA
1 CCCTCAAACTTTCTAAAAATTATA-TTTTGA
* *
24263 CCCTCAAACTTTCTAAAAATAACATTTTG-
1 CCCTCAAACTTTCTAAAAATTATATTTTGA
* * * * * *
24292 TCCTCGAACTTTCCAAAAATCACATTTTAA
1 CCCTCAAACTTTCTAAAAATTATATTTTGA
* *
24322 CCCTCAAACTTCCCAAAAAATTATA-TTTGA
1 CCCTCAAACTT-TCTAAAAATTATATTTTGA
* *
24352 CCCT-AGAACTTTC-CAAAATTA-AGATTTGA
1 CCCTCA-AACTTTCTAAAAATTATA-TTTTGA
* *
24381 CCC-CTAAACTTCCTAAAAATT-TAAATTT-A
1 CCCTC-AAACTTTCTAAAAATTAT-ATTTTGA
*
24410 TCCCT-AAACTTTCTAAAATTTCAT-TTTTGA
1 -CCCTCAAACTTTCTAAAAATT-ATATTTTGA
24440 CCC
1 CCC
24443 CATTTTTCCT
Statistics
Matches: 164, Mismatches: 26, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
27 1 0.01
28 9 0.05
29 88 0.54
30 54 0.33
31 12 0.07
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.35
Consensus pattern (30 bp):
CCCTCAAACTTTCTAAAAATTATATTTTGA
Found at i:24309 original size:59 final size:60
Alignment explanation
Indices: 24205--24400 Score: 181
Period size: 59 Copynumber: 3.3 Consensus size: 60
24195 CTCATGAGGT
* * * * * *
24205 CCCT-AAACTTTCTATAAATTATATTTTGACCCTCAAAC-TTGCAAAAATTTAGATTTGA
1 CCCTCAAACTTCCTAAAAATAATATTTTGACCCTCGAACTTTCCAAAAATTAAGATTTGA
* * * * * *
24263 CCCTCAAACTTTCTAAAAATAACATTTTG-TCCTCGAACTTTCCAAAAATCACA-TTTTAA
1 CCCTCAAACTTCCTAAAAATAATATTTTGACCCTCGAACTTTCCAAAAATTA-AGATTTGA
* * *
24322 CCCTCAAACTTCCCAAAAA-ATTATATTTGACCCTAGAACTTTCC-AAAATTAAGATTTGA
1 CCCTCAAACTTCCTAAAAATAATAT-TTTGACCCTCGAACTTTCCAAAAATTAAGATTTGA
24381 CCC-CTAAACTTCCTAAAAAT
1 CCCTC-AAACTTCCTAAAAAT
24401 TTAAATTTAT
Statistics
Matches: 110, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
58 16 0.15
59 81 0.74
60 13 0.12
ACGTcount: A:0.38, C:0.24, G:0.05, T:0.33
Consensus pattern (60 bp):
CCCTCAAACTTCCTAAAAATAATATTTTGACCCTCGAACTTTCCAAAAATTAAGATTTGA
Found at i:24415 original size:59 final size:58
Alignment explanation
Indices: 24248--24429 Score: 167
Period size: 59 Copynumber: 3.1 Consensus size: 58
24238 CAAACTTGCA
* * * *
24248 AAAATTTAGATTTGACCCTCAAACTTTCTAAAAA-TAACATTT-TGTCCTCGAACTTTCC
1 AAAATTAAGATTTGACCCTCAAACTTCCTAAAAATTAA-ATTTAT-CCCTAGAACTTTCC
* * * * * *
24306 AAAAATCACATTTTAACCCTCAAACTTCCCAAAAAATTATATTTGA-CCCTAGAACTTTCC
1 AAAATTAAGA-TTTGACCCTCAAACTT-CCTAAAAATTAAATTT-ATCCCTAGAACTTTCC
*
24366 AAAATTAAGATTTGACCC-CTAAACTTCCTAAAAATTTAAATTTATCCCTA-AACTTTCT
1 AAAATTAAGATTTGACCCTC-AAACTTCCTAAAAA-TTAAATTTATCCCTAGAACTTTCC
24424 AAAATT
1 AAAATT
24430 TCATTTTTGA
Statistics
Matches: 100, Mismatches: 16, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
58 29 0.29
59 40 0.40
60 29 0.29
61 2 0.02
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (58 bp):
AAAATTAAGATTTGACCCTCAAACTTCCTAAAAATTAAATTTATCCCTAGAACTTTCC
Found at i:24443 original size:59 final size:60
Alignment explanation
Indices: 24220--24429 Score: 166
Period size: 59 Copynumber: 3.5 Consensus size: 60
24210 AACTTTCTAT
* * * * * *
24220 AAATTATATTTTGACCCTCA-AACTTGCAAAAATTTAGATTTGA-CCCTCAAACTT-TCTAA
1 AAATTA-AATTTGACCCT-AGAACTTTCCAAAATTAAGATTTGACCCCTCAAACTTCCCAAA
* * * * * * *
24279 AAA-TAACATTTTG-TCCTCGAACTTTCCAAAAATCACATTTTAACCCTCAAACTTCCCAAA
1 AAATTAA-A-TTTGACCCTAGAACTTTCCAAAATTAAGATTTGACCCCTCAAACTTCCCAAA
* *
24339 AAATTATATTTGACCCTAGAACTTTCCAAAATTAAGATTTGACCCCT-AAACTTCCTAAA
1 AAATTAAATTTGACCCTAGAACTTTCCAAAATTAAGATTTGACCCCTCAAACTTCCCAAA
* *
24398 AATTTAAATTT-ATCCCTA-AACTTTCTAAAATT
1 AAATTAAATTTGA-CCCTAGAACTTTCCAAAATT
24430 TCATTTTTGA
Statistics
Matches: 120, Mismatches: 23, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
57 1 0.01
58 36 0.30
59 47 0.39
60 34 0.28
61 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (60 bp):
AAATTAAATTTGACCCTAGAACTTTCCAAAATTAAGATTTGACCCCTCAAACTTCCCAAA
Found at i:31059 original size:30 final size:30
Alignment explanation
Indices: 31023--31080 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
31013 AGTTTGCTAG
31023 CAATTCAAAATCAAGCATCACAATTCATCA
1 CAATTCAAAATCAAGCATCACAATTCATCA
31053 CAATTCAAAATCAAGCATCACAATTCAT
1 CAATTCAAAATCAAGCATCACAATTCAT
31081 TGCCCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.47, C:0.26, G:0.03, T:0.24
Consensus pattern (30 bp):
CAATTCAAAATCAAGCATCACAATTCATCA
Found at i:32668 original size:42 final size:41
Alignment explanation
Indices: 32615--32862 Score: 274
Period size: 42 Copynumber: 6.1 Consensus size: 41
32605 CAGATTGAAG
*
32615 CATCCTATCTCTTACCCCGATCATGGGGCAAATTGCAGACAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGCAG-CAT
* * * * *
32657 TATCCAATCTCTTACCCCGATCATAGGGAAAATTACAATCAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGC-AGCAT
* * *
32699 TATCAAATCTCTTACCCCGATCATGGGGTAAATTGCAGC--
1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGCAGCAT
* * * *
32738 CATCCGATCTTTTACCCCAATCATGGGGCAAATTACAG--T
1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGCAGCAT
*
32777 CATCCAATCTCTTACCCTGATCATGGGGCAAATTGCAGCTAT
1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGCAGC-AT
* * *
32819 CATCCAATCTCTTGCCCCGATCATAGGGCAGATTGCA--AT
1 CATCCAATCTCTTACCCCGATCATGGGGCAAATTGCAGCAT
32858 CATCC
1 CATCC
32863 GAAGCAATAA
Statistics
Matches: 174, Mismatches: 27, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
39 71 0.41
41 2 0.01
42 100 0.57
43 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.15, T:0.27
Consensus pattern (41 bp):
CATCCAATCTCTTACCCCGATCATGGGGCAAATTGCAGCAT
Found at i:32764 original size:39 final size:39
Alignment explanation
Indices: 32580--32855 Score: 239
Period size: 42 Copynumber: 6.9 Consensus size: 39
32570 ATTGAAGGCA
* * ** * * *
32580 CCAATATCTTACCTCGATCGCGAGGCAGATTGAAG-CAT
1 CCAATCTCTTACCCCGATCATGGGGCAAATTGCAGCCAT
* *
32618 CCTATCTCTTACCCCGATCATGGGGCAAATTGCAGACATTAT
1 CCAATCTCTTACCCCGATCATGGGGCAAATTGCAG-C--CAT
* * * * *
32660 CCAATCTCTTACCCCGATCATAGGGAAAATTACAATCATTAT
1 CCAATCTCTTACCCCGATCATGGGGCAAATTGC-AGC--CAT
* *
32702 CAAATCTCTTACCCCGATCATGGGGTAAATTGCAGCCAT
1 CCAATCTCTTACCCCGATCATGGGGCAAATTGCAGCCAT
* * * * *
32741 CCGATCTTTTACCCCAATCATGGGGCAAATTACAGTCAT
1 CCAATCTCTTACCCCGATCATGGGGCAAATTGCAGCCAT
*
32780 CCAATCTCTTACCCTGATCATGGGGCAAATTGCAGCTATCAT
1 CCAATCTCTTACCCCGATCATGGGGCAAATTGCAGC---CAT
* * *
32822 CCAATCTCTTGCCCCGATCATAGGGCAGATTGCA
1 CCAATCTCTTACCCCGATCATGGGGCAAATTGCA
32856 ATCATCCGAA
Statistics
Matches: 193, Mismatches: 37, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
38 27 0.14
39 64 0.33
41 2 0.01
42 99 0.51
43 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (39 bp):
CCAATCTCTTACCCCGATCATGGGGCAAATTGCAGCCAT
Found at i:33188 original size:85 final size:85
Alignment explanation
Indices: 33038--33205 Score: 201
Period size: 85 Copynumber: 2.0 Consensus size: 85
33028 ACTTCAAACC
* * * ** * *
33038 CCATCTTCCTGGTAAGATACAGAGAAGTGGGTCGAAGCAATAAAGTGGTCATCTTTCTGACGAGA
1 CCATCTTCCTGGTAAGATACAGAGAAGTGGATCAAAACAATAAAGCAGTCATATTCCTGACGAGA
*
33103 TGCAAAGAAGTAAACCAAAT
66 TACAAAGAAGTAAACCAAAT
* * * * *
33123 CCATCTTCCTGTTGAGATACAGAGAAGTGGATTAAAACAATGAAGCAGTCATATTCCTGATGAGA
1 CCATCTTCCTGGTAAGATACAGAGAAGTGGATCAAAACAATAAAGCAGTCATATTCCTGACGAGA
* *
33188 TACAGAGAAGTAGACCAA
66 TACAAAGAAGTAAACCAA
33206 TTTAATGAAG
Statistics
Matches: 68, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
85 68 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (85 bp):
CCATCTTCCTGGTAAGATACAGAGAAGTGGATCAAAACAATAAAGCAGTCATATTCCTGACGAGA
TACAAAGAAGTAAACCAAAT
Found at i:33220 original size:208 final size:208
Alignment explanation
Indices: 32864--33952 Score: 1541
Period size: 208 Copynumber: 5.2 Consensus size: 208
32854 CAATCATCCG
* * ** * * *
32864 AAGCAATAAAGTGGTCATCTTCCTAACAAGATGCAGAGAAGTGAACCAAATCCGTCTTCCTAATG
1 AAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATG
* **
32929 AGATACAGAGAAGTGGATTCAAACAATGAATCAGTCATCTTCCTGATGAGATATAGAGAAGTAGA
66 AGATACAGAGAAGTGGATTGAAACAATGAGGCAGTCATCTTCCTGATGAGATATAGAGAAGTAGA
* * * * *
32994 TCAAATCTATGAAGCGAAGCTCAACACGAATGAGACTTCAAACCCCATCTTCCTGGTAAGATACA
131 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
*
33059 GAGAAGTGGGTCG
196 GAGAAGTGGGTCA
* * * * * ** * *
33072 AAGCAATAAAGTGGTCATCTTTCTGACGAGATGCAAAGAAGTAAACCAAATCCATCTTCCTGTTG
1 AAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATG
* * * *
33137 AGATACAGAGAAGTGGATTAAAACAATGAAGCAGTCATATTCCTGATGAGATACAGAGAAGTAGA
66 AGATACAGAGAAGTGGATTGAAACAATGAGGCAGTCATCTTCCTGATGAGATATAGAGAAGTAGA
* * * *
33202 CCAATTTAATGAAGCGAAGCTCAATACGAATAAGACTTCAAACCTCATCTTCCTGATGAGATACA
131 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
*
33267 GAGAAGTGAGTCA
196 GAGAAGTGGGTCA
* *
33280 AAGCAATAAAGCGGTCATCTTCCTAATGAGATACAGAGAAGTGGACCAAATCCGTCTTTCTGATG
1 AAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATG
* * *
33345 AGCTACAGAGAAGTTGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATATAGAGAAGTAGA
66 AGATACAGAGAAGTGGATTGAAACAATGAGGCAGTCATCTTCCTGATGAGATATAGAGAAGTAGA
*
33410 ACAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
131 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
33475 GAGAAGTGGGTCA
196 GAGAAGTGGGTCA
* * * *
33488 AAGCAATAAAGTGGTCATCTTCTTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGTTG
1 AAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATG
* * *
33553 AGATACAGAGAAATGGATTTAAACAATGAGGCAGCCATCTTCCTGATGAGATATAGAGAAGTAGA
66 AGATACAGAGAAGTGGATTGAAACAATGAGGCAGTCATCTTCCTGATGAGATATAGAGAAGTAGA
* * ** * *
33618 CCAAATCAACGAAGCGATGCTCAATACGAAAAAGACTTCAAACCTCATCTTCTTGATGAGATACA
131 CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
33683 GAGAAGTGGGTCA
196 GAGAAGTGGGTCA
* * * *
33696 AAGCAATAAAGCGGTCATCTTTCTGATGAGATACAAAGAAGTGGACCAAATTCGTCTTCTTGATG
1 AAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATG
* * * *
33761 AGATATAGAGAAGTGGATTGAAACAATGAGGC-GATCATCTTCTTGATGAGATACAAAGAAGTAG
66 AGATACAGAGAAGTGGATTGAAACAATGAGGCAG-TCATCTTCCTGATGAGATATAGAGAAGTAG
* *
33825 ACCAAATCAATGAAGCGAAGCTCAATACGAATGAGAATTCAAACCCCATCTTCCTTATGAGATAC
130 ACCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATAC
* *
33890 AGAGAAGTGGATCG
195 AGAGAAGTGGGTCA
* * * *
33904 AAGTAATAAAACGGTCATCTTCCTGATAAGATACAGAGAAGTAGACCAA
1 AAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAA
33953 GAGATGAAGC
Statistics
Matches: 785, Mismatches: 95, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
207 1 0.00
208 784 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.23
Consensus pattern (208 bp):
AAGCAATAAAGCGGTCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCCTGATG
AGATACAGAGAAGTGGATTGAAACAATGAGGCAGTCATCTTCCTGATGAGATATAGAGAAGTAGA
CCAAATCAATGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTCCTGATGAGATACA
GAGAAGTGGGTCA
Found at i:33397 original size:85 final size:85
Alignment explanation
Indices: 33249--33416 Score: 230
Period size: 85 Copynumber: 2.0 Consensus size: 85
33239 TCAAACCTCA
33249 TCTTCCTGATGAGATACAGAGAAGTGAGTCAAAGCAATAAAGCGGTCATCTTCCTAATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGAGTCAAAGCAATAAAGCGGTCATCTTCCTAATGAGATAC
* *
33314 AGAGAAGTGGACCAAATCCG
66 AGAGAAGTAGAACAAATCCG
* * * * * * *
33334 TCTTTCTGATGAGCTACAGAGAAGTTGATTGAAA-CAATGAGGCGGTCATCTTCCTGATGAGATA
1 TCTTCCTGATGAGATACAGAGAAG-TGAGTCAAAGCAATAAAGCGGTCATCTTCCTAATGAGATA
*
33398 TAGAGAAGTAGAACAAATC
65 CAGAGAAGTAGAACAAATC
33417 AATGAAGCGA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 65 0.90
86 7 0.10
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGAGTCAAAGCAATAAAGCGGTCATCTTCCTAATGAGATAC
AGAGAAGTAGAACAAATCCG
Found at i:33808 original size:85 final size:85
Alignment explanation
Indices: 33665--33831 Score: 239
Period size: 85 Copynumber: 2.0 Consensus size: 85
33655 TCAAACCTCA
*
33665 TCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTTCTGATGAGATAC
1 TCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGATCATCTTTCTGATGAGATAC
*
33730 AAAGAAGTGGACCAAATTCG
66 AAAGAAGTAGACCAAATTCG
* * * * *
33750 TCTTCTTGATGAGATATAGAGAAGTGGATTGAAA-CAATGAGGCGATCATC-TTCTTGATGAGAT
1 TCTTCTTGATGAGATACAGAGAAGTGG-GTCAAAGCAATAAAGCGATCATCTTTC-TGATGAGAT
33813 ACAAAGAAGTAGACCAAAT
64 ACAAAGAAGTAGACCAAAT
33832 CAATGAAGCG
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
84 3 0.04
85 66 0.90
86 4 0.05
ACGTcount: A:0.37, C:0.14, G:0.24, T:0.26
Consensus pattern (85 bp):
TCTTCTTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGATCATCTTTCTGATGAGATAC
AAAGAAGTAGACCAAATTCG
Found at i:33836 original size:48 final size:48
Alignment explanation
Indices: 33750--33842 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
33740 ACCAAATTCG
* * * ** *
33750 TCTTCTTGATGAGATATAGAGAAGTGGATTGAAACAATGAGGCGATCA
1 TCTTCTTGATGAGATACAAAGAAGTAGATCCAAACAATGAAGCGATCA
33798 TCTTCTTGATGAGATACAAAGAAGTAGA-CCAAATCAATGAAGCGA
1 TCTTCTTGATGAGATACAAAGAAGTAGATCCAAA-CAATGAAGCGA
33843 AGCTCAATAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 3 0.08
48 35 0.92
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.25
Consensus pattern (48 bp):
TCTTCTTGATGAGATACAAAGAAGTAGATCCAAACAATGAAGCGATCA
Found at i:34796 original size:16 final size:14
Alignment explanation
Indices: 34753--34802 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
34743 TACTAACACC
**
34753 TATATATAAATATA
1 TATATATATTTATA
*
34767 CATATATATTTATA
1 TATATATATTTATA
34781 TATATATATTCGTATA
1 TATATATATT--TATA
34797 TATATA
1 TATATA
34803 CGCCTATTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 20 0.67
16 10 0.33
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (14 bp):
TATATATATTTATA
Found at i:38180 original size:30 final size:30
Alignment explanation
Indices: 38110--38278 Score: 173
Period size: 30 Copynumber: 5.7 Consensus size: 30
38100 ATAATGAAAA
* * *
38110 AGGG-TTAAAATACAAATTTT-GAAAAATTT
1 AGGGATTAAAATATAATTTTTAG-AAAGTTT
* *
38139 AGGGGTCAAAATATAATTTTTAGAAAGTTT
1 AGGGATTAAAATATAATTTTTAGAAAGTTT
* **
38169 AAGGATTAAAATGCAATTTTTAGAAAGTTT
1 AGGGATTAAAATATAATTTTTAGAAAGTTT
* *
38199 -GTGGGTTAAAATATAATTTTTAGAATGTTT
1 AG-GGATTAAAATATAATTTTTAGAAAGTTT
* *
38229 AGGGATCAAAATGTAATTTTTAGAAAGTTT
1 AGGGATTAAAATATAATTTTTAGAAAGTTT
**
38259 AGGGCCTAAAATATAATTTT
1 AGGGATTAAAATATAATTTT
38279 AAAATAAAAC
Statistics
Matches: 114, Mismatches: 22, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
29 4 0.04
30 108 0.95
31 2 0.02
ACGTcount: A:0.41, C:0.04, G:0.18, T:0.38
Consensus pattern (30 bp):
AGGGATTAAAATATAATTTTTAGAAAGTTT
Found at i:38211 original size:60 final size:60
Alignment explanation
Indices: 38136--38278 Score: 207
Period size: 60 Copynumber: 2.4 Consensus size: 60
38126 TTTTGAAAAA
* *
38136 TTTAGGGGTCAAAATATAATTTTTAGAAAGTTTAAGGATTAAAATGCAATTTTTAGAAAG
1 TTTAGGGGTTAAAATATAATTTTTAGAAAGTTTAAGGATCAAAATGCAATTTTTAGAAAG
* * *
38196 TTT-GTGGGTTAAAATATAATTTTTAGAATGTTTAGGGATCAAAATGTAATTTTTAGAAAG
1 TTTAG-GGGTTAAAATATAATTTTTAGAAAGTTTAAGGATCAAAATGCAATTTTTAGAAAG
**
38256 TTTAGGGCCTAAAATATAATTTT
1 TTTAGGGGTTAAAATATAATTTT
38279 AAAATAAAAC
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
59 1 0.01
60 72 0.97
61 1 0.01
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.40
Consensus pattern (60 bp):
TTTAGGGGTTAAAATATAATTTTTAGAAAGTTTAAGGATCAAAATGCAATTTTTAGAAAG
Found at i:38325 original size:29 final size:29
Alignment explanation
Indices: 38293--38351 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
38283 TAAAACAAAG
*
38293 GCTTCTTAGGTAATAAACCTAAAAATTTT
1 GCTTCCTAGGTAATAAACCTAAAAATTTT
38322 GCTTCCTAGGTAATAAACCTAAAAATTTT
1 GCTTCCTAGGTAATAAACCTAAAAATTTT
38351 G
1 G
38352 ACACGTAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.36
Consensus pattern (29 bp):
GCTTCCTAGGTAATAAACCTAAAAATTTT
Found at i:41615 original size:66 final size:66
Alignment explanation
Indices: 41545--41678 Score: 164
Period size: 66 Copynumber: 2.0 Consensus size: 66
41535 ACAAATTGCT
* **
41545 CAACTTAAAG-TAGAGGCAACAACGAAAGAAGCAGAGG-CTCAAAGAAAATATGATGAACTTCAG
1 CAACTTAAAGCTA-AGGCAACAACGAAAGAAGCAG-GGCCTCAAAGAAAATATGACGAACCGCAG
41608 CTA
64 CTA
* * ** *
41611 CAACTTGAAGCTAAGGCAGCAACGAGGGAAGCAGGGCCTCAAAGAAAGTATGACGAACCGCAGCT
1 CAACTTAAAGCTAAGGCAACAACGAAAGAAGCAGGGCCTCAAAGAAAATATGACGAACCGCAGCT
41676 A
66 A
41677 CA
1 CA
41679 GCTTCAAAAT
Statistics
Matches: 58, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 2 0.03
66 54 0.93
67 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.25, T:0.13
Consensus pattern (66 bp):
CAACTTAAAGCTAAGGCAACAACGAAAGAAGCAGGGCCTCAAAGAAAATATGACGAACCGCAGCT
A
Found at i:42001 original size:43 final size:43
Alignment explanation
Indices: 41954--42299 Score: 358
Period size: 43 Copynumber: 8.1 Consensus size: 43
41944 GTTAGTGGTA
* * * * *
41954 TTTGTAGGAAAAGTGTCACTAAAGACCATGTTCTATAGCGACA
1 TTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTATAGCGGCG
** * *
41997 TTTGTGGGAAAAATGCCGCTAAAGACCATGTTCTATAGCGGTG
1 TTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTATAGCGGCG
* ** *
42040 TTTGAGGGAAAA-TACCGCTAAAGA-CATGTTCTATAGCGGCG
1 TTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTATAGCGGCG
* * *
42081 TTTCTGAGAAAAGCGCTACTAAAGACCATGTTCTATAGCGGCG
1 TTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTATAGCGGCG
* * *
42124 CTTGTGGTGAAAA-CGCCAGCTAAAGACCAAGCTCTATAGCGGCG
1 TTTGTGG-GAAAAGCGCCA-CTAAAGACCATGTTCTATAGCGGCG
* * * *
42168 TTTGTGGGAAAAGCACCACTAAAAACCATGTTCTATAGCAGTG
1 TTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTATAGCGGCG
* *
42211 TTTGTGGGGAAAA-CGCGACTAAAAACCATGTTCTATAGCGGCG
1 TTTGT-GGGAAAAGCGCCACTAAAGACCATGTTCTATAGCGGCG
* ** ** *
42254 TTTGTGAGAAAAGCGCTGCTAAAGATAATGTTCTATAGCGGTG
1 TTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTATAGCGGCG
42297 TTT
1 TTT
42300 TTCCACATAA
Statistics
Matches: 255, Mismatches: 41, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
41 25 0.10
42 25 0.10
43 160 0.63
44 45 0.18
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (43 bp):
TTTGTGGGAAAAGCGCCACTAAAGACCATGTTCTATAGCGGCG
Found at i:42276 original size:86 final size:86
Alignment explanation
Indices: 41971--42299 Score: 394
Period size: 86 Copynumber: 3.8 Consensus size: 86
41961 GAAAAGTGTC
* * * ** *
41971 ACTAAAGACCATGTTCTATAGCGACATTTGTGGGAAAAATGCCGCTAAAGACCATGTTCTATAGC
1 ACTAAAGACCATGTTCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTATAGC
* *
42036 GGTGTTTGAGGGAAAATAC-CG
66 GGTGTTTGTGGGGAAA-ACGCG
* *
42057 -CTAAAGA-CATGTTCTATAGCGGCGTTTCTGAGAAAAGCGCTACTAAAGACCATGTTCTATAGC
1 ACTAAAGACCATGTTCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTATAGC
* * * *
42120 GGCGCTTGTGGTGAAAACGCC
66 GGTGTTTGTGGGGAAAACGCG
* * * * *
42141 AGCTAAAGACCAAGCTCTATAGCGGCGTTTGTGGGAAAAGCACCACTAAAAACCATGTTCTATAG
1 A-CTAAAGACCATGTTCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTATAG
*
42206 CAGTGTTTGTGGGGAAAACGCG
65 CGGTGTTTGTGGGGAAAACGCG
* ** **
42228 ACTAAAAACCATGTTCTATAGCGGCGTTTGTGAGAAAAGCGCTGCTAAAGATAATGTTCTATAGC
1 ACTAAAGACCATGTTCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTATAGC
42293 GGTGTTT
66 GGTGTTT
42300 TTCCACATAA
Statistics
Matches: 202, Mismatches: 37, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
83 2 0.01
84 60 0.30
85 7 0.03
86 67 0.33
87 66 0.33
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (86 bp):
ACTAAAGACCATGTTCTATAGCGGCGTTTGTGAGAAAAGCGCCACTAAAGACCATGTTCTATAGC
GGTGTTTGTGGGGAAAACGCG
Found at i:42293 original size:173 final size:171
Alignment explanation
Indices: 41972--42294 Score: 459
Period size: 171 Copynumber: 1.9 Consensus size: 171
41962 AAAAGTGTCA
* * ** * * *
41972 CTAAAGACCATGTTCTATAGCGACATTTGTGGGAAAAATGCCGCTAAAGACCATGTTCTATAGCG
1 CTAAAGACCAAGCTCTATAGCGACATTTGTGGGAAAAACACCACTAAAAACCATGTTCTATAGCA
*
42037 GTGTTTGAGGGAAAATACCGCTAAAGACATGTTCTATAGCGGCGTTTCTGAGAAAAGCGCTACTA
66 GTGTTTGAGGGAAAATACCGCTAAAAACATGTTCTATAGCGGCGTTTCTGAGAAAAGCGCTACTA
*
42102 AAGACCATGTTCTATAGCGGCGCTTGTGGTGAAAACGCCAG
131 AAGACAATGTTCTATAGCGGCGCTTGTGGTGAAAACGCCAG
* * *
42143 CTAAAGACCAAGCTCTATAGCGGCGTTTGTGGGAAAAGCACCACTAAAAACCATGTTCTATAGCA
1 CTAAAGACCAAGCTCTATAGCGACATTTGTGGGAAAAACACCACTAAAAACCATGTTCTATAGCA
* * * *
42208 GTGTTTGTGGGGAAA-ACGCGACTAAAAACCATGTTCTATAGCGGCGTTTGTGAGAAAAGCGCTG
66 GTGTTTGAGGGAAAATAC-CG-CTAAAAA-CATGTTCTATAGCGGCGTTTCTGAGAAAAGCGCTA
*
42272 CTAAAGATAATGTTCTATAGCGG
128 CTAAAGACAATGTTCTATAGCGG
42295 TGTTTTTCCA
Statistics
Matches: 132, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
170 2 0.02
171 70 0.53
172 6 0.05
173 54 0.41
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (171 bp):
CTAAAGACCAAGCTCTATAGCGACATTTGTGGGAAAAACACCACTAAAAACCATGTTCTATAGCA
GTGTTTGAGGGAAAATACCGCTAAAAACATGTTCTATAGCGGCGTTTCTGAGAAAAGCGCTACTA
AAGACAATGTTCTATAGCGGCGCTTGTGGTGAAAACGCCAG
Found at i:43785 original size:5 final size:5
Alignment explanation
Indices: 43775--43812 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
43765 TCCACCCTAA
* *
43775 ACCCC ACCCC ACCCT ACCCT ACCCT ACCCT ACCCT ACC
1 ACCCT ACCCT ACCCT ACCCT ACCCT ACCCT ACCCT ACC
43813 AAGTCTTTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.21, C:0.66, G:0.00, T:0.13
Consensus pattern (5 bp):
ACCCT
Found at i:44693 original size:46 final size:46
Alignment explanation
Indices: 44601--44704 Score: 118
Period size: 46 Copynumber: 2.3 Consensus size: 46
44591 ATATATAAAT
* ** * *
44601 AAAAAATTTAAAATTTTATAACTTTATAAAAATACAAAAATATATA
1 AAAAAATTAAAAAAGTTATAAATTTATAAAAAAACAAAAATATATA
* * *
44647 AAAAAATTAAAAAAGTTATAAATTTATAAAAAAATATAAATTTATA
1 AAAAAATTAAAAAAGTTATAAATTTATAAAAAAACAAAAATATATA
* *
44693 AAATAACTAAAA
1 AAAAAATTAAAA
44705 TCACATTGAA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (46 bp):
AAAAAATTAAAAAAGTTATAAATTTATAAAAAAACAAAAATATATA
Found at i:46280 original size:13 final size:13
Alignment explanation
Indices: 46247--46310 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 13
46237 TAATTTTTTA
*
46247 TTATATTTAAATT
1 TTATATTTAATTT
* * *
46260 TAAGATTTAATCT
1 TTATATTTAATTT
46273 TTATATTTTAATTTT
1 TTATA-TTTAA-TTT
46288 TAATATATTTAATTT
1 T--TATATTTAATTT
46303 TTATATTT
1 TTATATTT
46311 TATAATATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
13 19 0.47
14 5 0.12
15 7 0.17
16 5 0.12
17 4 0.10
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (13 bp):
TTATATTTAATTT
Found at i:46296 original size:17 final size:16
Alignment explanation
Indices: 46235--46305 Score: 62
Period size: 14 Copynumber: 4.7 Consensus size: 16
46225 AAATCTCATT
*
46235 TTTAATTTTTTATTATA
1 TTTAA-TTTTTAATATA
* *
46252 TTTAA-ATTT-A-AGA
1 TTTAATTTTTAATATA
*
46265 TTTAATCTTT-ATAT-
1 TTTAATTTTTAATATA
46279 TTTAATTTTTAATATA
1 TTTAATTTTTAATATA
46295 TTTAATTTTTA
1 TTTAATTTTTA
46306 TATTTTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
13 7 0.16
14 13 0.30
15 8 0.18
16 11 0.25
17 5 0.11
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (16 bp):
TTTAATTTTTAATATA
Found at i:46332 original size:25 final size:24
Alignment explanation
Indices: 46283--46332 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
46273 TTATATTTTA
**
46283 ATTTTTAATATATTTAATTTTTAT
1 ATTTTTAATATATTTAATTAATAT
46307 ATTTTATAATAT-TATTAATTAATAT
1 ATTTT-TAATATAT-TTAATTAATAT
46332 A
1 A
46333 AATATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTTTTAATATATTTAATTAATAT
Done.