Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004452.1 Hibiscus syriacus cultivar Beakdansim tig00009788_pilon, 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: 125500
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:2234 original size:23 final size:22
Alignment explanation
Indices: 2208--2250 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2198 TCTCAATGGT
* *
2208 TCTATCTTTATGACACGATTTCC
1 TCTACCTTCATGACAC-ATTTCC
2231 TCTACCTTCATGACACATTT
1 TCTACCTTCATGACACATTT
2251 TTTTCTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.23, C:0.28, G:0.07, T:0.42
Consensus pattern (22 bp):
TCTACCTTCATGACACATTTCC
Found at i:9875 original size:446 final size:449
Alignment explanation
Indices: 9064--9965 Score: 1461
Period size: 446 Copynumber: 2.0 Consensus size: 449
9054 CCCCATGGGC
*
9064 TTTATTTTATATCTTCTTAGGCTAATGATTTTTAAATTCATCTTTTAGTTCAACTAATAAGTGTT
1 TTTATTTTATATCTTCTTAGGCTAATGATTTTTAAATTCATCTTTTAGTTCAACTAATAACTGTT
*
9129 AAGTGGTCTCATCTCACATTAGCTTCATTTAAAGTTTGTTTTGTCTTTTTATTCAATTTTAGGGC
66 AAGTGGTCTCATCTCACATTAGCTTCATTTAAAGTTTGTTTTGTCTTTGTATTCAATTTTAGGGC
*
9194 CTCTGCACCTATTGCTATTAGTTCTAGGTTGGATGATCAACAAAACTACCTTCTATTTGTTTAAG
131 CTCTGCACATATTGCTATTAGTTCTAGGTTGGATGATCAACAAAACTACCTTCTATTTGTTTAAG
* * *
9259 ACTTTTTGGACTTTACCTTTCAACAATGGTAATGTACTTATGCATCCTTCTTACCTGCAGCCAAA
196 ACTTTTTGGACTTTACCTTTCAACAATGGTAATATACTTATGCATCATTCTTACCTGCAACCAAA
* * *
9324 TCAAATTTTTACTCACCCTGGGTTCGTTGGACCAGGATCCGTTGATGTCTTCCACTTTTGGACTG
261 TCAAATTTTTACTCACCCTGGGTTCGCTGGACCAGGATCCGTTGATGTCCTCCACTTTTGGAATG
* * *
9389 ACTGAATCTAATGGGAAAAATACATATTATGCATAATGAA-GG-TGCTAAAACATGGAATGATAG
326 ACTAAATCTAATGGAAAAAATACATATTATGCACAATGAAGGGTTGCTAAAACATGGAATGATAG
*
9452 CATTTATGTCAGCCTAGTATGCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCA
391 CATTTATGTCAGCCTAATATGCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCA
9511 TTTATTTTATATCTTCTTAGGCTAATGATTTTTAAATTCATCTTTTA-TTCAACTAATAACTGTT
1 TTTATTTTATATCTTCTTAGGCTAATGATTTTTAAATTCATCTTTTAGTTCAACTAATAACTGTT
* *
9575 AAGTGGTCTCATCTCATATTAGCTTCATTTACAGTTTGTTTTGTCTTTGTATTCAATTTTAGGGC
66 AAGTGGTCTCATCTCACATTAGCTTCATTTAAAGTTTGTTTTGTCTTTGTATTCAATTTTAGGGC
* *
9640 CTCTGCACATATTGCTATTAGTTCTAGGTTGGGTGATCAACAGAACTACCTTCTATTTGTTTAAG
131 CTCTGCACATATTGCTATTAGTTCTAGGTTGGATGATCAACAAAACTACCTTCTATTTGTTTAAG
* * * *
9705 CCTTTTT-GACTTTACCTTTGAACCATGGTAATATACTTATGCATCATTCTTACCTGCAACCGAA
196 ACTTTTTGGACTTTACCTTTCAACAATGGTAATATACTTATGCATCATTCTTACCTGCAACCAAA
* * ** *
9769 TCAAATTTTTACTCATCTTGGGTTCGCTGGACTTGGATCTGTTGATGTCCTCCACTTTTGGAATG
261 TCAAATTTTTACTCACCCTGGGTTCGCTGGACCAGGATCCGTTGATGTCCTCCACTTTTGGAATG
* *
9834 ACTAAATCTAATGGAAAAAAATACATATTCTGCACAATGAAGGTGGTTATGCTACAACATGGAAT
326 ACTAAATCTAATGG-AAAAAATACATATTATGCACAATGAA-G-GG-T-TGCTAAAACATGGAAT
* *
9899 GGTAGCATTTATGTCAGCCTAATGTGCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCA
386 GATAGCATTTATGTCAGCCTAATATGCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCA
9963 TTT
1 TTT
9966 GCATGAGCAA
Statistics
Matches: 418, Mismatches: 30, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
445 121 0.29
446 169 0.40
447 47 0.11
449 2 0.00
452 79 0.19
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (449 bp):
TTTATTTTATATCTTCTTAGGCTAATGATTTTTAAATTCATCTTTTAGTTCAACTAATAACTGTT
AAGTGGTCTCATCTCACATTAGCTTCATTTAAAGTTTGTTTTGTCTTTGTATTCAATTTTAGGGC
CTCTGCACATATTGCTATTAGTTCTAGGTTGGATGATCAACAAAACTACCTTCTATTTGTTTAAG
ACTTTTTGGACTTTACCTTTCAACAATGGTAATATACTTATGCATCATTCTTACCTGCAACCAAA
TCAAATTTTTACTCACCCTGGGTTCGCTGGACCAGGATCCGTTGATGTCCTCCACTTTTGGAATG
ACTAAATCTAATGGAAAAAATACATATTATGCACAATGAAGGGTTGCTAAAACATGGAATGATAG
CATTTATGTCAGCCTAATATGCTACCTTCAGGCTTTTTTCCAGTGACTTACAAAGCTCA
Found at i:16568 original size:53 final size:52
Alignment explanation
Indices: 16509--17329 Score: 999
Period size: 53 Copynumber: 15.5 Consensus size: 52
16499 CTCTCTATCG
** * * *
16509 CTTCAGGGAGTAAGAACTCGAACAATCTTCTGT-CTATGAGTCTGCTCTCTCTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCT-TCCTACGGGTCTGCTCTCTTTT
* ** * *
16562 CTTCAGGGAGTAGAACTCGAACAGTCTTCTT-CTCACGGG-CTCGATCTCTCTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCT-ACGGGTCT-GCTCTCTTTT
** * *
16614 CTTCAGGGAGTAGAACTCGAACAATCTTCTGCCTACGGGTCCGCTCTCTCTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCT-TTT
* * * *
16667 CCTCAGGGAGTAGAACTCGAACAATCATCTGCCTATGGG-CTTGCTCTCTCTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-TGCTCTCT-TTT
* ** *
16720 CTTCAGGGAGTAGAACTCGAAAAATCTTCTTCCTACGGGTCTGTTCTCTATTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCT-TTT
* * * *
16773 CTTCAGGGAGTAAGAACTCAAAAAATAATCTTCTTACGGGTCCGCTCTCTTTTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTC-TTTT
* * * *
16827 CTTCAGGGAGTAGAACTCGAACAGTAATCTTCCTACGGGTCCGCCCTATTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTT
* *
16879 CTTCAAGGAGTAGAACTCGAACAGTAATCTTCCTACGGG-CTCGCTCTCTATTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCT-GCTCTCT-TTT
*
16932 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGG-CTCACTCTCTATTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCT-GCTCTCT-TTT
*
16986 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTC-TTTT
* * *
17040 CTTCAGGGAGTAGAACTCGAACAGTAATCTTCCTACGGGTCTGCCCTATTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTT
* * *
17092 CTTCAGGGAGTAAGAACTCGAACAGTAATCTTCCTACGGGTCTGCCCTATTTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTT
17145 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGT-TCGCTCTCTTTTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCT-GCTCTC-TTTT
* *
17199 CTTCAGGGAGTAGAACTCAAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTC-TTTT
*
17252 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTC-TTTT
17305 CTTCAGGGAGTAGAACTCGAACAAT
1 CTTCAGGGAGTAGAACTCGAACAAT
17330 CTTCTGTTGC
Statistics
Matches: 699, Mismatches: 51, Indels: 36
0.89 0.06 0.05
Matches are distributed among these distances:
51 6 0.01
52 134 0.19
53 396 0.57
54 160 0.23
55 3 0.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (52 bp):
CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTT
Found at i:17393 original size:37 final size:37
Alignment explanation
Indices: 17339--17422 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
17329 TCTTCTGTTG
* *
17339 CTTCACTACCTCATTGTGAAGGC-TTCTGGATGATTTA
1 CTTCACTACCTCATTGTGAAGACTTTC-AGATGATTTA
* * *
17376 CTTCACTACTTCCTTGTGAAGACTTTCAGATGATTTG
1 CTTCACTACCTCATTGTGAAGACTTTCAGATGATTTA
17413 CTTCACTACC
1 CTTCACTACC
17423 CTTTCGTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
37 37 0.93
38 3 0.08
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (37 bp):
CTTCACTACCTCATTGTGAAGACTTTCAGATGATTTA
Found at i:18743 original size:19 final size:17
Alignment explanation
Indices: 18710--18826 Score: 63
Period size: 18 Copynumber: 7.1 Consensus size: 17
18700 TTTTGTTTTG
*
18710 TTTTT-TTTCTTCTTCT
1 TTTTTCTTTTTTCTTCT
18726 TCTTTTCTCTTTTTCTTCT
1 T-TTTTCT-TTTTTCTTCT
*
18745 TTTTTC--TTTT-TTCA
1 TTTTTCTTTTTTCTTCT
*
18759 TTTTTCATTTTT-TTCAT
1 TTTTTCTTTTTTCTTC-T
* *
18776 TTTTTC-TATTTC--AT
1 TTTTTCTTTTTTCTTCT
*
18790 TTTTTCATTTTT-TTCATT
1 TTTTTCTTTTTTCTTC--T
*
18808 TTTTTCTTTTTTTTTCT
1 TTTTTCTTTTTTCTTCT
18825 TT
1 TT
18827 CATCTTCAAG
Statistics
Matches: 80, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
14 16 0.20
15 8 0.10
16 12 0.15
17 13 0.16
18 18 0.22
19 13 0.16
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTCT
Found at i:18746 original size:9 final size:9
Alignment explanation
Indices: 18710--18826 Score: 54
Period size: 8 Copynumber: 13.3 Consensus size: 9
18700 TTTTGTTTTG
*
18710 TTTTTTTTC
1 TTTTTCTTC
*
18719 TTCTTCTTC
1 TTTTTCTTC
18728 -TTTTC-TC
1 TTTTTCTTC
18735 TTTTTCTTC
1 TTTTTCTTC
*
18744 TTTTTTCTTT
1 -TTTTTCTTC
*
18754 TTTCATTTTTC
1 TTT--TTCTTC
18765 ATTTTT-TTC
1 -TTTTTCTTC
*
18774 ATTTT-TTC
1 TTTTTCTTC
* *
18782 TATTTCAT-
1 TTTTTCTTC
18790 TTTTTCATT-
1 TTTTTC-TTC
18799 TTTTTCATT-
1 TTTTTC-TTC
18808 TTTTTCTT-
1 TTTTTCTTC
18816 TTTTT-TTC
1 TTTTTCTTC
18824 TTT
1 TTT
18827 CATCTTCAAG
Statistics
Matches: 87, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
7 4 0.05
8 34 0.39
9 32 0.37
10 10 0.11
11 4 0.05
12 3 0.03
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:18762 original size:23 final size:23
Alignment explanation
Indices: 18714--18829 Score: 82
Period size: 23 Copynumber: 5.0 Consensus size: 23
18704 GTTTTGTTTT
* * *
18714 TTTTCTTC-TTCTTCTTTTCTCT
1 TTTTCTTCTTTTTTCTTTTTTCA
18736 TTTTCTTCTTTTTTCTTTTTTCA
1 TTTTCTTCTTTTTTCTTTTTTCA
*
18759 TTTTTCAT-TTTTTTCATTTTTTC-
1 -TTTTCTTCTTTTTTC-TTTTTTCA
*
18782 TATTTC--ATTTTTTCATTTTTTTCA
1 T-TTTCTTCTTTTTTC--TTTTTTCA
*
18806 TTTTTTTCTTTTTT-TTTCTTTCA
1 TTTTCTTCTTTTTTCTTT-TTTCA
18829 T
1 T
18830 CTTCAAGCAA
Statistics
Matches: 77, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
22 19 0.25
23 38 0.49
24 14 0.18
25 6 0.08
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTCTTCTTTTTTCTTTTTTCA
Found at i:18770 original size:31 final size:31
Alignment explanation
Indices: 18712--18819 Score: 125
Period size: 31 Copynumber: 3.4 Consensus size: 31
18702 TTGTTTTGTT
18712 TTTTTTCTTCTTCTTC-TTTTCTC-TTTTTCTTC-
1 TTTTTTCTT-TT-TTCATTTT-TCATTTTT-TTCA
18744 TTTTTTCTTTTTTCATTTTTCATTTTTTTCA
1 TTTTTTCTTTTTTCATTTTTCATTTTTTTCA
*
18775 TTTTTTC-TATTTCATTTTTTCATTTTTTTCA
1 TTTTTTCTTTTTTCA-TTTTTCATTTTTTTCA
18806 TTTTTTTCTTTTTT
1 -TTTTTTCTTTTTT
18820 TTTCTTTCAT
Statistics
Matches: 68, Mismatches: 2, Indels: 11
0.84 0.02 0.14
Matches are distributed among these distances:
30 14 0.21
31 34 0.50
32 16 0.24
33 4 0.06
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (31 bp):
TTTTTTCTTTTTTCATTTTTCATTTTTTTCA
Found at i:18778 original size:6 final size:7
Alignment explanation
Indices: 18745--18801 Score: 53
Period size: 7 Copynumber: 7.7 Consensus size: 7
18735 TTTTTCTTCT
*
18745 TTTTTCT
1 TTTTTCA
18752 TTTTTCA
1 TTTTTCA
18759 TTTTTCA
1 TTTTTCA
18766 TTTTTTTCA
1 --TTTTTCA
18775 TTTTTTC-
1 -TTTTTCA
*
18782 TATTTCA
1 TTTTTCA
18789 TTTTTTCA
1 -TTTTTCA
18797 TTTTT
1 TTTTT
18802 TTCATTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
6 5 0.12
7 18 0.42
8 13 0.30
9 7 0.16
ACGTcount: A:0.11, C:0.12, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTCA
Found at i:18817 original size:16 final size:16
Alignment explanation
Indices: 18711--18819 Score: 86
Period size: 16 Copynumber: 6.9 Consensus size: 16
18701 TTTGTTTTGT
*
18711 TTTTTTTC-TTCTTC-
1 TTTTTTTCTTTTTTCA
* *
18725 TTCTTTTCTCTTTTTCT
1 TTTTTTTCT-TTTTTCA
18742 TCTTTTTTCTTTTTTCA
1 T-TTTTTTCTTTTTTCA
*
18759 TTTTTCAT-TTTTTTCA
1 TTTTT-TTCTTTTTTCA
*
18775 -TTTTTTC-TATTTCA
1 TTTTTTTCTTTTTTCA
18789 -TTTTTTCATTTTTTTCA
1 TTTTTTTC--TTTTTTCA
18806 TTTTTTTCTTTTTT
1 TTTTTTTCTTTTTT
18820 TTTCTTTCAT
Statistics
Matches: 77, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
14 21 0.27
15 4 0.05
16 23 0.30
17 15 0.19
18 14 0.18
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTCTTTTTTCA
Found at i:20902 original size:18 final size:18
Alignment explanation
Indices: 20876--20914 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
20866 CCTTCTTTGG
*
20876 CACTGGGACAATATTCGC
1 CACTAGGACAATATTCGC
20894 CACTAGGACAATATTCGC
1 CACTAGGACAATATTCGC
20912 CAC
1 CAC
20915 CCACTCAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (18 bp):
CACTAGGACAATATTCGC
Found at i:29265 original size:14 final size:14
Alignment explanation
Indices: 29246--29278 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29236 AAATAGATCT
29246 AACGGTCCAAAACA
1 AACGGTCCAAAACA
*
29260 AACGGTCCAAAATA
1 AACGGTCCAAAACA
29274 AACGG
1 AACGG
29279 CGGCGGGACA
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:0.48, C:0.24, G:0.18, T:0.09
Consensus pattern (14 bp):
AACGGTCCAAAACA
Found at i:29576 original size:2 final size:2
Alignment explanation
Indices: 29569--29595 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
29559 CTAAATAGTA
29569 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
29596 AAACGGAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36298 original size:15 final size:15
Alignment explanation
Indices: 36280--36335 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
36270 TAACCGGTTT
36280 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
36295 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
36312 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
36327 CGATTTTAA
1 CGGTTTTAA
36336 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:36308 original size:17 final size:17
Alignment explanation
Indices: 36283--36333 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
36273 CCGGTTTCGG
36283 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
36300 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
36315 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
36332 TT
1 TT
36334 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:36531 original size:21 final size:21
Alignment explanation
Indices: 36502--36558 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
36492 TTTTACACTT
*
36502 AGGGAACCGATTCCCTATGAG
1 AGGGTACCGATTCCCTATGAG
36523 AGGGTACCGATTCCCTATGAG
1 AGGGTACCGATTCCCTATGAG
36544 AGGGTACCGATTCCC
1 AGGGTACCGATTCCC
36559 CCACGCACCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (21 bp):
AGGGTACCGATTCCCTATGAG
Found at i:36776 original size:13 final size:13
Alignment explanation
Indices: 36755--36809 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
36745 AAGTTCGATA
*
36755 AATTCAAATACTT
1 AATTGAAATACTT
36768 AATTGAAATACTT
1 AATTGAAATACTT
* *
36781 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
36795 AATTGAAATACTT
1 AATTGAAATACTT
36808 AA
1 AA
36810 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:36891 original size:32 final size:33
Alignment explanation
Indices: 36795--36893 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
36785 AACTCAACAT
* * *
36795 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
36828 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
36861 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
36893 A
1 A
36894 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:36912 original size:21 final size:21
Alignment explanation
Indices: 36888--36927 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
36878 ACTTCAAGTT
36888 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
36909 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
36928 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:39254 original size:11 final size:12
Alignment explanation
Indices: 39233--39272 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 12
39223 TCCGGATAAA
39233 AACCGGTTTTTT
1 AACCGGTTTTTT
39245 AACCGGTTTTTTT
1 AACCGG-TTTTTT
39258 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
39272 A
1 A
39273 TCTGGTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 6 0.24
15 6 0.24
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:39263 original size:15 final size:14
Alignment explanation
Indices: 39232--39271 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
39222 TTCCGGATAA
39232 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
39245 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
39258 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
39272 ATCTGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:43542 original size:25 final size:25
Alignment explanation
Indices: 43508--43560 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
43498 AAGTGACATT
43508 GATAAGAGTAGTTGATTTACCCTTA
1 GATAAGAGTAGTTGATTTACCCTTA
43533 GATAAGAGTAGTTGATTTACCCTTA
1 GATAAGAGTAGTTGATTTACCCTTA
43558 GAT
1 GAT
43561 TTATTGGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (25 bp):
GATAAGAGTAGTTGATTTACCCTTA
Found at i:45164 original size:17 final size:17
Alignment explanation
Indices: 45142--45184 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
45132 TAACTTTATT
*
45142 TAAATTATTATTATAAA
1 TAAATTATTAATATAAA
*
45159 TAAATTTTTAATATAAA
1 TAAATTATTAATATAAA
45176 TATAATTAT
1 TA-AATTAT
45185 AAATGGGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAATTATTAATATAAA
Found at i:48180 original size:10 final size:10
Alignment explanation
Indices: 48151--48219 Score: 63
Period size: 10 Copynumber: 7.1 Consensus size: 10
48141 GATGCTGGAA
48151 AACCGGTTTG
1 AACCGGTTTG
*
48161 -ACCAGTTTTG
1 AACC-GGTTTG
48171 AACCGGTTTG
1 AACCGGTTTG
*
48181 -ACCGGTCTG
1 AACCGGTTTG
*
48190 AACCGGGTTG
1 AACCGGTTTG
*
48200 -ACCGGTCTG
1 AACCGGTTTG
*
48209 AACCGGGTTG
1 AACCGGTTTG
48219 A
1 A
48220 CCCGACCCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
9 18 0.39
10 25 0.54
11 3 0.07
ACGTcount: A:0.19, C:0.23, G:0.32, T:0.26
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:48193 original size:19 final size:19
Alignment explanation
Indices: 48169--48221 Score: 97
Period size: 19 Copynumber: 2.8 Consensus size: 19
48159 TGACCAGTTT
*
48169 TGAACCGGTTTGACCGGTC
1 TGAACCGGGTTGACCGGTC
48188 TGAACCGGGTTGACCGGTC
1 TGAACCGGGTTGACCGGTC
48207 TGAACCGGGTTGACC
1 TGAACCGGGTTGACC
48222 CGACCCGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.17, C:0.26, G:0.34, T:0.23
Consensus pattern (19 bp):
TGAACCGGGTTGACCGGTC
Found at i:48236 original size:14 final size:14
Alignment explanation
Indices: 48217--48244 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
48207 TGAACCGGGT
48217 TGACCCGACCCGAC
1 TGACCCGACCCGAC
48231 TGACCCGACCCGAC
1 TGACCCGACCCGAC
48245 CCGACTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.50, G:0.21, T:0.07
Consensus pattern (14 bp):
TGACCCGACCCGAC
Found at i:48259 original size:17 final size:17
Alignment explanation
Indices: 48215--48291 Score: 100
Period size: 17 Copynumber: 4.4 Consensus size: 17
48205 TCTGAACCGG
48215 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACT
**
48232 GACCCGACCCGACCCGACT
1 G--TTGACCCGACCCGACT
*
48251 GTTGACCCGGCCCGACT
1 GTTGACCCGACCCGACT
*
48268 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
48285 GTTGACC
1 GTTGACC
48292 GTTGACCGTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
17 36 0.71
19 15 0.29
ACGTcount: A:0.17, C:0.44, G:0.25, T:0.14
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:49242 original size:63 final size:63
Alignment explanation
Indices: 49174--49297 Score: 155
Period size: 63 Copynumber: 2.0 Consensus size: 63
49164 CTAATGTGAC
* * *
49174 TCTTAGGTAGG-CTCTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTG
1 TCTTAGGTAGGCCTC-ACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTG
49236 T
63 T
* *
49237 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
49298 TCCCTTAGGG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
62 1 0.02
63 48 0.91
64 4 0.08
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:49257 original size:32 final size:32
Alignment explanation
Indices: 49174--49297 Score: 80
Period size: 31 Copynumber: 4.0 Consensus size: 32
49164 CTAATGTGAC
* * *
49174 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
49204 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* *
49237 TCTTAGGTAGGC-CTCACGGCCCCGAA-ATCTA
1 TCTTAGGTAGGCTCTCACGG-CCCTAAGATGTA
*
49268 TCTTGGGTAGGCTCTCA-GGCCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
49298 TCCCTTAGGG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
30 5 0.07
31 42 0.58
32 20 0.28
33 5 0.07
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:54702 original size:17 final size:17
Alignment explanation
Indices: 54677--54713 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
54667 GATGATTAAT
54677 TTAGATAAACTTAATTA
1 TTAGATAAACTTAATTA
*
54694 TTAGTTAAACTTAATTA
1 TTAGATAAACTTAATTA
54711 TTA
1 TTA
54714 AAAAATCTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (17 bp):
TTAGATAAACTTAATTA
Found at i:54807 original size:13 final size:13
Alignment explanation
Indices: 54789--54815 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54779 TAATTTAAAA
54789 TTTAAATGATTCT
1 TTTAAATGATTCT
54802 TTTAAATGATTCT
1 TTTAAATGATTCT
54815 T
1 T
54816 ATGGGTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (13 bp):
TTTAAATGATTCT
Found at i:55814 original size:21 final size:23
Alignment explanation
Indices: 55790--55831 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
55780 TCTTATTTTC
55790 TTTCCTT-TT-TTTTTTCAAAAT
1 TTTCCTTATTATTTTTTCAAAAT
55811 TTTCCTTATTATTTTTTCAAA
1 TTTCCTTATTATTTTTTCAAA
55832 TGTTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (23 bp):
TTTCCTTATTATTTTTTCAAAAT
Found at i:65163 original size:18 final size:17
Alignment explanation
Indices: 65140--65187 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
65130 ACACATATAC
65140 CATCATTATCATCATCAA
1 CATCATTATCATCATC-A
* *
65158 CATCATTATCATGATCT
1 CATCATTATCATCATCA
65175 CTATCATTATCAT
1 C-ATCATTATCAT
65188 TAACCCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 1 0.04
18 26 0.96
ACGTcount: A:0.33, C:0.25, G:0.02, T:0.40
Consensus pattern (17 bp):
CATCATTATCATCATCA
Found at i:66026 original size:25 final size:25
Alignment explanation
Indices: 65998--66057 Score: 120
Period size: 25 Copynumber: 2.4 Consensus size: 25
65988 GCTCTATAAC
65998 TTATCTCACAGTTTTACATAATCAT
1 TTATCTCACAGTTTTACATAATCAT
66023 TTATCTCACAGTTTTACATAATCAT
1 TTATCTCACAGTTTTACATAATCAT
66048 TTATCTCACA
1 TTATCTCACA
66058 CTATTTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.43
Consensus pattern (25 bp):
TTATCTCACAGTTTTACATAATCAT
Found at i:66122 original size:2 final size:2
Alignment explanation
Indices: 66115--66145 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
66105 GCTTGTTACC
66115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
66146 TCTCATAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:80631 original size:30 final size:30
Alignment explanation
Indices: 80568--80631 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
80558 AACCAACATT
* * *
80568 AACTTTTTAAAATTATCATTTTGGTCTCTA
1 AACTTTTTAAAATTATCACTTTGGTCACCA
*
80598 AACTTTTTAAAGTTTAT-ACTTTGGTCACCA
1 AACTTTTTAAA-ATTATCACTTTGGTCACCA
80628 AACT
1 AACT
80632 GTACAAAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.31, C:0.16, G:0.08, T:0.45
Consensus pattern (30 bp):
AACTTTTTAAAATTATCACTTTGGTCACCA
Found at i:82274 original size:60 final size:61
Alignment explanation
Indices: 82197--82310 Score: 167
Period size: 61 Copynumber: 1.9 Consensus size: 61
82187 AATGGTCTCT
* * * *
82197 GACTATAGGGTGATGC-TTTGTTGAGTCTCTCGACTATTAAAAGTTATAAAATGATCTTTC
1 GACTATAGGGTGATGCTTTTGTTCAGTCCCCCGACTATTAAAAGTTACAAAATGATCTTTC
* *
82257 GACTATAGGGTGTTGCTTTTGTTCAGTCCCCCGACTATTGAAAGTTACAAAATG
1 GACTATAGGGTGATGCTTTTGTTCAGTCCCCCGACTATTAAAAGTTACAAAATG
82311 GTTATCCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
60 15 0.32
61 32 0.68
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (61 bp):
GACTATAGGGTGATGCTTTTGTTCAGTCCCCCGACTATTAAAAGTTACAAAATGATCTTTC
Found at i:82323 original size:61 final size:60
Alignment explanation
Indices: 82198--82323 Score: 146
Period size: 61 Copynumber: 2.1 Consensus size: 60
82188 ATGGTCTCTG
* * * * * *
82198 ACTATAGGGTGATGCTTTGTTGAGTCTCTCGACTATTAAAAGTTATAAAATGATCTTTCG
1 ACTATAGGGTGATGCTTTGTTCAGTCCCCCGACTATTAAAAGTTACAAAATGATCTTCCA
* * *
82258 ACTATAGGGTGTTGCTTTTGTTCAGTCCCCCGACTATTGAAAGTTACAAAATGGT-TATCCA
1 ACTATAGGGTGATGC-TTTGTTCAGTCCCCCGACTATTAAAAGTTACAAAATGATCT-TCCA
82319 ACTAT
1 ACTAT
82324 TTAGTATGTT
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
60 15 0.27
61 40 0.73
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.37
Consensus pattern (60 bp):
ACTATAGGGTGATGCTTTGTTCAGTCCCCCGACTATTAAAAGTTACAAAATGATCTTCCA
Found at i:82630 original size:60 final size:60
Alignment explanation
Indices: 82511--82631 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 60
82501 TCAGATGGTC
* * * * * *
82511 ATTTTGTAACTTTTAATAGTTGGAGGACTTGACAAAGAAACATCTTATAGTTGAAGGACT
1 ATTTTATAACTTTTAATAGTCGGAGGACTTAACAAAGAAACACCTTATAATCGAAGGACT
*
82571 ATTTTATAACTTTTAATAGTC-GAGAGACTTAACAAA-ACAACACCTTATAATCGAGGGACT
1 ATTTTATAACTTTTAATAGTCGGAG-GACTTAACAAAGA-AACACCTTATAATCGAAGGACT
82631 A
1 A
82632 CTTGTGTAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 4 0.08
60 48 0.92
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (60 bp):
ATTTTATAACTTTTAATAGTCGGAGGACTTAACAAAGAAACACCTTATAATCGAAGGACT
Found at i:88822 original size:10 final size:10
Alignment explanation
Indices: 88809--88851 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
88799 CAAACGGATG
88809 TAAACGAACA
1 TAAACGAACA
88819 TAAACGAACACAA
1 TAAACG-A-AC-A
*
88832 TAAACGAACG
1 TAAACGAACA
88842 TAAACGAACA
1 TAAACGAACA
88852 CATATGAACG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 15 0.54
11 3 0.11
12 3 0.11
13 7 0.25
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (10 bp):
TAAACGAACA
Found at i:88869 original size:24 final size:24
Alignment explanation
Indices: 88770--88869 Score: 105
Period size: 24 Copynumber: 4.2 Consensus size: 24
88760 CATTTAAATG
*
88770 ATAAACGAACACAAATGAAA-GAAC
1 ATAAACGAACACATAT-AAACGAAC
* ** *
88794 ATAAACAAACGGATGTAAACGAAC
1 ATAAACGAACACATATAAACGAAC
88818 ATAAACGAACACA-ATAAACGAAC
1 ATAAACGAACACATATAAACGAAC
* * *
88841 GTAAACGAACACATATGAACGTAC
1 ATAAACGAACACATATAAACGAAC
88865 ATAAA
1 ATAAA
88870 TGAATTTTTT
Statistics
Matches: 61, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
23 24 0.39
24 37 0.61
ACGTcount: A:0.57, C:0.18, G:0.13, T:0.12
Consensus pattern (24 bp):
ATAAACGAACACATATAAACGAAC
Found at i:89078 original size:24 final size:24
Alignment explanation
Indices: 89033--89110 Score: 84
Period size: 24 Copynumber: 3.2 Consensus size: 24
89023 GATTGAGCTA
* * * *
89033 AACATAAATGAGCGCACATAAATG
1 AACATAAACGAACGAACATAAACG
*
89057 AACATAAACGAACGAACGTAAACG
1 AACATAAACGAACGAACATAAACG
* * *
89081 AACATAAATGTATGAACATAAACG
1 AACATAAACGAACGAACATAAACG
89105 AACATA
1 AACATA
89111 TTACCGAACG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.54, C:0.17, G:0.14, T:0.15
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:90324 original size:29 final size:29
Alignment explanation
Indices: 90278--90387 Score: 139
Period size: 29 Copynumber: 3.8 Consensus size: 29
90268 CGTCGTACGG
*** * * *
90278 AAATAATTCGAAAATGGTGATATTTTGGG
1 AAATAATTCGATTTTGGTGCTATTCTGGT
*
90307 AAATAATTCGGTTTTGGTGCTATTCTGGT
1 AAATAATTCGATTTTGGTGCTATTCTGGT
*
90336 AAATAATTCGATTTTTGTGCTATTCTGGT
1 AAATAATTCGATTTTGGTGCTATTCTGGT
90365 AAATAATTCGATTTTGGGTGCTA
1 AAATAATTCGATTTT-GGTGCTA
90388 GATAAATAAT
Statistics
Matches: 70, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
29 64 0.91
30 6 0.09
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (29 bp):
AAATAATTCGATTTTGGTGCTATTCTGGT
Found at i:93124 original size:24 final size:24
Alignment explanation
Indices: 93018--93126 Score: 101
Period size: 24 Copynumber: 4.5 Consensus size: 24
93008 GAATATTTTA
*
93018 TCTGATTTCTGATTTGAATTCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* ** *
93042 TTTGACATCTGATCTGAAATCTGT
1 TCTGATTTCTGATCTGAATTCTGT
* * * * *
93066 TCTGATTCCTAACCTGGATTCTAT
1 TCTGATTTCTGATCTGAATTCTGT
* *
93090 TCTGATATCTGATCTGAATTATGT
1 TCTGATTTCTGATCTGAATTCTGT
*
93114 TTTGATTTCTGAT
1 TCTGATTTCTGAT
93127 ATCTCCGTTT
Statistics
Matches: 62, Mismatches: 23, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 62 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.48
Consensus pattern (24 bp):
TCTGATTTCTGATCTGAATTCTGT
Found at i:102049 original size:35 final size:35
Alignment explanation
Indices: 101976--102050 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
101966 CGTCACTAAC
* * **
101976 AGTAAGGTCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAACCGAGGAACCGCCA
* *
102011 AGTAAGGCCCTGAGCACACAACTGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAACCGAGGAACCGCCA
102046 AGTAA
1 AGTAA
102051 TCTTCCTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.35, C:0.27, G:0.27, T:0.12
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAACCGAGGAACCGCCA
Found at i:102155 original size:24 final size:24
Alignment explanation
Indices: 102128--102218 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
102118 CATAATTCAA
*
102128 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
102152 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
102176 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
102199 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
102219 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:102198 original size:47 final size:48
Alignment explanation
Indices: 102128--102218 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
102118 CATAATTCAA
* * *
102128 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
102176 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
102219 TCAAATTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:103381 original size:18 final size:18
Alignment explanation
Indices: 103358--103395 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
103348 TCCTTCCATC
*
103358 CAATCTTATTATTTAATT
1 CAATCTTATCATTTAATT
*
103376 CAATCTTATCATTTACTT
1 CAATCTTATCATTTAATT
103394 CA
1 CA
103396 GTCCTTTCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (18 bp):
CAATCTTATCATTTAATT
Found at i:105549 original size:2 final size:2
Alignment explanation
Indices: 105542--105598 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
105532 TGAGAAACCA
105542 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
105584 TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC T
105599 TCTAATTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:115809 original size:53 final size:52
Alignment explanation
Indices: 115750--116571 Score: 1012
Period size: 53 Copynumber: 15.5 Consensus size: 52
115740 CTCTCTATCG
** * *
115750 CTTCAGGGAGTAAGAACTCGAACAATCTTCTGT-CTACGAGTCTGCTCTCTCTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCT-TCCTACGGGTCTGCTCTCTTTT
* ** * *
115803 CTTCAGGGAGTAGAACTCGAACAGTCTTCTT-CTCACGGG-CTCGATCTCTCTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCT-ACGGGTCT-GCTCTCTTTT
** *
115855 CTTCAGGGAGTAGAACTCGAACAATCTTCTACCTACGGGTCTGCTCTCTCTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCT-TTT
* * *
115908 CCTCAGGGAGTAGAACTCGAACAATCATCTGCCTACGGG-CTTGCTCTCTCTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTC-TGCTCTCT-TTT
** *
115961 CTTCAGGGAGTAGAACTCGAACAATCTTCTTCCTACGGGTCTGTTCTCTATTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCT-TTT
* **
116014 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCTTACGGGTCCACTCTCTTTTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTC-TTTT
* * * *
116068 CTTCAGGGAGTAGAACTCGAACAGTAATCTTCCTACGGGTCCGCCCTATTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTT
* * *
116120 CTTCAAGGAGTAGAACTCGAACAGTAATCTTCCTACAGG-CTCGCTCTCTATTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCT-GCTCTCT-TTT
*
116173 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGG-CTCACTCTCTATTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCT-GCTCTCT-TTT
* *
116227 CTTCATGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTC-TTTT
* * * *
116281 CTTCAGGGAGTAGAACTCGAACAGTAATCTTCCTACGAGTCTGCCCTATTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTT
* *
116333 CTTCAGGGAGTAAGAACTCGAAGAATAATCTTCCTACGGGT-TCGCTATCTTTTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCT-GCTCTC-TTTT
116387 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGT-TCGCTCTCTTTTT
1 CTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCT-GCTCTC-TTTT
*
116441 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTC-TTTT
*
116494 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
1 CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTC-TTTT
116547 CTTCAGGGAGTAGAACTCGAACAAT
1 CTTCAGGGAGTAGAACTCGAACAAT
116572 CTTATGTTGC
Statistics
Matches: 698, Mismatches: 53, Indels: 36
0.89 0.07 0.05
Matches are distributed among these distances:
51 6 0.01
52 134 0.19
53 346 0.50
54 209 0.30
55 3 0.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (52 bp):
CTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTTTT
Found at i:116106 original size:160 final size:161
Alignment explanation
Indices: 115750--116571 Score: 1093
Period size: 160 Copynumber: 5.2 Consensus size: 161
115740 CTCTCTATCG
** *
115750 CTTCAGGGAGTAAGAACTCGAACAATCTTCTGT-CTACGAGTCTGCTCTCTC-TTCTTCAGGGAG
1 CTTCAGGGAGTAAGAACTCGAACAATAATCT-TCCTACGGGTCTGCTCTCTCTTTCTTCAGGGAG
** * *
115813 TAGAACTCGAACAGTCTTCTT-CTCACGGG-CTCGATCTCT-CTTCTTCAGGGAGT-AGAACTCG
65 TAGAACTCGAACAGTAATCTTCCT-ACGGGTCT-GCTCTCTATTTCTTCAGGGAGTAAGAACTCG
** * * *
115874 AACAATCTTCTACCTACGGGTCTGCTCTCTCTTT
128 AACAATAATCTTCCTACGGGTCCGCTCTCTTTTT
* * *
115908 CCTCAGGGAGT-AGAACTCGAACAATCATCTGCCTACGGG-CTTGCTCTCTCTTTCTTCAGGGAG
1 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTC-TGCTCTCTCTTTCTTCAGGGAG
* ** *
115971 TAGAACTCGAACAATCTTCTTCCTACGGGTCTGTTCTCTATTTCTTCAGGGAGTAAGAACTCGAA
65 TAGAACTCGAACAGTAATCTTCCTACGGGTCTGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAA
* *
116036 CAATAATCTTCTTACGGGTCCACTCTCTTTTT
130 CAATAATCTTCCTACGGGTCCGCTCTCTTTTT
* * * * *
116068 CTTCAGGGAGT-AGAACTCGAACAGTAATCTTCCTACGGGTCCGCCCTAT-TTTCTTCAAGGAGT
1 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTCTTTCTTCAGGGAGT
*
116131 AGAACTCGAACAGTAATCTTCCTACAGG-CTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAA
66 AGAACTCGAACAGTAATCTTCCTACGGGTCT-GCTCTCTATTTCTTCAGGGAGTAAGAACTCGAA
* *
116195 CAATAATCTTCCTACGGG-CTCACTCTCTATTT
130 CAATAATCTTCCTACGGGTC-CGCTCTCTTTTT
* * *
116227 CTTCATGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGAGT
1 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTCTTTCTTCAGGGAGT
*
116292 AGAACTCGAACAGTAATCTTCCTACGAGTCTGC-C-CTATTTTCTTCAGGGAGTAAGAACTCGAA
66 AGAACTCGAACAGTAATCTTCCTACGGGTCTGCTCTCTA-TTTCTTCAGGGAGTAAGAACTCGAA
* * *
116355 GAATAATCTTCCTACGGGTTCGCTATCTTTTT
130 CAATAATCTTCCTACGGGTCCGCTCTCTTTTT
*
116387 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGT-TCGCTCTCTTTTTCTTCAGGGAG
1 CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCT-GCTCTCTCTTTCTTCAGGGAG
* * *
116451 TAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTCAGGGAGT-AGAACTCGAA
65 TAGAACTCGAACAGTAATCTTCCTACGGGTCTGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAA
116515 CAATAATCTTCCTACGGGTCCGCTCTCTTTTT
130 CAATAATCTTCCTACGGGTCCGCTCTCTTTTT
116547 CTTCAGGGAGT-AGAACTCGAACAAT
1 CTTCAGGGAGTAAGAACTCGAACAAT
116572 CTTATGTTGC
Statistics
Matches: 596, Mismatches: 50, Indels: 35
0.88 0.07 0.05
Matches are distributed among these distances:
156 1 0.00
157 33 0.06
158 56 0.09
159 141 0.24
160 304 0.51
161 57 0.10
162 4 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (161 bp):
CTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCTGCTCTCTCTTTCTTCAGGGAGT
AGAACTCGAACAGTAATCTTCCTACGGGTCTGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAAC
AATAATCTTCCTACGGGTCCGCTCTCTTTTT
Found at i:116207 original size:213 final size:213
Alignment explanation
Indices: 115732--116571 Score: 1126
Period size: 213 Copynumber: 4.0 Consensus size: 213
115722 TCTCCAAAAT
* ** ** *
115732 CAGGTTCGCTCTCTATCGCTTCAGGGAGTAAGAACTCGAACAATCTTCTGT-CTACGAGTCT-GC
1 CAGGCTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCT-TCCTACGGGTCTCGC
* * ** * *
115795 TCTCT-CTTCTTCAGGGAGTAGAACTCGAACAGTCTTCTT-CTCACGGGCTCGA-TCTC-TCTTC
65 TCTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCT-ACGGG-TCCACTCTCTTTTTC
** * * * * *
115856 TTCAGGGAGTAGAACTCGAACAATCTTCTACCTACGGGTCTGCTCTCTCTTTCCTCAGGGAGTAG
128 TTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCCCTAT-TTTCTTCAGGGAGTAG
* *
115921 AACTCGAACAATCATCTGCCTA
192 AACTCGAACAATAATCTTCCTA
* * * ** *
115943 CGGGCTTGCTCTCTCTTTCTTCAGGGAGT-AGAACTCGAACAATCTTCTTCCTACGGGTCT-GTT
1 CAGGCTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCTCGCT
*
116006 CTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCTTACGGGTCCACTCTCTTTTTCTT
66 CTCTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCACTCTCTTTTTCTT
* *
116071 CAGGGAGTAGAACTCGAACAGTAATCTTCCTACGGGTCCGCCCTATTTTCTTCAAGGAGTAGAAC
130 CAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCCCTATTTTCTTCAGGGAGTAGAAC
*
116136 TCGAACAGTAATCTTCCTA
195 TCGAACAATAATCTTCCTA
*
116155 CAGGCTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGG-CTCACT
1 CAGGCTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCTCGCT
* *
116219 CTCTATTTCTTCATGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTT
66 CTCTATTTCTTCAGGGAGT-AGAACTCGAACAATAATCTTCCTACGGGTCCACTCTCTTTTTCTT
* * *
116284 CAGGGAGTAGAACTCGAACAGTAATCTTCCTACGAGTCTGCCCTATTTTCTTCAGGGAGTAAGAA
130 CAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCCCTATTTTCTTCAGGGAGT-AGAA
*
116349 CTCGAAGAATAATCTTCCTA
194 CTCGAACAATAATCTTCCTA
* * * *
116369 CGGGTTCGCTATCTTTTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGT-TCGCT
1 CAGGCTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCTCGCT
* *
116433 CTCTTTTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCTTTTTCTTC
66 CTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCACTCTCTTTTTCTTC
116498 AGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCTCTCT-TTTTCTTCAGGGAGTAGAA
131 AGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGC-C-CTATTTTCTTCAGGGAGTAGAA
116562 CTCGAACAAT
194 CTCGAACAAT
116572 CTTATGTTGC
Statistics
Matches: 564, Mismatches: 53, Indels: 22
0.88 0.08 0.03
Matches are distributed among these distances:
209 1 0.00
210 34 0.06
211 39 0.07
212 87 0.15
213 288 0.51
214 113 0.20
215 2 0.00
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (213 bp):
CAGGCTCGCTCTCTATTTCTTCAGGGAGTAAGAACTCGAACAATAATCTTCCTACGGGTCTCGCT
CTCTATTTCTTCAGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCACTCTCTTTTTCTTC
AGGGAGTAGAACTCGAACAATAATCTTCCTACGGGTCCGCCCTATTTTCTTCAGGGAGTAGAACT
CGAACAATAATCTTCCTA
Found at i:116635 original size:37 final size:37
Alignment explanation
Indices: 116581--116664 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
116571 TCTTATGTTG
* *
116581 CTTCACTACCTCATTGTGAAGGC-TTCTGGATGATTTA
1 CTTCACTACCTCATTGTGAAGACTTTC-AGATGATTTA
* * *
116618 CTTCACTACTTCCTTGTGAAGACTTTCAGATGATTTG
1 CTTCACTACCTCATTGTGAAGACTTTCAGATGATTTA
116655 CTTCACTACC
1 CTTCACTACC
116665 CTTTCGTTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
37 37 0.93
38 3 0.08
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.38
Consensus pattern (37 bp):
CTTCACTACCTCATTGTGAAGACTTTCAGATGATTTA
Found at i:117969 original size:16 final size:16
Alignment explanation
Indices: 117948--118003 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
117938 TTGTTTTGTT
117948 TTTTTTCTTCTTCTTC
1 TTTTTTCTTCTTCTTC
*
117964 TTTTTTCTTTTTCTTC
1 TTTTTTCTTCTTCTTC
*
117980 TTTTTTCTTCTTTTTTC
1 TTTTTTCTTC-TTCTTC
117997 TTTTTTC
1 TTTTTTC
118004 ATTTTTCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
16 24 0.67
17 12 0.33
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTCTTCTTCTTC
Found at i:117993 original size:9 final size:9
Alignment explanation
Indices: 117946--118072 Score: 58
Period size: 9 Copynumber: 14.3 Consensus size: 9
117936 TTTTGTTTTG
*
117946 TTTTTTTTC
1 TTTTTCTTC
*
117955 TTCTTCTTC
1 TTTTTCTTC
117964 -TTTT-TTC
1 TTTTTCTTC
117971 TTTTTCTTC
1 TTTTTCTTC
117980 TTTTTTCTTC
1 -TTTTTCTTC
117990 -TTTT-TTC
1 TTTTTCTTC
117997 -TTTT-TTC
1 TTTTTCTTC
*
118004 ATTTTTCATTT
1 -TTTTTC-TTC
*
118015 TTTTTCAT-
1 TTTTTCTTC
*
118023 TTTTTCTATT
1 TTTTTCT-TC
*
118033 TTTTTCCATTT
1 TTTTT-C-TTC
118044 TTTTTCTAT-
1 TTTTTCT-TC
118053 TTTTTCTAT-
1 TTTTTCT-TC
118062 TTTTT-TTC
1 TTTTTCTTC
118070 TTT
1 TTT
118073 CTTTTTTCTT
Statistics
Matches: 99, Mismatches: 6, Indels: 27
0.75 0.05 0.20
Matches are distributed among these distances:
7 14 0.14
8 21 0.21
9 31 0.31
10 22 0.22
11 10 0.10
12 1 0.01
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:118077 original size:9 final size:9
Alignment explanation
Indices: 117935--118083 Score: 95
Period size: 10 Copynumber: 15.0 Consensus size: 9
117925 CTTTTATTTG
*
117935 TTTTTGTTT
1 TTTTTCTTT
117944 TGTTTT-TTT
1 T-TTTTCTTT
117953 TCTTCTTCTTCT
1 T-TT-TTCTT-T
117965 TTTTTCTTT
1 TTTTTCTTT
*
117974 TTCTTCTTT
1 TTTTTCTTT
117983 TTTCTTCTTT
1 TTT-TTCTTT
*
117993 TTTCTTTTTT
1 TTT-TTCTTT
118003 CATTTTTCATTT
1 --TTTTTC-TTT
*
118015 TTTTTC-AT
1 TTTTTCTTT
118023 TTTTTCTATT
1 TTTTTCT-TT
118033 TTTTTCCATTT
1 TTTTT-C-TTT
118044 TTTTTCTATT
1 TTTTTCT-TT
*
118054 TTTTCTATTT
1 TTTT-TCTTT
118064 TTTTTCTTTCT
1 TTTTTC-TT-T
118075 TTTTTCTTT
1 TTTTTCTTT
118084 CATCTTCAAG
Statistics
Matches: 115, Mismatches: 9, Indels: 32
0.74 0.06 0.21
Matches are distributed among these distances:
8 7 0.06
9 21 0.18
10 55 0.48
11 23 0.20
12 9 0.08
ACGTcount: A:0.05, C:0.14, G:0.01, T:0.80
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:120148 original size:18 final size:18
Alignment explanation
Indices: 120122--120160 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
120112 CCTTCTTTGG
*
120122 CACTGGGACAATATTCGC
1 CACTAGGACAATATTCGC
120140 CACTAGGACAATATTCGC
1 CACTAGGACAATATTCGC
120158 CAC
1 CAC
120161 CCACTCAGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (18 bp):
CACTAGGACAATATTCGC
Done.