Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01005933.1 Kokia drynarioides strain JFW-HI SEQ_120314, 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: 141447
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 36 characters in sequence are not A, C, G, or T
Found at i:29 original size:17 final size:16
Alignment explanation
Indices: 2--67 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
1 A
*
2 AATTAATTTTAAACTT
1 AATTAAATTTAAACTT
18 AATTTAAATTTAAACTT
1 AA-TTAAATTTAAACTT
**
35 AAGAAAAGTTTAAACTTT
1 AATTAAA-TTTAAAC-TT
53 AAATTAAATTTAAAC
1 -AATTAAATTTAAAC
68 CCAAAATGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
16 5 0.12
17 22 0.54
18 9 0.22
19 5 0.12
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.41
Consensus pattern (16 bp):
AATTAAATTTAAACTT
Found at i:975 original size:206 final size:206
Alignment explanation
Indices: 485--1275 Score: 1182
Period size: 206 Copynumber: 3.9 Consensus size: 206
475 TTTGATCCAC
* * * * ** *
485 TTCTCTGTGTTTCATCAGGAAGATGGGGTTAGAAGATTTGTT--CATCGAGCATGGGTTTGATTT
1 TTCTCAGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCACATCGAGGGTGGGTTCGATTT
*
548 GCTCTTCTTCTCAGTATC-CTATCAGGAAGATGACCGCGTCATTTGTTTCAA-TCTGCTTCTCTG
66 GGTCTTCTTCTCAGTATCTC-ATCAGGAAGATGACCGCGTCATTTGTTTCAATTC-GCTTCTCTG
* * * ** * *
611 TATCTCAACAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAATAAGCTAACC-GTTTGT
129 TATCTCATCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTAT
* *
675 TGCTTCGACCTGC
194 TACTTCGACCTGT
*
688 TTCTCAGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGTTCACATCGAGGGTGGGTTCGATTT
1 TTCTCAGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCACATCGAGGGTGGGTTCGATTT
* ** * *
753 GGTCTTCTTCTCAGTATCTCATCAGGAATATGACCGCGTTGTTTGTTTCAATTTGCTTCTCAGTA
66 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATTCGCTTCTCTGTA
*
818 TCTCATCAGGAAGATGAATTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTA
131 TCTCATCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTA
883 CTTCGACCTGT
196 CTTCGACCTGT
*
894 TTCTCAGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTTACATCGAGGGTGGGTTCGATTT
1 TTCTCAGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCACATCGAGGGTGGGTTCGATTT
*
959 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCGTTTGTTTCAATTCGCTTC-CTTGT
66 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATTCGCTTCTC-TGT
* *
1023 ATCTCATCAGGAAGATGAATTTAGTCCACTTCTCAGTATCTCACCAGGAAGCTAA-CTGTTTTAT
130 ATCTCATCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCT-TTTTAT
*
1087 TACTTCAACCTGT
194 TACTTCGACCTGT
* *
1100 TTCTCAGTGTCTCATCAGGAAGTTGAGGTTCGAAGATTTGTTCACATCGAGGGTGGGTTTGATTT
1 TTCTCAGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCACATCGAGGGTGGGTTCGATTT
* * *
1165 GGTCTTCTTCTCAGTATCTCATCAGGAAAATGATCGCGTCATTTGTTTCAATTCGCTTCACTGTA
66 GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATTCGCTTCTCTGTA
*
1230 TCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAG
131 TCTCATCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATCAG
1276 CAAATGACCG
Statistics
Matches: 540, Mismatches: 40, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
203 38 0.07
205 126 0.23
206 375 0.69
207 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (206 bp):
TTCTCAGTGTCTCATCAGGAAGTTGGGGTTCGAAGATTTGTTCACATCGAGGGTGGGTTCGATTT
GGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCATTTGTTTCAATTCGCTTCTCTGTA
TCTCATCAGGAAGACGAATTTAGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTA
CTTCGACCTGT
Found at i:1804 original size:27 final size:27
Alignment explanation
Indices: 1781--1840 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
1771 TCAGAAATTC
*
1781 TATTAAAAAGAGGATCAAAGGAAACAA
1 TATTAAAAAGAAGATCAAAGGAAACAA
1808 TATTAAAAAGAAGATCAAAGGAAACAA
1 TATTAAAAAGAAGATCAAAGGAAACAA
1835 TCATTA
1 T-ATTA
1841 GTTGAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 27 0.87
28 4 0.13
ACGTcount: A:0.58, C:0.08, G:0.15, T:0.18
Consensus pattern (27 bp):
TATTAAAAAGAAGATCAAAGGAAACAA
Found at i:12603 original size:28 final size:27
Alignment explanation
Indices: 12542--12614 Score: 67
Period size: 28 Copynumber: 2.5 Consensus size: 27
12532 GTTGGACGAG
*
12542 AAAAATGGTAATTTCGGGAAAACTTGGGGTT
1 AAAAATGGTAATTT----AAAACTTGGGGGT
*
12573 AAAGATGG-AATTTAAAACATTCGGGGGT
1 AAAAATGGTAATTTAAAAC-TT-GGGGGT
12601 AAAAATGGTAATTT
1 AAAAATGGTAATTT
12615 TAAGAGTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
26 5 0.14
27 2 0.06
28 12 0.33
29 5 0.14
30 5 0.14
31 7 0.19
ACGTcount: A:0.40, C:0.05, G:0.26, T:0.29
Consensus pattern (27 bp):
AAAAATGGTAATTTAAAACTTGGGGGT
Found at i:12732 original size:29 final size:31
Alignment explanation
Indices: 12667--12733 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
12657 GAGTAAATTA
* * *
12667 GTAATTTTTGGATGTCCCGAGGTTAAAAATG
1 GTAATTTTAGGAGGTCCCGAGGGTAAAAATG
*
12698 G-GATTTTAGGAGGT-CCGAGGGT-AAAATG
1 GTAATTTTAGGAGGTCCCGAGGGTAAAAATG
12726 GTAATTTT
1 GTAATTTT
12734 TAAAACGTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
28 7 0.23
29 12 0.40
30 10 0.33
31 1 0.03
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.34
Consensus pattern (31 bp):
GTAATTTTAGGAGGTCCCGAGGGTAAAAATG
Found at i:12754 original size:59 final size:59
Alignment explanation
Indices: 12686--13087 Score: 432
Period size: 59 Copynumber: 6.8 Consensus size: 59
12676 GGATGTCCCG
* * * * * * *
12686 AGGTTAAAAATGGGATTTTAGGAGGTCCGAGGGTAAAATGGTAATTTTTAAAACGTTCA
1 AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCA
* * *
12745 AGGTCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAGATGGTAATGTTTAGAAGGTT-A
1 AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCA
* ** * * ** * *
12803 GAGGTTAAAAATGGGATTTTTAAAAGTTTGGGGGTAAATTGGTAATTTTGGGAAGATTCG
1 -AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCA
* * * **
12863 AGGTTAAAAATGGAATTTTTAGAAGTTCAAGGGTAAAATGGTAA-TTTTATGAAGGTTCA
1 AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTA-GAAGGTTCA
* **
12922 AGGTC-AAAATGGGATTTTTGGAACTTCGGGGGTAAAATGGTAATTTTGGGAAGGTTCA
1 AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCA
* * ** *
12980 TGGTAAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTGGGAAGGTTCG
1 AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCA
* * * **
13039 GGGTCAAAAATGGGATTTTTTGAAATTCAAGGGTAAAATGGTAATTTTT
1 AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTT
13088 GTACAGTTTA
Statistics
Matches: 287, Mismatches: 51, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
58 49 0.17
59 238 0.83
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (59 bp):
AGGTCAAAAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTTAGAAGGTTCA
Found at i:13024 original size:176 final size:177
Alignment explanation
Indices: 12684--13087 Score: 548
Period size: 176 Copynumber: 2.3 Consensus size: 177
12674 TTGGATGTCC
* * *
12684 CGAGGTTAAAAATGGGA-TTTTAGGAGGTCCGAGGGTAAAATGGTAATTTTTAAAACGTTCAAGG
1 CGAGGTTAAAAATGGGATTTTTA-GAAGTTCAAGGGTAAAATGGTAATTTTTAAAACGTTCAAGG
* * *
12748 TCAAAAATGAGATTTTTGGAAGTTCGGGGGTAAGATGGTAATGTTTAGAAGGTTAGAGGTTAAAA
65 TCAAAAATGAGATTTTTGGAACTTCGGGGGTAAAATGGTAATGTTTAGAAGGTTAGAGGTAAAAA
* *
12813 ATGGGATTTTTAAAAGTTTGGGGGTAAATTGGTAATTTTGGGAAGATT
130 ATGGGATTTTTAAAAGTTCGGGGGTAAAATGGTAATTTTGGGAAGATT
* * *
12861 CGAGGTTAAAAATGGAATTTTTAGAAGTTCAAGGGTAAAATGGTAA-TTTTATGAAGGTTCAAGG
1 CGAGGTTAAAAATGGGATTTTTAGAAGTTCAAGGGTAAAATGGTAATTTTTA-AAACGTTCAAGG
* * *
12925 TC-AAAATGGGATTTTTGGAACTTCGGGGGTAAAATGGTAAT-TTTGGGAAGGTTCA-TGGTAAA
65 TCAAAAATGAGATTTTTGGAACTTCGGGGGTAAAATGGTAATGTTT-AGAAGGTT-AGAGGTAAA
** *
12987 AAATGGGATTTTTGGAAGTTCGGGGGTAAAATGGTAATTTTGGGAAGGTT
128 AAATGGGATTTTTAAAAGTTCGGGGGTAAAATGGTAATTTTGGGAAGATT
* * * *
13037 CGGGGTCAAAAATGGGATTTTTTGAAATTCAAGGGTAAAATGGTAATTTTT
1 CGAGGTTAAAAATGGGATTTTTAGAAGTTCAAGGGTAAAATGGTAATTTTT
13088 GTACAGTTTA
Statistics
Matches: 200, Mismatches: 22, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
175 3 0.01
176 139 0.69
177 53 0.26
178 5 0.03
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.33
Consensus pattern (177 bp):
CGAGGTTAAAAATGGGATTTTTAGAAGTTCAAGGGTAAAATGGTAATTTTTAAAACGTTCAAGGT
CAAAAATGAGATTTTTGGAACTTCGGGGGTAAAATGGTAATGTTTAGAAGGTTAGAGGTAAAAAA
TGGGATTTTTAAAAGTTCGGGGGTAAAATGGTAATTTTGGGAAGATT
Found at i:14127 original size:21 final size:21
Alignment explanation
Indices: 14088--14187 Score: 73
Period size: 21 Copynumber: 4.8 Consensus size: 21
14078 TTTCCCTTTT
14088 TTATTAATATTATTTAATAATA
1 TTATTAATATTA-TTAATAATA
*
14110 TTATTATTATTATTAATAA-A
1 TTATTAATATTATTAATAATA
** **
14130 ACATT--TATTATTAATGCCT-
1 TTATTAATATTATTAAT-AATA
* *
14149 TTATTAATATTAATAATAATT
1 TTATTAATATTATTAATAATA
*
14170 TTATTAGTATCTATTAAT
1 TTATTAATAT-TATTAAT
14188 GCTAATTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
18 10 0.17
19 3 0.05
20 5 0.08
21 25 0.42
22 17 0.28
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
TTATTAATATTATTAATAATA
Found at i:14996 original size:17 final size:16
Alignment explanation
Indices: 14962--15015 Score: 65
Period size: 16 Copynumber: 3.2 Consensus size: 16
14952 AACTGGACTT
14962 TTTTAAATTAATTAAA
1 TTTTAAATTAATTAAA
14978 TTTTAAATTCAAATT-AA
1 TTTTAAATT--AATTAAA
14995 TTTTAAACTTAATTTAAA
1 TTTTAAA-TTAA-TTAAA
15013 TTT
1 TTT
15016 AAACTTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
16 11 0.33
17 11 0.33
18 11 0.33
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAATTAATTAAA
Found at i:15016 original size:17 final size:16
Alignment explanation
Indices: 14963--15054 Score: 80
Period size: 17 Copynumber: 5.4 Consensus size: 16
14953 ACTGGACTTT
14963 TTTAAA-TTAATTAAA
1 TTTAAACTTAATTAAA
*
14978 TTTTAAA-TTCAAATTAAT
1 -TTTAAACTT--AATTAAA
14996 TTTAAACTTAATTTAAA
1 TTTAAACTTAA-TTAAA
**
15013 TTTAAACTTAAGAAAA
1 TTTAAACTTAATTAAA
15029 GTTTAAACTTTAAATTAAA
1 -TTTAAAC-TT-AATTAAA
15048 TTTAAAC
1 TTTAAAC
15055 CCAAAATGAA
Statistics
Matches: 63, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
16 13 0.21
17 28 0.44
18 17 0.27
19 5 0.08
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.43
Consensus pattern (16 bp):
TTTAAACTTAATTAAA
Found at i:15017 original size:34 final size:33
Alignment explanation
Indices: 14962--15054 Score: 93
Period size: 35 Copynumber: 2.7 Consensus size: 33
14952 AACTGGACTT
*
14962 TTTTAAA-TTAATTAAATTTTAAA-TTCAA-ATTAA
1 TTTTAAACTTAATTAAA-TTTAAACTT-AAGA-AAA
14995 TTTTAAACTTAATTTAAATTTAAACTTAAGAAAA
1 TTTTAAACTTAA-TTAAATTTAAACTTAAGAAAA
*
15029 GTTTAAACTTTAAATTAAATTTAAAC
1 TTTTAAAC-TT-AATTAAATTTAAAC
15055 CCAAAATGAA
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
33 7 0.13
34 21 0.40
35 22 0.42
36 2 0.04
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (33 bp):
TTTTAAACTTAATTAAATTTAAACTTAAGAAAA
Found at i:15709 original size:29 final size:28
Alignment explanation
Indices: 15669--15736 Score: 109
Period size: 29 Copynumber: 2.4 Consensus size: 28
15659 TGTATGTATA
15669 TTTTTAAAAAACACAGATCTAAATTTTT
1 TTTTTAAAAAACACAGATCTAAATTTTT
15697 TTTTTAAAAAAACACAGATCTAAATTTTT
1 TTTTT-AAAAAACACAGATCTAAATTTTT
*
15726 TATTTTTAAAA
1 T-TTTTAAAAA
15737 CAAAGTTTTC
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
28 5 0.14
29 28 0.76
30 4 0.11
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (28 bp):
TTTTTAAAAAACACAGATCTAAATTTTT
Found at i:15826 original size:13 final size:13
Alignment explanation
Indices: 15808--15832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15798 TTTAAATGTT
15808 TAGATCTAAAAAC
1 TAGATCTAAAAAC
15821 TAGATCTAAAAA
1 TAGATCTAAAAA
15833 GTGAAAAGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (13 bp):
TAGATCTAAAAAC
Found at i:16673 original size:14 final size:13
Alignment explanation
Indices: 16646--16670 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16636 AGATTTTGAA
16646 GATTTTATTTTTG
1 GATTTTATTTTTG
16659 GATTTTATTTTT
1 GATTTTATTTTT
16671 TGGGCTCGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (13 bp):
GATTTTATTTTTG
Found at i:24685 original size:7 final size:7
Alignment explanation
Indices: 24673--24699 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
24663 TTGCTGCAAA
24673 AGCCAAT
1 AGCCAAT
24680 AGCCAAT
1 AGCCAAT
24687 AGCCAAT
1 AGCCAAT
24694 AGCCAA
1 AGCCAA
24700 CCATGTTAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.30, G:0.15, T:0.11
Consensus pattern (7 bp):
AGCCAAT
Found at i:28400 original size:15 final size:16
Alignment explanation
Indices: 28362--28400 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
28352 GATACAGTGA
28362 ATATAAAATTATAAAG
1 ATATAAAATTATAAAG
*
28378 ATAGAAAATTA-AAAG
1 ATATAAAATTATAAAG
*
28393 GTATAAAA
1 ATATAAAA
28401 CATAAATTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
ATATAAAATTATAAAG
Found at i:34556 original size:3 final size:3
Alignment explanation
Indices: 34512--34536 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
34502 CCAAAACTAT
34512 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
34537 GAAGAATAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:43725 original size:7 final size:7
Alignment explanation
Indices: 43713--43738 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43703 AGCGAGATTC
43713 GAACCTT
1 GAACCTT
43720 GAACCTT
1 GAACCTT
43727 GAACCTT
1 GAACCTT
43734 GAACC
1 GAACC
43739 GTTTTTGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (7 bp):
GAACCTT
Found at i:52618 original size:30 final size:31
Alignment explanation
Indices: 52543--52619 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
52533 TAAACTTTTT
* * *
52543 AAAATGATCAAATAAAGGTATAACCTTTTCG
1 AAAATGTTCAAATAAGGGTATAACCTTTTCA
* * *
52574 AAAGTGCTT-TAATAAGGGTA-AATCTTTTCA
1 AAAATG-TTCAAATAAGGGTATAACCTTTTCA
52604 AAAATGTTCAAATAAG
1 AAAATGTTCAAATAAG
52620 AGTTTTTCAG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
29 2 0.06
30 19 0.53
31 14 0.39
32 1 0.03
ACGTcount: A:0.44, C:0.10, G:0.14, T:0.31
Consensus pattern (31 bp):
AAAATGTTCAAATAAGGGTATAACCTTTTCA
Found at i:60670 original size:21 final size:21
Alignment explanation
Indices: 60631--60669 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
60621 TATTTGAGAA
60631 AAATATTTTTATCTAAAAAGT
1 AAATATTTTTATCTAAAAAGT
*
60652 AAATTTTTTTAT-TAAAAA
1 AAATATTTTTATCTAAAAA
60670 AATTATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (21 bp):
AAATATTTTTATCTAAAAAGT
Found at i:60699 original size:17 final size:18
Alignment explanation
Indices: 60677--60717 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
60667 AAAAATTATT
60677 TAAAAATA-TTTTTATC-C
1 TAAAAATAGTTTTT-TCTC
60694 TAAAAATAGTTTTTTCTC
1 TAAAAATAGTTTTTTCTC
60712 TAAAAA
1 TAAAAA
60718 ATATCCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAAAATAGTTTTTTCTC
Found at i:66953 original size:26 final size:26
Alignment explanation
Indices: 66917--66972 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
66907 ACTGTACTAG
*
66917 GAGCGATATACTGAATTGGCTCGTAA
1 GAGCGATATACTGAACTGGCTCGTAA
*
66943 GAGCGATATACTGAACTGGCTCGTAT
1 GAGCGATATACTGAACTGGCTCGTAA
66969 GAGC
1 GAGC
66973 TAAATTTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (26 bp):
GAGCGATATACTGAACTGGCTCGTAA
Found at i:71053 original size:31 final size:31
Alignment explanation
Indices: 71016--71153 Score: 117
Period size: 31 Copynumber: 4.5 Consensus size: 31
71006 GGATCCCAAA
* *
71016 AAGTTTAAGTACCAACTTAA-AAAAAAGTGTC
1 AAGTTTAAGTACCAAATTAAGAAAAAA-TATC
*
71047 AAGTTTAGGTACCAAATTAAGAAAAAATATC
1 AAGTTTAAGTACCAAATTAAGAAAAAATATC
* * *
71078 AAGTTTGAGTACCAAATT-GGACCAAAA-A--
1 AAGTTTAAGTACCAAATTAAGA-AAAAATATC
* * *
71106 AA-TTTAGGTATCAAATTAAAAAAAAAATATC
1 AAGTTTAAGTACCAAATT-AAGAAAAAATATC
*
71137 AAGTTTAAGTACGAAAT
1 AAGTTTAAGTACCAAAT
71154 ATTATATTAA
Statistics
Matches: 83, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
27 12 0.14
28 6 0.07
29 2 0.02
30 3 0.04
31 43 0.52
32 17 0.20
ACGTcount: A:0.51, C:0.10, G:0.13, T:0.26
Consensus pattern (31 bp):
AAGTTTAAGTACCAAATTAAGAAAAAATATC
Found at i:71080 original size:90 final size:90
Alignment explanation
Indices: 70970--71153 Score: 221
Period size: 90 Copynumber: 2.0 Consensus size: 90
70960 ATATTAAAAA
* * *
70970 AAATTAGAAAAAAGAGTCAAGTTCAG-GTACCAAATTGGATCCCAAAAAGTTTAAGTACCAACTT
1 AAATTAGAAAAAAGAGTCAAGTT-AGAGTACCAAATTGGA-CCAAAAAAATTTAAGTACCAAATT
* * *
71034 -AAAAAAAAGTGTCAAGTTTAGGTACC
64 AAAAAAAAAATATCAAGTTTAAGTACC
* * * *
71060 AAATTAAGAAAAAATA-TCAAGTTTGAGTACCAAATTGGACCAAAAAAATTTAGGTATCAAATTA
1 AAATT-AGAAAAAAGAGTCAAGTTAGAGTACCAAATTGGACCAAAAAAATTTAAGTACCAAATTA
*
71124 AAAAAAAAATATCAAGTTTAAGTACG
65 AAAAAAAAATATCAAGTTTAAGTACC
71150 AAAT
1 AAAT
71154 ATTATATTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
89 20 0.25
90 51 0.64
91 9 0.11
ACGTcount: A:0.50, C:0.11, G:0.14, T:0.24
Consensus pattern (90 bp):
AAATTAGAAAAAAGAGTCAAGTTAGAGTACCAAATTGGACCAAAAAAATTTAAGTACCAAATTAA
AAAAAAAATATCAAGTTTAAGTACC
Found at i:83371 original size:7 final size:7
Alignment explanation
Indices: 83355--83385 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
83345 TCAGCATGTT
83355 AAAT-AA
1 AAATAAA
83361 AAATAAA
1 AAATAAA
83368 AAATAAA
1 AAATAAA
83375 AAATAAA
1 AAATAAA
83382 AAAT
1 AAAT
83386 CCAATCTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AAATAAA
Found at i:85093 original size:16 final size:16
Alignment explanation
Indices: 85072--85155 Score: 69
Period size: 17 Copynumber: 5.1 Consensus size: 16
85062 ATTTGTCTGG
*
85072 ATTTATTGAAAATTGA
1 ATTTATTGAAAATTAA
* *
85088 ATTTATTTAAATTTAA
1 ATTTATTGAAAATTAA
* * *
85104 GTTTATTTTAAATTTAA
1 ATTTA-TTGAAAATTAA
*
85121 ATTTATTTGAAATTTAA
1 ATTTA-TTGAAAATTAA
*
85138 ATTTATTATAAAATTAA
1 ATTTATT-GAAAATTAA
85155 A
1 A
85156 AAGTCCAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
16 19 0.33
17 39 0.67
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (16 bp):
ATTTATTGAAAATTAA
Found at i:85115 original size:17 final size:17
Alignment explanation
Indices: 85087--85155 Score: 95
Period size: 17 Copynumber: 4.1 Consensus size: 17
85077 TTGAAAATTG
85087 AATTTA-TTTAAATTTA
1 AATTTATTTTAAATTTA
*
85103 AGTTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
85120 AATTTATTTGAAATTTA
1 AATTTATTTTAAATTTA
* *
85137 AATTTATTATAAAATTA
1 AATTTATTTTAAATTTA
85154 AA
1 AA
85156 AAGTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
16 5 0.11
17 41 0.89
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:85135 original size:7 final size:6
Alignment explanation
Indices: 85092--85142 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
85082 AATTGAATTT
* *
85092 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
85138 ATTTA
1 ATTTA
85143 TTATAAAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 4 0.11
5 4 0.11
6 26 0.68
7 4 0.11
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (6 bp):
ATTTAA
Found at i:85143 original size:34 final size:33
Alignment explanation
Indices: 85072--85155 Score: 107
Period size: 34 Copynumber: 2.5 Consensus size: 33
85062 ATTTGTCTGG
* *
85072 ATTTATT-GAAAATTGAATTTATTTAAATTTAA
1 ATTTATTATAAAATTAAATTTATTTAAATTTAA
* * *
85104 GTTTATTTTAAATTTAAATTTATTTGAAATTTAA
1 ATTTATTATAAAATTAAATTTATTT-AAATTTAA
85138 ATTTATTATAAAATTAAA
1 ATTTATTATAAAATTAAA
85156 AAGTCCAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 6 0.14
33 14 0.33
34 23 0.53
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (33 bp):
ATTTATTATAAAATTAAATTTATTTAAATTTAA
Found at i:85183 original size:25 final size:25
Alignment explanation
Indices: 85149--85203 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
85139 TTTATTATAA
* *
85149 AATTAAAAAGTCCAAAACAAAGTTC
1 AATTAAAAAGTCCAAAACAAAATCC
85174 AATTAAAAAGTCCAAAACAAAATCC
1 AATTAAAAAGTCCAAAACAAAATCC
85199 AATTA
1 AATTA
85204 CAAATGGCCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.58, C:0.16, G:0.05, T:0.20
Consensus pattern (25 bp):
AATTAAAAAGTCCAAAACAAAATCC
Found at i:85206 original size:13 final size:14
Alignment explanation
Indices: 85149--85222 Score: 52
Period size: 13 Copynumber: 5.6 Consensus size: 14
85139 TTTATTATAA
85149 AATTA-AAAAGTCC
1 AATTACAAAAGTCC
* *
85162 AA-AAC-AAAGTTC
1 AATTACAAAAGTCC
85174 AATTA-AAAAGTCC
1 AATTACAAAAGTCC
*
85187 AA-AACAAAA-TCC
1 AATTACAAAAGTCC
* *
85199 AATTACAAATGGCCC
1 AATTACAAA-AGTCC
85214 AATTACAAA
1 AATTACAAA
85223 CGACCCAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
12 15 0.33
13 20 0.43
15 11 0.24
ACGTcount: A:0.55, C:0.19, G:0.07, T:0.19
Consensus pattern (14 bp):
AATTACAAAAGTCC
Found at i:85229 original size:15 final size:15
Alignment explanation
Indices: 85197--85231 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
85187 AAAACAAAAT
* *
85197 CCAATTACAAATGGC
1 CCAATTACAAACGAC
85212 CCAATTACAAACGAC
1 CCAATTACAAACGAC
85227 CCAAT
1 CCAAT
85232 GGCACAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.43, C:0.31, G:0.09, T:0.17
Consensus pattern (15 bp):
CCAATTACAAACGAC
Found at i:87148 original size:59 final size:60
Alignment explanation
Indices: 86977--87411 Score: 576
Period size: 58 Copynumber: 7.4 Consensus size: 60
86967 CCCCTAAACT
* * * * *
86977 TTCTAAAAAGTACCATTTTACCCTCGAACTTCCAAAAATCCCTTTTTTGA-CCTTGAATC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAACC
* * *
87036 TTTTGAAAATTACCA-TTTACCCCTGAACTTCCAAAAATCCCATTTTTGA-CCTCGAA-C
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAACC
* * *
87093 TTCCAAAAATTACCATTTTGA-CCCCGAACCTTCTAAAAATTACCA-TTTT-ACCCTCGAACC
1 TTCTAAAAATTACCATTTT-ACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGACCCTCGAACC
*
87153 TTCTAAAAATTACCA-TTTACCCCCGAACTTCCAAAAATCCCATTTTT-AACCTCGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAACC
87211 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC-CGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAACC
*
87270 TTCCAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCC-CGAACC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAACC
* *
87328 TTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACTC-CGAACCC
1 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAA-CC
* *
87388 TTC--AAAACTACCATTTTGCCCCCG
1 TTCTAAAAATTACCATTTTACCCCCG
87412 TGCATCCGAA
Statistics
Matches: 340, Mismatches: 24, Indels: 25
0.87 0.06 0.06
Matches are distributed among these distances:
57 17 0.05
58 161 0.47
59 135 0.40
60 27 0.08
ACGTcount: A:0.32, C:0.32, G:0.06, T:0.31
Consensus pattern (60 bp):
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAACC
Found at i:87394 original size:29 final size:31
Alignment explanation
Indices: 86981--87404 Score: 354
Period size: 29 Copynumber: 14.5 Consensus size: 31
86971 TAAACTTTCT
*
86981 AAAAAGTACCA-TTTT-ACCCTCGAA-CTTCC
1 AAAAATTACCATTTTTGACCC-CGAACCTTCC
* * ** * **
87010 AAAAA-TCCCTTTTTTGACCTTGAATCTTTT
1 AAAAATTACCATTTTTGACCCCGAACCTTCC
*
87040 GAAAATTACCA--TTT-ACCCCTGAA-CTTCC
1 AAAAATTACCATTTTTGACCCC-GAACCTTCC
* *
87068 AAAAA-TCCCATTTTTGACCTCGAA-CTTCC
1 AAAAATTACCATTTTTGACCCCGAACCTTCC
*
87097 AAAAATTACCA-TTTTGACCCCGAACCTTCT
1 AAAAATTACCATTTTTGACCCCGAACCTTCC
*
87127 AAAAATTACCA-TTTT-ACCCTCGAACCTTCT
1 AAAAATTACCATTTTTGACCC-CGAACCTTCC
87157 AAAAATTACCA--TTT-ACCCCCGAA-CTTCC
1 AAAAATTACCATTTTTGA-CCCCGAACCTTCC
* * * *
87185 AAAAA-TCCCATTTTTAACCTCGAACCTTCT
1 AAAAATTACCATTTTTGACCCCGAACCTTCC
87215 AAAAATTACCA-TTTT-ACCCCCGAA-CTTCC
1 AAAAATTACCATTTTTGA-CCCCGAACCTTCC
*
87244 AAAAA-TCCCATTTTTGACCCCGAACCTTCC
1 AAAAATTACCATTTTTGACCCCGAACCTTCC
87274 AAAAATTACCA-TTTT-ACCCCGAA-CTTCC
1 AAAAATTACCATTTTTGACCCCGAACCTTCC
* *
87302 AAAAA-TCCCATTTTTGACCCCGAACCTTCT
1 AAAAATTACCATTTTTGACCCCGAACCTTCC
87332 AAAAATTACCA-TTTT-ATCCCCGAA-CTTCC
1 AAAAATTACCATTTTTGA-CCCCGAACCTTCC
* *
87361 AAAAA-TCCCATTTTTGACTCCGAACCCTT-C
1 AAAAATTACCATTTTTGACCCCGAA-CCTTCC
*
87391 -AAAACTACCATTTT
1 AAAAATTACCATTTT
87405 GCCCCCGTGC
Statistics
Matches: 328, Mismatches: 35, Indels: 63
0.77 0.08 0.15
Matches are distributed among these distances:
27 12 0.04
28 44 0.13
29 128 0.39
30 126 0.38
31 18 0.05
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (31 bp):
AAAAATTACCATTTTTGACCCCGAACCTTCC
Found at i:87411 original size:117 final size:116
Alignment explanation
Indices: 86977--87403 Score: 573
Period size: 117 Copynumber: 3.7 Consensus size: 116
86967 CCCCTAAACT
* * * * **
86977 TTCTAAAAAGTACCATTTTACCCTCGAACTTCCAAAAATCCCTTTTTTGA-CCTTGAATCTTTTG
1 TTCTAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCCTCGAA-CCTTCA
*
87041 AAAATTACCATTTACCCCTGAACTTCCAAAAATCCCATTTTTGACCTCGAA-C
64 AAAATTACCATTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACC
* * *
87093 TTCCAAAAATTACCATTTTGACCCCGAACCTTCTAAAAATTACCA-TTTT-ACCCTCGAACCTTC
1 TTCTAAAAATTACCATTTT-ACCCCGAA-CTTCCAAAAA-TCCCATTTTTGACCCTCGAACCTTC
*
87156 TAAAAATTACCATTTACCCCCGAACTTCCAAAAATCCCATTTTTAACCTCGAACC
63 -AAAAATTACCATTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACC
87211 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCC-CGAACCTTCCA
1 TTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAACCTT-CA
*
87275 AAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
64 AAAATTACCA-TTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACC
*
87328 TTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCCATTTTTGACTC-CGAACCCTTC-
1 TTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAA-CCTTCA
*
87391 AAAACTACCATTT
64 AAAATTACCATTT
87404 TGCCCCCGTG
Statistics
Matches: 280, Mismatches: 19, Indels: 25
0.86 0.06 0.08
Matches are distributed among these distances:
115 3 0.01
116 38 0.14
117 197 0.70
118 42 0.15
ACGTcount: A:0.33, C:0.31, G:0.05, T:0.31
Consensus pattern (116 bp):
TTCTAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCCTCGAACCTTCAAA
AATTACCATTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAACC
Found at i:88493 original size:13 final size:13
Alignment explanation
Indices: 88438--88494 Score: 55
Period size: 13 Copynumber: 4.2 Consensus size: 13
88428 TAATTATATA
88438 TTATTATTATT-ATT
1 TTATTA-TATTGA-T
88452 TTATGTATATTGAT
1 TTAT-TATATTGAT
*
88466 TTATTATA-CGAAT
1 TTATTATATTG-AT
88479 TTATTATATTGAT
1 TTATTATATTGAT
88492 TTA
1 TTA
88495 CTATCAGGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 1 0.03
13 19 0.51
14 14 0.38
15 3 0.08
ACGTcount: A:0.32, C:0.02, G:0.07, T:0.60
Consensus pattern (13 bp):
TTATTATATTGAT
Found at i:89554 original size:17 final size:16
Alignment explanation
Indices: 89527--89604 Score: 75
Period size: 17 Copynumber: 4.6 Consensus size: 16
89517 TTGGACATTT
89527 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTA-AA
**
89545 TAAATTTAAATTTCAGC
1 TAAATTTAAATTT-AAA
89562 TAAATTTAAATTTAGAA
1 TAAATTTAAATTTA-AA
* *
89579 TAAACTTAATTTTAAAA
1 TAAATTTAAATTT-AAA
89596 TAAATTTAA
1 TAAATTTAA
89605 GTTCATTGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.02
17 43 0.86
18 6 0.12
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:89600 original size:34 final size:34
Alignment explanation
Indices: 89527--89604 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
89517 TTGGACATTT
* * * **
89527 TAAATTTTAAATTTATAATAAATTTAAATTTCAGC
1 TAAA-TTTAAATTTAGAATAAACTTAAATTTAAAA
*
89562 TAAATTTAAATTTAGAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
89596 TAAATTTAA
1 TAAATTTAA
89605 GTTCATTGGG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
34 33 0.89
35 4 0.11
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.44
Consensus pattern (34 bp):
TAAATTTAAATTTAGAATAAACTTAAATTTAAAA
Found at i:93983 original size:2 final size:2
Alignment explanation
Indices: 93978--94002 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
93968 ATATATATAT
93978 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
94003 AGTAATTGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:100991 original size:6 final size:6
Alignment explanation
Indices: 100982--101041 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
100972 TCAAACTCAT
* * *
100982 TTTAAA TTT-AT TTTAAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
101028 TTTAAG TTTAAA TT
1 TTTAAA TTTAAA TT
101042 CATTTTCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 12 0.28
6 27 0.63
7 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:101005 original size:18 final size:17
Alignment explanation
Indices: 100982--101057 Score: 116
Period size: 17 Copynumber: 4.4 Consensus size: 17
100972 TCAAACTCAT
100982 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
101000 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
101017 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
*
101034 TTTAAATTCATTTTCAAA
1 TTTAAATTTATTTT-AAA
101052 TTTAAA
1 TTTAAA
101058 ATAAATAAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
17 32 0.59
18 22 0.41
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:101028 original size:35 final size:35
Alignment explanation
Indices: 100982--101057 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
100972 TCAAACTCAT
*
100982 TTTAAATTTATTTTAAAATTTAAATTTATTTT-AAA
1 TTTAAATTTATTTT-AAATTTAAATTCATTTTCAAA
*
101017 TTTAAATTTATTTTAAGTTTAAATTCATTTTCAAA
1 TTTAAATTTATTTTAAATTTAAATTCATTTTCAAA
101052 TTTAAA
1 TTTAAA
101058 ATAAATAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 15 0.39
35 23 0.61
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (35 bp):
TTTAAATTTATTTTAAATTTAAATTCATTTTCAAA
Found at i:101037 original size:11 final size:11
Alignment explanation
Indices: 100980--101020 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
100970 GCTCAAACTC
100980 ATTTTAAATTT
1 ATTTTAAATTT
100991 ATTTTAAA---
1 ATTTTAAATTT
100999 A-TTTAAATTT
1 ATTTTAAATTT
101009 ATTTTAAATTT
1 ATTTTAAATTT
101020 A
1 A
101021 AATTTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
7 6 0.23
8 1 0.04
10 1 0.04
11 18 0.69
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:101069 original size:34 final size:34
Alignment explanation
Indices: 100995--101069 Score: 80
Period size: 34 Copynumber: 2.2 Consensus size: 34
100985 AAATTTATTT
* * * **
100995 TAAAATTTAAATTTATTTTAAATTTAAATTTATT
1 TAAAGTTTAAATTCATTTTAAATTTAAATATAAA
*
101029 TTAAGTTTAAATTCATTTTCAAATTTAAA-ATAAA
1 TAAAGTTTAAATTCATTTT-AAATTTAAATATAAA
101063 TAAAGTT
1 TAAAGTT
101070 CAAACATAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
34 24 0.73
35 9 0.27
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (34 bp):
TAAAGTTTAAATTCATTTTAAATTTAAATATAAA
Found at i:101811 original size:3 final size:3
Alignment explanation
Indices: 101803--101870 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
101793 CTGATAGCAT
** **
101803 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA TTG TTT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
101849 TAA TAA TAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA
101871 AAAAGGGAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
3 52 0.90
4 6 0.10
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:103074 original size:60 final size:60
Alignment explanation
Indices: 102981--103187 Score: 199
Period size: 58 Copynumber: 3.5 Consensus size: 60
102971 CCCTAAATAA
* *
102981 TCCAAAAATTCCATTTTT-ACCCCCAAACTTCCAAAAATTTCAATCTTA-CCCTTAAACT
1 TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCAATCTTACCCCTCAAACT
* * * * * * * *
103039 TTCAAAAATTTCATTTTCTAACCCCGAAACTTCCAAAAATTTTATTTTTACCCCTCGAGCT
1 TCCAAAAATTCCATTTT-TAACCCCAAAACTTCCAAAAATTTCAATCTTACCCCTCAAACT
* * * ** *
103100 TCCAAAAATTCCATTTTTAACCCCAAAACTTCTAAAAATTACCAT-TT-TGCCTCGAA-T
1 TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCAATCTTACCCCTCAAACT
* *
103157 GTCCAAAAATTCCATTTTTGACCCCGAAACT
1 -TCCAAAAATTCCATTTTTAACCCCAAAACT
103188 CTCAAAATTA
Statistics
Matches: 123, Mismatches: 22, Indels: 8
0.80 0.14 0.05
Matches are distributed among these distances:
57 1 0.01
58 49 0.40
59 3 0.02
60 48 0.39
61 22 0.18
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (60 bp):
TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTTCAATCTTACCCCTCAAACT
Found at i:103145 original size:31 final size:29
Alignment explanation
Indices: 102981--103187 Score: 168
Period size: 29 Copynumber: 7.0 Consensus size: 29
102971 CCCTAAATAA
102981 TCCAAAAATTCCATTTTTACCCCCAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* * * **
103010 TCCAAAAATTTCAATCTTACCCTTAAACT
1 TCCAAAAATTCCATTTTTACCCCCAAACT
* * *
103039 TTCAAAAATTTCATTTTCTAACCCCGAAACT
1 TCCAAAAATTCCATTTT-T-ACCCCCAAACT
** * *
103070 TCCAAAAATTTTATTTTTACCCCTCGAGCT
1 TCCAAAAATTCCATTTTTACCCC-CAAACT
*
103100 TCCAAAAATTCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCCCCAAACT
* * * *
103130 TCTAAAAATTACCA-TTTT-GCCTCGAA-T
1 TCCAAAAATT-CCATTTTTACCCCCAAACT
*
103157 GTCCAAAAATTCCATTTTTGACCCCGAAACT
1 -TCCAAAAATTCCATTTTT-ACCCCCAAACT
103188 CTCAAAATTA
Statistics
Matches: 138, Mismatches: 30, Indels: 18
0.74 0.16 0.10
Matches are distributed among these distances:
27 4 0.03
28 17 0.12
29 43 0.31
30 41 0.30
31 33 0.24
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCCCCAAACT
Found at i:103167 original size:28 final size:27
Alignment explanation
Indices: 103133--103231 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 27
103123 CAAAACTTCT
*
103133 AAAAATTACCATTTTGCCTCGAATGTCC
1 AAAAATT-CCATTTTGCCCCGAATGTCC
**
103161 AAAAATTCCATTTTTGACCCCGAAACTCTC
1 AAAAATTCCA-TTTTG-CCCCGAATGTC-C
* * *
103191 -AAAATTACCCTTTTACCCCGAATGTCT
1 AAAAATT-CCATTTTGCCCCGAATGTCC
*
103218 AAAAAGTCCATTTT
1 AAAAATTCCATTTT
103232 TAATCCCGAA
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
27 9 0.16
28 26 0.46
29 18 0.32
30 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAAATTCCATTTTGCCCCGAATGTCC
Found at i:103222 original size:57 final size:57
Alignment explanation
Indices: 103100--103257 Score: 199
Period size: 57 Copynumber: 2.8 Consensus size: 57
103090 CCCTCGAGCT
* * * *
103100 TCCAAAAATTCCATTTTTAACCCCAAAACTTCTAAAAATTACCATTTTGCCTCGAATG
1 TCCAAAAATTCCATTTTTAACCCCGAAAC-TCTCAAAATTACCATTTTACCCCGAATG
* *
103158 TCCAAAAATTCCATTTTTGACCCCGAAACTCTCAAAATTACCCTTTTACCCCGAATG
1 TCCAAAAATTCCATTTTTAACCCCGAAACTCTCAAAATTACCATTTTACCCCGAATG
* * * ** *
103215 TCTAAAAAGTCCATTTTTAATCCCGAATTTCCCAAAATTACCA
1 TCCAAAAATTCCATTTTTAACCCCGAAACTCTCAAAATTACCA
103258 CTTCACCTCG
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 59 0.69
58 27 0.31
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.32
Consensus pattern (57 bp):
TCCAAAAATTCCATTTTTAACCCCGAAACTCTCAAAATTACCATTTTACCCCGAATG
Found at i:108362 original size:88 final size:88
Alignment explanation
Indices: 108213--108386 Score: 285
Period size: 88 Copynumber: 2.0 Consensus size: 88
108203 GGGAAGCTAA
* *
108213 TGATGTTTGTGCCTTCGAGGACGGAACGACTAAGGCTTATGAAAGCAATCGTCCTAAGGTGATTA
1 TGATGTTTGTGCCTCCAAGGACGGAACGACTAAGGCTTATGAAAGCAATCGTCCTAAGGTGATTA
*
108278 TTTGTTGCACGACAAGAGAATAG
66 TTTGTGGCACGACAAGAGAATAG
* *
108301 TGATGTTTGTGCGTCCAAGGACGGAACGACTAAGGCTTATGAAAGCAATCGTCTTAAGGTGATTA
1 TGATGTTTGTGCCTCCAAGGACGGAACGACTAAGGCTTATGAAAGCAATCGTCCTAAGGTGATTA
**
108366 TTTGTGGCACGGGAAGAGAAT
66 TTTGTGGCACGACAAGAGAAT
108387 CGATAACCCC
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 79 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (88 bp):
TGATGTTTGTGCCTCCAAGGACGGAACGACTAAGGCTTATGAAAGCAATCGTCCTAAGGTGATTA
TTTGTGGCACGACAAGAGAATAG
Found at i:115033 original size:206 final size:204
Alignment explanation
Indices: 114393--115156 Score: 1001
Period size: 205 Copynumber: 3.7 Consensus size: 204
114383 GCGATTATCC
* * * *
114393 ACAAACGATGCGGTCATCTTCTTGATAAGATACTGAGAAGAAGACCAAATTAAAACCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* *
114458 TGTGAGCAAATCTTCGAACCCTAGCTTCCTGATGAGACACTCAGAAGCAGGTCGAAGCAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* *
114523 GGTTAGCTTCTTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCAGATGAGATACAGAAAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCC-TATGAGATACAGAAAA
*
114588 GTGAATTGAA
195 GCGAATTGAA
* * *
114598 ACAAACAATGCGGTCATCTTCCTGATAAGATACTGAAAAGAAGACCAAATCAAACCCACGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* ** ** *
114663 TGTGAGTAAATCTTCGAACCTTAGCTTTTTGATGAGACACTGAGAAGTAGGTCGAAGCAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* * *
114728 GGTTAGCTTCCTGATGAGATACTGAGAAGTTGACCAAATTCATCTTCCTGATGAGATACAGAGAA
131 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCT-ATGAGATACAGAAAA
114793 GCGAATTGAA
195 GCGAATTGAA
* * * *
114803 ACAAACGACACGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATTAAACCCATGCTCGA
1 ACAAACGACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * * * * *
114868 TATGAGCGAATCCTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTTGAAGTAATAAAA
66 TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
* * *
114933 TGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTTGTCTTCCTATTGGGATACAAAAA
131 -GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTA-TGAGATACAGAAA
114998 AGC-AGATTGAA
194 AGCGA-ATTGAA
* * * * * *
115009 ACAAACGACGCGATCATCTTCCTGATAAGACACAGA-AGAGAAAATCAAATCAAACCCACGCCCG
1 ACAAACGACGCGGTCATCTTCCTGATAAGATACTGAGA-AGAAGACCAAATCAAACCCACGCTCG
* * * * * * * *
115073 ATGTGAGCAAATCTTCAAACCCCAACTTCCTGATAAGATACTAAGAAGTAGGTTGAAGTAATAAA
65 ATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAA
* *
115138 ACAGTTAGCTTCCTAATGA
130 A-GGTTAGCTTCCTGATGA
115157 AATATGGGGA
Statistics
Matches: 491, Mismatches: 63, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
205 301 0.61
206 190 0.39
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (204 bp):
ACAAACGACGCGGTCATCTTCCTGATAAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
TGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAA
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTATGAGATACAGAAAAG
CGAATTGAA
Found at i:115619 original size:17 final size:18
Alignment explanation
Indices: 115596--115688 Score: 113
Period size: 17 Copynumber: 5.3 Consensus size: 18
115586 TCAAACTCAT
115596 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAGA
* *
115614 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGA
115631 TTTAAATTTATTTTAA-A
1 TTTAAATTTATTTTAAGA
*
115648 TTTAAATTTAATTTAAG-
1 TTTAAATTTATTTTAAGA
*
115665 TTTAAATTCATTTTCAA-A
1 TTTAAATTTATTTT-AAGA
115683 TTTAAA
1 TTTAAA
115689 ATAAATAAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
17 43 0.66
18 22 0.34
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTAAATTTATTTTAAGA
Found at i:115639 original size:6 final size:6
Alignment explanation
Indices: 115628--115672 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
115618 ATTTGTTTTA
* *
115628 AAATTT AAATTT -ATTTT AAATTT AAATTT -AATTT AAGTTT AAATT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATT
115673 CATTTTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 9 0.27
6 24 0.73
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:115642 original size:35 final size:34
Alignment explanation
Indices: 115596--115688 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 34
115586 TCAAACTCAT
**
115596 TTTAAATTTATTTTAAGA-TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAA-ATTTAAATTTAATTT-AAA
*
115631 TTTAAATTTATTTTAAATTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
*
115665 TTTAAATTCATTTTCAAATTTAAA
1 TTTAAATTTATTTT-AAATTTAAA
115689 ATAAATAAAG
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
34 16 0.31
35 36 0.69
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTAATTTAAA
Found at i:115645 original size:11 final size:11
Alignment explanation
Indices: 115631--115686 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
115621 TGTTTTAAAA
115631 TTTAAATTTAT
1 TTTAAATTTAT
*
115642 TTTAAATTTAAA
1 TTTAAATTT-AT
*
115654 TTT-AATTTAAG
1 TTTAAATTT-AT
*
115665 TTTAAATTCAT
1 TTTAAATTTAT
115676 TTTCAAATTTA
1 TTT-AAATTTA
115687 AAATAAATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
11 23 0.62
12 14 0.38
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:116442 original size:3 final size:3
Alignment explanation
Indices: 116434--116492 Score: 64
Period size: 3 Copynumber: 19.0 Consensus size: 3
116424 CTGATAGCAT
** **
116434 TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TTG TTT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA
116480 TAA TAAA TAA TAA
1 TAA T-AA TAA TAA
116493 AAAAGGGAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
3 43 0.88
4 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:116461 original size:25 final size:25
Alignment explanation
Indices: 116432--116492 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
116422 TGCTGATAGC
116432 ATTAATAATAATAATAATAATAATA
1 ATTAATAATAATAATAATAATAATA
** **
116457 ATTAATAATTGTTTTAATAATAATA
1 ATTAATAATAATAATAATAATAATA
*
116482 ATAAATAATAA
1 ATTAATAATAA
116493 AAAAGGGAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (25 bp):
ATTAATAATAATAATAATAATAATA
Found at i:117691 original size:31 final size:31
Alignment explanation
Indices: 117636--117717 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
117626 TTTACCCCCG
* *
117636 AACTTCTAAAAATTCTA-TTTTTGACCCAAA
1 AACTTCCAAAAATTCCATTTTTTGACCCAAA
* **
117666 AACTTCGAAAAATTCCATTTTTTGACCCTGA
1 AACTTCCAAAAATTCCATTTTTTGACCCAAA
117697 AACTTCCAAAAATTCCATTTT
1 AACTTCCAAAAATTCCATTTT
117718 ACCCCCGAGC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 15 0.33
31 31 0.67
ACGTcount: A:0.37, C:0.22, G:0.05, T:0.37
Consensus pattern (31 bp):
AACTTCCAAAAATTCCATTTTTTGACCCAAA
Found at i:117765 original size:30 final size:30
Alignment explanation
Indices: 117605--117758 Score: 116
Period size: 30 Copynumber: 5.2 Consensus size: 30
117595 GGAGGTCCCT
* * * *
117605 AAACTGTCTAAAAATTAC-ATTTTTACCCCC
1 AAACT-TCCAAAAATTCCAATTTTGACCCCA
* * * * *
117635 GAACTTCTAAAAATTCTATTTTTGACCCAA
1 AAACTTCCAAAAATTCCAATTTTGACCCCA
* * **
117665 AAACTTCGAAAAATTCCATTTTTTGACCCTG
1 AAACTTCCAAAAATTCCA-ATTTTGACCCCA
*
117696 AAACTTCCAAAAATTCC-ATTTT-ACCCCC
1 AAACTTCCAAAAATTCCAATTTTGACCCCA
* * *
117724 GAGCTTCCAAAAATTCCAATTTTAACCCCA
1 AAACTTCCAAAAATTCCAATTTTGACCCCA
117754 AAACT
1 AAACT
117759 CTCAAAATTA
Statistics
Matches: 99, Mismatches: 21, Indels: 8
0.77 0.16 0.06
Matches are distributed among these distances:
28 19 0.19
29 19 0.19
30 35 0.35
31 26 0.26
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCAATTTTGACCCCA
Found at i:119471 original size:23 final size:23
Alignment explanation
Indices: 119427--119472 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
119417 ACATTGTTCG
* *
119427 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
119450 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
119473 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:126854 original size:18 final size:18
Alignment explanation
Indices: 126833--126867 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
126823 TAATTTTTTA
126833 ATAAATT-ATAATAATAAG
1 ATAAATTCA-AATAATAAG
126851 ATAAATTCAAATAATAA
1 ATAAATTCAAATAATAA
126868 ACTTGATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 15 0.94
19 1 0.06
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (18 bp):
ATAAATTCAAATAATAAG
Found at i:130616 original size:23 final size:21
Alignment explanation
Indices: 130585--130656 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 21
130575 AAACACATAA
130585 AAAAAATAACACCAAAACAAC
1 AAAAAATAACACCAAAACAAC
* *
130606 AAAAACTATA-ACCAAAACAAT
1 AAAAAATA-ACACCAAAACAAC
*
130627 AGCAAAAATAACAGCAAAACAAC
1 A--AAAAATAACACCAAAACAAC
130650 AATAAAA
1 AA-AAAA
130657 ATAATAACAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 19 0.46
22 6 0.15
23 16 0.39
ACGTcount: A:0.69, C:0.19, G:0.03, T:0.08
Consensus pattern (21 bp):
AAAAAATAACACCAAAACAAC
Found at i:130667 original size:23 final size:22
Alignment explanation
Indices: 130584--130668 Score: 75
Period size: 23 Copynumber: 3.8 Consensus size: 22
130574 AAAACACATA
*
130584 AAAAAAATAACACCAAAACAAC
1 AAAAAAATAACAACAAAACAAC
* *
130606 AAAAACTATAAC--CAAAACAAT
1 AAAAA-AATAACAACAAAACAAC
* *
130627 AGCAAAAATAACAGCAAAACAAC
1 A-AAAAAATAACAACAAAACAAC
*
130650 AATAAAAATAATAACAAAA
1 AA-AAAAATAACAACAAAA
130669 ATAGCACCAA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
21 14 0.28
22 8 0.16
23 28 0.56
ACGTcount: A:0.71, C:0.18, G:0.02, T:0.09
Consensus pattern (22 bp):
AAAAAAATAACAACAAAACAAC
Found at i:130668 original size:35 final size:35
Alignment explanation
Indices: 130619--130693 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
130609 AACTATAACC
* *
130619 AAAACAATAGCAAAAATAACAGCAAAACAACAATA
1 AAAACAATAACAAAAATAACACCAAAACAACAATA
* * *
130654 AAAATAATAACAAAAATAGCACCAAAACAAC-AGA
1 AAAACAATAACAAAAATAACACCAAAACAACAATA
130688 AAAACA
1 AAAACA
130694 CCAGCAACAA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 7 0.21
35 27 0.79
ACGTcount: A:0.69, C:0.17, G:0.05, T:0.08
Consensus pattern (35 bp):
AAAACAATAACAAAAATAACACCAAAACAACAATA
Found at i:131222 original size:36 final size:36
Alignment explanation
Indices: 131181--131260 Score: 92
Period size: 36 Copynumber: 2.2 Consensus size: 36
131171 CCTGACAAAA
* *
131181 TATTTTTAAAGTTTAT-TTTAT-AAATATATTCTTATT
1 TATTTTTAAA-TATATATTTATAAAATATAAT-TTATT
*
131217 TATTTTCAAATATATATTTATAAAATATAATTTATT
1 TATTTTTAAATATATATTTATAAAATATAATTTATT
*
131253 TTTTTTTA
1 TATTTTTA
131261 TAAAATTACA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
35 4 0.11
36 25 0.68
37 8 0.22
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (36 bp):
TATTTTTAAATATATATTTATAAAATATAATTTATT
Found at i:131451 original size:22 final size:22
Alignment explanation
Indices: 131423--131464 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
131413 AAATTTTATT
131423 TTTTTTAGTCAATTTGATTTAA
1 TTTTTTAGTCAATTTGATTTAA
* *
131445 TTTTTTATTCACTTTGATTT
1 TTTTTTAGTCAATTTGATTT
131465 TTAATCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (22 bp):
TTTTTTAGTCAATTTGATTTAA
Found at i:131624 original size:20 final size:22
Alignment explanation
Indices: 131601--131643 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
131591 CATTTTTAAA
131601 ATTTTATTAATT-TT-TTATGT
1 ATTTTATTAATTCTTATTATGT
*
131621 ATTTTTTTAATTCTTATTATGT
1 ATTTTATTAATTCTTATTATGT
131643 A
1 A
131644 AACGCAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 2 0.10
22 7 0.35
ACGTcount: A:0.26, C:0.02, G:0.05, T:0.67
Consensus pattern (22 bp):
ATTTTATTAATTCTTATTATGT
Found at i:132574 original size:36 final size:36
Alignment explanation
Indices: 132534--132607 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
132524 CTTGGTTAAT
132534 TAGGGAAAAGCTTGATCCCCAAGATCAGGAATTTTA
1 TAGGGAAAAGCTTGATCCCCAAGATCAGGAATTTTA
132570 TAGGGAAAAGCTTGATCCCCAAGATCAGGAATTTTA
1 TAGGGAAAAGCTTGATCCCCAAGATCAGGAATTTTA
132606 TA
1 TA
132608 ACATTATACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.26
Consensus pattern (36 bp):
TAGGGAAAAGCTTGATCCCCAAGATCAGGAATTTTA
Found at i:137376 original size:18 final size:19
Alignment explanation
Indices: 137353--137396 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
137343 GTTTGTTTGG
*
137353 AATTTTAGGATTTTA-GAA
1 AATTTTAGAATTTTATGAA
*
137371 AATTTTATAATTTTATGAA
1 AATTTTAGAATTTTATGAA
*
137390 ATTTTTA
1 AATTTTA
137397 AAGAATTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (19 bp):
AATTTTAGAATTTTATGAA
Found at i:137927 original size:12 final size:12
Alignment explanation
Indices: 137910--137942 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
137900 TTTAAATATT
*
137910 AATTATATAAAA
1 AATTATAAAAAA
137922 AATTATAAAAAA
1 AATTATAAAAAA
137934 AA-TATAAAA
1 AATTATAAAA
137943 TCACTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 7 0.35
12 13 0.65
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AATTATAAAAAA
Found at i:141280 original size:42 final size:42
Alignment explanation
Indices: 141228--141445 Score: 144
Period size: 42 Copynumber: 5.3 Consensus size: 42
141218 CCAGGTTTAC
* * *
141228 CACCACCACCTCCTGCACCTAGAAGTGCATCATTACCACCAG
1 CACCACCACCTCCTACACATAGAACTGCATCATTACCACCAG
* **
141270 CACCAGCACCTCCTATTCATAGAACTGCATCATTACCACCAG
1 CACCACCACCTCCTACACATAGAACTGCATCATTACCACCAG
* * * ** * * **
141312 CACCACCACCT-ATGGCACCTTCAACAGAATCAGGACCAATGCCAG
1 CACCACCACCTCCT-ACACATAGAACTGCATCATTACC-A--CCAG
* ** * * *
141357 CGCCACTGCCACC-AC-C-TGGAAGTGCATCATTACCACC--
1 CACCACCACCTCCTACACATAGAACTGCATCATTACCACCAG
**
141394 C-CCACCACCTCCTATTCATAGAACTGCATCATTACCACCAG
1 CACCACCACCTCCTACACATAGAACTGCATCATTACCACCAG
141435 CACCACCACCT
1 CACCACCACCT
141446 AT
Statistics
Matches: 128, Mismatches: 37, Indels: 22
0.68 0.20 0.12
Matches are distributed among these distances:
36 8 0.06
37 2 0.02
38 1 0.01
39 21 0.16
41 3 0.02
42 79 0.62
43 2 0.02
44 1 0.01
45 11 0.09
ACGTcount: A:0.29, C:0.42, G:0.11, T:0.17
Consensus pattern (42 bp):
CACCACCACCTCCTACACATAGAACTGCATCATTACCACCAG
Done.