Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003848.1 Hibiscus syriacus cultivar Beakdansim tig00008256_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: 200949
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2508 original size:25 final size:25
Alignment explanation
Indices: 2467--2565 Score: 164
Period size: 25 Copynumber: 4.0 Consensus size: 25
2457 CATTAGGGGA
* * *
2467 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGAT
2491 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2516 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2541 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
2566 GGGTTGGTTC
Statistics
Matches: 71, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
24 6 0.08
25 65 0.92
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:2665 original size:3 final size:3
Alignment explanation
Indices: 2657--2699 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
2647 TTTTGTAAAT
* **
2657 TAA TAA TAA TAG TAA TAA TAA TAA T-A TAA CGA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2700 TATATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3100 original size:88 final size:90
Alignment explanation
Indices: 2901--3144 Score: 316
Period size: 90 Copynumber: 2.7 Consensus size: 90
2891 TCTAAGGGTG
* * ** * * * *
2901 ACACGGCTCCTACGTGATGAGGA-GATCTGGTCA-GGGGATGACACTGCTCCTACATGATGAAGA
1 ACACGGTTCCTACGTGATGAGGACGA-CTGGTTATCAGGTTGACACGGCTCATACGTGATGAAGA
* * *
2964 ATTCTTGGCCATCTTTAGGGATGATA
65 GTTCTTGGCCATCTTAAAGGATGATA
*
2990 ACACGGTTCCTACGTGATGAGGACGACTGGTTATCAGGTTGACACGGCTCTTACGTGATGAAGAG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTTATCAGGTTGACACGGCTCATACGTGATGAAGAG
3055 TTCTTGGCCATC-TAAAGG-TGATA
66 TTCTTGGCCATCTTAAAGGATGATA
*
3078 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAG
1 ACACGGTTCCTACGTGATGAGGACGACTGGTTATC-A-GGTTGACACGGCTCATACGTGATGAAG
3143 AG
64 AG
3145 ATCTGGTCTG
Statistics
Matches: 138, Mismatches: 13, Indels: 7
0.87 0.08 0.04
Matches are distributed among these distances:
88 39 0.28
89 33 0.24
90 66 0.48
ACGTcount: A:0.25, C:0.20, G:0.29, T:0.26
Consensus pattern (90 bp):
ACACGGTTCCTACGTGATGAGGACGACTGGTTATCAGGTTGACACGGCTCATACGTGATGAAGAG
TTCTTGGCCATCTTAAAGGATGATA
Found at i:17769 original size:25 final size:25
Alignment explanation
Indices: 17731--17829 Score: 157
Period size: 25 Copynumber: 4.0 Consensus size: 25
17721 AGTTAGGGGA
*
17731 TTAGGG-TTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGAT
*
17755 TTAGGGTTTGAAACCCTAATCTAAT
1 TTAGGGTTTGAAACCCTAATCTGAT
17780 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
17805 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
17830 GGGTTGGTTC
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
24 9 0.13
25 61 0.87
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:17966 original size:3 final size:3
Alignment explanation
Indices: 17958--18007 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
17948 ATATATAATT
*
17958 TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAA TTAA TAA -AA TTA -AA
1 TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA -TAA TAA TAA TAA TAA
18003 TAA TA
1 TAA TA
18008 TAAAAAAGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 3 0.07
3 32 0.78
4 6 0.15
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:17985 original size:10 final size:10
Alignment explanation
Indices: 17946--18007 Score: 72
Period size: 10 Copynumber: 5.8 Consensus size: 10
17936 ACAAAATTTG
17946 TAATATATAATT
1 TAATA-ATAA-T
17958 TAATAATAAT
1 TAATAATAAT
17968 AATAATAATAAT
1 --TAATAATAAT
17980 TAATAATAAT
1 TAATAATAAT
17990 TAATAA-AAT
1 TAATAATAAT
17999 TAAATAATA
1 T-AATAATA
18008 TAAAAAAGAC
Statistics
Matches: 46, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
9 4 0.09
10 22 0.48
11 5 0.11
12 15 0.33
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
TAATAATAAT
Found at i:24321 original size:37 final size:36
Alignment explanation
Indices: 24266--24352 Score: 122
Period size: 37 Copynumber: 2.4 Consensus size: 36
24256 TGGTAACCAA
24266 CTTTGAAAAAGTGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAA-TGATTTTCAAAGTTTGGTAAATGTTT
* *
24303 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
24340 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
24353 AATGGGATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
35 2 0.04
36 10 0.22
37 33 0.73
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:28871 original size:21 final size:20
Alignment explanation
Indices: 28847--28910 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
28837 AACTTTGAAA
28847 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
28868 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
28882 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
28903 AAATGTTT
1 AAATGTTT
28911 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:28885 original size:35 final size:36
Alignment explanation
Indices: 28839--28960 Score: 176
Period size: 35 Copynumber: 3.4 Consensus size: 36
28829 TGGTAACCAA
28839 CTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTT
*
28876 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
* *
28911 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGGTAAATGTTT
*
28948 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
28961 AATGGGATAA
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
35 36 0.46
36 14 0.18
37 28 0.36
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTT
Found at i:31158 original size:13 final size:13
Alignment explanation
Indices: 31139--31171 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
31129 AAGGAGATAT
31139 TTTCTTCA-CTTC
1 TTTCTTCATCTTC
31151 TCTTCTTCATCTTC
1 T-TTCTTCATCTTC
31165 TTTCTTC
1 TTTCTTC
31172 TTCCTCATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.05
13 13 0.68
14 5 0.26
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (13 bp):
TTTCTTCATCTTC
Found at i:32316 original size:3 final size:3
Alignment explanation
Indices: 32310--32376 Score: 75
Period size: 3 Copynumber: 23.0 Consensus size: 3
32300 ATTTATTATT
* * * *
32310 TAA TAA TAA TGA TAA TAA TAA TAA TAA TGA TAA TAT TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
32358 TAA -AA TAA TAT TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
32377 AATGAGAAAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
2 4 0.08
3 48 0.92
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:32853 original size:42 final size:41
Alignment explanation
Indices: 32781--32907 Score: 164
Period size: 42 Copynumber: 3.0 Consensus size: 41
32771 GTCTTATGAT
* * * *
32781 TGACCCGAATGACTTATCATCTTGCTCGAAAGGCTTACAGA
1 TGACCCGAAAGATTTAACATCATGCTCGAAAGGCTTACAGA
*
32822 TGACCCGAAGGATTTAAGCATCATGCTCGAAAGGCTTACAGA
1 TGACCCGAAAGATTTAA-CATCATGCTCGAAAGGCTTACAGA
* * *
32864 TGACCTGAAAAATTTACACATCATGCTCGAAAGACTTACAGA
1 TGACCCGAAAGATTTA-ACATCATGCTCGAAAGGCTTACAGA
32906 TG
1 TG
32908 GCCCAAATGA
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
41 14 0.18
42 61 0.80
43 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (41 bp):
TGACCCGAAAGATTTAACATCATGCTCGAAAGGCTTACAGA
Found at i:32902 original size:22 final size:22
Alignment explanation
Indices: 32840--32903 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
32830 AGGATTTAAG
*
32840 CATCATGCTCGAAAGGCTTACA
1 CATCATGCTCGAAAGACTTACA
* * * * *
32862 GATGA-CCT-GAAAAATTTACA
1 CATCATGCTCGAAAGACTTACA
32882 CATCATGCTCGAAAGACTTACA
1 CATCATGCTCGAAAGACTTACA
32904 GATGGCCCAA
Statistics
Matches: 29, Mismatches: 11, Indels: 4
0.66 0.25 0.09
Matches are distributed among these distances:
20 12 0.41
21 4 0.14
22 13 0.45
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (22 bp):
CATCATGCTCGAAAGACTTACA
Found at i:36467 original size:9 final size:8
Alignment explanation
Indices: 36442--36472 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
36432 TCAATCTCTC
36442 TTTTTC-T
1 TTTTTCTT
36449 TTTTTCTT
1 TTTTTCTT
36457 TTTTTCTT
1 TTTTTCTT
36465 TTTTTCTT
1 TTTTTCTT
36473 GTTCTTCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTCTT
Found at i:41960 original size:20 final size:20
Alignment explanation
Indices: 41911--41960 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 20
41901 ATAGGATTAA
* *
41911 ATTAAAAAGTAATAAAAATT
1 ATTAAAAAATAAAAAAAATT
41931 ATGGTAAAAAAATAAAAAAAATT
1 AT--T-AAAAAATAAAAAAAATT
41954 ATTAAAA
1 ATTAAAA
41961 TATCAAGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
20 6 0.24
21 1 0.04
22 1 0.04
23 17 0.68
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (20 bp):
ATTAAAAAATAAAAAAAATT
Found at i:43280 original size:3 final size:3
Alignment explanation
Indices: 43274--43348 Score: 93
Period size: 3 Copynumber: 26.0 Consensus size: 3
43264 ATTTATTATT
* * *
43274 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAT TAA TAT TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
43321 TAA TAA TAA TAA TAT TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
43349 GAAAAAATTA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 6 0.10
3 55 0.90
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:45526 original size:6 final size:6
Alignment explanation
Indices: 45511--45547 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
45501 AATAGGGAGA
*
45511 ACGATG ACGATT ACGATG ACGATG ACGATG ACGATG A
1 ACGATG ACGATG ACGATG ACGATG ACGATG ACGATG A
45548 ACATGATGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.30, T:0.19
Consensus pattern (6 bp):
ACGATG
Found at i:45553 original size:18 final size:19
Alignment explanation
Indices: 45509--45553 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
45499 TCAATAGGGA
*
45509 GAACGATGACGATTACGAT
1 GAACGATGACGATGACGAT
45528 G-ACGATGACGATGACGAT
1 GAACGATGACGATGACGAT
45546 GAAC-ATGA
1 GAACGATGA
45554 TGAAGCTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.38, C:0.16, G:0.29, T:0.18
Consensus pattern (19 bp):
GAACGATGACGATGACGAT
Found at i:47847 original size:2 final size:2
Alignment explanation
Indices: 47842--47871 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
47832 GTGTGTGTAC
47842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47872 GTCATGGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50482 original size:60 final size:59
Alignment explanation
Indices: 50397--50581 Score: 160
Period size: 60 Copynumber: 3.1 Consensus size: 59
50387 TTTGGATGAA
* ** * * *
50397 TTTGGGGAT-AACATTGAAAGTTTCAAAAGTTTGGGGACCAATTTAGAAT-AAGGGTCATAT
1 TTTGGGGATGAA-ATTGAATG-TTCAAAAGTTTAAGGACCAATTTAAAATGAA-AGTCATAG
* * * *
50457 TTTGGGGATGAAATTGGAATGTTCAAAATTTTATGGACTAATATAAAATGAAAGTCATAG
1 TTTGGGGATGAAATT-GAATGTTCAAAAGTTTAAGGACCAATTTAAAATGAAAGTCATAG
* * * * *
50517 TTTAGAGATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTT-AAATGGAGGATCATAG
1 TTTGGGGATGAAATT-GAATGTTCAAAAGTTTAAGGACCAATTTAAAATGAAAG-TCATAG
50577 TTTGG
1 TTTGG
50582 AGACATGTGA
Statistics
Matches: 101, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
59 7 0.07
60 86 0.85
61 8 0.08
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (59 bp):
TTTGGGGATGAAATTGAATGTTCAAAAGTTTAAGGACCAATTTAAAATGAAAGTCATAG
Found at i:50885 original size:2 final size:2
Alignment explanation
Indices: 50878--50903 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
50868 CTTGCTAGTA
50878 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
50904 TAGTGTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52911 original size:74 final size:74
Alignment explanation
Indices: 52790--52937 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
52780 AGGACAGAGT
52790 TTGTTAACTCCAGGTTGAACGCCTCTTTGAAAATTTTCCCTTCGAAATACCCGAGTCCGGCTTCA
1 TTGTTAACTCCAGGTTGAACGCCTCTTTGAAAATTTTCCCTTCGAAATACCCGAGTCCGGCTTCA
52855 TTAAGACCA
66 TTAAGACCA
52864 TTGTTAACTCCAGGTTGAACGCCTCTTTGAAAATTTTCCCTTCGAAATACCCGAGTCCGGCTTCA
1 TTGTTAACTCCAGGTTGAACGCCTCTTTGAAAATTTTCCCTTCGAAATACCCGAGTCCGGCTTCA
52929 TTAAGACCA
66 TTAAGACCA
52938 CAAAGGACAT
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (74 bp):
TTGTTAACTCCAGGTTGAACGCCTCTTTGAAAATTTTCCCTTCGAAATACCCGAGTCCGGCTTCA
TTAAGACCA
Found at i:69621 original size:99 final size:99
Alignment explanation
Indices: 69504--69689 Score: 284
Period size: 99 Copynumber: 1.9 Consensus size: 99
69494 GTCTGAATAT
* * *
69504 CAACAAAGCTGATAGAAACTGAAA-TAGACAATCAACTCCAAGAGAGCCAAAAAGCCAACGGGAA
1 CAACAAAGCTGATAGAAACTGAAACTAG-CAATCAAATCCAAGAGAACCAAAAAGCCAACAGGAA
69568 AGAAGAATTGAGAAAAAGAAGGGGCGGAATAACAA
65 AGAAGAATTGAGAAAAAGAAGGGGCGGAATAACAA
* * * *
69603 CAACAAAGCTGATTGAAACTGAAACTTGCAATCAAATCCAAGAGAACCAAAAAGCTAGCAGGAAA
1 CAACAAAGCTGATAGAAACTGAAACTAGCAATCAAATCCAAGAGAACCAAAAAGCCAACAGGAAA
*
69668 GAAGAATTGAGATAAAGAAGGG
66 GAAGAATTGAGAAAAAGAAGGG
69690 ACAAAAGATT
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
99 76 0.97
100 2 0.03
ACGTcount: A:0.51, C:0.16, G:0.23, T:0.11
Consensus pattern (99 bp):
CAACAAAGCTGATAGAAACTGAAACTAGCAATCAAATCCAAGAGAACCAAAAAGCCAACAGGAAA
GAAGAATTGAGAAAAAGAAGGGGCGGAATAACAA
Found at i:75142 original size:22 final size:20
Alignment explanation
Indices: 75100--75143 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
75090 AATCTTTTAT
*
75100 TTATATTATTTATTTTAATA
1 TTATATTATATATTTTAATA
75120 TTATATTACTATATTCTTAATA
1 TTATATTA-TATATT-TTAATA
75142 TT
1 TT
75144 GTATGTGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 5 0.24
22 8 0.38
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
TTATATTATATATTTTAATA
Found at i:75575 original size:23 final size:23
Alignment explanation
Indices: 75528--75575 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
75518 AATAACATAT
**
75528 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
75551 TAGGTAGCGCTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
75574 TA
1 TA
75576 AGCATTTAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.40, C:0.08, G:0.19, T:0.33
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:75637 original size:87 final size:87
Alignment explanation
Indices: 75491--75653 Score: 317
Period size: 87 Copynumber: 1.9 Consensus size: 87
75481 AATATTATAT
75491 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
75556 AGCGCTTATATAATAAAATAAG
66 AGCGCTTATATAATAAAATAAG
*
75578 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCTCTTATATAATGTAATAGGT
1 CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
75643 AGCGCTTATAT
66 AGCGCTTATAT
75654 TAACCTATTT
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 75 1.00
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (87 bp):
CATTTAACCAGAAATATTATCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAAG
Found at i:76323 original size:200 final size:199
Alignment explanation
Indices: 75671--76378 Score: 806
Period size: 199 Copynumber: 3.5 Consensus size: 199
75661 TTTTCGAAGT
* * *
75671 AAACCGGTATATTTATACCGGTAACATTGCAAATTTACCTATTACATTATTATTATCGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
*** * * *
75736 TGTTTTTTATATCGATACAATTT--TAAATGTATCGACACTTTATGCTTGCACCTCGTTGGACAT
66 TGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTG---T
* * * * *
75799 TCATATTTCATTCTGGAAAAAAGTATCGGCACAAACTAACAAAGTGTCGATACATGAT-TTAGAC
127 GC--A-TTCATTCTGGACAAAAGTATCGACACAAATTAAC-AAGTGTCGATACATTATGTT-GAC
*
75863 CTATTCTCTCATA
187 CTATTTTCTCATA
* * * *
75876 AAACCGGTATATTTATATCGGTTACATTGAAAATTTACCTATTACATTATACTTATGGGTTTCGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* * *
75941 TGTTTCTGTGATCGATACTTTTTATAAATGTATCGACACTTTATG-GTTGCACC-C-TTT-TCGA
66 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG-TGCACCTCGTTTGT-G-
* * **
76002 CATTCATTCTGGACCAAAAGTATCGACACAAATTTACAAGTGTCGATACTTTATGCGGACCTATT
128 CATTCATTCTGGA-CAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTTGACCTATT
*
76067 TTATCATA
192 TTCTCATA
* * * *
76075 AAACCGATATATTTATATCGGTTACATTGTAAATTTACCTAATACATTATAATTATCGGTATCGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
76140 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGTGCAT
66 TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGTGCAT
* * * *
76205 TCATCCTGGACAATAAGTATCGACACAAATTCCACAAGTGTCGATACATTATGTTGACATGTTTT
131 TCATTCTGGACAA-AAGTATCGACACAAATT-AACAAGTGTCGATACATTATGTTGACCTATTTT
*
76270 CTAAT-
194 CTCATA
* * * * *
76275 TAACCGGTATACTTATACCGGTTACATTGTTAATTTACCTATTACATTATAATTATTGGTTTTGA
1 AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
* *
76340 TGTTTGTTGGG-TCGATACTTGTAGA-AAATATATCGACAC
66 TGTTT-TTGGGATCGATACTTTTA-ATAAATGTATCGACAC
76379 ATATTTAGGT
Statistics
Matches: 435, Mismatches: 53, Indels: 35
0.83 0.10 0.07
Matches are distributed among these distances:
199 150 0.34
200 137 0.31
201 40 0.09
202 2 0.00
204 5 0.01
205 74 0.17
206 27 0.06
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (199 bp):
AAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGA
TGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCGTGCACCTCGTTTGTGCAT
TCATTCTGGACAAAAGTATCGACACAAATTAACAAGTGTCGATACATTATGTTGACCTATTTTCT
CATA
Found at i:79180 original size:200 final size:199
Alignment explanation
Indices: 78826--79434 Score: 862
Period size: 200 Copynumber: 3.0 Consensus size: 199
78816 TCTCCATATA
* *
78826 ACCCTTTTTGGCATCCATTCTGGACATAAAGTATCGACACAATATTAAAAAGTGTCGATACATGT
1 ACCCTTTTTGGCATCCATTCTGGACAAAAAGTATCGACACAA-ATTTAAAAGTGTCGATACATGT
* * * *
78891 TGTAGACCTATTCTCTCATAAAATCGATATATTTATACCGATTATATTACAAAATTACCTATTAC
65 TATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTAC
* *
78956 ATTATAATTATGGGTTTCGATGTTTTCGGGATCGACACTTTTAATAAATGTATCGACACTTTGTG
130 ATTATAATTATGAGTTTCGATGTTTTCGGGATCGACACTTTTAATAAATGTATCGACACTTTATG
79021 CGTTC
195 CGTTC
** * * * *
79026 TTCCTTTTTGGCATCTATTCTAGACAAAAAGTATCGACACAAATTTATATAGTGTCGATACATAT
1 ACCCTTTTTGGCATCCATTCTGGACAAAAAGTATCGACACAAATTTA-AAAGTGTCGATACATGT
* ** *
79091 TATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTACATTGTAAATTTACCTATTAC
65 TATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTAC
* * *
79156 ATTATAATTATGAGTTTTGATGTTTTCGGGATCGACACTTTTTGA-AAATATATCGACACTTTAT
130 ATTATAATTATGAGTTTCGATGTTTTCGGGATCGACAC-TTTTAATAAATGTATCGACACTTTAT
79220 GCGTTC
194 GCGTTC
* *
79226 ACCCTTTTTGGCATCCATTCTGGACAAAAATTATCGATAC-AATATTAAGAAGTGTCGATACATG
1 ACCCTTTTTGGCATCCATTCTGGACAAAAAGTATCGACACAAAT-TTAA-AAGTGTCGATACATG
* * *
79290 TTATAGACCTATTATCTCATAAAACCGGTATATGTATATCGGTTATATTACAAAATTACCTATTA
64 TTATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTA
* * * * *
79355 CATTATAATTATGAGTTTCAATATTTTTGGGATTGACACTTTTAATAAATGTATCGAAACTTTAT
129 CATTATAATTATGAGTTTCGATGTTTTCGGGATCGACACTTTTAATAAATGTATCGACACTTTAT
*
79420 GCGTGC
194 GCGTTC
79426 AACCCTTTT
1 -ACCCTTTT
79435 GGATCGACAC
Statistics
Matches: 358, Mismatches: 45, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
199 13 0.04
200 332 0.93
201 13 0.04
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (199 bp):
ACCCTTTTTGGCATCCATTCTGGACAAAAAGTATCGACACAAATTTAAAAGTGTCGATACATGTT
ATAGACCTATTCTCTCATAAAACCGGTATATTTATACCGGTTATATTACAAAATTACCTATTACA
TTATAATTATGAGTTTCGATGTTTTCGGGATCGACACTTTTAATAAATGTATCGACACTTTATGC
GTTC
Found at i:79486 original size:51 final size:52
Alignment explanation
Indices: 79378--79487 Score: 145
Period size: 51 Copynumber: 2.1 Consensus size: 52
79368 AGTTTCAATA
*
79378 TTTTTGGGATTGACACTTTTAATAAATGTATCGAAACTTTATGCGTGCAACCC
1 TTTTT-GGATCGACACTTTTAATAAATGTATCGAAACTTTATGCGTGCAACCC
* * *
79431 -TTTTGGATCGACACTCTTTGA-AAATGTATCGACACTTTATGCGTTC-ACCC
1 TTTTTGGATCGACACT-TTTAATAAATGTATCGAAACTTTATGCGTGCAACCC
79481 TTTTTGG
1 TTTTTGG
79488 CATCCATTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
50 4 0.08
51 39 0.76
52 8 0.16
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.39
Consensus pattern (52 bp):
TTTTTGGATCGACACTTTTAATAAATGTATCGAAACTTTATGCGTGCAACCC
Found at i:79539 original size:251 final size:251
Alignment explanation
Indices: 79184--79636 Score: 721
Period size: 251 Copynumber: 1.8 Consensus size: 251
79174 GATGTTTTCG
*
79184 GGATCGACACTTTTTGAAAATATATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
1 GGATCGACACTCTTTGAAAATATATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
* *
79249 ACAAAAATTATCGATACAATATTAAGAAGTGTCGATACATGTTATAGACCTATTATCTCATAAAA
66 ACAAAAAGTATCGACACAATATTAAGAAGTGTCGATACATGTTATAGACCTATTATCTCATAAAA
* * *
79314 CCGGTATATGTATATCGGTTATATT-ACAAAATTACCTATTACATTATAATTAT-GAGTTTCAAT
131 CCGGTATATGTATACCGGTTACATTGA-AAAATTACCCATTACATTATAATTATCG-GTTTCAAT
79377 ATTTTTGGGATTGACACTTTTAATAAATGTATCGAAACTTTATGCGTGCAACCCTTTT
194 ATTTTTGGGATTGACACTTTTAATAAATGTATCGAAACTTTATGCGTGCAACCCTTTT
*
79435 GGATCGACACTCTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
1 GGATCGACACTCTTTGAAAATATATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
* ** * * *
79500 ATAAAAAGTATCGACACAATATTATTAAGTGTCGATACATGTTGTAGACCTATTTTTTCATAAAA
66 ACAAAAAGTATCGACACAATATTAAGAAGTGTCGATACATGTTATAGACCTATTATCTCATAAAA
* * * *
79565 CTGGTATATTTATACCGGTTACATTGAAAAATTACCCATTACATTATAATTATCGGTTTCGATGT
131 CCGGTATATGTATACCGGTTACATTGAAAAATTACCCATTACATTATAATTATCGGTTTCAATAT
79630 TTTTGGG
196 TTTTGGG
79637 GTCGTTACTT
Statistics
Matches: 183, Mismatches: 17, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
251 181 0.99
252 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (251 bp):
GGATCGACACTCTTTGAAAATATATCGACACTTTATGCGTTCACCCTTTTTGGCATCCATTCTGG
ACAAAAAGTATCGACACAATATTAAGAAGTGTCGATACATGTTATAGACCTATTATCTCATAAAA
CCGGTATATGTATACCGGTTACATTGAAAAATTACCCATTACATTATAATTATCGGTTTCAATAT
TTTTGGGATTGACACTTTTAATAAATGTATCGAAACTTTATGCGTGCAACCCTTTT
Found at i:80262 original size:17 final size:17
Alignment explanation
Indices: 80240--80279 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
80230 CCAGATTATA
80240 AATCATTTTTTCCGCTG
1 AATCATTTTTTCCGCTG
80257 AATCATTTTTTCCGCTG
1 AATCATTTTTTCCGCTG
80274 AATCAT
1 AATCAT
80280 CAACCAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (17 bp):
AATCATTTTTTCCGCTG
Found at i:85097 original size:21 final size:21
Alignment explanation
Indices: 85073--85122 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
85063 AATTTTGTGT
* *
85073 ACTGTAGCAGTGTATCGATGC
1 ACTGTAGCAATGCATCGATGC
85094 ACTGTAGCAATGCATCGATGC
1 ACTGTAGCAATGCATCGATGC
*
85115 ACTTTAGC
1 ACTGTAGC
85123 CATTCAAAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (21 bp):
ACTGTAGCAATGCATCGATGC
Found at i:85162 original size:21 final size:21
Alignment explanation
Indices: 85136--85177 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
85126 TCAAAGTTTT
* *
85136 ATGCATCGATGCACTGTAGCA
1 ATGCATCGATACACTATAGCA
85157 ATGCATCGATACACTATAGCA
1 ATGCATCGATACACTATAGCA
85178 CTGTAGCAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
ATGCATCGATACACTATAGCA
Found at i:88766 original size:47 final size:47
Alignment explanation
Indices: 88712--88805 Score: 188
Period size: 47 Copynumber: 2.0 Consensus size: 47
88702 CTTACTCCCT
88712 AAACACAAAATCGTTCCGACCCCTCTTTGCAAACCGTTCCGGTTGTC
1 AAACACAAAATCGTTCCGACCCCTCTTTGCAAACCGTTCCGGTTGTC
88759 AAACACAAAATCGTTCCGACCCCTCTTTGCAAACCGTTCCGGTTGTC
1 AAACACAAAATCGTTCCGACCCCTCTTTGCAAACCGTTCCGGTTGTC
88806 GATCCGAGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.26, C:0.34, G:0.15, T:0.26
Consensus pattern (47 bp):
AAACACAAAATCGTTCCGACCCCTCTTTGCAAACCGTTCCGGTTGTC
Found at i:89439 original size:18 final size:18
Alignment explanation
Indices: 89416--89459 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
89406 TGATTTCCTC
*
89416 AGAAGAATCGTT-TGTTTG
1 AGAAGAA-CGTTGTGGTTG
*
89434 AGAAGAAGGTTGTGGTTG
1 AGAAGAACGTTGTGGTTG
89452 AGAAGAAC
1 AGAAGAAC
89460 TGGGTTGATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 3 0.14
18 19 0.86
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.27
Consensus pattern (18 bp):
AGAAGAACGTTGTGGTTG
Found at i:90126 original size:200 final size:199
Alignment explanation
Indices: 89768--90726 Score: 1526
Period size: 200 Copynumber: 4.8 Consensus size: 199
89758 TATTTAAATT
* *
89768 AGTATAGAAACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
** * * *
89833 TATTTATATTGATTACTTTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGT
66 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG-
* *
89898 GATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGA
130 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCATTTTTGGCATTCATTCTGGA
89963 CCAAA
195 CCAAA
* *
89968 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAATCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
*
90033 AATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTCG
66 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT-G
90098 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCATTTTTGGCATTCATTCTGGA
130 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCATTTTTGGCATTCATTCTGGA
90163 CCAAA
195 CCAAA
* *
90168 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAATCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
* * * * *
90233 AATTTATACCAGTTACATTGAAAAATTACTTGTTACATTATACTTATGGGTTTCGATATTTCTGA
66 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG-
* * * *
90298 GATTGATACTTTTTATAAATGGATCGACACTTTATGGTTACACCCTTTTT-GCATTCATTCTGAA
130 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCATTTTTGGCATTCATTCTGGA
*
90362 CTAAA
195 CCAAA
* *
90367 AGTATCGACACAAAATTAAAAAGTGTGGATACATGTTGTAGACCTATTCTCTCATAAAACCAGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
*
90432 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATGTTTCTGG
66 TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT-G
* * * *
90497 GATCGATACTTTTTATAAATGGATAGACACTTTATGGTTTCACCATTTTCGGCATTCATTCTAGA
130 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCATTTTTGGCATTCATTCTGGA
90562 CCAAA
195 CCAAA
*
90567 AGTATCGAC-CAAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGAT
1 AGTATCGACAC-AAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
* * * *
90631 ATATTTATACTGATTACATTGAAAAATTACATATTACATTATACTTATGGGTTTCGATGTTTATA
65 ATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT-
90696 GGATCGATACTTTTTATAAATGGATCGACAC
129 GGATCGATACTTTTTATAAATGGATCGACAC
90727 ATATGTTTAC
Statistics
Matches: 705, Mismatches: 49, Indels: 10
0.92 0.06 0.01
Matches are distributed among these distances:
199 182 0.26
200 522 0.74
201 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (199 bp):
AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
TATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGG
ATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCATTTTTGGCATTCATTCTGGAC
CAAA
Found at i:90516 original size:399 final size:400
Alignment explanation
Indices: 89768--90726 Score: 1575
Period size: 399 Copynumber: 2.4 Consensus size: 400
89758 TATTTAAATT
* *
89768 AGTATAGAAACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
* * * * *
89833 TATTTATATTGATTACTTTGAAAATTTACCTATTACATTATACTTATGGGTTTCGATGTTTCTGT
66 TATTTATACTGATTACATTGAAAAATTACATATTACATTATACTTATGGGTTTCGATGTTTCTGA
* * *
89898 GATCGATACTTTTTATAAATGTATCGACACTTTATGGTTGCACCCTTTTTGGCATTCATTCTGGA
131 GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTACACCCTTTTTGGCATTCATTCTGAA
* *
89963 CCAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAAT
196 CCAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
* *
90028 CGGTAAATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTT
261 CAGTAAATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATGTT
* *
90093 TCTCGGATCGATACTTTTTATAAATGGATCGACACTTTATGGTTGCACCATTTTTGGCATTCATT
326 TCTCGGATCGATACTTTTTATAAATGGATAGACACTTTATGGTTGCACCATTTTCGGCATTCATT
*
90158 CTGGACCAAA
391 CTAGACCAAA
* *
90168 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCGTAAAATCGGTA
1 AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
* * * * *
90233 AATTTATAC-CAGTTACATTGAAAAATTACTTGTTACATTATACTTATGGGTTTCGATATTTCTG
66 TATTTATACTGA-TTACATTGAAAAATTACATATTACATTATACTTATGGGTTTCGATGTTTCTG
*
90297 AGATTGATACTTTTTATAAATGGATCGACACTTTATGGTTACACCCTTTTT-GCATTCATTCTGA
130 AGATCGATACTTTTTATAAATGGATCGACACTTTATGGTTACACCCTTTTTGGCATTCATTCTGA
* *
90361 ACTAAAAGTATCGACACAAAATTAAAAAGTGTGGATACATGTTGTAGACCTATTCTCTCATAAAA
195 ACCAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAA
*
90426 CCAGTATATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATGT
260 CCAGTAAATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATGT
* *
90491 TTCTGGGATCGATACTTTTTATAAATGGATAGACACTTTATGGTTTCACCATTTTCGGCATTCAT
325 TTCTCGGATCGATACTTTTTATAAATGGATAGACACTTTATGGTTGCACCATTTTCGGCATTCAT
90556 TCTAGACCAAA
390 TCTAGACCAAA
*
90567 AGTATCGAC-CAAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGAT
1 AGTATCGACAC-AAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGT
*
90631 ATATTTATACTGATTACATTGAAAAATTACATATTACATTATACTTATGGGTTTCGATGTTTAT-
65 ATATTTATACTGATTACATTGAAAAATTACATATTACATTATACTTATGGGTTTCGATGTTTCTG
90695 AGGATCGATACTTTTTATAAATGGATCGACAC
130 A-GATCGATACTTTTTATAAATGGATCGACAC
90727 ATATGTTTAC
Statistics
Matches: 516, Mismatches: 39, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
398 2 0.00
399 351 0.68
400 163 0.32
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (400 bp):
AGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
TATTTATACTGATTACATTGAAAAATTACATATTACATTATACTTATGGGTTTCGATGTTTCTGA
GATCGATACTTTTTATAAATGGATCGACACTTTATGGTTACACCCTTTTTGGCATTCATTCTGAA
CCAAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
CAGTAAATTTATACCGGTTACATTGAAAAATTACCTATTACATTATACTTATGGGTTTCAATGTT
TCTCGGATCGATACTTTTTATAAATGGATAGACACTTTATGGTTGCACCATTTTCGGCATTCATT
CTAGACCAAA
Found at i:90977 original size:18 final size:19
Alignment explanation
Indices: 90950--91016 Score: 91
Period size: 19 Copynumber: 3.6 Consensus size: 19
90940 TTCTCATCTC
* *
90950 ATACATAATTAT-ATTCAT
1 ATACAAAATTATAAATCAT
*
90968 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCAT
*
90987 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
91006 ATACAAAATTA
1 ATACAAAATTA
91017 ACCCTACATT
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
18 11 0.25
19 33 0.75
ACGTcount: A:0.52, C:0.10, G:0.01, T:0.36
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:91631 original size:4 final size:4
Alignment explanation
Indices: 91598--94361 Score: 4268
Period size: 4 Copynumber: 705.2 Consensus size: 4
91588 TCCTTTCATG
* * *
91598 CATA CATG CATA CATG CATA CATG CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
91646 CATA CATA CATA CATA CATA CATA CATG CATG CATG CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
91694 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
91742 CATA CATA CATA CATA CATTA CATA CATA CATA TACTA CATA CATG CATG
1 CATA CATA CATA CATA CA-TA CATA CATA CATA CA-TA CATA CATA CATA
* *
91792 CATG CA-G CATA CATA CATA CATA CATA CATA CATA CA-A CATA TGCATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA --CATA
* * * * * *
91840 CATA CATA CATA CATG CATG CATG CATA CATA CATA CATG C-TG CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
91887 CATG CATA CATA CATA CATA CATA CATG CATG C-TA CATA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * *
91934 CATG CATGCA CATA CATA CAT- CAT- CATG CATG CATA CATA CATG CATG
1 CATA CAT--A CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * *
91982 CATG CATG CATA TATA CATA CATA CATA CATA CATA CATA CATA -ATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * * * *
92029 TATG CATG CATG CATG TATA TATA CATA CATA CATT CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
92077 CATA CATA CATA CATA CATA CATA CATA TATA CATA CATA CATA CATG
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * * * * *
92125 CATG CATG CATA CATA TGCATA CATA CATA CATT CATG CATG CATG CATG
1 CATA CATA CATA CATA --CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
92175 CATA CATT CATG CATA CATG CATG CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92223 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
92271 CATG CATG CATA CATA CATA C--A CATG CATG CATA CATA CATA CATCA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT-A
* * * * *
92318 CATG CATG CATA CAT- CATG CATA CATG CATG CATA -ATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* *
92364 -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATG CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
92411 CATA CATA -ATA CATA C--A CATA CATA CATA CATA CATG CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92456 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT-
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92503 -ATA CATA CAT- -ATA CATA CATA CATA C-TA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92547 CATA CATA CATA CATA CATA CATA CATA CATA CA-A CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92594 CATA CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
92640 CATA CATA CAAA CATA CA-A -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
92686 CATA CATA CCATA CATA CATA CATA CATA CATA CATA CAGA CATA CATA
1 CATA CATA -CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92735 CATA CATA CA-A CATA CATA CA-A CATA CATA CATA CATA -ATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92780 CATA CATA CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92826 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92874 CATA CATA CATA CATA -ATA CATA CATA C-TA CATA CATA C-TA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
92919 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
92967 CATA CATA CAGA CATA CATA CATA CATA CATA CATA CATA CAATA -ATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA C-ATA CATA
93015 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
93063 CATA AATA CATA CATA CATA CATA CATA CA-A CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93110 CATA CATA CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93156 CATA CATA CATA CAT- CATA CATA CATAA CATA CATA CATA CATA C--A
1 CATA CATA CATA CATA CATA CATA CAT-A CATA CATA CATA CATA CATA
*
93202 CATA CATA CATA CATA CATA CATA CATA TATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93250 CATA CATA CATA CATA CATA -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93297 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93344 CATA CATA CATA CATA CATA CATA -ATA CATA CATA CACTA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-TA CATA CATA
93392 CATA CATA CATA CATA CATA CA-A CATA CATA CATA C-TA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93438 CATA CATA CATA CATA CATA CATA CAATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA C-ATA CATA CATA CATA CATA CATA
93487 CATA CATA C--A CATA CATA CAT- CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93532 CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93579 CATA CATA -ATA CATA CATA CATA CATA CATA CA-A CATA CATA C-TA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93624 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93672 CATA CATA -ATA CAT- -ATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93717 CATA CATA CATA CATA CATA CATA CATA -ATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93764 CATA CATA CATA CATA CATA CATA CATA CATA CAT- CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93811 CATA C-TA CATA CATA CATA CATA CATA CATA CATA -ATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93857 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATAA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT-A
93906 CATA CATA CATA CATA CATA C-TA CATA CA-A CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93952 CATA CATA CATA CATA C-TA CATA CATA CATA CATA CATA CATA CAT-
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
93998 -ATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
94045 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
94093 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
94141 CATA CATA CATA CATA CATA CATA CATA CATA CATA CA-A CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
94188 CATA CATA CATA CATA CATA CATA CATA -ATA CATA CATA CATA -ATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
94234 CATA CATA CATA CATA CATA CATA C--A CATA CATA C-TA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
94279 CATA CATA CATA CATA CATA -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
94326 CATA CATA CATA CATA CATA C-TA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA C
94362 CAATCTCTTA
Statistics
Matches: 2606, Mismatches: 68, Indels: 172
0.92 0.02 0.06
Matches are distributed among these distances:
2 25 0.01
3 139 0.05
4 2397 0.92
5 34 0.01
6 11 0.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:95357 original size:21 final size:21
Alignment explanation
Indices: 95331--95371 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
95321 CCTCCTCATT
*
95331 TCCTCCATCTTTTCTTCTTCC
1 TCCTCCATATTTTCTTCTTCC
*
95352 TCCTCCCTATTTTCTTCTTC
1 TCCTCCATATTTTCTTCTTC
95372 ATATTTTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (21 bp):
TCCTCCATATTTTCTTCTTCC
Found at i:95593 original size:33 final size:33
Alignment explanation
Indices: 95556--95621 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
95546 CATCTTAAGA
*
95556 TCACCCCTTAACACCTCAACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
*
95589 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTCTTTCACCACT
95622 CCATCTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTCTTTCACCACT
Found at i:95680 original size:21 final size:21
Alignment explanation
Indices: 95655--95719 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
95645 CCCCTTATGC
* *
95655 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
95676 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
95697 CTCTCAAGTTTCTTTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
95718 CT
1 CT
95720 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.15, C:0.31, G:0.11, T:0.43
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:98007 original size:20 final size:20
Alignment explanation
Indices: 97961--98007 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
97951 TCCGGTAGCG
97961 CTTTACCGGTTTTATCATTT
1 CTTTACCGGTTTTATCATTT
**
97981 CGATACCGGTTTTATCATATT
1 CTTTACCGGTTTTATCAT-TT
98002 -TTTACC
1 CTTTACC
98008 TGTTATATTG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.19, C:0.21, G:0.11, T:0.49
Consensus pattern (20 bp):
CTTTACCGGTTTTATCATTT
Found at i:98237 original size:182 final size:182
Alignment explanation
Indices: 97928--98402 Score: 738
Period size: 182 Copynumber: 2.6 Consensus size: 182
97918 CGTACTTATG
*
97928 AAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTACCGGTTTTATCATTTCGATACCGGTTT
1 AAAGTATTGACACTTTCAATATATCCGATAGCGCTTTACCGGTTTTATCATTTCGATACCGGTTT
97993 TATCATATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
* *
98058 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGACACTTATATT
131 AGGCGCTAAAACTGCTTCTCTTTAAAATTCACAAAGTATCGACACTTATATT
*
98110 AAAGTATTGACACTTTAAATATATCCGATAGCGCTTTACCGGTTTTATCATTTCGATACCGGTTT
1 AAAGTATTGACACTTTCAATATATCCGATAGCGCTTTACCGGTTTTATCATTTCGATACCGGTTT
* * * * *
98175 TGTCATATTTTTACATGTTATATCGTTGTGGGTCGATACATTTTTATAAAGTATCTACACTTTAT
66 TATCATATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
**
98240 AGGCGCTAAAACTGCTTCTCTTTAAAATTCACAAAGTATCGATTCTTATATT
131 AGGCGCTAAAACTGCTTCTCTTTAAAATTCACAAAGTATCGACACTTATATT
* * * * * * *
98292 AAAGTATCGACACATTCAATATATCC-AGTAGGGCTTTACCGGTATTGTCTTTTCG-TGACCAGT
1 AAAGTATTGACACTTTCAATATATCCGA-TAGCGCTTTACCGGTTTTATCATTTCGAT-ACCGGT
* *
98355 TTTATCATATTTTTACCTGTTATATTGATATGGATCGATACATTTTTA
64 TTTATCATATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTA
98403 ATTTGGATCG
Statistics
Matches: 266, Mismatches: 25, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
181 2 0.01
182 264 0.99
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (182 bp):
AAAGTATTGACACTTTCAATATATCCGATAGCGCTTTACCGGTTTTATCATTTCGATACCGGTTT
TATCATATTTTTACCTGTTATATTGTTGTGGATCGATACATTTTTATAAAGTATCGACACTTTAT
AGGCGCTAAAACTGCTTCTCTTTAAAATTCACAAAGTATCGACACTTATATT
Found at i:101512 original size:21 final size:22
Alignment explanation
Indices: 101458--101542 Score: 102
Period size: 23 Copynumber: 3.9 Consensus size: 22
101448 AATCAAGATA
101458 ATTCTACGTGGTCCTTCGGGAC
1 ATTCTACGTGGTCCTTCGGGAC
101480 AATTCTACGTGGTCCTTCGGGAC
1 -ATTCTACGTGGTCCTTCGGGAC
* * *
101503 A-TCTATGTGGTACTTCAGGAC
1 ATTCTACGTGGTCCTTCGGGAC
*
101524 ATTCTATGTGG-CACTTCGG
1 ATTCTACGTGGTC-CTTCGG
101543 TGCAATTTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
21 18 0.33
22 15 0.27
23 22 0.40
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.33
Consensus pattern (22 bp):
ATTCTACGTGGTCCTTCGGGAC
Found at i:101561 original size:24 final size:24
Alignment explanation
Indices: 101525--101570 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
101515 CTTCAGGACA
**
101525 TTCTATGTGGCACTTCGGTGCAAT
1 TTCTATGCAGCACTTCGGTGCAAT
*
101549 TTCTATGCAGCACTTCGTTGCA
1 TTCTATGCAGCACTTCGGTGCA
101571 TTTTATACGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (24 bp):
TTCTATGCAGCACTTCGGTGCAAT
Found at i:108304 original size:23 final size:23
Alignment explanation
Indices: 108270--108338 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
108260 CACCACAGCT
*
108270 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
108293 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
108316 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
108339 TACAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:112665 original size:11 final size:11
Alignment explanation
Indices: 112649--112682 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
112639 AACACCCCCA
*
112649 ACCCGTATCTG
1 ACCCGTATCCG
112660 ACCCGTATCCG
1 ACCCGTATCCG
*
112671 ACCCGGATCCG
1 ACCCGTATCCG
112682 A
1 A
112683 GTCTGAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.21, C:0.41, G:0.21, T:0.18
Consensus pattern (11 bp):
ACCCGTATCCG
Found at i:113407 original size:23 final size:23
Alignment explanation
Indices: 113373--113435 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
113363 CACCACAGCT
*
113373 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * * *
113396 CGTAGAATTGCACCGTAGTGTCG
1 CGTAGAAATGCACCGAAGTGCCA
113419 CGTAGAAATGCACCGAA
1 CGTAGAAATGCACCGAA
113436 ATTCCATATA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.32, C:0.24, G:0.25, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:113838 original size:2 final size:2
Alignment explanation
Indices: 113831--113867 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
113821 TGTCTTATCC
*
113831 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
113868 TCACATGTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:114591 original size:20 final size:19
Alignment explanation
Indices: 114546--114597 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 19
114536 TCTCAAAGAT
* *
114546 TATCACATAACTTCTTTTA
1 TATCATATAACTTCTTTCA
*
114565 TATTCATATAATTTCTTATCA
1 TA-TCATATAACTTCTT-TCA
114586 TATCATCATAAC
1 TATCAT-ATAAC
114598 ATAGCATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 2 0.08
20 16 0.62
21 8 0.31
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (19 bp):
TATCATATAACTTCTTTCA
Found at i:116173 original size:17 final size:17
Alignment explanation
Indices: 116151--116189 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
116141 TGAAAACTCA
116151 ATAATAATA-ATGTGATG
1 ATAATAATATATGTG-TG
*
116168 ATAATATTATATGTGTG
1 ATAATAATATATGTGTG
116185 ATAAT
1 ATAAT
116190 TAGAAGAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (17 bp):
ATAATAATATATGTGTG
Found at i:118724 original size:13 final size:13
Alignment explanation
Indices: 118701--118741 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
118691 AGTACTATGG
118701 TATTA-TTTATAT
1 TATTATTTTATAT
118713 TATTATTTTATAT
1 TATTATTTTATAT
* *
118726 AATTATATTAT-T
1 TATTATTTTATAT
118738 TATT
1 TATT
118742 TACTTATCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 9 0.36
13 16 0.64
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTATTTTATAT
Found at i:118742 original size:4 final size:4
Alignment explanation
Indices: 118703--118762 Score: 50
Period size: 4 Copynumber: 14.5 Consensus size: 4
118693 TACTATGGTA
* * * *
118703 TTAT TTAT ATTA- TTATT TTAT ATAA TTAT ATTAT TTAT TTAC TTAT CTAT
1 TTAT TTAT -TTAT TTA-T TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT
118753 TTAT TTAT TT
1 TTAT TTAT TT
118763 CGTTTCAGGT
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
3 3 0.07
4 31 0.70
5 10 0.23
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (4 bp):
TTAT
Found at i:121156 original size:15 final size:15
Alignment explanation
Indices: 121136--121167 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
121126 GGAGAACAAT
121136 ATATGTAATATGATA
1 ATATGTAATATGATA
121151 ATATGTAATATGATA
1 ATATGTAATATGATA
121166 AT
1 AT
121168 GAAATATAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (15 bp):
ATATGTAATATGATA
Found at i:121159 original size:7 final size:8
Alignment explanation
Indices: 121136--121167 Score: 50
Period size: 7 Copynumber: 4.2 Consensus size: 8
121126 GGAGAACAAT
121136 ATATG-TA
1 ATATGATA
121143 ATATGATA
1 ATATGATA
121151 ATATG-TA
1 ATATGATA
121158 ATATGATA
1 ATATGATA
121166 AT
1 AT
121168 GAAATATAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 12 0.52
8 11 0.48
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (8 bp):
ATATGATA
Found at i:122260 original size:103 final size:103
Alignment explanation
Indices: 121937--122252 Score: 587
Period size: 103 Copynumber: 3.1 Consensus size: 103
121927 GGGTCTACGC
*
121937 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
122002 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
122040 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
122105 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
122143 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
122208 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
*
122246 AGTCCTT
1 GGTCCTT
122253 ATGGACATTA
Statistics
Matches: 208, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 208 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
Found at i:122331 original size:23 final size:23
Alignment explanation
Indices: 122268--122336 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
122258 CATTATTATA
*
122268 TGGCACTACGGTACAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * * *
122291 CGGCACTCCAGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
122314 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
122337 AGCTGTGGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:128653 original size:2 final size:2
Alignment explanation
Indices: 128646--128690 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
128636 TTTAATAAAT
* *
128646 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA AA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
128687 TA TA
1 TA TA
128691 AAAAATCATC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:142075 original size:21 final size:21
Alignment explanation
Indices: 142051--142124 Score: 59
Period size: 19 Copynumber: 3.5 Consensus size: 21
142041 CCAAATTAAG
142051 AAATAAAATTACAAAATAAAT
1 AAATAAAATTACAAAATAAAT
*
142072 AAAT-AAA-TACTAAAATTGAATAA
1 AAATAAAATTAC-AAAA-T-AA-AT
142095 AAATAAAATTAC-AAAT-AAT
1 AAATAAAATTACAAAATAAAT
142114 AAA-AGAAATTA
1 AAATA-AAATTA
142125 ACATATTCAA
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
18 1 0.02
19 13 0.30
20 8 0.18
21 5 0.11
22 3 0.07
23 8 0.18
24 3 0.07
25 3 0.07
ACGTcount: A:0.69, C:0.04, G:0.03, T:0.24
Consensus pattern (21 bp):
AAATAAAATTACAAAATAAAT
Found at i:143922 original size:41 final size:41
Alignment explanation
Indices: 143877--143987 Score: 132
Period size: 42 Copynumber: 2.7 Consensus size: 41
143867 GGATGGCCCT
*
143877 AAGGACTTATCATCTTGCTCGAAAGACTGACAGATAACCCG
1 AAGGACTTATCATCTTGCTCAAAAGACTGACAGATAACCCG
* * * * **
143918 AAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCG
1 AAGGACTT-ATCATCTTGCTCAAAAGACTGACAGATAACCCG
**
143960 AAGGACTTATCATCTCACTCAAAAGACT
1 AAGGACTTATCATCTTGCTCAAAAGACT
143988 TATTAATGGC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 24 0.41
42 34 0.59
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (41 bp):
AAGGACTTATCATCTTGCTCAAAAGACTGACAGATAACCCG
Found at i:143988 original size:41 final size:40
Alignment explanation
Indices: 143868--144009 Score: 140
Period size: 41 Copynumber: 3.5 Consensus size: 40
143858 AAGTCTTATG
* * * *
143868 GATGGCCCTAAGGACTTATCATCTTGCTCGAAAGACTGACA
1 GATGGCCCGAAGGACTTATCATC-TGCTCAAAAGACTTACT
** *
143909 GATAACCCGAAGGATTTAATCATCATGCTCAAAAGACTTACT
1 GATGGCCCGAAGGACTT-ATCATC-TGCTCAAAAGACTTACT
* *
143951 GATGGCCCGAAGGACTTATCATCTCACTCAAAAGACTTATT
1 GATGGCCCGAAGGACTTATCATCT-GCTCAAAAGACTTACT
* * *
143992 AATGGCCCAAAAGACTTA
1 GATGGCCCGAAGGACTTA
144010 CTAATTTTGG
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
40 1 0.01
41 48 0.58
42 34 0.41
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.25
Consensus pattern (40 bp):
GATGGCCCGAAGGACTTATCATCTGCTCAAAAGACTTACT
Found at i:144219 original size:300 final size:299
Alignment explanation
Indices: 143678--144268 Score: 943
Period size: 300 Copynumber: 2.0 Consensus size: 299
143668 AATCATCATG
* * * * * * *
143678 CTCAAAAGACTTAATGATGGTCCGAAGGACTTATTAATTTTGGAAATAATTTATTGGGTAAGAAA
1 CTCAAAAGACTTAATAATGGCCCAAAAGACTTACTAATTTTGGAAATAATTTACTAGGTAAGAAA
*
143743 CTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAACATTAAATGAGAAACTTT
66 CTTTGGAAATCGCATTCTTACTTTTCAAAAATTTCATTTTCTGAAAACATTAAATGAGAAACTTT
*
143808 GGAAATCGCTTTCTCTTTTTTCGAAAATCATGTGAAAACATCTTGCCCGAAAGTCTTATGGATGG
131 GGAAATCGCTTTCTCTTTTTTCGAAAATCATGTGAAAACATCTTGCCCGAAAGTCTTATAGATGG
* *
143873 CCCTAAGGACTTATCATCTTGCTCGAAAGACTGACAGATAACCCGAAGGATTTAATCATCATGCT
196 CCCTAAGGACTTATCAGCTTGCTCAAAAGACTGACAGATAACCCGAAGGATTTAATCATCATGCT
*
143938 CAAAAGACTTACTGATGGCCCGAAGGACTTATCATCTCA
261 CAAAAGACTAACTGATGGCCCGAAGGACTTATCATCTCA
* *
143977 CTCAAAAGACTTATTAATGGCCCAAAAGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAAA
1 CTCAAAAGACTTAATAATGGCCCAAAAGACTTACTAATTTTGGAAATAATTTACTAGGTAAGAAA
* *
144042 CTTTGGAAATCGCATTCTTACTTTTCAAAAATTTCATTTTCTTAAAAGATTTAAATGAGAAACTT
66 CTTTGGAAATCGCATTCTTACTTTTCAAAAATTTCATTTTCTGAAAACA-TTAAATGAGAAACTT
*
144107 TGGAAATCGCTTTCTCATTTTTT-GAAAATCATGTGAAAACATCTTGCCCGAAGGTCTTATAGAT
130 TGGAAATCGCTTTCTC-TTTTTTCGAAAATCATGTGAAAACATCTTGCCCGAAAGTCTTATAGAT
*
144171 GG-CCTGAAGGACTTATCAGCTTGCTCAAAAGACTGACAGATGACCCGAAGGATTTAATCATCAT
194 GGCCCT-AAGGACTTATCAGCTTGCTCAAAAGACTGACAGATAACCCGAAGGATTTAATCATCAT
* ** *
144235 TCTTGAAAGACTAACTGATGGCTCGAAGGACTTA
258 GCTCAAAAGACTAACTGATGGCCCGAAGGACTTA
144269 CCAATTTGGG
Statistics
Matches: 267, Mismatches: 22, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
299 105 0.39
300 156 0.58
301 6 0.02
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (299 bp):
CTCAAAAGACTTAATAATGGCCCAAAAGACTTACTAATTTTGGAAATAATTTACTAGGTAAGAAA
CTTTGGAAATCGCATTCTTACTTTTCAAAAATTTCATTTTCTGAAAACATTAAATGAGAAACTTT
GGAAATCGCTTTCTCTTTTTTCGAAAATCATGTGAAAACATCTTGCCCGAAAGTCTTATAGATGG
CCCTAAGGACTTATCAGCTTGCTCAAAAGACTGACAGATAACCCGAAGGATTTAATCATCATGCT
CAAAAGACTAACTGATGGCCCGAAGGACTTATCATCTCA
Found at i:144521 original size:251 final size:251
Alignment explanation
Indices: 143915--144752 Score: 945
Period size: 251 Copynumber: 3.3 Consensus size: 251
143905 GACAGATAAC
* * * * *
143915 CCGAAGGATTTAATCATCAT-GCTC-AAAAGACTTACTGATGGCCCGAAGGACTT-ATCATC-TC
1 CCGAAGGACTT-ATCATC-TCGCTCGAAAA-ACTTACAGATGACCCGAAAGATTTAATCATCAT-
* * * * * * * * *
143976 ACTCAAAAGACTTATTAATGGCCCAAAAGACTTACTAATTTTGGAAATAGTTTACTAGGTAAGAA
62 GCTCGAAAGACTAACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACT-GGTAAGAA
* * * *
144041 ACTTTGGAAATCGCATTCTTACTTTTCAAAAATTTCATTTTCTTAAAAGATTTAAATGAGAAACT
126 ACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATA-CTAAATGAGAAACT
* * * * * *
144106 TTGGAAATCGCTTTCTCATTTTTTGAAAATCATGTGAAAACATCTTGCCCGAAGGTCTTATAGAT
190 TTGGAAA---CTTTCTCA--TTTTCAAATTCATGTGAAAACATCCTACCCAAAGGTCTTATGGAT
144171 GG
250 GG
* * * * *
144173 CCTGAAGGACTTATCAGCTTGCTC-AAAAGACTGACAGATGACCCGAAGGATTTAATCATCATTC
1 CC-GAAGGACTTATCATCTCGCTCGAAAA-ACTTACAGATGACCCGAAAGATTTAATCATCATGC
* *
144237 TTGAAAGACTAACTGATGGCTCGAAGGACTTACCAATTTGGGAAATAGTTTACTGGATAAGAAAC
64 TCGAAAGACTAACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACTGG-TAAGAAAC
* * *
144302 TTTGGAAATCGCTTTCTTACTTTTCCAAATTTTCATTTTCTGAAAATACTAAATGGGAAACTTTG
128 TTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTG
*
144367 G-AA-TTTCTCATTTTCAAATTCATGTGAAAATATCCTACCCAAAGGTCTTATGGATGG
193 GAAACTTTCTCATTTTCAAATTCATGTGAAAACATCCTACCCAAAGGTCTTATGGATGG
* * * * ** *
144424 CTCGAATGACTTATCATCTCACTCGAAAAACTTACAAATGACCTGAATTATTTAATCATCACGCT
1 C-CGAAGGACTTATCATCTCGCTCGAAAAACTTACAGATGACCCGAAAGATTTAATCATCATGCT
* *
144489 CGAAATACTTACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACTGGGTAAGAAACT
65 CGAAAGACTAACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACT-GGTAAGAAACT
**
144554 TTGGAAATCATTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGG
129 TTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGG
* * * *
144619 AAATCGCTTTCTTATTTTCAAATTCATATG-AAACATCCTACCTAAAGGTCTTACGGATGG
194 AAA---CTTTCTCATTTTCAAATTCATGTGAAAACATCCTACCCAAAGGTCTTATGGATGG
* * * *
144679 CCCGAAGGACTTATCATCTCGTTTGAAAGACTTACAGATGACCCGAAAGATTTCATCATCATGCT
1 -CCGAAGGACTTATCATCTCGCTCGAAAAACTTACAGATGACCCGAAAGATTTAATCATCATGCT
*
144744 CGAAGGACT
65 CGAAAGACT
144753 TATCATCTCG
Statistics
Matches: 497, Mismatches: 69, Indels: 31
0.83 0.12 0.05
Matches are distributed among these distances:
251 205 0.41
252 9 0.02
253 7 0.01
255 86 0.17
256 22 0.04
257 3 0.01
258 54 0.11
259 110 0.22
260 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (251 bp):
CCGAAGGACTTATCATCTCGCTCGAAAAACTTACAGATGACCCGAAAGATTTAATCATCATGCTC
GAAAGACTAACTGATGGCCCGAAGGACTTACCAATTTGGGAAATAGTTTACTGGTAAGAAACTTT
GGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTCTGAAAATACTAAATGAGAAACTTTGGAA
ACTTTCTCATTTTCAAATTCATGTGAAAACATCCTACCCAAAGGTCTTATGGATGG
Found at i:162899 original size:2 final size:2
Alignment explanation
Indices: 162885--163013 Score: 79
Period size: 2 Copynumber: 69.0 Consensus size: 2
162875 GGACACATTA
162885 AT AT AT -T AT -T AT AT AGT AT -T AT AT AT AT -T AT AT -T AGT -T
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT
*
162923 AT AT -T AT AT AT AT -T AT AT AT AT AT AT -T AT AT TT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
162961 AT AT A- AT AGT AT AA AT GT AT -T AT AT AT -T AT AT AGT AT AT AGT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T
*
163003 AT -T AT TT AT AT
1 AT AT AT AT AT AT
163014 TCTTTAATGA
Statistics
Matches: 100, Mismatches: 8, Indels: 38
0.68 0.05 0.26
Matches are distributed among these distances:
1 14 0.14
2 77 0.77
3 9 0.09
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (2 bp):
AT
Found at i:162915 original size:9 final size:9
Alignment explanation
Indices: 162885--163014 Score: 85
Period size: 9 Copynumber: 14.0 Consensus size: 9
162875 GGACACATTA
162885 ATATATTATT
1 ATATA-TATT
162895 ATATAGTATT
1 ATATA-TATT
162905 ATATATATT
1 ATATATATT
162914 ATAT-TAGTT
1 ATATATA-TT
162923 ATAT-TA-T
1 ATATATATT
162930 ATATATTATAT
1 ATATA-TAT-T
162941 ATATATATT
1 ATATATATT
162950 ATATTTATATT
1 ATA--TATATT
162961 ATATA-A-T
1 ATATATATT
*
162968 AGTATAAATGT
1 A-TATATAT-T
162979 ATTATATATT
1 A-TATATATT
162989 ATATAGTA-T
1 ATATA-TATT
*
162998 ATA-GTATT
1 ATATATATT
*
163006 ATTTATATT
1 ATATATATT
163015 CTTTAATGAA
Statistics
Matches: 100, Mismatches: 6, Indels: 29
0.74 0.04 0.21
Matches are distributed among these distances:
7 9 0.09
8 10 0.10
9 37 0.37
10 21 0.21
11 23 0.23
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.54
Consensus pattern (9 bp):
ATATATATT
Found at i:162918 original size:5 final size:5
Alignment explanation
Indices: 162891--162964 Score: 79
Period size: 5 Copynumber: 15.6 Consensus size: 5
162881 ATTAATATAT
*
162891 TATTA TA-TA GTATTA TA-TA TATTA TATTA -GTTA TATTA TA-TA TATTA
1 TATTA TATTA -TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
162938 TA-TA TA-TA TATTA TATTTA TATTA TAT
1 TATTA TATTA TATTA TA-TTA TATTA TAT
162965 AATAGTATAA
Statistics
Matches: 60, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
4 21 0.35
5 32 0.53
6 7 0.12
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.57
Consensus pattern (5 bp):
TATTA
Found at i:162932 original size:7 final size:7
Alignment explanation
Indices: 162886--163014 Score: 89
Period size: 7 Copynumber: 19.1 Consensus size: 7
162876 GACACATTAA
162886 TATATTAT
1 TATA-TAT
*
162894 TATATAG
1 TATATAT
162901 TAT-TA-
1 TATATAT
162906 TATATAT
1 TATATAT
162913 TATATTAGT
1 TATA-TA-T
162922 TATAT-T
1 TATATAT
162928 ATATATAT
1 -TATATAT
162936 TATATA-
1 TATATAT
162942 TATATA-
1 TATATAT
162948 T-TATAT
1 TATATAT
162954 T-TATAT
1 TATATAT
*
162960 TATATAA
1 TATATAT
162967 TAGTATA-
1 TA-TATAT
* *
162974 AATGTAT
1 TATATAT
162981 TATATAT
1 TATATAT
*
162988 TATATAG
1 TATATAT
*
162995 TATATAG
1 TATATAT
163002 TAT-TAT
1 TATATAT
163008 T-TATAT
1 TATATAT
163014 T
1 T
163015 CTTTAATGAA
Statistics
Matches: 102, Mismatches: 8, Indels: 24
0.76 0.06 0.18
Matches are distributed among these distances:
5 8 0.08
6 29 0.28
7 48 0.47
8 12 0.12
9 5 0.05
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (7 bp):
TATATAT
Found at i:166561 original size:14 final size:14
Alignment explanation
Indices: 166542--166575 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
166532 GTATAGATCA
166542 GAATGTTTCGATGG
1 GAATGTTTCGATGG
166556 GAATGTTTCGATGG
1 GAATGTTTCGATGG
*
166570 GCATGT
1 GAATGT
166576 GGTAGGACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.09, G:0.35, T:0.35
Consensus pattern (14 bp):
GAATGTTTCGATGG
Found at i:173936 original size:21 final size:20
Alignment explanation
Indices: 173912--173956 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
173902 TAGTTAGATT
*
173912 AAAATATTTTTAAAACGTTTA
1 AAAATATATTTAAAA-GTTTA
*
173933 AAAATGTATTTAAAAGTTTTA
1 AAAATATATTTAAAAG-TTTA
173954 AAA
1 AAA
173957 CATAAAAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.40
Consensus pattern (20 bp):
AAAATATATTTAAAAGTTTA
Found at i:176414 original size:2 final size:2
Alignment explanation
Indices: 176407--176435 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
176397 CTCTTTGTGT
176407 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 T
176436 TCGTTCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:180077 original size:30 final size:30
Alignment explanation
Indices: 180031--180096 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 30
180021 AAATCATTTT
*
180031 GACCA-CCAACGTTTT-AATTTTATCAATCA
1 GACCACCCAACGTTTTAAATGTT-TCAATCA
180060 GACCACCCAAC-TATTTAAATGTTTCAATCA
1 GACCACCCAACGT-TTTAAATGTTTCAATCA
*
180090 AACCACC
1 GACCACC
180097 GACCTTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 6 0.19
30 21 0.66
31 5 0.16
ACGTcount: A:0.36, C:0.29, G:0.06, T:0.29
Consensus pattern (30 bp):
GACCACCCAACGTTTTAAATGTTTCAATCA
Found at i:183629 original size:34 final size:32
Alignment explanation
Indices: 183566--183672 Score: 124
Period size: 32 Copynumber: 3.0 Consensus size: 32
183556 TTTTCTAACT
183566 TACTAACATTCTAACTTTTATTTTATTGTTCA
1 TACTAACATTCTAACTTTTATTTTATTGTTCA
183598 TACTAACATTCTAACTTTTTATTTTTATTGTTCTTA
1 TACTAACATTCTAAC-TTTTA-TTTTATTGTTC--A
183634 CTAACTTACTAGCATTCTAACTTTTATTTTATTGTTCA
1 -T-AC-TA--A-CATTCTAACTTTTATTTTATTGTTCA
183672 T
1 T
183673 TGTTGAGTTA
Statistics
Matches: 65, Mismatches: 0, Indels: 15
0.81 0.00 0.19
Matches are distributed among these distances:
32 15 0.23
33 5 0.08
34 11 0.17
36 1 0.02
37 2 0.03
38 3 0.05
39 2 0.03
40 11 0.17
41 6 0.09
42 9 0.14
ACGTcount: A:0.26, C:0.16, G:0.04, T:0.54
Consensus pattern (32 bp):
TACTAACATTCTAACTTTTATTTTATTGTTCA
Found at i:184478 original size:65 final size:64
Alignment explanation
Indices: 184384--184536 Score: 182
Period size: 65 Copynumber: 2.4 Consensus size: 64
184374 TACACTTGGG
* * * ** *
184384 GTGCATCTGTACACTAATTACATCCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACACAAAATACATTTGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGG-T
184448 T
64 T
* * * * *
184449 GTGCATCGGTACATAAAATGCATTTGATGTTTCAATAAAATCAGGAGTGCGTCGATTCATGGTT
1 GTGCATCGGTACACAAAATACATTTGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGTT
184513 GTGCATCGGTACACAAAATACATT
1 GTGCATCGGTACACAAAATACATT
184537 CGAATTAGGG
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
64 24 0.32
65 48 0.65
66 2 0.03
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (64 bp):
GTGCATCGGTACACAAAATACATTTGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGTT
Found at i:184918 original size:13 final size:13
Alignment explanation
Indices: 184900--184933 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
184890 TAAGATTTTC
*
184900 TTTGAAAATCATT
1 TTTGAAAATCAAT
184913 TTTG-AAATCAAT
1 TTTGAAAATCAAT
184925 TTTGAAAAT
1 TTTGAAAAT
184934 TATTCCCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:186001 original size:44 final size:44
Alignment explanation
Indices: 185938--186040 Score: 145
Period size: 44 Copynumber: 2.3 Consensus size: 44
185928 AAACCCAACG
* *
185938 AGTGTATCGATGCACATTCAA-GACATGCATCGGTGTACCTTCAT
1 AGTGTATCGATGCACATTCAAGGA-ATGCATCGGTATACCTTAAT
* * *
185982 AGTGTATTGATGCATATTCAAGGAATGCATCGGTATACTTTAAT
1 AGTGTATCGATGCACATTCAAGGAATGCATCGGTATACCTTAAT
186026 AGTGTATCGATGCAC
1 AGTGTATCGATGCAC
186041 TATGCACAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
44 49 0.96
45 2 0.04
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (44 bp):
AGTGTATCGATGCACATTCAAGGAATGCATCGGTATACCTTAAT
Found at i:189745 original size:20 final size:21
Alignment explanation
Indices: 189706--189745 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
189696 GAAGCTTTAA
* *
189706 GATCATCAATTTTCTTTTGAT
1 GATCATCAATTTACTCTTGAT
189727 GATCATC-ATTTACTCTTGA
1 GATCATCAATTTACTCTTGA
189746 AAGTAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (21 bp):
GATCATCAATTTACTCTTGAT
Found at i:193730 original size:16 final size:16
Alignment explanation
Indices: 193709--193751 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
193699 AAATATTTAG
193709 TTTAAATTATTTTAAA
1 TTTAAATTATTTTAAA
*
193725 TTTAAATTTATTTTAGA
1 TTTAAA-TTATTTTAAA
193742 TTTAAATTAT
1 TTTAAATTAT
193752 GATGAATGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.40
17 15 0.60
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Done.