Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 29 of 135
Found at i:7603584 original size:2 final size:2
Alignment explanation
Indices: 7603577--7603603 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7603567 GGCTTTAATT
7603577 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 T
7603604 CTAATAAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7604837 original size:51 final size:51
Alignment explanation
Indices: 7604761--7605009 Score: 232
Period size: 51 Copynumber: 4.6 Consensus size: 51
7604751 TTATAAACGA
*
7604761 AAAGGTCCGATGACTAAGAGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
7604812 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATAATGAATAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGT--G------A-G--TAAATGAATCCTTTACGGATT
* * * * **
7604874 AAAGGTTCGATGACTAAATGTCATCGTGAGTAAATGAATCCATGATAGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * * **
7604925 AAAGGTCTGATGACTCAA-TGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACT-AAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
7604977 AAGAGGTCCGATGACTATAG-GTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
7605010 TTAAATGAAA
Statistics
Matches: 165, Mismatches: 17, Indels: 30
0.78 0.08 0.14
Matches are distributed among these distances:
51 75 0.45
52 12 0.07
53 28 0.17
54 1 0.01
59 1 0.01
60 2 0.01
62 46 0.28
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:7604888 original size:62 final size:62
Alignment explanation
Indices: 7604791--7604908 Score: 218
Period size: 62 Copynumber: 1.9 Consensus size: 62
7604781 TCATCGTGAG
*
7604791 TAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATAATGAA
1 TAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAATGTCATCGTGAGTAAATAATGAA
*
7604853 TAAATGAATCCTTTACGGATTAAAGGTTCGATGACTAAATGTCATCGTGAGTAAAT
1 TAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAATGTCATCGTGAGTAAAT
7604909 GAATCCATGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 54 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (62 bp):
TAAATGAATCCTTTACGGATTAAAGGTCCGATGACTAAATGTCATCGTGAGTAAATAATGAA
Found at i:7611199 original size:112 final size:112
Alignment explanation
Indices: 7611002--7611225 Score: 439
Period size: 112 Copynumber: 2.0 Consensus size: 112
7610992 ATATTACACT
*
7611002 GTGAATAGGCATTAAATAATTAAGTATACCAAATGGTAGGGAAAATATAAGGAAATGAGCATGCA
1 GTGAATAGGCATTAAATAATTAAGTATACCAAATGGTAGGGAAAATATAAGGAAATGAGCATACA
7611067 AGTATGAATAATAGATGACTAGAATTGTGATTACTTAGTTGATTAAA
66 AGTATGAATAATAGATGACTAGAATTGTGATTACTTAGTTGATTAAA
7611114 GTGAATAGGCATTAAATAATTAAGTATACCAAATGGTAGGGAAAATATAAGGAAATGAGCATACA
1 GTGAATAGGCATTAAATAATTAAGTATACCAAATGGTAGGGAAAATATAAGGAAATGAGCATACA
7611179 AGTATGAATAATAGATGACTAGAATTGTGATTACTTAGTTGATTAAA
66 AGTATGAATAATAGATGACTAGAATTGTGATTACTTAGTTGATTAAA
7611226 TTCATGAATA
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 111 1.00
ACGTcount: A:0.44, C:0.06, G:0.21, T:0.29
Consensus pattern (112 bp):
GTGAATAGGCATTAAATAATTAAGTATACCAAATGGTAGGGAAAATATAAGGAAATGAGCATACA
AGTATGAATAATAGATGACTAGAATTGTGATTACTTAGTTGATTAAA
Found at i:7625178 original size:59 final size:58
Alignment explanation
Indices: 7625059--7625204 Score: 145
Period size: 59 Copynumber: 2.5 Consensus size: 58
7625049 AAGCGACACG
* * * *
7625059 TTTTCTTGA-TTGGTACTTAAATTTTTTTGATCTAATTTGACATCTGAACTTGACACTT
1 TTTTCTTAATTTGGTACTTAAATTTTTTTGACCCAATTTGACACCTGAACTTGACA-TT
* * *
7625117 TTTTC-TAATTTGGTA-TATAAATTTTTTTTGACCCAATTTGATACCTGAATTTGATATT
1 TTTTCTTAATTTGGTACT-TAAA-TTTTTTTGACCCAATTTGACACCTGAACTTGACATT
** *
7625175 TTTTCTTAATTTATTACTTAAGCTTTTTTT
1 TTTTCTTAATTTGGTACTTAA-ATTTTTTT
7625205 AAGATTCAAT
Statistics
Matches: 72, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
57 3 0.04
58 22 0.31
59 46 0.64
60 1 0.01
ACGTcount: A:0.25, C:0.12, G:0.10, T:0.54
Consensus pattern (58 bp):
TTTTCTTAATTTGGTACTTAAATTTTTTTGACCCAATTTGACACCTGAACTTGACATT
Found at i:7625469 original size:31 final size:29
Alignment explanation
Indices: 7625421--7625552 Score: 101
Period size: 31 Copynumber: 4.5 Consensus size: 29
7625411 CCCCAAAAAA
* *
7625421 TTTAAGTACCAACTTAAAAAAAAGTGTCAAG
1 TTTAGGTACCAAATTAAAAAAAA--GTCAAG
7625452 TTTAGGTACCAAATTAAAAAAAAGTCAAG
1 TTTAGGTACCAAATTAAAAAAAAGTCAAG
* * *
7625481 TTT-GAGTATCAAATTGGATAAAAA---AAG
1 TTTAG-GTACCAAATT-AAAAAAAAGTCAAG
* *
7625508 TTTAAGTACCAAATTTAAAAAAAGTGTCAAG
1 TTTAGGTACCAAA-TTAAAAAAA-AGTCAAG
* *
7625539 TTCAGATACCAAAT
1 TTTAGGTACCAAAT
7625553 ATTATATTAA
Statistics
Matches: 80, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
27 18 0.22
28 3 0.04
29 18 0.22
30 7 0.09
31 34 0.43
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (29 bp):
TTTAGGTACCAAATTAAAAAAAAGTCAAG
Found at i:7625898 original size:30 final size:30
Alignment explanation
Indices: 7625831--7625898 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
7625821 AAAATTTATG
* * *
7625831 TACCAACTTAAAAAAAGTGTCAAGTTTAGG
1 TACCAAATTAAAAAAAATGTCAAGTTTAGC
*
7625861 TATCAAATTAAAAAAAATGTCAAGTTTAGC
1 TACCAAATTAAAAAAAATGTCAAGTTTAGC
*
7625891 TGCCAAAT
1 TACCAAAT
7625899 ATTATATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.28
Consensus pattern (30 bp):
TACCAAATTAAAAAAAATGTCAAGTTTAGC
Found at i:7633898 original size:29 final size:29
Alignment explanation
Indices: 7633849--7634088 Score: 163
Period size: 29 Copynumber: 8.2 Consensus size: 29
7633839 CTTTTAATGG
* *
7633849 TAAAAATGTAATTTCAGGAAAATTTGGGGT
1 TAAAAATGGAATTT-TGGAAAATTTGGGGT
*
7633879 TAAAAATGGAATTTTGGAAAGTTTGCGGG-
1 TAAAAATGGAATTTTGGAAAATTTG-GGGT
* * * * **
7633908 TAAAATTGTAATTTGGGTGAAA-TCAGGGT
1 TAAAAATGGAATTTTGG-AAAATTTGGGGT
* *
7633937 TAAAAATGGAATTTTGG-AAGTTTGGGGG
1 TAAAAATGGAATTTTGGAAAATTTGGGGT
* **
7633965 T-AAAATGGTAATTTTTAGAAGTTTTGGGGT
1 TAAAAATGG-AA-TTTTGGAAAATTTGGGGT
* * *
7633995 CAAAAATGGAATTTTGGAAAGTTTAGGGGG
1 TAAAAATGGAATTTTGGAAAATTT-GGGGT
*
7634025 T-AAAATGGTAATTTTAGGTGAAA-TTGGGGT
1 TAAAAATGG-AATTTT-GG-AAAATTTGGGGT
7634055 TAAAAATGGAATTTT-GAAAAGTTTAGGGG-
1 TAAAAATGGAATTTTGGAAAA-TTT-GGGGT
7634084 TAAAA
1 TAAAA
7634089 CGATAATTTT
Statistics
Matches: 163, Mismatches: 31, Indels: 33
0.72 0.14 0.15
Matches are distributed among these distances:
27 12 0.07
28 11 0.07
29 67 0.41
30 53 0.33
31 18 0.11
32 2 0.01
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (29 bp):
TAAAAATGGAATTTTGGAAAATTTGGGGT
Found at i:7633942 original size:58 final size:58
Alignment explanation
Indices: 7633872--7634097 Score: 273
Period size: 58 Copynumber: 3.9 Consensus size: 58
7633862 TCAGGAAAAT
* *
7633872 TTGGGGTTAAAAATGGAATTTTGGAAAGTTT-GCGGGTAAAATTGTAATTTGGGTGAAA
1 TTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGGTAAAATGGTAATTT-GGTGAAA
** * *
7633930 TCAGGGTTAAAAATGGAATTTTGG-AAGTTT-GGGGGTAAAATGGTAATTT-TTAGAAGTT
1 TTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGGTAAAATGGTAATTTGGT-GAA--A
*
7633988 TTGGGGTCAAAAATGGAATTTTGGAAAGTTTAGGGGGTAAAATGGTAATTTTAGGTGAAA
1 TTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGGTAAAATGGTAA-TTT-GGTGAAA
* * *
7634048 TTGGGGTTAAAAATGGAATTTTGAAAAGTTTA-GGGGTAAAACGATAATTT
1 TTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGGTAAAATGGTAATTT
7634098 TTGGAAGTTT
Statistics
Matches: 145, Mismatches: 15, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
55 1 0.01
56 3 0.02
57 23 0.16
58 46 0.32
59 19 0.13
60 46 0.32
61 3 0.02
62 3 0.02
63 1 0.01
ACGTcount: A:0.35, C:0.02, G:0.30, T:0.34
Consensus pattern (58 bp):
TTGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGGTAAAATGGTAATTTGGTGAAA
Found at i:7634069 original size:30 final size:28
Alignment explanation
Indices: 7633849--7634070 Score: 123
Period size: 30 Copynumber: 7.6 Consensus size: 28
7633839 CTTTTAATGG
* * *
7633849 TAAAAATGTAATTTCAGGAAAATTTGGGGT
1 TAAAAATGGAATTT-TGGGAAA-TTGGGGT
7633879 TAAAAATGGAATTTT-GGAAAGTTTGCGGG-
1 TAAAAATGGAATTTTGGGAAA--TTG-GGGT
* * * **
7633908 TAAAATTGTAATTTGGGTGAAATCAGGGT
1 TAAAAATGGAATTTTGG-GAAATTGGGGT
* *
7633937 TAAAAATGGAATTTT-GGAAGTTTGGGGG
1 TAAAAATGGAATTTTGGGAA-ATTGGGGT
** *
7633965 T-AAAATGGTAATTTTTAGAAGTTTTGGGGT
1 TAAAAATGG-AATTTTGGGAA--ATTGGGGT
* *
7633995 CAAAAATGGAATTTT-GGAAAGTTTAGGGGG
1 TAAAAATGGAATTTTGGGAAA--TT-GGGGT
7634025 T-AAAATGGTAATTTTAGGTGAAATTGGGGT
1 TAAAAATGG-AATTTT-GG-GAAATTGGGGT
7634055 TAAAAATGGAATTTTG
1 TAAAAATGGAATTTTG
7634071 AAAAGTTTAG
Statistics
Matches: 150, Mismatches: 24, Indels: 37
0.71 0.11 0.18
Matches are distributed among these distances:
27 10 0.07
28 19 0.13
29 45 0.30
30 51 0.34
31 20 0.13
32 1 0.01
33 4 0.03
ACGTcount: A:0.35, C:0.02, G:0.29, T:0.34
Consensus pattern (28 bp):
TAAAAATGGAATTTTGGGAAATTGGGGT
Found at i:7634100 original size:30 final size:31
Alignment explanation
Indices: 7634066--7634171 Score: 89
Period size: 29 Copynumber: 3.5 Consensus size: 31
7634056 AAAAATGGAA
7634066 TTTTGAAAAGTTTAGGGGT-AAAACGATAAT
1 TTTTGAAAAGTTTAGGGGTCAAAACGATAAT
* *
7634096 TTTTG-GAAGTTTCA-GGGTCAAAATG-TAAT
1 TTTTGAAAAGTTT-AGGGGTCAAAACGATAAT
* * *
7634125 TTTT-TAAAGTTTTGGGATCACAAAC-ATAAT
1 TTTTGAAAAGTTTAGGGGTCA-AAACGATAAT
* *
7634155 TTCTGAATAGTTTAGGG
1 TTTTGAAAAGTTTAGGG
7634172 ACCTATAAGC
Statistics
Matches: 59, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
29 29 0.49
30 21 0.36
31 9 0.15
ACGTcount: A:0.34, C:0.07, G:0.22, T:0.38
Consensus pattern (31 bp):
TTTTGAAAAGTTTAGGGGTCAAAACGATAAT
Found at i:7635320 original size:15 final size:15
Alignment explanation
Indices: 7635300--7635329 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
7635290 TTAAAACGTC
7635300 TTTAATACTTATTAA
1 TTTAATACTTATTAA
7635315 TTTAATACTTATTAA
1 TTTAATACTTATTAA
7635330 AAACTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATACTTATTAA
Found at i:7635896 original size:14 final size:14
Alignment explanation
Indices: 7635875--7635917 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
7635865 CATTGGGCCT
7635875 ATTTGGGCCATTGTA
1 ATTTGGGCC-TTGTA
7635890 A-TTGGGCCTT-TA
1 ATTTGGGCCTTGTA
7635902 ATTTGGGCCTTTGTA
1 ATTTGGGCC-TTGTA
7635917 A
1 A
7635918 ATGGACTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 3 0.12
13 9 0.36
14 9 0.36
15 4 0.16
ACGTcount: A:0.19, C:0.14, G:0.26, T:0.42
Consensus pattern (14 bp):
ATTTGGGCCTTGTA
Found at i:7636003 original size:17 final size:18
Alignment explanation
Indices: 7635981--7636021 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
7635971 TTTCAAATAT
*
7635981 TTTAAATTTAA-AATGAA
1 TTTAAATTTAATAATAAA
7635998 TTTAAATTTAATAATAAA
1 TTTAAATTTAATAATAAA
7636016 TTTAAA
1 TTTAAA
7636022 CCTAAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
TTTAAATTTAATAATAAA
Found at i:7636793 original size:201 final size:200
Alignment explanation
Indices: 7636365--7636809 Score: 698
Period size: 201 Copynumber: 2.2 Consensus size: 200
7636355 TTCATTGACC
* * *
7636365 TGGTCTTCTTCTCTGTGTCTCATCAGGAAGATGACCG-CAATC-ATCTGTTTTAATTCGCTTCTC
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGTC--TCGCTCTGTTTTAATTCGCTTCTC
* * *
7636428 TGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTGTCTCATTAGGAAGCTAACTTTTTA
64 TGGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACATTTTA
* *
7636493 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGCGTTGAGC
129 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGCGTTGAGC
7636558 GTTGAGT
194 GTTGAGT
*
7636565 TGGTATTCTTCTCTGTATCCCATCAGGAAGATGACCGTCTCGCT-TGTTTTTAATTCGCTTCTCT
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGTCTCGCTCTG-TTTTAATTCGCTTCTCT
7636629 GGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTA
65 GGATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAA-CATTTTA
* * * *
7636694 TTGTTTCGATCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGTGTTGAGC
129 TTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGCGTTGAGC
7636759 GTTGAGT
194 GTTGAGT
* *
7636766 TGGTATTCTTCTCTGTATCTTATCAGGAAGATGACTGTCTCGCT
1 TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGTCTCGCT
7636810 GTCTTGTTGA
Statistics
Matches: 225, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
199 4 0.02
200 107 0.48
201 114 0.51
ACGTcount: A:0.19, C:0.22, G:0.22, T:0.36
Consensus pattern (200 bp):
TGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGTCTCGCTCTGTTTTAATTCGCTTCTCTG
GATCTCCTCAGGAAGACGAATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACATTTTATT
GCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTACGAAGATTGGCTCGCGTTGAGCGT
TGAGT
Found at i:7644329 original size:29 final size:29
Alignment explanation
Indices: 7644292--7644386 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 29
7644282 AAAATCTAAT
7644292 TTTTGGAAAAATCAGGGTTAAAAATGGAA
1 TTTTGGAAAAATCAGGGTTAAAAATGGAA
* ** * *
7644321 TTTTAGAAAGTTTAGGGGT-AAAATGGTAA
1 TTTTGGAAAAATCAGGGTTAAAAATGG-AA
** * *
7644350 TTTTGGGTATATCGGGGTTAAAAATGGAA
1 TTTTGGAAAAATCAGGGTTAAAAATGGAA
7644379 TTTTGGAA
1 TTTTGGAA
7644387 GTTTAGGGGT
Statistics
Matches: 49, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
28 7 0.14
29 35 0.71
30 7 0.14
ACGTcount: A:0.37, C:0.02, G:0.27, T:0.34
Consensus pattern (29 bp):
TTTTGGAAAAATCAGGGTTAAAAATGGAA
Found at i:7644354 original size:58 final size:57
Alignment explanation
Indices: 7644292--7644708 Score: 428
Period size: 58 Copynumber: 7.1 Consensus size: 57
7644282 AAAATCTAAT
7644292 TTTTGGAAAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAA
1 TTTTGGAAAAATC-GGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAA
** * * *
7644350 TTTTGGGTATATCGGGGTTAAAAATGGAATTTT-GGAAGTTTAGGGGTAAAACGGTAA
1 TTTTGGAAAAATC-GGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAA
* *** * * * *
7644407 TTTTTAGAAGTTTTGGAGTTAAAAATGAAATTTT-GGAAGTTTAGGGGTAAAACGGTAA
1 -TTTTGGAAAAATCGG-GTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAA
** *
7644465 TTTTGGGTGAAATCGAGGTT-AAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAA
1 TTTT-GGAAAAATCG-GGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAA
** * *
7644523 TTTTGAGTGAAATCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAACGGTAA
1 TTTTG-GAAAAATCG-GGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAA
*** * *
7644582 TTTTTGGAAGTTTTGGAGTTAAAAATGGAATTTTGGAAAGTTT-GAGGGTAAAATGGTAA
1 -TTTTGGAAAAATCGG-GTTAAAAATGGAATTTTAGAAAGTTTAG-GGGTAAAATGGTAA
** *
7644641 TTTTGGGTGAAATCGAGGTTAAAAATGGAATTTTAAAAAGTTTAGGGGTAAAATGGTAA
1 TTTT-GGAAAAATCG-GGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAA
7644700 TTTTTGGAA
1 -TTTTGGAA
7644709 GTTTCAGGGT
Statistics
Matches: 301, Mismatches: 44, Indels: 27
0.81 0.12 0.07
Matches are distributed among these distances:
57 41 0.14
58 127 0.42
59 122 0.41
60 11 0.04
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (57 bp):
TTTTGGAAAAATCGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAA
Found at i:7644395 original size:29 final size:29
Alignment explanation
Indices: 7644306--7644741 Score: 221
Period size: 29 Copynumber: 14.9 Consensus size: 29
7644296 GGAAAAATCA
*
7644306 GGGTTAAAAATGG-AATTTTAGAAAGTTTAG
1 GGGTT-AAAATGGTAATTTT-GGAAGTTTAG
*
7644336 GGG-TAAAATGGTAATTTTGG--GTATATCG
1 GGGTTAAAATGGTAATTTTGGAAGT-T-TAG
7644364 GGGTTAAAAATGG-AATTTTGGAAGTTTAG
1 GGGTT-AAAATGGTAATTTTGGAAGTTTAG
* * *
7644393 GGG-TAAAACGGTAATTTTTAGAAGTTTTG
1 GGGTTAAAATGGTAA-TTTTGGAAGTTTAG
* *
7644422 GAGTTAAAAAT-GAAATTTTGGAAGTTTAG
1 GGGTT-AAAATGGTAATTTTGGAAGTTTAG
* ** ** *
7644451 GGG-TAAAACGGTAATTTTGGGTGAAATCG
1 GGGTTAAAATGGTAATTTTGGAAG-TTTAG
* *
7644480 AGGTTAAAATGG-AATTTTAGAAAGTTT-G
1 GGGTTAAAATGGTAATTTT-GGAAGTTTAG
* * *
7644508 GGGGTAAAATGGTAATTTT-G-AGTGAAATCG
1 GGGTTAAAATGGTAATTTTGGAAGT---TTAG
*
7644538 AGGTTAAAAATGG-AATTTTGGAAAGTTTAG
1 GGGTT-AAAATGGTAATTTTGG-AAGTTTAG
* *
7644568 GGG-TAAAACGGTAATTTTTGGAAGTTTTG
1 GGGTTAAAATGGTAA-TTTTGGAAGTTTAG
*
7644597 GAGTTAAAAATGG-AATTTTGGAAAGTTT-G
1 GGGTT-AAAATGGTAATTTTGG-AAGTTTAG
** ** *
7644626 AGGG-TAAAATGGTAATTTTGGGTGAAATCG
1 -GGGTTAAAATGGTAATTTTGGAAG-TTTAG
* **
7644656 AGGTTAAAAATGG-AATTTTAAAAAGTTTAG
1 GGGTT-AAAATGGTAATTTT-GGAAGTTTAG
7644686 GGG-TAAAATGGTAATTTTTGGAAGTTTCA-
1 GGGTTAAAATGGTAA-TTTTGGAAGTTT-AG
* *
7644715 GGGTCAAAAT-GTAATTTTTTGAAGTTT
1 GGGTTAAAATGGTAA-TTTTGGAAGTTT
7644742 TGGGATCACA
Statistics
Matches: 309, Mismatches: 57, Indels: 81
0.69 0.13 0.18
Matches are distributed among these distances:
26 5 0.02
27 11 0.04
28 59 0.19
29 126 0.41
30 77 0.25
31 28 0.09
33 3 0.01
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (29 bp):
GGGTTAAAATGGTAATTTTGGAAGTTTAG
Found at i:7644574 original size:59 final size:59
Alignment explanation
Indices: 7644307--7644703 Score: 493
Period size: 59 Copynumber: 6.8 Consensus size: 59
7644297 GAAAAATCAG
* * *
7644307 GGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATGGTAATTTTGGGT-ATATCGG
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATCGA
* * ** *** *
7644365 GGTTAAAAATGGAATTTTGG-AAGTTTAGGGGTAAAACGGTAATTTTTAGAAGTTTTGGA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAA-TTTTGGGTGAAATCGA
* *
7644424 -GTTAAAAATGAAATTTTGG-AAGTTTAGGGGTAAAACGGTAATTTTGGGTGAAATCGA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATCGA
* * *
7644481 GGTT-AAAATGGAATTTTAGAAAGTTTGGGGGTAAAATGGTAATTTTGAGTGAAATCGA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATCGA
* ** *** *
7644539 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAACGGTAATTTTTGGAAGTTTTGGA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAA-TTTTGGGTGAAATCGA
7644599 -GTTAAAAATGGAATTTTGGAAAGTTT-GAGGGTAAAATGGTAATTTTGGGTGAAATCGA
1 GGTTAAAAATGGAATTTTGGAAAGTTTAG-GGGTAAAATGGTAATTTTGGGTGAAATCGA
**
7644657 GGTTAAAAATGGAATTTTAAAAAGTTTAGGGGTAAAATGGTAATTTT
1 GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTT
7644704 TGGAAGTTTC
Statistics
Matches: 289, Mismatches: 41, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
57 43 0.15
58 117 0.40
59 119 0.41
60 10 0.03
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (59 bp):
GGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTGGGTGAAATCGA
Found at i:7646562 original size:16 final size:17
Alignment explanation
Indices: 7646554--7646601 Score: 69
Period size: 18 Copynumber: 2.8 Consensus size: 17
7646544 TTTCAAATAT
7646554 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATGAA
*
7646571 TTTAAATTTAATAATAAA
1 TTTAAATTTAA-AATGAA
*
7646589 TTTAAACTTAAAA
1 TTTAAATTTAAAA
7646602 AATCCAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATGAA
Found at i:7646576 original size:17 final size:17
Alignment explanation
Indices: 7646516--7646601 Score: 75
Period size: 17 Copynumber: 4.8 Consensus size: 17
7646506 AGACTTTTTT
* *
7646516 ATTTAAATTTTAATTAA
1 ATTTAAATTTAAAATAA
7646533 ATTTAAATTTATTTCAAAT-A
1 ATTTAAATTTA----AAATAA
* *
7646553 TTTTAAATTTAAAATGA
1 ATTTAAATTTAAAATAA
7646570 ATTTAAATTTAATAATAA
1 ATTTAAATTTAA-AATAA
*
7646588 ATTTAAACTTAAAA
1 ATTTAAATTTAAAA
7646602 AATCCAATCA
Statistics
Matches: 57, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
16 4 0.07
17 24 0.42
18 15 0.26
20 11 0.19
21 3 0.05
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:7656298 original size:22 final size:22
Alignment explanation
Indices: 7656256--7656299 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
7656246 TTAAAAAATG
* *
7656256 TTAATATATATAGTACTTTAGA
1 TTAATATATATAGGACATTAGA
7656278 TTAATAT-TATAGAGACATTAGA
1 TTAATATATATAG-GACATTAGA
7656300 ACGGTTCGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (22 bp):
TTAATATATATAGGACATTAGA
Found at i:7658692 original size:16 final size:16
Alignment explanation
Indices: 7658671--7658715 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
7658661 AATGGAATGA
7658671 AAATAAATTTTTAATT
1 AAATAAATTTTTAATT
7658687 AAATAAA--TTTAATT
1 AAATAAATTTTTAATT
*
7658701 AATTAAAATTTTTAA
1 AAAT-AAATTTTTAA
7658716 ACCCTAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 7 0.28
17 5 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAAATTTTTAATT
Found at i:7659219 original size:12 final size:12
Alignment explanation
Indices: 7659202--7659228 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
7659192 ATAAAATATG
7659202 TTTTGGTATTAA
1 TTTTGGTATTAA
7659214 TTTTGGTATTAA
1 TTTTGGTATTAA
7659226 TTT
1 TTT
7659229 GCTTTTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.00, G:0.15, T:0.63
Consensus pattern (12 bp):
TTTTGGTATTAA
Found at i:7660026 original size:3 final size:3
Alignment explanation
Indices: 7660018--7660064 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
7660008 TATACAAGTT
* *
7660018 ATA ATA ATA ATA ATA ATA GTA GTA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7660065 CATCCTCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:7660190 original size:28 final size:29
Alignment explanation
Indices: 7660128--7660191 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
7660118 TATGCAAAAG
* *
7660128 AGTTTTTTTTCATAATTTTTGGAATTATA
1 AGTTTTATTTCATAATTTTTGAAATTATA
*
7660157 AGTTTTATTT-ATAATTTTTTGAAATTCTA
1 AGTTTTATTTCATAA-TTTTTGAAATTATA
7660186 A-TTTTA
1 AGTTTTA
7660192 ACATTTGTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.30, C:0.03, G:0.08, T:0.59
Consensus pattern (29 bp):
AGTTTTATTTCATAATTTTTGAAATTATA
Found at i:7664168 original size:32 final size:34
Alignment explanation
Indices: 7664114--7664192 Score: 81
Period size: 32 Copynumber: 2.3 Consensus size: 34
7664104 TAACTATATC
7664114 TTTATAATTTTTAAAGGATTAAA-T-TAATTTTT
1 TTTATAATTTTTAAAGGATTAAAGTGTAATTTTT
* ** *
7664146 TTTATCATTTTTAGGGGGTTAAAGTGTAATTTTAT
1 TTTATAATTTTTAAAGGATTAAAGTGTAATTTT-T
7664181 CTTTATTAATTT
1 -TTTA-TAATTT
7664193 AAAATTTTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
32 19 0.51
33 1 0.03
34 7 0.19
35 1 0.03
36 4 0.11
37 5 0.14
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (34 bp):
TTTATAATTTTTAAAGGATTAAAGTGTAATTTTT
Found at i:7669148 original size:34 final size:34
Alignment explanation
Indices: 7669067--7669148 Score: 114
Period size: 33 Copynumber: 2.4 Consensus size: 34
7669057 TGTTTCTATG
* *
7669067 TTTAAATCGATTGTCATGTTGAAATATTGATTCT
1 TTTAAATCGATTGTTATGTTGAAATACTGATTCT
*
7669101 TTT-AATCGATTGTTATGTT-AGAATACTGCTTCT
1 TTTAAATCGATTGTTATGTTGA-AATACTGATTCT
7669134 TTTAAATCGATTGTT
1 TTTAAATCGATTGTT
7669149 TATATATCCC
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 1 0.02
33 28 0.65
34 14 0.33
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.49
Consensus pattern (34 bp):
TTTAAATCGATTGTTATGTTGAAATACTGATTCT
Found at i:7670880 original size:12 final size:12
Alignment explanation
Indices: 7670863--7670984 Score: 113
Period size: 12 Copynumber: 10.2 Consensus size: 12
7670853 ATAACATCCA
* *
7670863 AACAACCAAAAT
1 AACAACAAAAAC
*
7670875 AACAACCAAAAC
1 AACAACAAAAAC
* * *
7670887 ATCAATAAAAAT
1 AACAACAAAAAC
7670899 AA-AAGCAAAAAC
1 AACAA-CAAAAAC
*
7670911 AATAACAACAAA-
1 AACAACAA-AAAC
7670923 AACAACAAAAAC
1 AACAACAAAAAC
*
7670935 AACAACAAAAAT
1 AACAACAAAAAC
* *
7670947 AACAGCAAAAAT
1 AACAACAAAAAC
*
7670959 AGCAACAAAAAC
1 AACAACAAAAAC
7670971 AACAACAAAAAC
1 AACAACAAAAAC
7670983 AA
1 AA
7670985 TAGCATCAAA
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
11 5 0.05
12 81 0.89
13 5 0.05
ACGTcount: A:0.71, C:0.20, G:0.02, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:7670917 original size:6 final size:6
Alignment explanation
Indices: 7670908--7670984 Score: 55
Period size: 6 Copynumber: 12.8 Consensus size: 6
7670898 TAAAAGCAAA
* * * * * * *
7670908 AACAAT AACAAC AAAAAC AACAAA AACAAC AACAAA AATAAC AGCAAA
1 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC
* * * *
7670956 AATAGC AACAAA AACAAC AACAAA AACAA
1 AACAAC AACAAC AACAAC AACAAC AACAA
7670985 TAGCATCAAA
Statistics
Matches: 51, Mismatches: 20, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.73, C:0.21, G:0.03, T:0.04
Consensus pattern (6 bp):
AACAAC
Found at i:7670923 original size:21 final size:22
Alignment explanation
Indices: 7670889--7670984 Score: 81
Period size: 21 Copynumber: 4.4 Consensus size: 22
7670879 ACCAAAACAT
* * *
7670889 CAATAAAAATAAAAGCAA-AAA
1 CAATAACAACAAAAACAACAAA
7670910 CAATAACAACAAAAACAACAAA
1 CAATAACAACAAAAACAACAAA
* *
7670932 -AACAACAACAAAAATAACAGCAA
1 CAATAACAACAAAAACAACA--AA
* *
7670955 AAATAGCAACAAAAACAAC-AA
1 CAATAACAACAAAAACAACAAA
*
7670976 CAAAAACAA
1 CAATAACAA
7670985 TAGCATCAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
21 40 0.67
22 3 0.05
23 2 0.03
24 15 0.25
ACGTcount: A:0.73, C:0.19, G:0.03, T:0.05
Consensus pattern (22 bp):
CAATAACAACAAAAACAACAAA
Found at i:7670926 original size:9 final size:9
Alignment explanation
Indices: 7670908--7670984 Score: 61
Period size: 9 Copynumber: 8.6 Consensus size: 9
7670898 TAAAAGCAAA
*
7670908 AACAATAAC
1 AACAAAAAC
7670917 AACAAAAAC
1 AACAAAAAC
7670926 AACAAAAAC
1 AACAAAAAC
7670935 AACAACAAA-
1 AACAA-AAAC
* * *
7670944 AATAACAGC
1 AACAAAAAC
*
7670953 AA-AAATAGC
1 AACAAA-AAC
7670962 AACAAAAAC
1 AACAAAAAC
7670971 AACAACAAA-
1 AACAA-AAAC
7670980 AACAA
1 AACAA
7670985 TAGCATCAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
8 3 0.05
9 45 0.79
10 9 0.16
ACGTcount: A:0.73, C:0.21, G:0.03, T:0.04
Consensus pattern (9 bp):
AACAAAAAC
Found at i:7670934 original size:48 final size:48
Alignment explanation
Indices: 7670863--7670984 Score: 147
Period size: 48 Copynumber: 2.5 Consensus size: 48
7670853 ATAACATCCA
* * * * *
7670863 AACAACCAAAATAACAACCAAAACATCAATAAAAATAAAAGCAAAAAC
1 AACAACAAAAACAACAACAAAAACAACAACAAAAATAAAAGCAAAAAC
* * *
7670911 AATAACAACAAA-AACAACAAAAACAACAACAAAAATAACAGCAAAAAT
1 AACAACAA-AAACAACAACAAAAACAACAACAAAAATAAAAGCAAAAAC
*
7670959 AGCAACAAAAACAACAACAAAAACAA
1 AACAACAAAAACAACAACAAAAACAA
7670985 TAGCATCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
47 3 0.05
48 57 0.90
49 3 0.05
ACGTcount: A:0.71, C:0.20, G:0.02, T:0.06
Consensus pattern (48 bp):
AACAACAAAAACAACAACAAAAACAACAACAAAAATAAAAGCAAAAAC
Found at i:7686651 original size:22 final size:22
Alignment explanation
Indices: 7686624--7686669 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
7686614 AATTTAAAAT
7686624 ATTATATAAAT-TTAATTATAAA
1 ATTATATAAATATTAA-TATAAA
**
7686646 ATTATATTGATATTAATATAAA
1 ATTATATAAATATTAATATAAA
7686668 AT
1 AT
7686670 AATACATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (22 bp):
ATTATATAAATATTAATATAAA
Found at i:7687779 original size:27 final size:28
Alignment explanation
Indices: 7687749--7687804 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
7687739 TTTTCGTTTA
*
7687749 ATTTAGAGTTAAATTGA-TTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTTAAATTT
* *
7687776 ATTTAAATTTAAATTTATTTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTTAAATTT
7687804 A
1 A
7687805 AATTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
ATTTAAAGTTAAATTGATTTTTAAATTT
Found at i:7687785 original size:6 final size:6
Alignment explanation
Indices: 7687767--7687867 Score: 82
Period size: 6 Copynumber: 16.8 Consensus size: 6
7687757 TTAAATTGAT
**
7687767 TTTAAA TTT--A TTTAAA TTTAAA TTTATT TTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A
* * ** * *
7687815 TTTAAA TTT-AT TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
7687863 TTTAA
1 TTTAA
7687868 CATTAAAAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
4 4 0.05
5 4 0.05
6 59 0.77
7 4 0.05
8 6 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:7687851 original size:49 final size:49
Alignment explanation
Indices: 7687767--7687861 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
7687757 TTAAATTGAT
** ** *
7687767 TTTAAATTTATTTAAATTTAAATTTATTTTTAAATTTAAAT-TTAATTA
1 TTTAAATTTATTTAAATTTAAATTTAAATAAAAATTAAAATATTAATTA
*
7687815 TTTAAATTTATTTTGAATTTAAATTTAAATAAAAATTAAAATATTAA
1 TTTAAATTTA-TTTAAATTTAAATTTAAATAAAAATTAAAATATTAA
7687862 GTTTAACATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 10 0.26
49 25 0.64
50 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (49 bp):
TTTAAATTTATTTAAATTTAAATTTAAATAAAAATTAAAATATTAATTA
Found at i:7689564 original size:30 final size:30
Alignment explanation
Indices: 7689526--7689910 Score: 474
Period size: 30 Copynumber: 12.9 Consensus size: 30
7689516 CCAAATTGGA
* *
7689526 CCAAAATTATATTTTGTCCCCAAAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
* * * *
7689556 CTACAATTACATTTTGACCCCAAAAATATT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
* *
7689586 CCTAAATTACATTTTGACCCCTAAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
*
7689616 CCAAAATTACATTTTAACCCCAAAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
* * *
7689646 CCAAAATTATATTTTGA-CTCGAAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
7689675 CCAAAATTACATTTTGACCCCAAAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
*
7689705 CCAAAATTACATTTTAACCCCAAAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
* * ** *
7689735 CCAAAATTATATTTTAACCTTAAAACTTTA
1 CCAAAATTACATTTTGACCCCAAAACTTTT
* * *
7689765 CCAAAATTACAATTTGACCTC-GAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
**
7689794 CCAAAATTACATTTCAACCCCAAAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
* *
7689824 CCATAATTACATTTTGACCCCGAAACTTTT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
*
7689854 CCAAAATTACATTTTGACCCCGAAAC--TT
1 CCAAAATTACATTTTGACCCCAAAACTTTT
*
7689882 CCAAAAATTACCATTTT-ACCCCCAAACTT
1 CC-AAAATTA-CATTTTGACCCCAAAACTT
7689911 CTCTAAATCC
Statistics
Matches: 305, Mismatches: 44, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
28 4 0.01
29 65 0.21
30 236 0.77
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
CCAAAATTACATTTTGACCCCAAAACTTTT
Found at i:7689683 original size:119 final size:118
Alignment explanation
Indices: 7689525--7689881 Score: 482
Period size: 119 Copynumber: 3.0 Consensus size: 118
7689515 ACCAAATTGG
* * * * * * *
7689525 ACCAAAATTATATTTTGTCCCCAAAACTTTTCTACAATTACATTTTGACCCCAAAAATATTCCTA
1 ACCAAAATTATATTTTG-ACTCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC-A
*
7689590 AATTACATTTTGACCCCTAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
64 AATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
*
7689645 TCCAAAATTATATTTTGACTCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAA
1 ACCAAAATTATATTTTGACTCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCC-AA
* * **
7689710 ATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTAACCTTAAAACTTT
65 ATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
* * **
7689764 ACCAAAATTACAATTTGACCTCG-AACTTTTCCAAAATTACATTTCAACCCCAAAACTTTTCCAT
1 ACCAAAATTATATTTTGA-CTCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCA-
* * *
7689828 AATTACATTTTGACCCCGAAACTTTTCCAAAATTACATTTTGACCCCGAAACTT
64 AATTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTT
7689882 CCAAAAATTA
Statistics
Matches: 209, Mismatches: 26, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
118 1 0.00
119 188 0.90
120 20 0.10
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (118 bp):
ACCAAAATTATATTTTGACTCGAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAA
TTACATTTTGACCCCAAAACTTTTCCAAAATTACATTTTAACCCCAAAACTTT
Found at i:7689714 original size:89 final size:89
Alignment explanation
Indices: 7689526--7689907 Score: 491
Period size: 89 Copynumber: 4.3 Consensus size: 89
7689516 CCAAATTGGA
* ** * * * * *
7689526 CCAAAATTATATTTTGTCCCCAAAACTTTTCTACAATTACATTTTGACCCCAAAAATATTCCTAA
1 CCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAA
7689591 ATTACATTTTGACCCCTAAACTTTT
66 ATTACATTTTGACCCC-AAACTTTT
* * *
7689616 CCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTGA-CTCGAAACTTTTCCAAA
1 CCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAA
7689680 ATTACATTTTGACCCCAAAACTTTT
66 ATTACATTTTGACCCC-AAACTTTT
* * ** *
7689705 CCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTATATTTTAACCTTAAAACTTTACCAAA
1 CCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAA
* * *
7689770 ATTACAATTTGACCTCGAACTTTT
66 ATTACATTTTGACCCCAAACTTTT
* * *
7689794 CCAAAATTACATTTCAACCCCAAAACTTTTCCATAATTACATTTTGACCCCGAAACTTTTCCAAA
1 CCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAA
7689859 ATTACATTTTGACCCCGAAAC--TT
66 ATTACATTTTGACCCC-AAACTTTT
*
7689882 CCAAAAATTACCATTTTACCCCCAAA
1 CC-AAAATTA-CATTTTAACCCCAAA
7689908 CTTCTCTAAA
Statistics
Matches: 256, Mismatches: 32, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
88 4 0.02
89 167 0.65
90 85 0.33
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (89 bp):
CCAAAATTACATTTTAACCCCAAAACTTTTCCAAAATTACATTTTGACCCCAAAACTTTTCCAAA
ATTACATTTTGACCCCAAACTTTT
Found at i:7689945 original size:59 final size:58
Alignment explanation
Indices: 7689882--7690078 Score: 171
Period size: 59 Copynumber: 3.4 Consensus size: 58
7689872 CCCGAAACTT
* ** *
7689882 CCAAAAATTACCATTTTACCCCCAAACTTCTCTAAATCCCAATTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTT-TCAAAATTTCATTTTTAACCCCGATTTCA
* * * * * * * ** * **
7689941 CCAAAACTTATCGTTTTGCCTCCGAACTTTCCAAAATTTCATTTTTGACCTTGTTTTTG
1 CCAAAAATTACCATTTTACCCCCAAACTTT-CAAAATTTCATTTTTAACCCCGATTTCA
* * * * *
7690000 CCAGAATTTACCATTTTATTCCCCAAACTTTCCAAATTTCATTTTTAGCCCCGATTTCA
1 CCAAAAATTACCATTTTA-CCCCCAAACTTTCAAAATTTCATTTTTAACCCCGATTTCA
7690059 -CAAAAATTACCATTTTACCC
1 CCAAAAATTACCATTTTACCC
7690079 TAAAAGCCCA
Statistics
Matches: 101, Mismatches: 35, Indels: 6
0.71 0.25 0.04
Matches are distributed among these distances:
57 2 0.02
58 16 0.16
59 74 0.73
60 9 0.09
ACGTcount: A:0.29, C:0.29, G:0.05, T:0.37
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCAAAATTTCATTTTTAACCCCGATTTCA
Found at i:7701913 original size:31 final size:31
Alignment explanation
Indices: 7701878--7702337 Score: 166
Period size: 31 Copynumber: 13.4 Consensus size: 31
7701868 TCTTTATCTC
*
7701878 TGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 TGAAATTGAAGTAAGAGCAACGTCATCCTCT
** * **
7701909 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCTCT
* *
7701945 CTGAAATTGAAGTAAGAACAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCTCT
** * **
7701977 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCTCT
7702013 CTGAAATTGAAGTAAGAGCAACGTCATCCTCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCTCT
* * * *
7702045 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCT
1 TGAAATTGAAGTA-AG--AG-CAAC--GTCATCCTCT
*
7702082 CTGAAATTG-AGTAAGAGTAACATCGTTTCCTATCCTCT
1 -TGAAATTGAAGTAAGAG---CAACG--T-C-ATCCTCT
* * * **
7702120 TGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCT
1 TGAAATTGAAGTAAGA--GCA-A-C--GTCATCCTCT
*
7702157 CTGAAATTGAAGTAAGAGCAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCTCT
* * * * * **
7702189 TGAAATTGAAATAGAGTGGGTAACACTTCTTTATCT
1 TGAAATTGAAGTA-A--GAG-CA-ACGTCATCCTCT
* *
7702225 CTGAAATTGAAGTAAGAACAACGTCATCCCCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCTCT
** * **
7702257 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCT
1 TGAAATTGAAGTA-A---GAGCA-ACGTCATCCTCT
7702293 CTGAAATTGAAGTAAGAGCAACGTCATCCTCT
1 -TGAAATTGAAGTAAGAGCAACGTCATCCTCT
7702325 TGAAATTGAAGTA
1 TGAAATTGAAGTA
7702338 GAGTTGGATA
Statistics
Matches: 312, Mismatches: 72, Indels: 90
0.66 0.15 0.19
Matches are distributed among these distances:
31 77 0.25
32 45 0.14
33 10 0.03
34 7 0.02
35 14 0.04
36 43 0.14
37 77 0.25
38 35 0.11
39 2 0.01
40 1 0.00
41 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (31 bp):
TGAAATTGAAGTAAGAGCAACGTCATCCTCT
Found at i:7701948 original size:68 final size:68
Alignment explanation
Indices: 7701834--7702458 Score: 865
Period size: 68 Copynumber: 8.9 Consensus size: 68
7701824 ATCATTTCCA
*
7701834 ATCCGCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
7701899 GTC
66 GTC
*
7701902 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAACAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
7701967 GTC
66 GTC
7701970 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
7702035 GTC
66 GTC
* * *
7702038 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTG-AGTAAGAGTAA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG---
*
7702102 CATCGTTTCC
62 CAACG--T-C
* * * * *
7702112 TATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 -ATCCCCTTGAAATTGAAGT-AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
7702177 ACGTC
64 ACGTC
* * * *
7702182 ATCCCCTTGAAATTGAAATAGAGTGGGTAACACTTCTTTATCTCTGAAATTGAAGTAAGAACAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
7702247 GTC
66 GTC
7702250 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
1 ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
7702315 GTC
66 GTC
* * *
7702318 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGTAA
1 ATCCCCTTGAAATTGAAGTAGAG-TGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAG---
*
7702383 CATCGTTTCC
62 CAACG--T-C
* * * * *
7702393 TATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCA
1 -ATCCCCTTGAAATTGAAGT-AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCA
7702458 A
64 A
7702459 GATCATTTCC
Statistics
Matches: 504, Mismatches: 34, Indels: 33
0.88 0.06 0.06
Matches are distributed among these distances:
68 291 0.58
69 80 0.16
70 1 0.00
71 5 0.01
72 4 0.01
73 7 0.01
74 2 0.00
75 47 0.09
76 65 0.13
77 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (68 bp):
ATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAAGAGCAAC
GTC
Found at i:7702089 original size:38 final size:35
Alignment explanation
Indices: 7701841--7702453 Score: 289
Period size: 37 Copynumber: 17.4 Consensus size: 35
7701831 CCAATCCGCT
* *
7701841 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTA-AGTGG-TAACAAGTCTTCATCTC
* * * **
7701878 TGAAATTGAAGTAAG-AGCAAC--GTCATCCCCT-
1 TGAAATTGAAGTAAGTGGTAACAAGTCTTCATCTC
* *
7701909 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTA-AGTGG-TAACAAGTCTTCATCTC
* **
7701946 TGAAATTGAAGTAA---G-AACAACGTCATCCCCT-
1 TGAAATTGAAGTAAGTGGTAACAA-GTCTTCATCTC
* *
7701977 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTA-AGTGG-TAACAAGTCTTCATCTC
* * * *
7702014 TGAAATTGAAGTAAG-AGCAAC--GTCATCCTCT-
1 TGAAATTGAAGTAAGTGGTAACAAGTCTTCATCTC
7702045 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
1 TGAAATTGAAGTA-AG-TGG-TAACAAGTCTTCATCTC
* *
7702083 TGAAATTG-AGTAAG-AGTAACATCGT-TTCCTATCCTC
1 TGAAATTGAAGTAAGTGGTAACA-AGTCTT-C-AT-CTC
* * *
7702119 TTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGT--AAGTGG-TAACAAGTCTTCATCTC
* * * **
7702158 TGAAATTGAAGTAAG-AGCAAC--GTCATCCCCT-
1 TGAAATTGAAGTAAGTGGTAACAAGTCTTCATCTC
* ** *
7702189 TGAAATTGAAATAGAGTGGGTAACACTTCTTTATCTC
1 TGAAATTGAAGTA-AGT-GGTAACAAGTCTTCATCTC
* **
7702226 TGAAATTGAAGTAA---G-AACAACGTCATCCCCT-
1 TGAAATTGAAGTAAGTGGTAACAA-GTCTTCATCTC
* *
7702257 TGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTC
1 TGAAATTGAAGTA-AGTGG-TAACAAGTCTTCATCTC
* * * *
7702294 TGAAATTGAAGTAAG-AGCAAC--GTCATCCTCT-
1 TGAAATTGAAGTAAGTGGTAACAAGTCTTCATCTC
7702325 TGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTC
1 TGAAATTGAAGTA-AG-TGG-TAACAAGTCTTCATCTC
* *
7702363 TGAAATTGAAGTAAG-AGTAACATCGT-TTCCTATCCTC
1 TGAAATTGAAGTAAGTGGTAACA-AGTCTT-C-AT-CTC
* * *
7702400 TTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTC
1 -TGAAATTGAAGT--AAGTGG-TAACAAGTCTTCATCTC
7702439 TGAAATTGAAGTAAG
1 TGAAATTGAAGTAAG
7702454 AGCAAGATCA
Statistics
Matches: 430, Mismatches: 83, Indels: 127
0.67 0.13 0.20
Matches are distributed among these distances:
31 85 0.20
32 48 0.11
33 9 0.02
34 31 0.07
35 18 0.04
36 42 0.10
37 105 0.24
38 60 0.14
39 6 0.01
40 8 0.02
41 6 0.01
42 12 0.03
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (35 bp):
TGAAATTGAAGTAAGTGGTAACAAGTCTTCATCTC
Found at i:7702368 original size:280 final size:281
Alignment explanation
Indices: 7701828--7702458 Score: 1167
Period size: 280 Copynumber: 2.3 Consensus size: 281
7701818 AAAAAGATCA
* * * * * *
7701828 TTTCCAATCCGCTTGAAATTGAAGT-AGAGTGGATAACACGTCTTTATCTCTGAAATTGAAGTAA
1 TTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
*
7701892 GAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAG
66 GAGCAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAG
7701957 TAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
131 TAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
7702022 AAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAA
196 AAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAA
7702087 ATTG-AGTAAGAGTAACATCG
261 ATTGAAGTAAGAGTAACATCG
7702107 TTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
1 TTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
* *
7702172 GAGCAACGTCATCCCCTTGAAATTGAAATAGAGTGGGTAACACTTCTTTATCTCTGAAATTGAAG
66 GAGCAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAG
7702237 TAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
131 TAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
7702302 AAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAA
196 AAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAA
7702367 ATTGAAGTAAGAGTAACATCG
261 ATTGAAGTAAGAGTAACATCG
7702388 TTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
1 TTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
7702453 GAGCAA
66 GAGCAA
7702459 GATCATTTCC
Statistics
Matches: 341, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
279 23 0.07
280 231 0.68
281 87 0.26
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (281 bp):
TTTCCTATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAA
GAGCAACGTCATCCCCTTGAAATTGAAATAGAGTGGATAACACGTCTTTATCTCTGAAATTGAAG
TAAGAACAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTTATCTCTGAAATTG
AAGTAAGAGCAACGTCATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAA
ATTGAAGTAAGAGTAACATCG
Found at i:7702444 original size:76 final size:76
Alignment explanation
Indices: 7702318--7702515 Score: 288
Period size: 76 Copynumber: 2.6 Consensus size: 76
7702308 GAGCAACGTC
* * *
7702318 ATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTCATCTCTGAAATTGAAGTAAGAGTAA
1 ATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
*
7702383 CATCGTTTCCT
66 CATCATTTCCT
** *
7702394 ATCCTCTTGAAATTGAAGTAAAACTGGATATCAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
1 ATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
*
7702459 GATCATTTCCT
66 CATCATTTCCT
* * *
7702470 ATCTTCTAGAAATTGAAGTAAAGTTGGATAGCAAAGTCTTTATCTC
1 ATCCTCTTGAAATTGAAGTAAAGTTGGATAAC-AAGTCTTTATCTC
7702516 CCTGAAGAGC
Statistics
Matches: 108, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
76 95 0.88
77 13 0.12
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (76 bp):
ATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAA
CATCATTTCCT
Found at i:7702482 original size:38 final size:36
Alignment explanation
Indices: 7702288--7702490 Score: 116
Period size: 38 Copynumber: 5.6 Consensus size: 36
7702278 AACACGTCTT
*
7702288 TATCTCTGAAATTGAAGTAAGAGCAACGTCA--TCC
1 TATCTCTGAAATTGAAGTAAGAGCAACATCATTTCC
* * ** *
7702322 --TCT-TGAAATTGAAGTAGAGTTGGATA-A-CAAGTCT
1 TATCTCTGAAATTGAAGTA-AG-AGCA-ACATCATTTCC
* *
7702356 TCATCTCTGAAATTGAAGTAAGAGTAACATCGTTTCC
1 T-ATCTCTGAAATTGAAGTAAGAGCAACATCATTTCC
* * * ** *
7702393 TATCCTCTTGAAATTGAAGTAA-AACTGGATATCAAGTCTT
1 TAT-CTC-TGAAATTGAAGTAAGAGC--AACATCATTTC-C
*
7702433 TATCTCTGAAATTGAAGTAAGAGCAAGATCATTTCC
1 TATCTCTGAAATTGAAGTAAGAGCAACATCATTTCC
7702469 TATCTTCTAGAAATTGAAGTAA
1 TATC-TCT-GAAATTGAAGTAA
7702491 AGTTGGATAG
Statistics
Matches: 126, Mismatches: 24, Indels: 34
0.68 0.13 0.18
Matches are distributed among these distances:
31 13 0.10
32 7 0.06
33 2 0.02
34 3 0.02
35 1 0.01
36 9 0.07
37 23 0.18
38 54 0.43
39 11 0.09
40 3 0.02
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.32
Consensus pattern (36 bp):
TATCTCTGAAATTGAAGTAAGAGCAACATCATTTCC
Found at i:7702824 original size:27 final size:28
Alignment explanation
Indices: 7702794--7702849 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
7702784 TTTTCGTTTA
*
7702794 ATTTAGAGTTAAATTGA-TTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTTAAATTT
* *
7702821 ATTTAAATTTAAATTTATTTTTAAATTT
1 ATTTAAAGTTAAATTGATTTTTAAATTT
7702849 A
1 A
7702850 AATTTAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (28 bp):
ATTTAAAGTTAAATTGATTTTTAAATTT
Found at i:7702830 original size:6 final size:6
Alignment explanation
Indices: 7702812--7702912 Score: 82
Period size: 6 Copynumber: 16.8 Consensus size: 6
7702802 TTAAATTGAT
**
7702812 TTTAAA TTT--A TTTAAA TTTAAA TTTATT TTTAAA TTTAAA TTTAATTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA--A
* * ** * *
7702860 TTTAAA TTT-AT TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA TATTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA
7702908 TTTAA
1 TTTAA
7702913 CATTAAAAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
4 4 0.05
5 4 0.05
6 59 0.77
7 4 0.05
8 6 0.08
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:7702896 original size:49 final size:49
Alignment explanation
Indices: 7702812--7702906 Score: 120
Period size: 49 Copynumber: 1.9 Consensus size: 49
7702802 TTAAATTGAT
** ** *
7702812 TTTAAATTTATTTAAATTTAAATTTATTTTTAAATTTAAAT-TTAATTA
1 TTTAAATTTATTTAAATTTAAATTTAAATAAAAATTAAAATATTAATTA
*
7702860 TTTAAATTTATTTTGAATTTAAATTTAAATAAAAATTAAAATATTAA
1 TTTAAATTTA-TTTAAATTTAAATTTAAATAAAAATTAAAATATTAA
7702907 GTTTAACATT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 10 0.26
49 25 0.64
50 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (49 bp):
TTTAAATTTATTTAAATTTAAATTTAAATAAAAATTAAAATATTAATTA
Found at i:7704739 original size:30 final size:30
Alignment explanation
Indices: 7704698--7705074 Score: 526
Period size: 30 Copynumber: 12.6 Consensus size: 30
7704688 AATTATCTAG
*
7704698 AAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
7704728 AAATTATATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
7704758 AAATTACATTTTGACCCCAAAACTTTTCCT
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
7704788 AAATTACATTTTGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
7704818 AAATTACATTTTAACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
7704848 AAATTATATTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
*
7704878 AAATTACATTTTGACCCAAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * *
7704908 AAATTATATTTTGACCCTAAAACTTTACCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * *
7704938 AAATAACATTTTAACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
7704968 AAATTACATTTCGACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* * *
7704998 CAATTACATTTTAACCCTAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTTCCA
* *
7705028 AAATTACATTTTGACCTCGAAAC--TTCCAA
1 AAATTACATTTTGACCCCAAAACTTTTCC-A
7705057 AAATTACCATTTT-ACCCC
1 AAATTA-CATTTTGACCCC
7705075 TCAAACTTCT
Statistics
Matches: 314, Mismatches: 31, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
28 4 0.01
29 11 0.04
30 299 0.95
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTTCCA
Found at i:7708741 original size:14 final size:14
Alignment explanation
Indices: 7708722--7708748 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
7708712 AACATTTAGC
7708722 AAAAAGAAAGAAAG
1 AAAAAGAAAGAAAG
7708736 AAAAAGAAAGAAA
1 AAAAAGAAAGAAA
7708749 AATATGGGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAAAG
Found at i:7713570 original size:50 final size:50
Alignment explanation
Indices: 7713495--7713598 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
7713485 ATTCTCTATT
* *
7713495 CATCTATTTTAGAATAATGATTAAAGTTTTTGCGATATAATTTTAAATCC
1 CATCTATTTTAGAATAATGACTAAAGTTTTTGCGATATAATTTTAAACCC
*
7713545 CATCTCTTTTAGAATAATGACTAAAGTTTTTGCGATATAATTTTAAACCC
1 CATCTATTTTAGAATAATGACTAAAGTTTTTGCGATATAATTTTAAACCC
7713595 CATC
1 CATC
7713599 AATCTCTATT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (50 bp):
CATCTATTTTAGAATAATGACTAAAGTTTTTGCGATATAATTTTAAACCC
Found at i:7713638 original size:114 final size:113
Alignment explanation
Indices: 7713439--7713662 Score: 306
Period size: 114 Copynumber: 2.0 Consensus size: 113
7713429 CTGACACATG
* ** *
7713439 TTTAGAACAATGACTAAAGTTTCTGCCATTTGGTTTCAAACCCATCATTCTCTATTCATCTATTT
1 TTTAGAACAATGACTAAAGTTTCTGCCATATAATTTCAAACCCATCAATCTCTATTCATCTATTT
*
7713504 TAGAATAATGATTAAAGTTTTTGCGATATAATTTTAAATCCCATCTCT
66 TAGAATAATGATTAAAGTTTTTGCGATATAATTTCAAATCCCATCTCT
* * * * *
7713552 TTTAGAATAATGACTAAAGTTTTTGCGATATAATTTTAAACCCCATCAATCTCTATTCATCTCTT
1 TTTAGAACAATGACTAAAGTTTCTGCCATATAATTTCAAA-CCCATCAATCTCTATTCATCTATT
* * *
7713617 TTA-AAGTAATGATTGAAGTTTTTGCGATATAGTTTCAAATCTCATC
65 TTAGAA-TAATGATTAAAGTTTTTGCGATATAATTTCAAATCCCATC
7713663 ATTCTCTATT
Statistics
Matches: 96, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
113 35 0.36
114 61 0.64
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.42
Consensus pattern (113 bp):
TTTAGAACAATGACTAAAGTTTCTGCCATATAATTTCAAACCCATCAATCTCTATTCATCTATTT
TAGAATAATGATTAAAGTTTTTGCGATATAATTTCAAATCCCATCTCT
Found at i:7713646 original size:64 final size:64
Alignment explanation
Indices: 7713545--7713746 Score: 273
Period size: 64 Copynumber: 3.2 Consensus size: 64
7713535 TTTTAAATCC
* * * *
7713545 CATCTCTTTTAGAATAATGACTAAAGTTTTTGCGATATAATTTTAAACCCCATCAATCTCTATT
1 CATCTCTTTTAGAATAATGATTAAAGTTTTTGCGATATAGTTTCAAACCCCATCATTCTCTATT
* * *
7713609 CATCTCTTTTA-AAGTAATGATTGAAGTTTTTGCGATATAGTTTCAAATCTCATCATTCTCTATT
1 CATCTCTTTTAGAA-TAATGATTAAAGTTTTTGCGATATAGTTTCAAACCCCATCATTCTCTATT
* * * *
7713673 CATCTCTTTTAGAATAATAATTAAAGTTTTTGCGATATAGTTTCAAACTCCAT-ATTTTTTATT
1 CATCTCTTTTAGAATAATGATTAAAGTTTTTGCGATATAGTTTCAAACCCCATCATTCTCTATT
*
7713736 CATTTCTTTTA
1 CATCTCTTTTA
7713747 ATCTTGTATT
Statistics
Matches: 121, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
63 20 0.17
64 99 0.82
65 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (64 bp):
CATCTCTTTTAGAATAATGATTAAAGTTTTTGCGATATAGTTTCAAACCCCATCATTCTCTATT
Found at i:7727941 original size:21 final size:21
Alignment explanation
Indices: 7727915--7727958 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
7727905 ATAGAAAAAA
7727915 GGGACTGATTTACTAGGCTTT
1 GGGACTGATTTACTAGGCTTT
7727936 GGGACTGATTTACTAGGCTTT
1 GGGACTGATTTACTAGGCTTT
7727957 GG
1 GG
7727959 CTTAATATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.14, G:0.32, T:0.36
Consensus pattern (21 bp):
GGGACTGATTTACTAGGCTTT
Found at i:7734552 original size:3 final size:3
Alignment explanation
Indices: 7734544--7734592 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
7734534 AGATGTCATT
7734544 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
7734592 A
1 A
7734593 AACTTTCCTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:7736202 original size:21 final size:21
Alignment explanation
Indices: 7736176--7736217 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
7736166 TAGGTCACGT
*
7736176 TTGGTTCGCTGTAATGGAATA
1 TTGGTTCGCTATAATGGAATA
7736197 TTGGTTCGCTATAATGGAATA
1 TTGGTTCGCTATAATGGAATA
7736218 GAGCTCTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (21 bp):
TTGGTTCGCTATAATGGAATA
Found at i:7736438 original size:54 final size:54
Alignment explanation
Indices: 7736378--7736494 Score: 164
Period size: 54 Copynumber: 2.1 Consensus size: 54
7736368 TTAATAAGAT
* * *
7736378 TATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACA
1 TATTATTAAATACAATGTAAT-AAAATAATAAATAATTTAATAATATTTTTAACA
* *
7736432 TATTATTAAATACAATGTAATAAAATAATATATAATTTAATAATATTTTTAATA
1 TATTATTAAATACAATGTAATAAAATAATAAATAATTTAATAATATTTTTAACA
7736486 TAATTATTA
1 T-ATTATTA
7736495 TTAAAATATA
Statistics
Matches: 56, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
53 22 0.39
54 27 0.48
55 7 0.12
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (54 bp):
TATTATTAAATACAATGTAATAAAATAATAAATAATTTAATAATATTTTTAACA
Found at i:7736539 original size:24 final size:24
Alignment explanation
Indices: 7736491--7736549 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
7736481 TAATATAATT
*
7736491 ATTATTAAAATATAAATTAGTAAAA
1 ATTA-TAATATATAAATTAGTAAAA
7736516 ATTATAATATATAATATTAG-AAAA
1 ATTATAATATATAA-ATTAGTAAAA
*
7736540 ATAAT-ATATA
1 ATTATAATATA
7736550 ACTTATTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.16
24 17 0.55
25 9 0.29
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
ATTATAATATATAAATTAGTAAAA
Found at i:7739506 original size:28 final size:27
Alignment explanation
Indices: 7739442--7739506 Score: 62
Period size: 28 Copynumber: 2.4 Consensus size: 27
7739432 ATAAAATATT
*
7739442 TTTTTTATATTTGTATACTTTTTAATA
1 TTTTTTAAATTTGTATACTTTTTAATA
* * *
7739469 ATATTT-AATTTTTATAATCTTTTTAA-A
1 TTTTTTAAATTTGTAT-A-CTTTTTAATA
7739496 TTTTTTAAATT
1 TTTTTTAAATT
7739507 AATTAATTGT
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
26 7 0.24
27 10 0.34
28 12 0.41
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTTTAAATTTGTATACTTTTTAATA
Found at i:7749640 original size:21 final size:21
Alignment explanation
Indices: 7749615--7749654 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
7749605 TTTTTTTTTA
7749615 AAATT-AAAAGTCAAAATTATT
1 AAATTAAAAAGT-AAAATTATT
7749636 AAATTAAAAAGTAAAATTA
1 AAATTAAAAAGTAAAATTA
7749655 CGTTATTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (21 bp):
AAATTAAAAAGTAAAATTATT
Found at i:7749697 original size:67 final size:67
Alignment explanation
Indices: 7749574--7749703 Score: 172
Period size: 67 Copynumber: 1.9 Consensus size: 67
7749564 TCAAAATAAG
* * * * * *
7749574 AAAAAGTAAAATTATGTTTTTTTGATAAATGTTTTTTTTTAAAATTAAAAGTCAAAATTATTAAA
1 AAAAAGTAAAATTACGTTATTTTCATAAATGTTTTTTATTAAAATTAAAAGACAAAACTATTAAA
7749639 TT
66 TT
* *
7749641 AAAAAGTAAAATTACGTTATTTTCATAAATGTTTATTTATT-AAGTTGAAAGACAAAACTATTA
1 AAAAAGTAAAATTACGTTATTTTCATAAATGTTT-TTTATTAAAATTAAAAGACAAAACTATTA
7749704 TATTGTTATG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
67 49 0.91
68 5 0.09
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (67 bp):
AAAAAGTAAAATTACGTTATTTTCATAAATGTTTTTTATTAAAATTAAAAGACAAAACTATTAAA
TT
Found at i:7755609 original size:13 final size:13
Alignment explanation
Indices: 7755574--7755636 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
7755564 TTTAGCATTA
*
7755574 CTTTTGATAAGTG
1 CTTTTGAAAAGTG
*
7755587 CTTTTAAAAAGTG
1 CTTTTGAAAAGTG
* *
7755600 CTTTGGAAAAATG
1 CTTTTGAAAAGTG
*
7755613 ATTTTGAAAAGTAG
1 CTTTTGAAAAGT-G
7755627 -TTTTGAAAAG
1 CTTTTGAAAAG
7755637 CTTGGTTTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
13 40 0.98
14 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.38
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:7761300 original size:49 final size:49
Alignment explanation
Indices: 7761243--7761350 Score: 198
Period size: 49 Copynumber: 2.2 Consensus size: 49
7761233 TACATCATAT
*
7761243 GAAATTGAATCATCTTTAAACTAAGTTTCTTCAAGCTACATTCTGCTCA
1 GAAATTGAATCATCTTTAAACAAAGTTTCTTCAAGCTACATTCTGCTCA
7761292 GAAATTGAATCATCTTTAAACAAAGTTTCTTCAAGCTACATTCTGCTCA
1 GAAATTGAATCATCTTTAAACAAAGTTTCTTCAAGCTACATTCTGCTCA
7761341 GAAATGTGAA
1 GAAAT-TGAA
7761351 CATGACTCAA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
49 53 0.93
50 4 0.07
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.34
Consensus pattern (49 bp):
GAAATTGAATCATCTTTAAACAAAGTTTCTTCAAGCTACATTCTGCTCA
Found at i:7765845 original size:51 final size:50
Alignment explanation
Indices: 7765698--7765846 Score: 119
Period size: 51 Copynumber: 2.9 Consensus size: 50
7765688 ATAGATATGG
* * *
7765698 TGAAAATGGAGAAATAAGAAA-CATTTGGAAATTA-TTATGGTTTTCTCCAAAA
1 TGAAAATGGA-AAA-ATGAAATAATTTGGAAATAATTTAT-GTTTT-TCCAAAA
* * * *
7765750 TGAAAATGGAGAAATGAAATCATTT-GAGAATAAATGTAAT-TTTTTGCAAAA
1 TGAAAATGGAAAAATGAAATAATTTGGA-AAT-AAT-TTATGTTTTTCCAAAA
7765801 TGAAAAT-GAAAAATGAAAATAATTTGGAAATGAATTTATGTTTTTC
1 TGAAAATGGAAAAATG-AAATAATTTGGAAAT-AATTTATGTTTTTC
7765847 GAATTAAATA
Statistics
Matches: 79, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
50 17 0.22
51 42 0.53
52 17 0.22
54 3 0.04
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.33
Consensus pattern (50 bp):
TGAAAATGGAAAAATGAAATAATTTGGAAATAATTTATGTTTTTCCAAAA
Found at i:7772328 original size:17 final size:17
Alignment explanation
Indices: 7772306--7772344 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
7772296 CTCCACCTTG
* *
7772306 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
7772323 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
7772340 ACAAG
1 ACAAG
7772345 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:7777629 original size:20 final size:19
Alignment explanation
Indices: 7777605--7777656 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
7777595 ATTATTATTT
7777605 TTAAAATTTAATTTAAATA
1 TTAAAATTTAATTTAAATA
* *
7777624 -TATAAATTATATTTTACATA
1 TTA-AAATT-TAATTTAAATA
*
7777644 TTAAAATATAATT
1 TTAAAATTTAATT
7777657 ATTACAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
18 2 0.08
19 9 0.35
20 13 0.50
21 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (19 bp):
TTAAAATTTAATTTAAATA
Found at i:7777671 original size:21 final size:21
Alignment explanation
Indices: 7777623--7777676 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
7777613 TAATTTAAAT
*
7777623 ATATAAAT-TATATTTTACAT
1 ATATAAATATATATTTTACAA
7777643 AT-TAAA-ATATAATTATTACAA
1 ATATAAATATAT-ATT-TTACAA
7777664 ATATAAATATATA
1 ATATAAATATATA
7777677 ATGATATATT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
19 7 0.25
20 5 0.18
21 7 0.25
22 5 0.18
23 4 0.14
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
ATATAAATATATATTTTACAA
Found at i:7781190 original size:7 final size:7
Alignment explanation
Indices: 7781178--7781574 Score: 654
Period size: 7 Copynumber: 55.3 Consensus size: 7
7781168 CTGAAGCATA
7781178 TCCCCGT
1 TCCCCGT
7781185 TCCCCGT
1 TCCCCGT
7781192 TCCCCGT
1 TCCCCGT
7781199 TCCCCGT
1 TCCCCGT
*
7781206 TCCCCGG
1 TCCCCGT
*
7781213 TCCCCGG
1 TCCCCGT
7781220 TCCCCGGT
1 TCCCC-GT
7781228 TCCCCGGT
1 TCCCC-GT
7781236 TCCCCGGT
1 TCCCC-GT
7781244 TCCCCCGGT
1 T-CCCC-GT
7781253 TCCCCGGT
1 TCCCC-GT
7781261 TCCCCCGGT
1 T-CCCC-GT
7781270 TCCCCCGGT
1 T-CCCC-GT
7781279 TCCCCCCGT
1 T--CCCCGT
7781288 TCCCCGT
1 TCCCCGT
7781295 TCCCCGT
1 TCCCCGT
7781302 TCCCCGT
1 TCCCCGT
7781309 TCCCCGT
1 TCCCCGT
7781316 TCCCCGT
1 TCCCCGT
7781323 TCCCCGT
1 TCCCCGT
7781330 TCCCCGT
1 TCCCCGT
7781337 T-CCCGT
1 TCCCCGT
7781343 TCCCCGT
1 TCCCCGT
7781350 TCCCCGT
1 TCCCCGT
7781357 TCCCCGT
1 TCCCCGT
7781364 TCCCCGT
1 TCCCCGT
7781371 TCCCCGT
1 TCCCCGT
7781378 TCCCCGT
1 TCCCCGT
7781385 TCCCCGT
1 TCCCCGT
7781392 TCCCCGT
1 TCCCCGT
7781399 TCCCCGT
1 TCCCCGT
7781406 TCCCCGT
1 TCCCCGT
7781413 T-CCCGT
1 TCCCCGT
7781419 TCCCCGT
1 TCCCCGT
7781426 TCCCCGT
1 TCCCCGT
7781433 TCCCCGT
1 TCCCCGT
7781440 TCCCCGT
1 TCCCCGT
7781447 TCCCCGT
1 TCCCCGT
7781454 TCCCCGT
1 TCCCCGT
7781461 TCCCCGT
1 TCCCCGT
7781468 TCCCCGT
1 TCCCCGT
7781475 TCCCCGT
1 TCCCCGT
7781482 TCCCCGT
1 TCCCCGT
7781489 TCCCCGT
1 TCCCCGT
7781496 TCCCCGT
1 TCCCCGT
7781503 TCCCCGT
1 TCCCCGT
7781510 TCCCCGT
1 TCCCCGT
7781517 TCCCCGT
1 TCCCCGT
7781524 TCCCCGT
1 TCCCCGT
7781531 TCCCCGT
1 TCCCCGT
7781538 TCCCCGT
1 TCCCCGT
7781545 TCCCCGT
1 TCCCCGT
7781552 TCCCCGT
1 TCCCCGT
7781559 TCCCCGT
1 TCCCCGT
7781566 TCCCCGT
1 TCCCCGT
7781573 TC
1 TC
7781575 AAAGAAACAG
Statistics
Matches: 382, Mismatches: 2, Indels: 12
0.96 0.01 0.03
Matches are distributed among these distances:
6 12 0.03
7 311 0.81
8 26 0.07
9 28 0.07
10 5 0.01
ACGTcount: A:0.00, C:0.56, G:0.16, T:0.27
Consensus pattern (7 bp):
TCCCCGT
Found at i:7781251 original size:9 final size:9
Alignment explanation
Indices: 7781221--7781292 Score: 114
Period size: 9 Copynumber: 8.3 Consensus size: 9
7781211 GGTCCCCGGT
7781221 CCCCGGTT-
1 CCCCGGTTC
7781229 CCCCGGTT-
1 CCCCGGTTC
7781237 CCCCGGTTC
1 CCCCGGTTC
7781246 CCCCGGTT-
1 CCCCGGTTC
7781254 CCCCGGTTC
1 CCCCGGTTC
7781263 CCCCGGTTC
1 CCCCGGTTC
7781272 CCCCGGTTC
1 CCCCGGTTC
*
7781281 CCCCCGTTC
1 CCCCGGTTC
7781290 CCC
1 CCC
7781293 GTTCCCCGTT
Statistics
Matches: 61, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
8 24 0.39
9 37 0.61
ACGTcount: A:0.00, C:0.57, G:0.21, T:0.22
Consensus pattern (9 bp):
CCCCGGTTC
Found at i:7783718 original size:21 final size:24
Alignment explanation
Indices: 7783672--7783723 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 24
7783662 ACATTTAATC
7783672 TTTAATACTTACATATTTTATCAA
1 TTTAATACTTACATATTTTATCAA
7783696 TTTAAT-CTTA-AT-TTTTAAT-AA
1 TTTAATACTTACATATTTT-ATCAA
7783717 TTTAATA
1 TTTAATA
7783724 AATTTAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 12 0.46
22 4 0.15
23 4 0.15
24 6 0.23
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTAATACTTACATATTTTATCAA
Found at i:7783752 original size:23 final size:24
Alignment explanation
Indices: 7783703--7783750 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 24
7783693 CAATTTAATC
7783703 TTAATTTTTAATAATTTAATAAAT
1 TTAATTTTTAATAATTTAATAAAT
7783727 TTAACTTTTT-AT-ATTT-ATAAAT
1 TTAA-TTTTTAATAATTTAATAAAT
7783749 TT
1 TT
7783751 TATTAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
23 4 0.17
24 6 0.26
25 5 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (24 bp):
TTAATTTTTAATAATTTAATAAAT
Found at i:7784863 original size:15 final size:15
Alignment explanation
Indices: 7784845--7784875 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7784835 TTTAATTGTA
*
7784845 TATATTTTATAAATT
1 TATATTATATAAATT
7784860 TATATTATATAAATT
1 TATATTATATAAATT
7784875 T
1 T
7784876 CTAAAATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TATATTATATAAATT
Found at i:7784882 original size:24 final size:23
Alignment explanation
Indices: 7784828--7784875 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
7784818 TTCCAAAACA
* * *
7784828 TTATATATTTAATTGTATATATT
1 TTATAAATTTAATTATATAAATT
7784851 TTATAAATTTATATTATATAAATT
1 TTATAAATTTA-ATTATATAAATT
7784875 T
1 T
7784876 CTAAAATAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATAAATTTAATTATATAAATT
Found at i:7785547 original size:19 final size:19
Alignment explanation
Indices: 7785504--7785547 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
7785494 ATTAATTATT
7785504 TTAAAATTTAATTTGAATA
1 TTAAAATTTAATTTGAATA
*
7785523 TATAAAATTT-ATTTTACATA
1 T-TAAAATTTAATTTGA-ATA
7785543 TTAAA
1 TTAAA
7785548 GTATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAAAATTTAATTTGAATA
Found at i:7786483 original size:15 final size:15
Alignment explanation
Indices: 7786463--7786508 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
7786453 ACAAAATAAT
7786463 AACATAAGTGACTAA
1 AACATAAGTGACTAA
* *
7786478 AACATAA-T-ATTTCA
1 AACATAAGTGA-CTAA
7786492 AACATAAGTGACTAA
1 AACATAAGTGACTAA
7786507 AA
1 AA
7786509 TGTAACTTGA
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 12 0.50
16 1 0.04
ACGTcount: A:0.54, C:0.13, G:0.09, T:0.24
Consensus pattern (15 bp):
AACATAAGTGACTAA
Found at i:7787487 original size:38 final size:36
Alignment explanation
Indices: 7787421--7787520 Score: 96
Period size: 38 Copynumber: 2.7 Consensus size: 36
7787411 CTTTTCTATA
* * *
7787421 TTTACATAATTTTCTAAATTTATA-ATATACTATAAATT
1 TTTATATATTTTTCAAAATTTATATATATA-T-TAAA-T
*
7787459 TTTATATATTTTTCAAAATATTATATATATATTTAAT
1 TTTATATATTTTTCAAAAT-TTATATATATATTAAAT
*
7787496 TGTATATATTTTT-ATAAATTTATAT
1 TTTATATATTTTTCA-AAATTTATAT
7787521 TTTATATATT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
36 7 0.13
37 17 0.31
38 19 0.35
39 6 0.11
40 5 0.09
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (36 bp):
TTTATATATTTTTCAAAATTTATATATATATTAAAT
Found at i:7787504 original size:25 final size:25
Alignment explanation
Indices: 7787476--7787531 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
7787466 ATTTTTCAAA
*
7787476 ATATTATATATATATTTA-ATTGTAT
1 ATATT-TATATAAATTTATATTGTAT
* *
7787501 ATATTTTTATAAATTTATATTTTAT
1 ATATTTATATAAATTTATATTGTAT
7787526 ATATTT
1 ATATTT
7787532 CTAAAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
ATATTTATATAAATTTATATTGTAT
Found at i:7792351 original size:31 final size:30
Alignment explanation
Indices: 7792283--7792341 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
7792273 ACTTATTCGG
7792283 ATCAACTCGAATAAAAAATTAAAATTTTCC
1 ATCAACTCGAATAAAAAATTAAAATTTTCC
7792313 ATCAACTCGAATAAAAAATTAAAATTTTC
1 ATCAACTCGAATAAAAAATTAAAATTTTC
7792342 AGTTTAACTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (30 bp):
ATCAACTCGAATAAAAAATTAAAATTTTCC
Found at i:7810624 original size:16 final size:17
Alignment explanation
Indices: 7810603--7810635 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
7810593 GAAAATTTTA
7810603 GCTTTTT-CTCAAAAGT
1 GCTTTTTGCTCAAAAGT
7810619 GCTTTTTGGCTCAAAAG
1 GCTTTTT-GCTCAAAAG
7810636 CACTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (17 bp):
GCTTTTTGCTCAAAAGT
Found at i:7813965 original size:22 final size:22
Alignment explanation
Indices: 7813937--7813990 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
7813927 CTAGATGCTT
7813937 GAAACAAAAGATAAAATAACTC
1 GAAACAAAAGATAAAATAACTC
7813959 GAAACAAAAGATAAAATAACTC
1 GAAACAAAAGATAAAATAACTC
7813981 GAAACAAAAG
1 GAAACAAAAG
7813991 CTACTAAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.65, C:0.13, G:0.11, T:0.11
Consensus pattern (22 bp):
GAAACAAAAGATAAAATAACTC
Found at i:7815550 original size:22 final size:21
Alignment explanation
Indices: 7815510--7815551 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
7815500 AAAGTATTGT
**
7815510 AAAAATATTTTAATTTTTTTG
1 AAAAATATTTTAAAATTTTTG
7815531 AAAAATATTTTTAAAATTTTT
1 AAAAATA-TTTTAAAATTTTT
7815552 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
AAAAATATTTTAAAATTTTTG
Found at i:7816076 original size:46 final size:44
Alignment explanation
Indices: 7816019--7816116 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 44
7816009 TGAATAGAGT
* * * *
7816019 TGTAATGGAATAAAATTGTAATCAGTA-ATTTAATTGTTTGGTTGAA
1 TGTAATAGAATAAAACTATAAT-AGTATATTT-A-TGTTTGGTTAAA
7816065 TGTAATAGAATAAAACTATAATAGTATATTTATGTTTGGTTAAA
1 TGTAATAGAATAAAACTATAATAGTATATTTATGTTTGGTTAAA
7816109 TG-AATAGA
1 TGTAATAGA
7816117 TGTTGTAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
43 6 0.13
44 13 0.28
45 5 0.11
46 23 0.49
ACGTcount: A:0.41, C:0.02, G:0.17, T:0.40
Consensus pattern (44 bp):
TGTAATAGAATAAAACTATAATAGTATATTTATGTTTGGTTAAA
Found at i:7816250 original size:12 final size:12
Alignment explanation
Indices: 7816227--7816262 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
7816217 ATTATTAAAT
7816227 ATAATTTAATAA
1 ATAATTTAATAA
7816239 A-AATTATAATAA
1 ATAATT-TAATAA
7816251 ATAATTTAATAA
1 ATAATTTAATAA
7816263 CATTCCTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.18
12 14 0.64
13 4 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATTTAATAA
Found at i:7816312 original size:32 final size:32
Alignment explanation
Indices: 7816275--7816367 Score: 111
Period size: 32 Copynumber: 2.9 Consensus size: 32
7816265 TTCCTAATAT
7816275 AATTAATTTTATATTAAAATATTTTTATTTTA
1 AATTAATTTTATATTAAAATATTTTTATTTTA
* *
7816307 TATTAA-ATTATATTAAAATA-TTTTATTTTA
1 AATTAATTTTATATTAAAATATTTTTATTTTA
*
7816337 AATTATATTTTGA-AATAAAATATTTTATATT
1 AATTA-ATTTT-ATATTAAAATATTTT-TATT
7816368 AAAATATTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
30 14 0.27
31 14 0.27
32 15 0.29
33 4 0.08
34 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (32 bp):
AATTAATTTTATATTAAAATATTTTTATTTTA
Found at i:7816317 original size:15 final size:15
Alignment explanation
Indices: 7816280--7816376 Score: 88
Period size: 15 Copynumber: 6.3 Consensus size: 15
7816270 AATATAATTA
7816280 ATTTTATATTAAAAT
1 ATTTTATATTAAAAT
* * *
7816295 ATTTTTATTTTATATT
1 A-TTTTATATTAAAAT
**
7816311 AAATTATATTAAAAT
1 ATTTTATATTAAAAT
*
7816326 ATTTTATTTTAAATTAT
1 ATTTTATATTAAA--AT
*
7816343 ATTTTGA-AATAAAAT
1 ATTTT-ATATTAAAAT
7816358 ATTTTATATTAAAAT
1 ATTTTATATTAAAAT
7816373 ATTT
1 ATTT
7816377 CAAATATTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
14 1 0.02
15 38 0.60
16 12 0.19
17 11 0.17
18 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (15 bp):
ATTTTATATTAAAAT
Found at i:7816333 original size:30 final size:30
Alignment explanation
Indices: 7816283--7816397 Score: 112
Period size: 30 Copynumber: 3.9 Consensus size: 30
7816273 ATAATTAATT
7816283 TTATATTAAAATATTTTTATTTTATATTAAA
1 TTATATTAAAATA-TTTTATTTTATATTAAA
*
7816314 TTATATTAAAATATTTTATTTTAAATT--A
1 TTATATTAAAATATTTTATTTTATATTAAA
* * ***
7816342 -TATTTTGAAATAAAATATTTTATATTAAA
1 TTATATTAAAATATTTTATTTTATATTAAA
* *
7816371 ATAT-TTCAAATATTTTATTTTTATATT
1 TTATATTAAAATATTTTA-TTTTATATT
7816398 TTCAGAGTCC
Statistics
Matches: 69, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
27 20 0.29
28 1 0.01
29 10 0.14
30 25 0.36
31 13 0.19
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.57
Consensus pattern (30 bp):
TTATATTAAAATATTTTATTTTATATTAAA
Found at i:7816508 original size:12 final size:12
Alignment explanation
Indices: 7816486--7816519 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
7816476 GTGTAAATGA
7816486 ATGAA-CGTTCG
1 ATGAACCGTTCG
7816497 ATGAACCGTTCG
1 ATGAACCGTTCG
7816509 -TGAACCGTTCG
1 ATGAACCGTTCG
7816520 TTTATGTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 16 0.73
12 6 0.27
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (12 bp):
ATGAACCGTTCG
Found at i:7816651 original size:12 final size:12
Alignment explanation
Indices: 7816633--7816679 Score: 60
Period size: 12 Copynumber: 4.0 Consensus size: 12
7816623 TTCACGAACA
7816633 AGCTCGTTTATT
1 AGCTCGTTTATT
*
7816645 GGCTCGTTTATT
1 AGCTCGTTTATT
*
7816657 AACTCGTTTA-T
1 AGCTCGTTTATT
*
7816668 AGCTTGTTTATT
1 AGCTCGTTTATT
7816680 TATTAATGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.17, C:0.15, G:0.17, T:0.51
Consensus pattern (12 bp):
AGCTCGTTTATT
Found at i:7816819 original size:23 final size:23
Alignment explanation
Indices: 7816759--7816866 Score: 144
Period size: 23 Copynumber: 4.7 Consensus size: 23
7816749 ATTCATTAAC
* *
7816759 ATTGTTCGTGAACGTGTTCAATT
1 ATTGTTCGTGAACATGTTCGATT
* * *
7816782 ATATGTTCATAAACATGTTCGTTT
1 AT-TGTTCGTGAACATGTTCGATT
7816806 ATTGTTCGTGAACATGTTCGATT
1 ATTGTTCGTGAACATGTTCGATT
*
7816829 AATGTTCGTGAACATGTTCGATT
1 ATTGTTCGTGAACATGTTCGATT
*
7816852 AATGTTCGTGAACAT
1 ATTGTTCGTGAACAT
7816867 TAAACAAACG
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
23 57 0.76
24 18 0.24
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.42
Consensus pattern (23 bp):
ATTGTTCGTGAACATGTTCGATT
Found at i:7816825 original size:12 final size:12
Alignment explanation
Indices: 7816808--7816866 Score: 54
Period size: 12 Copynumber: 5.1 Consensus size: 12
7816798 GTTCGTTTAT
7816808 TGTTCGTGAACA
1 TGTTCGTGAACA
*
7816820 TGTTCGAT-TA-A
1 TGTTCG-TGAACA
7816831 TGTTCGTGAACA
1 TGTTCGTGAACA
*
7816843 TGTTCGAT-TA-A
1 TGTTCG-TGAACA
7816854 TGTTCGTGAACA
1 TGTTCGTGAACA
7816866 T
1 T
7816867 TAAACAAACG
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
10 2 0.05
11 16 0.43
12 17 0.46
13 2 0.05
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (12 bp):
TGTTCGTGAACA
Found at i:7817741 original size:20 final size:19
Alignment explanation
Indices: 7817716--7817762 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
7817706 GGCTCGTTCA
*
7817716 AAAAATAAGAGGATTTGAAT
1 AAAAATAAGAGG-TTTGAAC
*
7817736 AAAAAT-ATAGGTTTGAAC
1 AAAAATAAGAGGTTTGAAC
7817754 AAAAA-AAGA
1 AAAAATAAGA
7817763 AGCTCGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 13 0.57
19 4 0.17
20 6 0.26
ACGTcount: A:0.60, C:0.02, G:0.17, T:0.21
Consensus pattern (19 bp):
AAAAATAAGAGGTTTGAAC
Found at i:7817758 original size:19 final size:21
Alignment explanation
Indices: 7817714--7817759 Score: 53
Period size: 19 Copynumber: 2.3 Consensus size: 21
7817704 AGGGCTCGTT
7817714 CAAAAAATAAGAGGATTTGAA
1 CAAAAAATAAGAGGATTTGAA
* *
7817735 -TAAAAAT-ATAGG-TTTGAA
1 CAAAAAATAAGAGGATTTGAA
7817753 CAAAAAA
1 CAAAAAA
7817760 AGAAGCTCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 4
0.75 0.11 0.14
Matches are distributed among these distances:
18 6 0.29
19 9 0.43
20 6 0.29
ACGTcount: A:0.59, C:0.04, G:0.15, T:0.22
Consensus pattern (21 bp):
CAAAAAATAAGAGGATTTGAA
Found at i:7823204 original size:42 final size:42
Alignment explanation
Indices: 7823125--7823485 Score: 372
Period size: 42 Copynumber: 8.4 Consensus size: 42
7823115 GAATCACTTG
* *
7823125 ATGTATAAATGGAAGGCTCATGTCTC-GAGATGAGCATGAGATT
1 ATGTTTAAA-GGAAGACTCATGTCTCAG-GATGAGCATGAGATT
* *
7823168 ATGTTTAAAGGAAGATTCATGTCTCAGGATGTGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
** * * *
7823210 ATGTTTAAAGGAAGACTCATGTCTTGGGATGGGTATGGGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
*
7823252 ATGTTTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
7823294 ATGTTTAAAGGAAGACTCGTGACTCGTGACTC-GAGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTC---A-T-GT--CTCAG-GATGAGCATGAGATT
* * *
7823343 ATGTTTAAAGGAAAACTCGTGACTCAGGATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
** * * * * *
7823385 ATAATTAAAGGAAGACTCGTGTCTCGGGAAGAGCATTAGGTT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
* *
7823427 ATGTTTAAAGGAAGACTTATGTCTCA--ATAGAGCATAAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGGAT-GAGCATGAGATT
7823468 -TGTTTAAAAAGGAAGACT
1 ATGTTT--AAAGGAAGACT
7823486 TATGACTCGG
Statistics
Matches: 272, Mismatches: 33, Indels: 27
0.82 0.10 0.08
Matches are distributed among these distances:
40 6 0.02
41 10 0.04
42 204 0.75
43 10 0.04
44 1 0.00
45 2 0.01
46 1 0.00
47 2 0.01
48 1 0.00
49 35 0.13
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCATGTCTCAGGATGAGCATGAGATT
Found at i:7823337 original size:49 final size:48
Alignment explanation
Indices: 7823278--7823410 Score: 179
Period size: 49 Copynumber: 2.9 Consensus size: 48
7823268 TCATGTCTCG
7823278 GGATGAGCATGAGATTATGTTTAAAGGAAGACTCGTGACTCGTGACTC
1 GGATGAGCATGAGATTATGTTTAAAGGAAGACTCGTGACTCGTGACTC
*
7823326 GAGATGAGCATGAGATTATGTTTAAAGGAAAACTCGTGACTC---A---
1 G-GATGAGCATGAGATTATGTTTAAAGGAAGACTCGTGACTCGTGACTC
** *
7823369 GGATGAGCATGAGATTATAATTAAAGGAAGACTCGTGTCTCG
1 GGATGAGCATGAGATTATGTTTAAAGGAAGACTCGTGACTCG
7823411 GGAAGAGCAT
Statistics
Matches: 78, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
42 36 0.46
43 1 0.01
46 1 0.01
48 1 0.01
49 39 0.50
ACGTcount: A:0.33, C:0.13, G:0.28, T:0.26
Consensus pattern (48 bp):
GGATGAGCATGAGATTATGTTTAAAGGAAGACTCGTGACTCGTGACTC
Found at i:7823439 original size:175 final size:174
Alignment explanation
Indices: 7823148--7823494 Score: 466
Period size: 175 Copynumber: 2.0 Consensus size: 174
7823138 AGGCTCATGT
* * * * *
7823148 CTCGAGATGAGCATGAGATTATGTTTAAAGGAAGATTCATGTCTCAGGATGTGCATGAGATTATG
1 CTCGAGATGAGCATGAGATTATGTTTAAAGGAAAACTCATGACTCAGGATGAGCATGAGATTATA
* * * * * *
7823213 TTTAAAGGAAGACTCATGTCTTGGGATGGGTATGGGATTATGTTTAAAGGAAGACTCATGTCTCG
66 ATTAAAGGAAGACTCATGTCTCGGGAAGAGCATAGGATTATGTTTAAAGGAAGACTCATGTCTC-
* * *
7823278 GGAT-GAGCATGAGATTATGTTT-AAAGGAAGACTCGTGACTCGTGA
130 -AATAGAGCATAAGATT-TGTTTAAAAGGAAGACTCATGACTCGTGA
*
7823323 CTCGAGATGAGCATGAGATTATGTTTAAAGGAAAACTCGTGACTCAGGATGAGCATGAGATTATA
1 CTCGAGATGAGCATGAGATTATGTTTAAAGGAAAACTCATGACTCAGGATGAGCATGAGATTATA
* *
7823388 ATTAAAGGAAGACTCGTGTCTCGGGAAGAGCATTAGG-TTATGTTTAAAGGAAGACTTATGTCTC
66 ATTAAAGGAAGACTCATGTCTCGGGAAGAGCA-TAGGATTATGTTTAAAGGAAGACTCATGTCTC
*
7823452 AATAGAGCATAAGATTTGTTTAAAAAGGAAGACTTATGACTCG
130 AATAGAGCATAAGATTTGTTT-AAAAGGAAGACTCATGACTCG
7823495 GTTGGAGCAT
Statistics
Matches: 150, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
173 7 0.05
174 11 0.07
175 129 0.86
176 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (174 bp):
CTCGAGATGAGCATGAGATTATGTTTAAAGGAAAACTCATGACTCAGGATGAGCATGAGATTATA
ATTAAAGGAAGACTCATGTCTCGGGAAGAGCATAGGATTATGTTTAAAGGAAGACTCATGTCTCA
ATAGAGCATAAGATTTGTTTAAAAGGAAGACTCATGACTCGTGA
Found at i:7829796 original size:6 final size:6
Alignment explanation
Indices: 7829785--7829823 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
7829775 TGATCAAAAT
* * *
7829785 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
7829824 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:7830728 original size:19 final size:19
Alignment explanation
Indices: 7830704--7830740 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
7830694 GGTAAAGTTT
7830704 TTATATAATTTTAGGGGGA
1 TTATATAATTTTAGGGGGA
7830723 TTATATAATTTTAGGGGG
1 TTATATAATTTTAGGGGG
7830741 TTAGTTTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (19 bp):
TTATATAATTTTAGGGGGA
Found at i:7835843 original size:97 final size:97
Alignment explanation
Indices: 7835674--7835863 Score: 292
Period size: 97 Copynumber: 2.0 Consensus size: 97
7835664 TTGAAAAAGG
* * * *
7835674 GTATTCGATTATCCTAGTTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
1 GTATTCGATTATCCGAGTTGGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
7835739 CCAAAATAAAGGAATATTGCCTCAATTTAAGA
66 CCAAAATAAAGGAATATTGCCTCAATTTAAGA
*
7835771 GTATTCGATTATCTCGA-TTGGAAGAAAAATCACGCCTAGTAAGTTAAGGCACGAATTTTCAAAA
1 GTATTCGATTATC-CGAGTTGGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAA
* * *
7835835 CTCGAAATAAAGGAATATTGCCTCGATTT
65 CCCAAAATAAAGGAATATTGCCTCAATTT
7835864 TAAATATTTT
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
97 82 0.98
98 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.28
Consensus pattern (97 bp):
GTATTCGATTATCCGAGTTGGAAGAAAAATCACGCCTAGTAAGTTAAGGCACAAATTTTCAAAAC
CCAAAATAAAGGAATATTGCCTCAATTTAAGA
Found at i:7836011 original size:14 final size:14
Alignment explanation
Indices: 7835992--7836039 Score: 55
Period size: 15 Copynumber: 3.5 Consensus size: 14
7835982 ACAAACATAC
7835992 GAAAATAAATATGA
1 GAAAATAAATATGA
*
7836006 GAAAATAAAATACGA
1 GAAAAT-AAATATGA
*
7836021 AAAAAT-AA-ATGA
1 GAAAATAAATATGA
7836033 GAAAATA
1 GAAAATA
7836040 TAAAATTAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 8 0.29
13 2 0.07
14 6 0.21
15 12 0.43
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (14 bp):
GAAAATAAATATGA
Found at i:7836043 original size:14 final size:13
Alignment explanation
Indices: 7835992--7836039 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
7835982 ACAAACATAC
7835992 GAAAATAAATATGA
1 GAAAATAAA-ATGA
7836006 GAAAATAAAAT-A
1 GAAAATAAAATGA
*
7836018 CGAAAAAATAAATGA
1 -GAAAATA-AAATGA
7836033 GAAAATA
1 GAAAATA
7836040 TAAAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 1 0.03
13 8 0.28
14 19 0.66
15 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.12, T:0.17
Consensus pattern (13 bp):
GAAAATAAAATGA
Found at i:7836045 original size:29 final size:27
Alignment explanation
Indices: 7835988--7836039 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
7835978 ATGAACAAAC
*
7835988 ATACGAAAATAAATATGAGAAAATAAA
1 ATACGAAAATAAAAATGAGAAAATAAA
7836015 ATACGAAAA-AATAAATGAGAAAATA
1 ATACGAAAATAA-AAATGAGAAAATA
7836040 TAAAATTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 2 0.09
27 21 0.91
ACGTcount: A:0.67, C:0.04, G:0.12, T:0.17
Consensus pattern (27 bp):
ATACGAAAATAAAAATGAGAAAATAAA
Found at i:7836156 original size:28 final size:28
Alignment explanation
Indices: 7836112--7836442 Score: 149
Period size: 29 Copynumber: 11.5 Consensus size: 28
7836102 AAGGGGGTCG
* *
7836112 AAAATG-AAGTTTCAGAGAGTTTAGGGTT
1 AAAATGTAA-TTTTAGAGAGTTTAGGGTA
7836140 AAAATGTAATTTTAGAGAGTTTTAGGGGTA
1 AAAATGTAATTTTAGAGAG-TTTA-GGGTA
* * **
7836170 AAAATGTCATTTT-GGGAAAATTAGGGATA
1 AAAATGTAATTTTAGAG-AGTTTAGGG-TA
* * * *
7836199 AAAATGTGATTTTTG-GAAGTTCGAGGGCA
1 AAAATGTAATTTTAGAG-AGTT-TAGGGTA
* * * *
7836228 AAAATGTGATTTTTGAAAGTTTAGGGGCA
1 AAAATGTAATTTTAGAGAGTTTA-GGGTA
* *
7836257 AAAATGTAATTTT-GAAAGCTTGAGGGTA
1 AAAATGTAATTTTAGAGAG-TTTAGGGTA
* *
7836285 AAAATGTAATTTTTGAGAAG-TTCGTGGTCA
1 AAAATGTAATTTTAGAG-AGTTTAG-GGT-A
* * * *
7836315 AATATG-ATTTTTGGA-AGTTCGAGGGTA
1 AAAATGTAATTTTAGAGAGTT-TAGGGTA
* * * *
7836342 AAAATGCAATTTTTGAGAAG-TTCGGGGA
1 AAAATGTAATTTTAGAG-AGTTTAGGGTA
7836370 TAAAATGTAATTTTTAGA-AGTTTAAGGGTA
1 -AAAATGTAA-TTTTAGAGAGTTT-AGGGTA
** * * *
7836400 AATTTGTAATTTTTAAAAAGTTTGAGGGTC
1 AAAATGTAA-TTTTAGAGAGTTT-AGGGTA
7836430 AAAATGTAATTTT
1 AAAATGTAATTTT
7836443 GGAAAAAGTT
Statistics
Matches: 238, Mismatches: 41, Indels: 47
0.73 0.13 0.14
Matches are distributed among these distances:
27 8 0.03
28 60 0.25
29 111 0.47
30 59 0.25
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (28 bp):
AAAATGTAATTTTAGAGAGTTTAGGGTA
Found at i:7836297 original size:57 final size:55
Alignment explanation
Indices: 7836140--7836443 Score: 209
Period size: 57 Copynumber: 5.3 Consensus size: 55
7836130 GTTTAGGGTT
* * * * * **
7836140 AAAATGTAATTTTAGAGAGTTTTAGGGGTAAAAATGTCATTTTGGGAAAATTAGGGATA
1 AAAATGTAATTTT-GAAAG-TTGA-GGGTAAAAATGTAATTTT-TGAAAGTTAGGGGCA
* * * *
7836199 AAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATGTGATTTTTGAAAGTTTAGGGGCA
1 AAAATGT-AATTTTGAAAGTT-GAGGGTAAAAATGTAATTTTTGAAAG-TTAGGGGCA
* *
7836257 AAAATGTAATTTTGAAAGCTTGAGGGTAAAAATGTAATTTTTGAGAAGTTCGTGGTCA
1 AAAATGTAATTTTGAAAG-TTGAGGGTAAAAATGTAATTTTTGA-AAGTTAG-GGGCA
* * * * *
7836315 AATATG-ATTTTTGGAAGTTCGAGGGTAAAAATGCAATTTTTGAGAAGTTCGGGG-A
1 AAAATGTAATTTTGAAAGTT-GAGGGTAAAAATGTAATTTTTGA-AAGTTAGGGGCA
* * ** * *
7836370 TAAAATGTAATTTTTAGAAGTTTAAGGGTAAATTTGTAATTTTTAAAAAGTTTGAGGGTC-
1 -AAAATGTAATTTTGA-AAG-TTGAGGGTAAAAATGTAATTTTT-GAAAG-TT-AGGGGCA
7836430 AAAATGTAATTTTG
1 AAAATGTAATTTTG
7836444 GAAAAAGTTT
Statistics
Matches: 197, Mismatches: 33, Indels: 30
0.76 0.13 0.12
Matches are distributed among these distances:
55 1 0.01
56 9 0.05
57 81 0.41
58 69 0.35
59 29 0.15
60 8 0.04
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (55 bp):
AAAATGTAATTTTGAAAGTTGAGGGTAAAAATGTAATTTTTGAAAGTTAGGGGCA
Found at i:7836411 original size:58 final size:58
Alignment explanation
Indices: 7836139--7836442 Score: 239
Period size: 58 Copynumber: 5.2 Consensus size: 58
7836129 AGTTTAGGGT
** * * * *
7836139 TAAAATGTAA-TTTTAGAGAGTTTTAGGGGTAAAAATGTCA-TTTTGGGAAAATT-AGGGA
1 TAAAATGTAATTTTTAGA-AGTTCGA-GGGTAAAAATGTAATTTTTGAG-AAGTTCGGGGA
* * * * *
7836197 TAAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATGTGATTTTTGA-AAGTTTAGGGGCA
1 T-AAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAG-TTCGGGG-A
* *
7836257 -AAAATGTAATTTTGA-AAGCTT-GAGGGTAAAAATGTAATTTTTGAGAAGTTCGTGG-
1 TAAAATGTAATTTTTAGAAG-TTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGGGGA
* * * * *
7836312 TCAAATATGATTTTTGGAAGTTCGAGGGTAAAAATGCAATTTTTGAGAAGTTCGGGGA
1 TAAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGGGGA
** ** * * *
7836370 TAAAATGTAATTTTTAGAAGTTTAAGGGTAAATTTGTAATTTTTAAAAAGTTTGAGGG-
1 TAAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCG-GGGA
7836428 TCAAAATGTAATTTT
1 T-AAAATGTAATTTT
7836443 GGAAAAAGTT
Statistics
Matches: 197, Mismatches: 35, Indels: 27
0.76 0.14 0.10
Matches are distributed among these distances:
56 12 0.06
57 66 0.34
58 75 0.38
59 37 0.19
60 7 0.04
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.36
Consensus pattern (58 bp):
TAAAATGTAATTTTTAGAAGTTCGAGGGTAAAAATGTAATTTTTGAGAAGTTCGGGGA
Found at i:7836473 original size:31 final size:31
Alignment explanation
Indices: 7836406--7836473 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
7836396 GGTAAATTTG
* *
7836406 TAATTTT-TAAAAAGTTTGAGGGTCAAAATG
1 TAATTTTGGAAAAAGTTTGAGGGTCAAAATA
7836436 TAATTTTGGAAAAAGTTT-AGGGGTCAAAATA
1 TAATTTTGGAAAAAGTTTGA-GGGTCAAAATA
*
7836467 TGATTTT
1 TAATTTT
7836474 TGAACAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
30 8 0.24
31 25 0.76
ACGTcount: A:0.38, C:0.03, G:0.21, T:0.38
Consensus pattern (31 bp):
TAATTTTGGAAAAAGTTTGAGGGTCAAAATA
Found at i:7838143 original size:17 final size:16
Alignment explanation
Indices: 7838121--7838168 Score: 71
Period size: 17 Copynumber: 3.0 Consensus size: 16
7838111 TTAAATTTTA
*
7838121 AATTTAAATTCAAAAT
1 AATTTAAATTTAAAAT
7838137 AAGTTTAAATTTAAAAT
1 AA-TTTAAATTTAAAAT
7838154 AA-TTAAATTTAAAAT
1 AATTTAAATTTAAAAT
7838169 TTTGAAATTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 13 0.43
16 2 0.07
17 15 0.50
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
AATTTAAATTTAAAAT
Found at i:7838177 original size:15 final size:15
Alignment explanation
Indices: 7838108--7838168 Score: 72
Period size: 15 Copynumber: 4.1 Consensus size: 15
7838098 TTGGACTTTT
*
7838108 TAATTAAATTTTAAA
1 TAATTAAATTTAAAA
*
7838123 T--TTAAATTCAAAA
1 TAATTAAATTTAAAA
7838136 TAAGTTTAAATTTAAAA
1 TAA--TTAAATTTAAAA
7838153 TAATTAAATTTAAAA
1 TAATTAAATTTAAAA
7838168 T
1 T
7838169 TTTGAAATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
13 11 0.28
15 14 0.36
17 14 0.36
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TAATTAAATTTAAAA
Found at i:7845791 original size:15 final size:15
Alignment explanation
Indices: 7845768--7845801 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7845758 CTTTGTAAAT
* *
7845768 TTTATTTTATTTTAA
1 TTTAGTTTAATTTAA
7845783 TTTAGTTTAATTTAA
1 TTTAGTTTAATTTAA
7845798 TTTA
1 TTTA
7845802 ATTTTTATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTAGTTTAATTTAA
Found at i:7845925 original size:15 final size:15
Alignment explanation
Indices: 7845907--7845943 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
7845897 CTTTTTTATT
7845907 TTTATTTA-TTGTTTA
1 TTTATTTATTTG-TTA
7845922 TTTATTTATTTGTTA
1 TTTATTTATTTGTTA
7845937 TTTATTT
1 TTTATTT
7845944 TCATGCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (15 bp):
TTTATTTATTTGTTA
Found at i:7846111 original size:28 final size:28
Alignment explanation
Indices: 7846080--7846135 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
7846070 TTAATTTCAT
7846080 TTATTGTTTTATG-TATTT-TATTTGTTTG
1 TTATT-TTTT-TGCTATTTATATTTGTTTG
*
7846108 TTATTTTTTTGCTATTTATATTTTTTTG
1 TTATTTTTTTGCTATTTATATTTGTTTG
7846136 CCTTATTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 9 0.36
28 14 0.56
ACGTcount: A:0.14, C:0.02, G:0.11, T:0.73
Consensus pattern (28 bp):
TTATTTTTTTGCTATTTATATTTGTTTG
Found at i:7846129 original size:17 final size:19
Alignment explanation
Indices: 7846109--7846149 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
7846099 ATTTGTTTGT
7846109 TATTTTTTTG-C-TATTTA
1 TATTTTTTTGCCTTATTTA
7846126 TATTTTTTTGCCTTATTTA
1 TATTTTTTTGCCTTATTTA
7846145 -ATTTT
1 TATTTT
7846150 GTTTATTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.45
18 6 0.27
19 6 0.27
ACGTcount: A:0.17, C:0.07, G:0.05, T:0.71
Consensus pattern (19 bp):
TATTTTTTTGCCTTATTTA
Found at i:7846135 original size:67 final size:66
Alignment explanation
Indices: 7846064--7846203 Score: 142
Period size: 67 Copynumber: 2.1 Consensus size: 66
7846054 ACATTCTTGC
* * * * * *
7846064 TTTTGTTTAATTTCATTTAT-TGT-TTTATGTATTTTATTTGTTTGTTATTTTTTTGCTAT-TTA
1 TTTTGTTT-ATTTAATTT-TGTGTATTTATGAATCTT-TTTATTTGTTATTTATTTG-TATGTCA
7846126 TATTT
62 TATTT
* *
7846131 TTTTGCCTTATTTAATTTTGTTTATTTATGAATCTTTTTATTTGTTATTTATTTGTATGTCATAT
1 TTTTG-TTTATTTAATTTTGTGTATTTATGAATCTTTTTATTTGTTATTTATTTGTATGTCATAT
7846196 TT
65 TT
7846198 TTTTGT
1 TTTTGT
7846204 CTTTAAATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
66 4 0.07
67 44 0.73
68 12 0.20
ACGTcount: A:0.17, C:0.04, G:0.09, T:0.69
Consensus pattern (66 bp):
TTTTGTTTATTTAATTTTGTGTATTTATGAATCTTTTTATTTGTTATTTATTTGTATGTCATATT
T
Found at i:7846336 original size:22 final size:22
Alignment explanation
Indices: 7846306--7846352 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
7846296 TTATTAATTA
7846306 ATTAATATT-TATTGTCATTATT
1 ATTAATATTATATTGTCATT-TT
* *
7846328 ATTATTATTATATTGTTATTTT
1 ATTAATATTATATTGTCATTTT
7846350 ATT
1 ATT
7846353 TAGGGATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (22 bp):
ATTAATATTATATTGTCATTTT
Found at i:7846435 original size:29 final size:30
Alignment explanation
Indices: 7846371--7846451 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 30
7846361 AATCCCAAAA
* *
7846371 TTATACATGAACTATGGTTTAATGTGCAATT
1 TTATACATGAACTTTGATTT-ATGTGCAATT
* *
7846402 GTATACATGAACTTTGATTT-TGTGTAATT
1 TTATACATGAACTTTGATTTATGTGCAATT
* *
7846431 TTATATATGAAATTTTGATTT
1 TTATACATG-AACTTTGATTT
7846452 GATCCAATTC
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 15 0.36
30 10 0.24
31 17 0.40
ACGTcount: A:0.31, C:0.06, G:0.15, T:0.48
Consensus pattern (30 bp):
TTATACATGAACTTTGATTTATGTGCAATT
Found at i:7846679 original size:29 final size:30
Alignment explanation
Indices: 7846643--7846704 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 30
7846633 GTTTTACATG
* *
7846643 TATAATTGCAC-TAAATTAAAGTTCATGTA
1 TATAATTGCACATAAATCAAAATTCATGTA
7846672 TATAATTGCACATTAAATCAAAATTCATGTA
1 TATAATTGCACA-TAAATCAAAATTCATGTA
7846703 TA
1 TA
7846705 ATTTTGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 11 0.38
31 18 0.62
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (30 bp):
TATAATTGCACATAAATCAAAATTCATGTA
Found at i:7846705 original size:29 final size:27
Alignment explanation
Indices: 7846639--7846707 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 27
7846629 TAGAGTTTTA
* *
7846639 CATGTATAATTGCACTAAATTAAAGTT
1 CATGTATAATTGCACTAAATCAAAATT
7846666 CATGTATATAATTGCACATTAAATCAAAATT
1 CATG--TATAATTGCAC--TAAATCAAAATT
7846697 CATGTATAATT
1 CATGTATAATT
7846708 TTGAGATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
27 4 0.11
29 18 0.50
31 14 0.39
ACGTcount: A:0.42, C:0.12, G:0.09, T:0.38
Consensus pattern (27 bp):
CATGTATAATTGCACTAAATCAAAATT
Found at i:7855662 original size:31 final size:31
Alignment explanation
Indices: 7855622--7855715 Score: 118
Period size: 31 Copynumber: 3.0 Consensus size: 31
7855612 CAGTTTACAC
* * * *
7855622 TTTGGTCACTTACCTATTAATAAGTTTATAA
1 TTTGATCACTTAACTATTAGTAAATTTATAA
*
7855653 TTTGATCACTTAATTATTAGTAAATTTATAA
1 TTTGATCACTTAACTATTAGTAAATTTATAA
*
7855684 TTTAATCA-TTCAACTATTAGTAAATTTATAA
1 TTTGATCACTT-AACTATTAGTAAATTTATAA
7855715 T
1 T
7855716 AGTCACTCTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
30 2 0.04
31 53 0.96
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (31 bp):
TTTGATCACTTAACTATTAGTAAATTTATAA
Found at i:7857830 original size:23 final size:21
Alignment explanation
Indices: 7857804--7857846 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
7857794 CCATCATCCA
7857804 CCTTAAAAATGATTTTGATCTTG
1 CCTTAAAAATG-TTTT-ATCTTG
**
7857827 CCTTTGAAATGTTTTATCTT
1 CCTTAAAAATGTTTTATCTT
7857847 CAACCAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.49
Consensus pattern (21 bp):
CCTTAAAAATGTTTTATCTTG
Done.