Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 123 of 193
Found at i:38818804 original size:12 final size:12
Alignment explanation
Indices: 38818784--38818817 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
38818774 TTGTTTATTC
38818784 TCTTCTTCTTGT
1 TCTTCTTCTTGT
* *
38818796 TCTTGTTCTTTT
1 TCTTCTTCTTGT
38818808 TCTTCTTCTT
1 TCTTCTTCTT
38818818 CTACTACATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.24, G:0.06, T:0.71
Consensus pattern (12 bp):
TCTTCTTCTTGT
Found at i:38824757 original size:3 final size:3
Alignment explanation
Indices: 38824749--38824773 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38824739 ATTCAATATT
38824749 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
38824774 CTAATATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:38825540 original size:29 final size:29
Alignment explanation
Indices: 38825485--38825540 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
38825475 TATATTTATG
* * * * *
38825485 ATTTTTAAAGGATTAAATTTTATTTTTCT
1 ATTTTTAAAAGATCAAAATATAATTTTCT
38825514 ATTTTTAAAAGATCAAAATATAATTTT
1 ATTTTTAAAAGATCAAAATATAATTTT
38825541 ACCGTTATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (29 bp):
ATTTTTAAAAGATCAAAATATAATTTTCT
Found at i:38825653 original size:33 final size:33
Alignment explanation
Indices: 38825608--38825674 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
38825598 CAAATGTTGG
*
38825608 AACCCAAATGAATAATAAGCTAAATTATATTGA
1 AACCCAAATGAATAATAAACTAAATTATATTGA
* * *
38825641 AACCCAACTGAATAATAAATTAATTTATATTGA
1 AACCCAAATGAATAATAAACTAAATTATATTGA
38825674 A
1 A
38825675 TCTCAAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (33 bp):
AACCCAAATGAATAATAAACTAAATTATATTGA
Found at i:38829645 original size:24 final size:24
Alignment explanation
Indices: 38829613--38829659 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
38829603 GAGTTTAAAA
38829613 CGTATAGTGG-CTGACGAGCATAAG
1 CGTATAGTGGAC-GACGAGCATAAG
*
38829637 CGTATAGTGGACGATGAGCATAA
1 CGTATAGTGGACGACGAGCATAA
38829660 ACGTGTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.21
Consensus pattern (24 bp):
CGTATAGTGGACGACGAGCATAAG
Found at i:38832523 original size:29 final size:31
Alignment explanation
Indices: 38832468--38832536 Score: 99
Period size: 29 Copynumber: 2.3 Consensus size: 31
38832458 AATCTCAAAA
38832468 TTATACATGGACTTTAGTCTAATGTGTAATT
1 TTATACATGGACTTTAGTCTAATGTGTAATT
*
38832499 TTATACATGGACTTT-GAT-T-TTGTGTAATT
1 TTATACATGGACTTTAG-TCTAATGTGTAATT
38832528 TTATACATG
1 TTATACATG
38832537 AAAATTTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 18 0.50
30 2 0.06
31 16 0.44
ACGTcount: A:0.28, C:0.09, G:0.16, T:0.48
Consensus pattern (31 bp):
TTATACATGGACTTTAGTCTAATGTGTAATT
Found at i:38832547 original size:30 final size:29
Alignment explanation
Indices: 38832490--38832548 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
38832480 TTTAGTCTAA
* *
38832490 TGTGTAATTTTATACATGGACTTTGATTT
1 TGTGTAATTTTATACATGAAATTTGATTT
38832519 TGTGTAATTTTATACATGAAAATTTGATTT
1 TGTGTAATTTTATACATG-AAATTTGATTT
38832549 AATATAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.29, C:0.05, G:0.15, T:0.51
Consensus pattern (29 bp):
TGTGTAATTTTATACATGAAATTTGATTT
Found at i:38832557 original size:30 final size:29
Alignment explanation
Indices: 38832494--38832557 Score: 74
Period size: 30 Copynumber: 2.2 Consensus size: 29
38832484 GTCTAATGTG
* * ** *
38832494 TAATTTTATACATGGACTTTGATTTTGTG
1 TAATTTTATACATGAAATTTGATTTAATA
38832523 TAATTTTATACATGAAAATTTGATTTAATA
1 TAATTTTATACATG-AAATTTGATTTAATA
38832553 TAATT
1 TAATT
38832558 CTCTCAAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 14 0.48
30 15 0.52
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (29 bp):
TAATTTTATACATGAAATTTGATTTAATA
Found at i:38843761 original size:2 final size:2
Alignment explanation
Indices: 38843754--38843786 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
38843744 AAGAAAAACA
38843754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38843787 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38843791 original size:2 final size:2
Alignment explanation
Indices: 38843786--38843811 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38843776 ATATATATAT
38843786 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
38843812 TATATTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:38844009 original size:15 final size:15
Alignment explanation
Indices: 38843960--38844009 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
38843950 ATTCCAATGT
*
38843960 AATGTGATT-CTTTAG
1 AATGTGATTGC-TGAG
*
38843975 AATGTGATTGCTGGG
1 AATGTGATTGCTGAG
*
38843990 GATGTGATTGCTGAG
1 AATGTGATTGCTGAG
38844005 AATGT
1 AATGT
38844010 TGCTTTACAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 28 0.97
16 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.32, T:0.38
Consensus pattern (15 bp):
AATGTGATTGCTGAG
Found at i:38851861 original size:39 final size:39
Alignment explanation
Indices: 38851818--38851898 Score: 153
Period size: 39 Copynumber: 2.1 Consensus size: 39
38851808 AAAGGCATAA
*
38851818 CTAGAGATTTAAATACTTGATCAATGGGCATGGTTCATT
1 CTAGAGATTTAAATACTTGATCAATGGGCATAGTTCATT
38851857 CTAGAGATTTAAATACTTGATCAATGGGCATAGTTCATT
1 CTAGAGATTTAAATACTTGATCAATGGGCATAGTTCATT
38851896 CTA
1 CTA
38851899 TACTAGATGC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.36
Consensus pattern (39 bp):
CTAGAGATTTAAATACTTGATCAATGGGCATAGTTCATT
Found at i:38856725 original size:17 final size:18
Alignment explanation
Indices: 38856687--38856727 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38856677 CTTTACTTTT
* *
38856687 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACACAGA
38856705 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
38856722 ATTTTA
1 ATTTTA
38856728 GTCACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:38865437 original size:12 final size:12
Alignment explanation
Indices: 38865420--38865448 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
38865410 CTTCAATCAA
38865420 CTAGCTGTTACC
1 CTAGCTGTTACC
38865432 CTAGCTGTTACC
1 CTAGCTGTTACC
38865444 CTAGC
1 CTAGC
38865449 AGTATCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.34, G:0.17, T:0.31
Consensus pattern (12 bp):
CTAGCTGTTACC
Found at i:38868748 original size:3 final size:3
Alignment explanation
Indices: 38868740--38868767 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
38868730 GAGCTTTCCT
38868740 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
38868768 GTTAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:38871362 original size:53 final size:53
Alignment explanation
Indices: 38871299--38871407 Score: 200
Period size: 53 Copynumber: 2.1 Consensus size: 53
38871289 GGTAAAGAGG
38871299 AACTGTGACTTAATAATCAAAATTGTTTCTATAATTTTTTCTCTCAGGACACA
1 AACTGTGACTTAATAATCAAAATTGTTTCTATAATTTTTTCTCTCAGGACACA
* *
38871352 AACTGTGACTTAATAATCAAAATTGTTTTTGTAATTTTTTCTCTCAGGACACA
1 AACTGTGACTTAATAATCAAAATTGTTTCTATAATTTTTTCTCTCAGGACACA
38871405 AAC
1 AAC
38871408 ACCGTCTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (53 bp):
AACTGTGACTTAATAATCAAAATTGTTTCTATAATTTTTTCTCTCAGGACACA
Found at i:38877617 original size:28 final size:28
Alignment explanation
Indices: 38877577--38877654 Score: 102
Period size: 28 Copynumber: 2.7 Consensus size: 28
38877567 AAATGAAATT
* *
38877577 AAAATAATATAATAATTTTATATTTTAA
1 AAAATAATTTAATAATTTTATATTTCAA
*
38877605 AAAAGAATTTAATAATTTTATATTTCAA
1 AAAATAATTTAATAATTTTATATTTCAA
*
38877633 AACGATAATTTTAATAATTTTA
1 AA-AATAA-TTTAATAATTTTA
38877655 AAACTATTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
28 27 0.63
29 3 0.07
30 13 0.30
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (28 bp):
AAAATAATTTAATAATTTTATATTTCAA
Found at i:38883612 original size:11 final size:11
Alignment explanation
Indices: 38883592--38883666 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
38883582 AAGCCTCTCA
*
38883592 TCTTTCCTTTC
1 TCTTTTCTTTC
*
38883603 TCTTTTCTTTT
1 TCTTTTCTTTC
*
38883614 TCTCATTCATTTC
1 TCT-TTTC-TTTC
38883627 T-TATTTCTTTC
1 TCT-TTTCTTTC
38883638 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
38883650 TATTTTCTTCC
1 TCTTTTCTTTC
38883661 TCTTTT
1 TCTTTT
38883667 AATCATACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 29 0.57
12 18 0.35
13 4 0.08
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:38883653 original size:22 final size:22
Alignment explanation
Indices: 38883599--38883663 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
38883589 TCATCTTTCC
*
38883599 TTTCTCTTTTCTTTTTCTCATTCA
1 TTTCT-TTTTCTTTCTCTC-TTCA
* *
38883623 TTTCTTATTTCTTTCTCTTTTCT
1 TTTCTT-TTTCTTTCTCTCTTCA
*
38883646 TTTCTATTTTCTTCCTCT
1 TTTCT-TTTTCTTTCTCT
38883664 TTTAATCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCTCTTCA
Found at i:38884109 original size:14 final size:15
Alignment explanation
Indices: 38884078--38884112 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
38884068 TTTTAAATCT
*
38884078 AACCAAACCCATTTG
1 AACCAAACCCAATTG
38884093 AACCAAA-CCAATTG
1 AACCAAACCCAATTG
38884107 AACCAA
1 AACCAA
38884113 GTCTAACCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.49, C:0.31, G:0.06, T:0.14
Consensus pattern (15 bp):
AACCAAACCCAATTG
Found at i:38884151 original size:10 final size:10
Alignment explanation
Indices: 38884138--38884164 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
38884128 AGTCAAACCA
38884138 TTGACCGGCG
1 TTGACCGGCG
38884148 TTGACCGGCG
1 TTGACCGGCG
38884158 TTGACCG
1 TTGACCG
38884165 ACCGTTGACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.30, G:0.37, T:0.22
Consensus pattern (10 bp):
TTGACCGGCG
Found at i:38884189 original size:20 final size:19
Alignment explanation
Indices: 38884164--38884252 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 19
38884154 GGCGTTGACC
38884164 GACCGTTGACTTTGACTGTT
1 GACCGTTGACTTTGACT-TT
* * *
38884184 GACCGTTAACCGTTGAATTT
1 GACCGTTGA-CTTTGACTTT
*
38884204 GACCGTTGAC---CAC--T
1 GACCGTTGACTTTGACTTT
38884218 GACCGTTGACTTTGACTATT
1 GACCGTTGACTTTGACT-TT
*
38884238 TACCGTTGACTTTGA
1 GACCGTTGACTTTGA
38884253 TCGTTGGCTT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
14 11 0.20
16 1 0.02
17 2 0.04
19 1 0.02
20 33 0.61
21 6 0.11
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.36
Consensus pattern (19 bp):
GACCGTTGACTTTGACTTT
Found at i:38884212 original size:7 final size:7
Alignment explanation
Indices: 38884164--38884227 Score: 51
Period size: 7 Copynumber: 9.4 Consensus size: 7
38884154 GGCGTTGACC
38884164 GACCGTT
1 GACCGTT
*
38884171 GA-CTTT
1 GACCGTT
*
38884177 GACTGTT
1 GACCGTT
38884184 GACCGTT
1 GACCGTT
*
38884191 AACCGTT
1 GACCGTT
**
38884198 GA-ATTT
1 GACCGTT
38884204 GACCGTT
1 GACCGTT
**
38884211 GACCACT
1 GACCGTT
38884218 GACCGTT
1 GACCGTT
38884225 GAC
1 GAC
38884228 TTTGACTATT
Statistics
Matches: 41, Mismatches: 14, Indels: 4
0.69 0.24 0.07
Matches are distributed among these distances:
6 9 0.22
7 32 0.78
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.31
Consensus pattern (7 bp):
GACCGTT
Found at i:38884247 original size:27 final size:27
Alignment explanation
Indices: 38884164--38884247 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
38884154 GGCGTTGACC
38884164 GACCGTTGACTTTGACTGTTGACCGTT
1 GACCGTTGACTTTGACTGTTGACCGTT
* * * **
38884191 AACCGTTGAATTTGACCGTTGACCACT
1 GACCGTTGACTTTGACTGTTGACCGTT
* *
38884218 GACCGTTGACTTTGACTATTTACCGTT
1 GACCGTTGACTTTGACTGTTGACCGTT
38884245 GAC
1 GAC
38884248 TTTGATCGTT
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (27 bp):
GACCGTTGACTTTGACTGTTGACCGTT
Found at i:38885317 original size:3 final size:3
Alignment explanation
Indices: 38885309--38885333 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
38885299 TATTCTATTC
38885309 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
38885334 TTGGGATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:38890737 original size:11 final size:11
Alignment explanation
Indices: 38890717--38890791 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
38890707 AAGCCTCTCA
*
38890717 TCTTTCCTTTC
1 TCTTTTCTTTC
*
38890728 TCTTTTCTTTT
1 TCTTTTCTTTC
*
38890739 TCTCATTCATTTC
1 TCT-TTTC-TTTC
38890752 T-TATTTCTTTC
1 TCT-TTTCTTTC
38890763 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
38890775 TATTTTCTTCC
1 TCTTTTCTTTC
38890786 TCTTTT
1 TCTTTT
38890792 AATCACACTC
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 29 0.57
12 18 0.35
13 4 0.08
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:38890778 original size:22 final size:22
Alignment explanation
Indices: 38890724--38890788 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
38890714 TCATCTTTCC
*
38890724 TTTCTCTTTTCTTTTTCTCATTCA
1 TTTCT-TTTTCTTTCTCTC-TTCA
* *
38890748 TTTCTTATTTCTTTCTCTTTTCT
1 TTTCTT-TTTCTTTCTCTCTTCA
*
38890771 TTTCTATTTTCTTCCTCT
1 TTTCT-TTTTCTTTCTCT
38890789 TTTAATCACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCTCTTCA
Found at i:38891233 original size:14 final size:15
Alignment explanation
Indices: 38891202--38891236 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
38891192 TTTTAAATCT
*
38891202 AACCAAACCCATTTG
1 AACCAAACCCAATTG
38891217 AACCAAA-CCAATTG
1 AACCAAACCCAATTG
38891231 AACCAA
1 AACCAA
38891237 GTCTAATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.49, C:0.31, G:0.06, T:0.14
Consensus pattern (15 bp):
AACCAAACCCAATTG
Found at i:38891303 original size:20 final size:19
Alignment explanation
Indices: 38891278--38891327 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
38891268 GGCGTTGACC
* *
38891278 GACCGTTGACTTTGACTGTT
1 GACCGTTGACGTTGAAT-TT
*
38891298 GACCGTTAACCGTTGAATTT
1 GACCGTTGA-CGTTGAATTT
38891318 GACCGTTGAC
1 GACCGTTGAC
38891328 CACTGACCGT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
19 1 0.04
20 18 0.72
21 6 0.24
ACGTcount: A:0.20, C:0.22, G:0.24, T:0.34
Consensus pattern (19 bp):
GACCGTTGACGTTGAATTT
Found at i:38891309 original size:27 final size:27
Alignment explanation
Indices: 38891279--38891351 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
38891269 GCGTTGACCG
* **
38891279 ACCGTTGACTTTGACTGTTGACCGTTA
1 ACCGTTGACTTTGACCGTTGACCACTA
* *
38891306 ACCGTTGAATTTGACCGTTGACCACTG
1 ACCGTTGACTTTGACCGTTGACCACTA
38891333 ACCG-TGACTTTGACCGTTG
1 ACCGTTGACTTTGACCGTTG
38891352 GCTTTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
26 14 0.35
27 26 0.65
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (27 bp):
ACCGTTGACTTTGACCGTTGACCACTA
Found at i:38895834 original size:136 final size:135
Alignment explanation
Indices: 38895590--38895864 Score: 424
Period size: 136 Copynumber: 2.0 Consensus size: 135
38895580 AGTAAAAAAT
* * * * * *
38895590 TTATGACTCGACTCGTCGGAGTTGTGATCCTGAAATCACTATTTTCGACACTATTGAAAATCGGG
1 TTATGACTCGACTCGTCGGAGTTGTGATCCCGAAATCACTATTTCCGACACCACTGAAAACCGAG
* *
38895655 CTATTACAATGTTACCCTCATAGGATATCCTTAATCTCTTTGGGACAATATACGCTCTCTCAATA
66 CTATTACAATGTTACCCTCATAAGATATCCTTAATCTCTTTGGGACAACATACGCTCTCTCAATA
38895720 TGATCC
131 TGAT-C
* *
38895726 TTATGACTCGACTCGTCGGAGTTGTGATCCCGAAATCATTGTTTCCGACACCACTGAAAACCGAG
1 TTATGACTCGACTCGTCGGAGTTGTGATCCCGAAATCACTATTTCCGACACCACTGAAAACCGAG
* * *
38895791 CTGTTACAATGTTACCCTCATAAGATATCCTTAATCTCTTTGGGATAACATCCGCTCTCTCAATA
66 CTATTACAATGTTACCCTCATAAGATATCCTTAATCTCTTTGGGACAACATACGCTCTCTCAATA
38895856 TGATC
131 TGATC
38895861 TTAT
1 TTAT
38895865 TTATATCATG
Statistics
Matches: 126, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
135 5 0.04
136 121 0.96
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.33
Consensus pattern (135 bp):
TTATGACTCGACTCGTCGGAGTTGTGATCCCGAAATCACTATTTCCGACACCACTGAAAACCGAG
CTATTACAATGTTACCCTCATAAGATATCCTTAATCTCTTTGGGACAACATACGCTCTCTCAATA
TGATC
Found at i:38898284 original size:16 final size:16
Alignment explanation
Indices: 38898265--38898295 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38898255 GAATTTAAAC
*
38898265 TAAAAAAAATTAAAAT
1 TAAAAAAAAATAAAAT
38898281 TAAAAAAAAATAAAA
1 TAAAAAAAAATAAAA
38898296 CCCCTAACAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAAAAAATAAAAT
Found at i:38898955 original size:180 final size:180
Alignment explanation
Indices: 38898629--38898974 Score: 464
Period size: 180 Copynumber: 1.9 Consensus size: 180
38898619 TGCTCAAATT
** * *
38898629 TTCGAGTAAGCATATATTTAGCTGATTTGTTTTAGGGTTCATAAAAAATTGTGAATTTTTATTTT
1 TTCGAGTAAGCATATATTTAGCCAATTTGTTTTA-GATTCATAAAAAATTGGGAATTTTTATTTT
* * *
38898694 TTTATTATTGTGTCGGTTGGACTAAATTGGTGCTACAATTCATCATAGAATTAGAATTAGGAAGG
65 TTTATTATTGTGTCGGCTGGACTAAATTGGTGCTAAAATTCATCATAGAATTAAAATTAGGAAGG
* * *
38898759 GAATTGTTGGGTTTATATAATACAAAGTCGAATTTTTTTATTTGAAATGTA
130 GAATTGTAGAGTTTATATAATAAAAAGTCGAATTTTTTTATTTGAAATGTA
* * *
38898810 TTCGGGTAAGCATAT-TTTAGCCAATTTG-TTT-GATTCATAAGAAATTGAGGATTTTTTAATTT
1 TTCGAGTAAGCATATATTTAGCCAATTTGTTTTAGATTCATAAAAAATTG-GGAATTTTT-ATTT
* * * **
38898872 TTTTGATTATTGTGTCGGCTGGATTAAATTGGTGGTAAAATTCGTCATATCATTAAAATTAGGAA
64 TTTT-ATTATTGTGTCGGCTGGACTAAATTGGTGCTAAAATTCATCATAGAATTAAAATTAGGAA
*
38898937 GGGAATTGTAGAGTTTATATAATAAAAAGTTGAATTTT
128 GGGAATTGTAGAGTTTATATAATAAAAAGTCGAATTTT
38898975 GTGTGTGAAT
Statistics
Matches: 143, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
177 14 0.10
178 7 0.05
179 11 0.08
180 97 0.68
181 14 0.10
ACGTcount: A:0.32, C:0.06, G:0.20, T:0.42
Consensus pattern (180 bp):
TTCGAGTAAGCATATATTTAGCCAATTTGTTTTAGATTCATAAAAAATTGGGAATTTTTATTTTT
TTATTATTGTGTCGGCTGGACTAAATTGGTGCTAAAATTCATCATAGAATTAAAATTAGGAAGGG
AATTGTAGAGTTTATATAATAAAAAGTCGAATTTTTTTATTTGAAATGTA
Found at i:38900539 original size:17 final size:17
Alignment explanation
Indices: 38900517--38900549 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38900507 GATTCAATAC
*
38900517 TTTAATTCGGTTAATTT
1 TTTAATTCGATTAATTT
38900534 TTTAATTCGATTAATT
1 TTTAATTCGATTAATT
38900550 CGGGTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.06, G:0.09, T:0.58
Consensus pattern (17 bp):
TTTAATTCGATTAATTT
Found at i:38901430 original size:158 final size:156
Alignment explanation
Indices: 38900959--38901431 Score: 547
Period size: 159 Copynumber: 3.0 Consensus size: 156
38900949 ATATGCCATC
* * * * *
38900959 CTTTTTTGGCTTCTAGTTCTCATACTTGTACCAGATTGAGA-AAAAAAAATCAGAAACCCAAATT
1 CTTTTTTGGCTTCTAGTTCTCGTACTCGTACCAAACTAAGACAAAAAAAATCAG-AACCCAAATT
* * * *
38901023 AGATTTAAATAATTTGGAATTGATATTAAAAAAGTGTTTACGATATACCTGTAATCCAATTATGT
65 AGATTT-AATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACCTGTGATCCAATTGTGT
* * *
38901088 TCGACTGAATGCATGGTGTTTTGTTGTT
129 TAGAATGAATGCATGGTATTTTGTTGTT
* * * *
38901116 CTTTTTTGACTTCTAGTT-TGCGTACTCGTACCATAGTAAGACCAAAAAAAATCATAACCTCAAA
1 CTTTTTTGGCTTCTAGTTCT-CGTACTCGTACCAAACTAAGA-CAAAAAAAATCAGAACC-CAAA
* ** ** *
38901180 TTAGATTAAAATATTTTTTAATTGACATTAAAAAAGTGTCCACGATATACTTGTGATCCAATTGT
63 TTAGATT-TAATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACCTGTGATCCAATTGT
* *
38901245 GTTAGGATGAATGCATGGTATTATGTTGTT
127 GTTAGAATGAATGCATGGTATTTTGTTGTT
* * *
38901275 ATTTTTTTGGCTTCTAGTTCTCGTACTCGTACCAAACTAAGACAAAAAAAATTAGAATCCAAATT
1 -CTTTTTTGGCTTCTAGTTCTCGTACTCGTACCAAACTAAGACAAAAAAAATCAGAACCCAAATT
* * * *
38901340 AGATTGTAATATTTTGGAATTGACAATGAAAAAGTGTTTACGATATACCTGTGTTCTC-GTTGTG
65 AGATT-TAATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACCTGTGATC-CAATTGTG
* *
38901404 TTAGAATGAATGCATGATCTTTTGTTGT
128 TTAGAATGAATGCATGGTATTTTGTTGT
38901432 GACCCTCACA
Statistics
Matches: 264, Mismatches: 44, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
156 1 0.00
157 33 0.12
158 85 0.32
159 109 0.41
160 35 0.13
161 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (156 bp):
CTTTTTTGGCTTCTAGTTCTCGTACTCGTACCAAACTAAGACAAAAAAAATCAGAACCCAAATTA
GATTTAATATTTTGGAATTGACATTAAAAAAGTGTTTACGATATACCTGTGATCCAATTGTGTTA
GAATGAATGCATGGTATTTTGTTGTT
Found at i:38902133 original size:96 final size:95
Alignment explanation
Indices: 38901965--38902146 Score: 226
Period size: 96 Copynumber: 1.9 Consensus size: 95
38901955 AAATTTGAAG
* * * *
38901965 AAGGATATTTGATTACCTCGATTTGAAGAAAGGTTGCACCTAGTGAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTACCTCGATTTGAAGAAAGATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
38902030 TAATCGAAGATAAGAA-AATATTGCCTCGATT
66 TAATCGAA-ATAA-AAGAATATTGCCTCGATT
** *
38902061 AAGGATATTCGATTATTTCGATTTGAAG-AAGAATCGCACCTAGTAAGTTAAGGCGCAAAATTTT
1 AAGGATATTCGATTACCTCGATTTGAAGAAAG-ATCGCACCTAGTAAGTTAAGGCAC-AAATTTT
* *
38902125 GA-ACTCGAAATAAAAGAATATT
64 CATAATCGAAATAAAAGAATATT
38902147 ATCTCGGTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
94 2 0.03
95 13 0.18
96 51 0.69
97 8 0.11
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (95 bp):
AAGGATATTCGATTACCTCGATTTGAAGAAAGATCGCACCTAGTAAGTTAAGGCACAAATTTTCA
TAATCGAAATAAAAGAATATTGCCTCGATT
Found at i:38902538 original size:59 final size:57
Alignment explanation
Indices: 38902475--38902681 Score: 209
Period size: 58 Copynumber: 3.6 Consensus size: 57
38902465 TAGATATCCG
* * * * * *
38902475 AGGGGTAAAATGCTACTTTTTGGTGACATCGGGGTTTAAAATGGAATTTTAAAGAGTTC
1 AGGGGTAAAATGGTAATTTTTGATAAAATCGGGG-TAAAAATGGAATTTTAAA-AGTTC
* * ** * *
38902534 AGGGGTAAAATGGTAATTTTCGATAAAATTTGGGCCAAAAATAGAATTTCAAAAAGTTC
1 AGGGGTAAAATGGTAATTTTTGATAAAA-TCGGGGTAAAAATGGAATTT-TAAAAGTTC
* * * *
38902593 -GAGGTAAAATGGTAATTTTTGATAAAATCGAGGTCAAAATGGAATTTTGGAAAGTTC
1 AGGGGTAAAATGGTAATTTTTGATAAAATCGGGGTAAAAATGGAATTTT-AAAAGTTC
*
38902650 AGGGGTAAAATGGTAATTTTTGGTAAAATCGG
1 AGGGGTAAAATGGTAATTTTTGATAAAATCGG
38902682 AAAGTTTGGG
Statistics
Matches: 119, Mismatches: 25, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
57 21 0.18
58 53 0.45
59 38 0.32
60 7 0.06
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (57 bp):
AGGGGTAAAATGGTAATTTTTGATAAAATCGGGGTAAAAATGGAATTTTAAAAGTTC
Found at i:38902610 original size:28 final size:28
Alignment explanation
Indices: 38902578--38902668 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
38902568 CCAAAAATAG
38902578 AATTTCAAAAAGTTCGAGGTAAAATGGT
1 AATTTCAAAAAGTTCGAGGTAAAATGGT
*
38902606 AATTTTTGATAAAA--TCGAGGTCAAAATGG-
1 AA--TTTCA-AAAAGTTCGAGGT-AAAATGGT
*** *
38902635 AATTTTGGAAAGTTCAGGGGTAAAATGGT
1 AATTTCAAAAAGTTC-GAGGTAAAATGGT
38902664 AATTT
1 AATTT
38902669 TTGGTAAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
26 3 0.06
27 3 0.06
28 11 0.22
29 18 0.36
30 11 0.22
31 4 0.08
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (28 bp):
AATTTCAAAAAGTTCGAGGTAAAATGGT
Found at i:38902610 original size:58 final size:59
Alignment explanation
Indices: 38902512--38902678 Score: 214
Period size: 58 Copynumber: 2.9 Consensus size: 59
38902502 ATCGGGGTTT
* * *
38902512 AAAATGGAATTTTAAAGAGTTCAGGGGTAAAATGGTAATTTTCGATAAAATTTG-GGCC
1 AAAATGGAATTTTAAAAAGTTCAGGGGTAAAATGGTAATTTTTGATAAAATTCGAGGCC
* * * *
38902570 AAAAATAGAATTTCAAAAAGTTC-GAGGTAAAATGGTAATTTTTGATAAAA-TCGAGGTC
1 -AAAATGGAATTTTAAAAAGTTCAGGGGTAAAATGGTAATTTTTGATAAAATTCGAGGCC
** *
38902628 AAAATGGAATTTTGGAAAGTTCAGGGGTAAAATGGTAATTTTTGGTAAAAT
1 AAAATGGAATTTTAAAAAGTTCAGGGGTAAAATGGTAATTTTTGATAAAAT
38902679 CGGAAAGTTT
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
57 20 0.22
58 53 0.58
59 19 0.21
ACGTcount: A:0.41, C:0.05, G:0.23, T:0.31
Consensus pattern (59 bp):
AAAATGGAATTTTAAAAAGTTCAGGGGTAAAATGGTAATTTTTGATAAAATTCGAGGCC
Found at i:38902638 original size:29 final size:29
Alignment explanation
Indices: 38902591--38902680 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
38902581 TTCAAAAAGT
38902591 TCGAGGTAAAATGGTAATTTTTGATAAAA
1 TCGAGGTAAAATGGTAATTTTTGATAAAA
* **
38902620 TCGAGGTCAAAATGG-AATTTTGGA-AAGT
1 TCGAGGT-AAAATGGTAATTTTTGATAAAA
* *
38902648 TCAGGGGTAAAATGGTAATTTTTGGTAAAA
1 TC-GAGGTAAAATGGTAATTTTTGATAAAA
38902678 TCG
1 TCG
38902681 GAAAGTTTGG
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
28 11 0.22
29 27 0.55
30 11 0.22
ACGTcount: A:0.37, C:0.06, G:0.26, T:0.32
Consensus pattern (29 bp):
TCGAGGTAAAATGGTAATTTTTGATAAAA
Found at i:38902676 original size:18 final size:18
Alignment explanation
Indices: 38902653--38902711 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
38902643 AAAGTTCAGG
38902653 GGTAAAATGGTAATTTTT
1 GGTAAAATGGTAATTTTT
* **
38902671 GGTAAAATCGGAAAGTTTGGG
1 GGTAAAAT-GGTAA-TTT-TT
38902692 GGTAAAATGGTAATTTTT
1 GGTAAAATGGTAATTTTT
38902710 GG
1 GG
38902712 AAGTTTCGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
18 10 0.31
19 7 0.22
20 7 0.22
21 8 0.25
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.36
Consensus pattern (18 bp):
GGTAAAATGGTAATTTTT
Found at i:38902715 original size:29 final size:28
Alignment explanation
Indices: 38902683--38902801 Score: 87
Period size: 30 Copynumber: 4.0 Consensus size: 28
38902673 TAAAATCGGA
* *
38902683 AAGTTTGGGGGTAAAATGGTAATTTTTGG
1 AAGTTTGAGGGTAAAAT-ATAATTTTTGG
** * *
38902712 AAGTTTCGAGGCAAAAATATACTTTTAGG
1 AAGTTT-GAGGGTAAAATATAATTTTTGG
* *
38902741 AAGTTTTTG-GGGTCAAAATGTAATTTCTGAG
1 AAG--TTTGAGGGT-AAAATATAATTTTTG-G
*
38902772 AAGTTTGAGGGTTAAAGTATAATTTTTGG
1 AAGTTTGAGGG-TAAAATATAATTTTTGG
38902801 A
1 A
38902802 CAATTTAGGG
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
29 25 0.37
30 35 0.51
31 8 0.12
ACGTcount: A:0.32, C:0.04, G:0.27, T:0.37
Consensus pattern (28 bp):
AAGTTTGAGGGTAAAATATAATTTTTGG
Found at i:38903612 original size:20 final size:20
Alignment explanation
Indices: 38903587--38903646 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
38903577 AGATCTGGAA
38903587 TTTAAAATCATTTTATTTTT-
1 TTTAAAATC-TTTTATTTTTG
38903607 TTTAAACATCTTCTT-TTTTTG
1 TTTAAA-ATCTT-TTATTTTTG
38903628 TTTAAAA-CTTTTGATTTTT
1 TTTAAAATCTTTT-ATTTTT
38903647 CCATTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.06
19 3 0.09
20 19 0.54
21 11 0.31
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTAAAATCTTTTATTTTTG
Found at i:38903866 original size:18 final size:17
Alignment explanation
Indices: 38903843--38903885 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
38903833 TATTACCATT
38903843 TATTATTATTTAAAAAAA
1 TATTATTA-TTAAAAAAA
*
38903861 TATTATTATTAAAATAA
1 TATTATTATTAAAAAAA
38903878 TAATTATT
1 T-ATTATT
38903886 GCTATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TATTATTATTAAAAAAA
Found at i:38904591 original size:18 final size:18
Alignment explanation
Indices: 38904568--38904624 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
38904558 GTAATTGGAC
38904568 ATTTTAAACTTAATTTTA
1 ATTTTAAACTTAATTTTA
** *
38904586 ATTTTAAAAATCATTTTA
1 ATTTTAAACTTAATTTTA
* * *
38904604 AATTT-AACTAAATTTAA
1 ATTTTAAACTTAATTTTA
38904621 ATTT
1 ATTT
38904625 AAAAAAATTT
Statistics
Matches: 29, Mismatches: 10, Indels: 1
0.73 0.25 0.03
Matches are distributed among these distances:
17 10 0.34
18 19 0.66
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTAAACTTAATTTTA
Found at i:38904621 original size:16 final size:16
Alignment explanation
Indices: 38904600--38904637 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
38904590 TAAAAATCAT
**
38904600 TTTAAATTTAACTAAA
1 TTTAAATTTAAAAAAA
38904616 TTTAAATTTAAAAAAA
1 TTTAAATTTAAAAAAA
38904632 TTTAAA
1 TTTAAA
38904638 ATCAATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TTTAAATTTAAAAAAA
Found at i:38906937 original size:24 final size:24
Alignment explanation
Indices: 38906910--38906967 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
38906900 CCCTTACCAC
*
38906910 CCTCATCACCTTTACTGCGAACAA
1 CCTCACCACCTTTACTGCGAACAA
* * *
38906934 CCTCACCACCTTTATTTCTAACAA
1 CCTCACCACCTTTACTGCGAACAA
38906958 CCTCACCACC
1 CCTCACCACC
38906968 CAATCCCTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.28, C:0.43, G:0.03, T:0.26
Consensus pattern (24 bp):
CCTCACCACCTTTACTGCGAACAA
Found at i:38907063 original size:69 final size:69
Alignment explanation
Indices: 38906934--38907063 Score: 183
Period size: 69 Copynumber: 1.9 Consensus size: 69
38906924 CTGCGAACAA
* * ** *
38906934 CCTCACCACCTTTATTTCTAACAACCTCACCACCCAATCCCTCACCCTCACCACCTTCACCACCA
1 CCTCACCACCTTTATTGCTAACAACCTCACCACCAAATCCCTCACCCGAACCACCATCACCACCA
38906999 TTAC
66 TTAC
38907003 CCTCACCACCTTTATTGC-AATCAACCTCACCACCAAATCCCTCACCCGAACC-CTCATCACC
1 CCTCACCACCTTTATTGCTAA-CAACCTCACCACCAAATCCCTCACCCGAACCAC-CATCACC
38907064 TTTACTACCA
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 3 0.06
69 51 0.94
ACGTcount: A:0.27, C:0.50, G:0.02, T:0.22
Consensus pattern (69 bp):
CCTCACCACCTTTATTGCTAACAACCTCACCACCAAATCCCTCACCCGAACCACCATCACCACCA
TTAC
Found at i:38907127 original size:24 final size:24
Alignment explanation
Indices: 38907080--38907128 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
38907070 ACCAACAACC
* *
38907080 TCACCTCCTTCATCACCCTCACCA
1 TCACCACCTTCATCACCATCACCA
* *
38907104 TCACCACCTTCATTACCATTACCA
1 TCACCACCTTCATCACCATCACCA
38907128 T
1 T
38907129 AAAATTGCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.24, C:0.47, G:0.00, T:0.29
Consensus pattern (24 bp):
TCACCACCTTCATCACCATCACCA
Found at i:38909954 original size:32 final size:32
Alignment explanation
Indices: 38909886--38909986 Score: 87
Period size: 32 Copynumber: 3.2 Consensus size: 32
38909876 TAACAAACGT
* * ** * *
38909886 TAAACTCGAAAGTCCTCAAAATTGACGGACCA
1 TAAACTTGAAAATCCTCAAAATAAATGAACCA
*
38909918 TAAACTTGAAAATCCTCAAAATAAATGAACCC
1 TAAACTTGAAAATCCTCAAAATAAATGAACCA
* * * *
38909950 TAAAC-TCAAAATTCCTCAAAATCAATAAACCT
1 TAAACTTGAAAA-TCCTCAAAATAAATGAACCA
38909982 TAAAC
1 TAAAC
38909987 CCAAAATTCC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
31 5 0.09
32 52 0.91
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.22
Consensus pattern (32 bp):
TAAACTTGAAAATCCTCAAAATAAATGAACCA
Found at i:38909992 original size:32 final size:32
Alignment explanation
Indices: 38909926--38910002 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
38909916 CATAAACTTG
* *
38909926 AAAA-TCCTCAAAATAAATGAACCCTAAACTC
1 AAAATTCCTCAAAATAAATAAACCCTAAACCC
* *
38909957 AAAATTCCTCAAAATCAATAAACCTTAAACCC
1 AAAATTCCTCAAAATAAATAAACCCTAAACCC
38909989 AAAATTCC-CAAAAT
1 AAAATTCCTCAAAAT
38910003 TGATAATTCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
31 10 0.24
32 31 0.76
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21
Consensus pattern (32 bp):
AAAATTCCTCAAAATAAATAAACCCTAAACCC
Found at i:38910740 original size:18 final size:20
Alignment explanation
Indices: 38910699--38910740 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
38910689 TATGACAAAT
*
38910699 TTTTTAATACATTATTTTAA
1 TTTTTAACACATTATTTTAA
*
38910719 TTTTTAACAC-TT-TTTTAC
1 TTTTTAACACATTATTTTAA
38910737 TTTT
1 TTTT
38910741 ACTTTAACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.45
19 2 0.10
20 9 0.45
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTTTAACACATTATTTTAA
Found at i:38918399 original size:31 final size:31
Alignment explanation
Indices: 38918351--38918419 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
38918341 TAACCTAGTT
* *
38918351 AAAGTTTAGGTATCTATTTGAGATAAA-AAGA
1 AAAGTTTAGGTACCTATTTGA-AAAAATAAGA
* *
38918382 AAAGTTTTGGTACCTATTTGAAAAAATAAGG
1 AAAGTTTAGGTACCTATTTGAAAAAATAAGA
38918413 AAAGTTT
1 AAAGTTT
38918420 GGGGTCTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.33
Consensus pattern (31 bp):
AAAGTTTAGGTACCTATTTGAAAAAATAAGA
Found at i:38920072 original size:18 final size:18
Alignment explanation
Indices: 38920051--38920088 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
38920041 GATTTACATA
38920051 TTAATTAATATTTCTATT
1 TTAATTAATATTTCTATT
* *
38920069 TTAATTAATTTTTTTATT
1 TTAATTAATATTTCTATT
38920087 TT
1 TT
38920089 TTAAATAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTAATTAATATTTCTATT
Found at i:38921834 original size:56 final size:56
Alignment explanation
Indices: 38921732--38921838 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
38921722 ATCTATATTC
* * **
38921732 AATTATGAAAAATTATAAAATATTCACTTAGTTATTAATAAATTTTTTTATCACTT
1 AATTATGAAAAATTATAAAATAATCACTCAACTATTAATAAATTTTTTTATCACTT
* *
38921788 AATTATGAAAAATTTATAAAATAATCACTCAACTATTCA-AATTTTTTTTAT
1 AATTATGAAAAA-TTATAAAATAATCACTCAACTATTAATAAATTTTTTTAT
38921839 TATCAATTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 23 0.52
57 21 0.48
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (56 bp):
AATTATGAAAAATTATAAAATAATCACTCAACTATTAATAAATTTTTTTATCACTT
Found at i:38922016 original size:56 final size:57
Alignment explanation
Indices: 38921929--38922037 Score: 130
Period size: 57 Copynumber: 1.9 Consensus size: 57
38921919 TGAGTGATTA
* * * * * * *
38921929 TTTTGTAACTTTTTATAGTTGAGTGA-TAAAAAAATTTACTAATAATTAGATGACCG
1 TTTTATAACTTTTCATAATTGAATGACAAAAAAAATTAACTAACAATTAGATGACCG
* *
38921985 TTTTATAACTTTTCATAATTTAATGACAAAAAAAATTAACTTACAATTAGATG
1 TTTTATAACTTTTCATAATTGAATGACAAAAAAAATTAACTAACAATTAGATG
38922038 TAATTTACCT
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
56 21 0.49
57 22 0.51
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.40
Consensus pattern (57 bp):
TTTTATAACTTTTCATAATTGAATGACAAAAAAAATTAACTAACAATTAGATGACCG
Found at i:38933833 original size:35 final size:34
Alignment explanation
Indices: 38933773--38933853 Score: 128
Period size: 35 Copynumber: 2.4 Consensus size: 34
38933763 AACTCTTCAC
38933773 TTTTAATTTAAAAAATTTAATCATTCTACTT-AA
1 TTTTAATTTAAAAAATTTAATCATTCTACTTAAA
*
38933806 TTTTAATTTAGAAAATATTTAATCATTCTATTTAAA
1 TTTTAATTTA-AAAA-ATTTAATCATTCTACTTAAA
38933842 TTTTAATTTAAA
1 TTTTAATTTAAA
38933854 GATATAGACA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
33 10 0.23
34 4 0.09
35 18 0.41
36 12 0.27
ACGTcount: A:0.42, C:0.06, G:0.01, T:0.51
Consensus pattern (34 bp):
TTTTAATTTAAAAAATTTAATCATTCTACTTAAA
Found at i:38943212 original size:16 final size:16
Alignment explanation
Indices: 38943191--38943229 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
38943181 ATATGATTAG
*
38943191 CCTATACACCATTCAC
1 CCTATACACCATCCAC
38943207 CCTATACACCATCCAC
1 CCTATACACCATCCAC
*
38943223 GCTATAC
1 CCTATAC
38943230 TAGCCAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.44, G:0.03, T:0.23
Consensus pattern (16 bp):
CCTATACACCATCCAC
Found at i:38943874 original size:29 final size:29
Alignment explanation
Indices: 38943825--38943883 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
38943815 TCTTCACGGC
38943825 TAAGGAGGAAAAACTAAGGTTTTTCATTG
1 TAAGGAGGAAAAACTAAGGTTTTTCATTG
* *
38943854 TAAGGAGGAAAAATTAGGGTTTTTCATTG
1 TAAGGAGGAAAAACTAAGGTTTTTCATTG
38943883 T
1 T
38943884 CAATCTTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.05, G:0.25, T:0.34
Consensus pattern (29 bp):
TAAGGAGGAAAAACTAAGGTTTTTCATTG
Found at i:38944692 original size:61 final size:61
Alignment explanation
Indices: 38944597--38944980 Score: 660
Period size: 61 Copynumber: 6.3 Consensus size: 61
38944587 GTAAATGCAA
* *
38944597 AAAGGTCTGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATCGATT
1 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
*
38944658 AAAGGTCCGATGTCTTTATTTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
1 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
38944719 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
1 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
* *
38944780 AAAGGTTCGATGTCTTTATGTCATCGTGAATATTACATGAAAATGAATCCTATTATGGATT
1 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
* * * *
38944841 AAAGATTCGATGTCTTTATGTCATCGTGAGTATTACACGAAAATGAATCCTATTATGAATT
1 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
**
38944902 AAAGGTTTGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
1 AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
*
38944963 AAAGGTCTGATGTCTTTA
1 AAAGGTCCGATGTCTTTA
38944981 CGGGATCGTG
Statistics
Matches: 308, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 308 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (61 bp):
AAAGGTCCGATGTCTTTATGTCATCGTGAGTATTACATGAAAATGAATCCTATTATGGATT
Found at i:38947980 original size:21 final size:21
Alignment explanation
Indices: 38947942--38948012 Score: 65
Period size: 21 Copynumber: 3.4 Consensus size: 21
38947932 GTTTTCAGTA
*
38947942 TTGGTAGAAGTAAT-ACTTGTT
1 TTGGTAGAAG-AGTCACTTGTT
*
38947963 TTGGTAGAAGAGTCACTTGTA
1 TTGGTAGAAGAGTCACTTGTT
* **
38947984 TCGGTAGAATTGTCACTTG-T
1 TTGGTAGAAGAGTCACTTGTT
*
38948004 ATGGTAGAA
1 TTGGTAGAA
38948013 ATCTACACTT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
20 9 0.22
21 32 0.78
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (21 bp):
TTGGTAGAAGAGTCACTTGTT
Found at i:38948011 original size:20 final size:20
Alignment explanation
Indices: 38947964--38948012 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
38947954 ATACTTGTTT
38947964 TGGTAGAAGAGTCACTTGTA
1 TGGTAGAAGAGTCACTTGTA
**
38947984 TCGGTAGAATTGTCACTTGTA
1 T-GGTAGAAGAGTCACTTGTA
38948005 TGGTAGAA
1 TGGTAGAA
38948013 ATCTACACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (20 bp):
TGGTAGAAGAGTCACTTGTA
Found at i:38948021 original size:21 final size:21
Alignment explanation
Indices: 38947975--38948023 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
38947965 GGTAGAAGAG
* *
38947975 TCACTTGTATCGGTAGAATTG
1 TCACTTGTATCGGTAGAAATC
38947996 TCACTTGTAT-GGTAGAAATC
1 TCACTTGTATCGGTAGAAATC
38948016 TACACTTG
1 T-CACTTG
38948024 AATTATTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (21 bp):
TCACTTGTATCGGTAGAAATC
Found at i:38951232 original size:33 final size:33
Alignment explanation
Indices: 38951164--38951238 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
38951154 TCCCCTTCAA
* **
38951164 CTTGTAACCCTCCTACATCACCCTACCCATTAG
1 CTTGTACCCCTCCTACATCACCCTACCCAACAG
* * *
38951197 CTTGTACCCCTTCTACATCACTCTCCCCAACAG
1 CTTGTACCCCTCCTACATCACCCTACCCAACAG
*
38951230 CTTTTACCC
1 CTTGTACCC
38951239 TTTTCAAATC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.21, C:0.44, G:0.05, T:0.29
Consensus pattern (33 bp):
CTTGTACCCCTCCTACATCACCCTACCCAACAG
Found at i:38951283 original size:33 final size:34
Alignment explanation
Indices: 38951263--38951357 Score: 117
Period size: 33 Copynumber: 2.9 Consensus size: 34
38951253 TCACCATTAG
*
38951263 ATTCTTCCCCTTCATCATCA-CTCTCCTCATCAA
1 ATTCTACCCCTTCATCATCACCTCTCCTCATCAA
38951296 ATTCTACCCCTTCATCATCA-CTCTCC-CTATCAA
1 ATTCTACCCCTTCATCATCACCTCTCCTC-ATCAA
* * *
38951329 CTTCCACCCTTTCATCATCACC-CTCCTCA
1 ATTCTACCCCTTCATCATCACCTCTCCTCA
38951358 ATAGTCAACA
Statistics
Matches: 55, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
32 1 0.02
33 52 0.95
34 2 0.04
ACGTcount: A:0.21, C:0.45, G:0.00, T:0.34
Consensus pattern (34 bp):
ATTCTACCCCTTCATCATCACCTCTCCTCATCAA
Found at i:38952393 original size:16 final size:16
Alignment explanation
Indices: 38952372--38952409 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
38952362 AGATGTTATG
*
38952372 GATTTGGGGATTTCAT
1 GATTTGGGGATTTCAC
*
38952388 GATTTGGGGGTTTCAC
1 GATTTGGGGATTTCAC
38952404 GATTTG
1 GATTTG
38952410 AGAAATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.16, C:0.08, G:0.34, T:0.42
Consensus pattern (16 bp):
GATTTGGGGATTTCAC
Found at i:38952817 original size:9 final size:9
Alignment explanation
Indices: 38952803--38952881 Score: 51
Period size: 9 Copynumber: 9.1 Consensus size: 9
38952793 ACAGTGTTAA
38952803 ACATAACAT
1 ACATAACAT
*
38952812 ACATAATAT
1 ACATAACAT
38952821 ACAT-ACAT
1 ACATAACAT
38952829 AACA-AACAT
1 -ACATAACAT
* * *
38952838 A-TTTATA-
1 ACATAACAT
*
38952845 ACAGTAATAT
1 ACA-TAACAT
*
38952855 ACATGACAT
1 ACATAACAT
38952864 ACATAACAT
1 ACATAACAT
38952873 ACAT-ACAT
1 ACATAACAT
38952881 A
1 A
38952882 ACAGATGTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
7 1 0.02
8 11 0.20
9 39 0.72
10 3 0.06
ACGTcount: A:0.53, C:0.18, G:0.03, T:0.27
Consensus pattern (9 bp):
ACATAACAT
Found at i:38952826 original size:13 final size:13
Alignment explanation
Indices: 38952802--38952884 Score: 66
Period size: 13 Copynumber: 6.3 Consensus size: 13
38952792 AACAGTGTTA
38952802 AACATAACATACAT
1 AACAT-ACATACAT
*
38952816 AATATACATACAT
1 AACATACATACAT
* *
38952829 AACAAACATATTTAT
1 AACATACATA--CAT
38952844 AACAGTA-AT--AT
1 AACA-TACATACAT
38952855 -ACATGACATACAT
1 AACAT-ACATACAT
38952868 AACATACATACAT
1 AACATACATACAT
38952881 AACA
1 AACA
38952885 GATGTAACAA
Statistics
Matches: 56, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
9 1 0.02
10 4 0.07
11 4 0.07
13 30 0.54
14 8 0.14
15 8 0.14
16 1 0.02
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.25
Consensus pattern (13 bp):
AACATACATACAT
Found at i:38952848 original size:52 final size:51
Alignment explanation
Indices: 38952786--38952884 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 51
38952776 ATATACTTAC
** *
38952786 TATTTAAACAGTGTTAAACATAACATACATAATATACATACATAACAAACA
1 TATTTAAACAGTAATAAACATAACATACATAACATACATACATAACAAACA
* *
38952837 TATTTATAACAGTAATATACATGACATACATAACATACATACATAACA
1 TATTTA-AACAGTAATAAACATAACATACATAACATACATACATAACA
38952885 GATGTAACAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
51 6 0.14
52 36 0.86
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.28
Consensus pattern (51 bp):
TATTTAAACAGTAATAAACATAACATACATAACATACATACATAACAAACA
Found at i:38954968 original size:13 final size:13
Alignment explanation
Indices: 38954872--38954970 Score: 58
Period size: 13 Copynumber: 7.5 Consensus size: 13
38954862 CATATTTCAT
*
38954872 AACATACAAAACA
1 AACATACATAACA
* *
38954885 TACATATATAACA
1 AACATACATAACA
*
38954898 GACATA-ATAAC-
1 AACATACATAACA
38954909 AACATACATAACA
1 AACATACATAACA
*
38954922 GTAATATACATAACA
1 --AACATACATAACA
* * *** *
38954937 TACTTTGGTAAAGA
1 AACATACAT-AACA
38954951 AACATACATAACA
1 AACATACATAACA
38954964 AACATAC
1 AACATAC
38954971 CTTTCACCTT
Statistics
Matches: 62, Mismatches: 19, Indels: 10
0.68 0.21 0.11
Matches are distributed among these distances:
11 5 0.08
12 10 0.16
13 28 0.45
14 7 0.11
15 12 0.19
ACGTcount: A:0.56, C:0.18, G:0.05, T:0.21
Consensus pattern (13 bp):
AACATACATAACA
Found at i:38955357 original size:31 final size:30
Alignment explanation
Indices: 38955316--38955377 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
38955306 CGAATGCTAT
38955316 CAAAAACAAAAATTAGAAGTCAAATATAATA
1 CAAAAAC-AAAATTAGAAGTCAAATATAATA
* * *
38955347 CAAATACAAAATTTGAAGTCAGATATAATA
1 CAAAAACAAAATTAGAAGTCAAATATAATA
38955377 C
1 C
38955378 GAACAAAAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.58, C:0.11, G:0.08, T:0.23
Consensus pattern (30 bp):
CAAAAACAAAATTAGAAGTCAAATATAATA
Found at i:38955517 original size:279 final size:278
Alignment explanation
Indices: 38954994--38955552 Score: 1023
Period size: 276 Copynumber: 2.0 Consensus size: 278
38954984 TCTTAATCTG
38954994 TTTAACCCTTGAAAAAAAAATCCACTCCAGTCACGAATGCTACTATCAAAAACAAAAATTAGAAG
1 TTTAACCCTTGAAAAAAAAATCCACTCCAGTCACGAATG--ACTATCAAAAACAAAAATTAGAAG
**
38955059 TCAAATATAATATGAATACAAAATTTGAAGTCAGATAAAATACGAACAAAAACAAAAATTTGTCA
64 TCAAATATAATACAAATACAAAATTTGAAGTCAGATAAAATACGAACAAAAACAAAAATTTGTCA
38955124 ATATAAAACTAGAAAATTTTGTTTTCCTAAACCCTAAACCAAAAAACCGAATGTTCCAAAAAATT
129 ATATAAAACTAGAAAATTTTGTTTTCCTAAACCCTAAACCAAAAAACCGAATGTTCCAAAAAATT
38955189 AGAAAAAATTGTGTCCCTACACCCTATACCAGAAAATAGAATGTTCCCAAAAAATTGTCAATTTT
194 AGAAAAAATTGTGTCCCTACACCCTATACCAGAAAATAGAATGTTCCCAAAAAATTGTCAATTTT
38955254 TGAGAACGAGTCAAAACAAA
259 TGAGAACGAGTCAAAACAAA
38955274 TTTAACCCTTG-AAAAAAAATCCACTCCAGTCACGAATG-CTATCAAAAACAAAAATTAGAAGTC
1 TTTAACCCTTGAAAAAAAAATCCACTCCAGTCACGAATGACTATCAAAAACAAAAATTAGAAGTC
*
38955337 AAATATAATACAAATACAAAATTTGAAGTCAGATATAATACGAACAAAAACAAAAATTTGTCAAT
66 AAATATAATACAAATACAAAATTTGAAGTCAGATAAAATACGAACAAAAACAAAAATTTGTCAAT
*
38955402 ATAAAACTAGAAAATTTTGTTTTCCTAAACCTTAAACCAAAAAAAACCGAATGTTCCAAAAAAAT
131 ATAAAACTAGAAAATTTTGTTTTCCTAAACCCTAAACC--AAAAAACCGAATGTTCC-AAAAAAT
38955467 TAGAAAAAATTGTGTCCCTACACCCTATACCAGAAAATAGAATGTTCCCAAAAAATTGTCAATTT
193 TAGAAAAAATTGTGTCCCTACACCCTATACCAGAAAATAGAATGTTCCCAAAAAATTGTCAATTT
38955532 TTGAGAACGAGTCAAAACAAA
258 TTGAGAACGAGTCAAAACAAA
38955553 AAGGTTTTAT
Statistics
Matches: 272, Mismatches: 4, Indels: 7
0.96 0.01 0.02
Matches are distributed among these distances:
276 124 0.46
278 17 0.06
279 120 0.44
280 11 0.04
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.24
Consensus pattern (278 bp):
TTTAACCCTTGAAAAAAAAATCCACTCCAGTCACGAATGACTATCAAAAACAAAAATTAGAAGTC
AAATATAATACAAATACAAAATTTGAAGTCAGATAAAATACGAACAAAAACAAAAATTTGTCAAT
ATAAAACTAGAAAATTTTGTTTTCCTAAACCCTAAACCAAAAAACCGAATGTTCCAAAAAATTAG
AAAAAATTGTGTCCCTACACCCTATACCAGAAAATAGAATGTTCCCAAAAAATTGTCAATTTTTG
AGAACGAGTCAAAACAAA
Found at i:38961840 original size:14 final size:14
Alignment explanation
Indices: 38961801--38961841 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
38961791 ATTATTATTT
38961801 AATTAAATAATTGA
1 AATTAAATAATTGA
38961815 AATTCAAA-AATTG-
1 AATT-AAATAATTGA
38961828 AATTAAATTAATTG
1 AATTAAA-TAATTG
38961842 GTTATTATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.12
13 4 0.17
14 14 0.58
15 3 0.12
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (14 bp):
AATTAAATAATTGA
Found at i:38962186 original size:156 final size:154
Alignment explanation
Indices: 38961992--38962302 Score: 604
Period size: 156 Copynumber: 2.0 Consensus size: 154
38961982 TTAATAAATA
38961992 CAGTCTATTTTGGGAAAAAAAAAATATACTGGGTTGGATTAAACTATAAAATGTTTGGTTAAAAG
1 CAGTCTATTTTGGGAAAAAAAAAATATACTGGGTTGGATTAAACTATAAAATGTTTGGTTAAAAG
38962057 TCCAAAAAACATAGATTTGAATCCAATACAAGAGAGACCCGATCCCATCATAATACATATGAGGG
66 TCCAAAAAACATAGATTTGAATCCAATACAAGAGAGACCCGATCCCATCATAATACATATGAGGG
38962122 GAGGCACATCCTATTAGCCCCCCT
131 GAGGCACATCCTATTAGCCCCCCT
38962146 CAGTCTATTTTGGGAAATAAAAAAAATATACTGGGTTGGATTAAACTATAAAATGTTTGGTTAAA
1 CAGTCTATTTTGGG-AA-AAAAAAAATATACTGGGTTGGATTAAACTATAAAATGTTTGGTTAAA
38962211 AGTCCAAAAAACATAGATTTGAATCCAATACAAGAGAGACCCGATCCCATCATAATACATATGAG
64 AGTCCAAAAAACATAGATTTGAATCCAATACAAGAGAGACCCGATCCCATCATAATACATATGAG
38962276 GGGAGGCACATCCTATTAGCCCCCCT
129 GGGAGGCACATCCTATTAGCCCCCCT
38962302 C
1 C
38962303 TCTCCTAATT
Statistics
Matches: 155, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
154 14 0.09
155 2 0.01
156 139 0.90
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (154 bp):
CAGTCTATTTTGGGAAAAAAAAAATATACTGGGTTGGATTAAACTATAAAATGTTTGGTTAAAAG
TCCAAAAAACATAGATTTGAATCCAATACAAGAGAGACCCGATCCCATCATAATACATATGAGGG
GAGGCACATCCTATTAGCCCCCCT
Found at i:38963674 original size:17 final size:18
Alignment explanation
Indices: 38963654--38963687 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38963644 TAGAATTGAG
38963654 TTGAAAAAATT-ATTTAA
1 TTGAAAAAATTAATTTAA
*
38963671 TTGAAAATATTAATTTA
1 TTGAAAAAATTAATTTA
38963688 TAGAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (18 bp):
TTGAAAAAATTAATTTAA
Found at i:38978175 original size:37 final size:37
Alignment explanation
Indices: 38978125--38978380 Score: 343
Period size: 37 Copynumber: 6.9 Consensus size: 37
38978115 CTTTATGATT
*
38978125 CACCGGCACAAAGCCTACTAGGCACAAAGCCTGAATA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCCGAATA
* *
38978162 CACCGGCGCAAAGCCTATTAGGCACAAAGCCCGAATA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCCGAATA
* * *
38978199 CATCGGTATAAAGCCTACTAGGCACACAA-CCCGAATA
1 CACCGGCACAAAGCCTACTAGGCACA-AAGCCCGAATA
* *
38978236 TACCGGCACAAAGCTTACTAGGCACAAAGCCCGAATA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCCGAATA
* * *
38978273 CACCAGCACAAAGCCTACTAGGCACACAGCTCGAATA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCCGAATA
* * **
38978310 TACCGACACAAAGCCTACTAGGCACAAAGCTTGAATA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCCGAATA
* *
38978347 CACCGGCACAAAGTCTACTAGACACAAAGCCCGA
1 CACCGGCACAAAGCCTACTAGGCACAAAGCCCGA
38978381 TTATTTAAAT
Statistics
Matches: 188, Mismatches: 29, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
36 2 0.01
37 184 0.98
38 2 0.01
ACGTcount: A:0.38, C:0.32, G:0.18, T:0.12
Consensus pattern (37 bp):
CACCGGCACAAAGCCTACTAGGCACAAAGCCCGAATA
Found at i:38978191 original size:16 final size:16
Alignment explanation
Indices: 38978129--38978192 Score: 56
Period size: 16 Copynumber: 3.7 Consensus size: 16
38978119 ATGATTCACC
*
38978129 GGCACAAAGCCTACTA
1 GGCACAAAGCCTATTA
*
38978145 GGCACAAAGCCTGAATACA
1 GGCACAAAGCCT--AT-TA
*
38978164 CCGGCGCAAAGCCTATTA
1 --GGCACAAAGCCTATTA
38978182 GGCACAAAGCC
1 GGCACAAAGCC
38978193 CGAATACATC
Statistics
Matches: 38, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 22 0.58
18 2 0.05
19 3 0.08
21 11 0.29
ACGTcount: A:0.36, C:0.31, G:0.22, T:0.11
Consensus pattern (16 bp):
GGCACAAAGCCTATTA
Found at i:38997745 original size:2 final size:2
Alignment explanation
Indices: 38997738--38997797 Score: 104
Period size: 2 Copynumber: 30.0 Consensus size: 2
38997728 AGTCAGTCGG
38997738 AT AT AT AT GA- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38997780 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
38997798 TGCTTTTCAA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.02
2 54 0.96
3 1 0.02
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39003465 original size:16 final size:17
Alignment explanation
Indices: 39003431--39003473 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 17
39003421 TAAGGTTAAA
39003431 AATTATTAAGTTTGATT
1 AATTATTAAGTTTGATT
39003448 AATT-TTAAGTTT-AGTT
1 AATTATTAAGTTTGA-TT
39003464 AATTAATTAA
1 AATT-ATTAA
39003474 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 14 0.61
17 4 0.17
18 4 0.17
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (17 bp):
AATTATTAAGTTTGATT
Found at i:39004589 original size:170 final size:170
Alignment explanation
Indices: 39004301--39004613 Score: 522
Period size: 170 Copynumber: 1.8 Consensus size: 170
39004291 ATGTAAATAT
* *
39004301 TGATTATTTGTCTCAAACGTGAGAAATAAAATTATGTACAGGAATTGGTTTTGACATTTATACGA
1 TGATTATTTGTCTCAAACATGAGAAATAAAATTATGCACAGGAATTGGTTTTGACATTTATACGA
* *
39004366 AAATGATACCCGAGTGAACTTCGTAAAAGATTAGGATACGTATGGCGTGCCATTAAGG-TTATAC
66 AAATGATACCCGAGTGAACTTCGTAAAAGATTAGGATACGTATAGCATGCCATT-AGGCTTATAC
*
39004430 GCAGGATTAATAAGACGCAAGATGTAAAAGTGATTGTTGAC
130 GCACGATTAATAAGACGCAAGATGTAAAAGTGATTGTTGAC
39004471 TGATTATTTGTCTCGAAA-ATGAGAAATAAAATTATGCACAGGAATTGGTTTTGACATTTATACG
1 TGATTATTTGTCTC-AAACATGAGAAATAAAATTATGCACAGGAATTGGTTTTGACATTTATACG
* * *
39004535 AAAATGATAGCCGAGTGAACTTTGTAAAAGGTTAGGATACGTATAGCATGCCATTAGGCTTATAC
65 AAAATGATACCCGAGTGAACTTCGTAAAAGATTAGGATACGTATAGCATGCCATTAGGCTTATAC
39004600 GCACGATTAATAAG
130 GCACGATTAATAAG
39004614 GGATTTTACA
Statistics
Matches: 133, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
169 3 0.02
170 127 0.95
171 3 0.02
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.30
Consensus pattern (170 bp):
TGATTATTTGTCTCAAACATGAGAAATAAAATTATGCACAGGAATTGGTTTTGACATTTATACGA
AAATGATACCCGAGTGAACTTCGTAAAAGATTAGGATACGTATAGCATGCCATTAGGCTTATACG
CACGATTAATAAGACGCAAGATGTAAAAGTGATTGTTGAC
Found at i:39004755 original size:30 final size:30
Alignment explanation
Indices: 39004694--39004756 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
39004684 CTCTACGGGT
* *
39004694 AACCTCGATATAATGTCAACTTATGTGAGC
1 AACCTCGATATAATGTCAACATATGTAAGC
* * * *
39004724 AACCTTGATATACTGTCAGCATGTGTAAGC
1 AACCTCGATATAATGTCAACATATGTAAGC
39004754 AAC
1 AAC
39004757 TTATTCTCAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (30 bp):
AACCTCGATATAATGTCAACATATGTAAGC
Found at i:39011302 original size:50 final size:50
Alignment explanation
Indices: 39011227--39011326 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
39011217 ATGGGTATAT
39011227 AATCTTTCTTTTTATCACAAATGGGTAATTAATCCCTTTATGACTTTTCC
1 AATCTTTCTTTTTATCACAAATGGGTAATTAATCCCTTTATGACTTTTCC
39011277 AATCTTTCTTTTTATCACAAATGGGTAATTAATCCCTTTATGACTTTTCC
1 AATCTTTCTTTTTATCACAAATGGGTAATTAATCCCTTTATGACTTTTCC
39011327 CTTAGGGAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.26, C:0.20, G:0.08, T:0.46
Consensus pattern (50 bp):
AATCTTTCTTTTTATCACAAATGGGTAATTAATCCCTTTATGACTTTTCC
Found at i:39019906 original size:21 final size:22
Alignment explanation
Indices: 39019882--39019931 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
39019872 TAAAGTTTTG
* *
39019882 ATTTAATCTTTTAAAAATTAC-
1 ATTTAATATTGTAAAAATTACA
**
39019903 ATTTTTTATTGTAAAAATTACA
1 ATTTAATATTGTAAAAATTACA
39019925 ATTTAAT
1 ATTTAAT
39019932 TTCGATTCCT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.42, C:0.06, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTTAATATTGTAAAAATTACA
Found at i:39043140 original size:15 final size:15
Alignment explanation
Indices: 39043122--39043155 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39043112 TAAACACCTC
39043122 TATTTTAAATCAA-AT
1 TATTTTAAAT-AATAT
39043137 TATTTTAAATAATAT
1 TATTTTAAATAATAT
39043152 TATT
1 TATT
39043156 CTATTGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 2 0.11
15 16 0.89
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTTTAAATAATAT
Found at i:39047033 original size:16 final size:15
Alignment explanation
Indices: 39047000--39047029 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39046990 AATTTTTTAA
39047000 AAATTATAAAAATAT
1 AAATTATAAAAATAT
*
39047015 AAATTATTAAAATAT
1 AAATTATAAAAATAT
39047030 TAAAATTCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTATAAAAATAT
Found at i:39050500 original size:2 final size:2
Alignment explanation
Indices: 39050493--39050534 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
39050483 GGAAAATAGA
39050493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39050535 TTAAAATAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39050858 original size:11 final size:11
Alignment explanation
Indices: 39050842--39050866 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39050832 TGATCGTGCA
39050842 TTAGATTGTTT
1 TTAGATTGTTT
39050853 TTAGATTGTTT
1 TTAGATTGTTT
39050864 TTA
1 TTA
39050867 TAATCATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.16, T:0.64
Consensus pattern (11 bp):
TTAGATTGTTT
Found at i:39050949 original size:21 final size:22
Alignment explanation
Indices: 39050924--39050975 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
39050914 GATATGCTCA
*
39050924 AATTAATTGA-TAT-ATCATATC
1 AATTAATTGAGAATGAT-ATATC
39050945 AATTAATTTGAGAATGATATATC
1 AATTAA-TTGAGAATGATATATC
39050968 AATTAATT
1 AATTAATT
39050976 TGAGCATGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 6 0.22
22 6 0.22
23 13 0.48
24 2 0.07
ACGTcount: A:0.44, C:0.06, G:0.08, T:0.42
Consensus pattern (22 bp):
AATTAATTGAGAATGATATATC
Found at i:39058554 original size:30 final size:30
Alignment explanation
Indices: 39058520--39058584 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
39058510 CAACATAAAA
* *
39058520 AACAAATGCTTTTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
39058550 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
39058580 AACAA
1 AACAA
39058585 TAAATAAGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:39066256 original size:21 final size:21
Alignment explanation
Indices: 39066230--39066278 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
39066220 TTTTAGTACT
* * *
39066230 GGTAGAAGCATGATTTGTTTC
1 GGTAGAAGCATCACTTGTATC
*
39066251 GGTAGAAGCTTCACTTGTATC
1 GGTAGAAGCATCACTTGTATC
39066272 GGTAGAA
1 GGTAGAA
39066279 CTGTCAGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.33
Consensus pattern (21 bp):
GGTAGAAGCATCACTTGTATC
Found at i:39067682 original size:12 final size:12
Alignment explanation
Indices: 39067665--39067698 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
39067655 CACAATCCAC
*
39067665 CATTTCATATTT
1 CATTTCACATTT
39067677 CATTTCACATTT
1 CATTTCACATTT
39067689 CATTTC-CATT
1 CATTTCACATT
39067699 CCTCATCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.53
Consensus pattern (12 bp):
CATTTCACATTT
Found at i:39068968 original size:52 final size:52
Alignment explanation
Indices: 39068855--39069036 Score: 226
Period size: 52 Copynumber: 3.6 Consensus size: 52
39068845 ATTTCATTTA
* * * ** * *
39068855 ATACCCACGATGACACATAGTAATCGGACCTC-TTGTTC--AAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
39068904 ACACTCACGATGACACATAGTCATTAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
39068956 ATACTCACGATGACATATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
* *
39069008 ATACTCATGATGACACATAGTTATCAGAC
1 ATACTCACGATGACACATAGTCATCAGAC
39069037 TTTAGTCATT
Statistics
Matches: 113, Mismatches: 17, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
49 27 0.24
50 3 0.03
52 83 0.73
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAGGATTCAT
Found at i:39071310 original size:59 final size:60
Alignment explanation
Indices: 39071191--39071349 Score: 203
Period size: 59 Copynumber: 2.6 Consensus size: 60
39071181 AACCTTAGGA
* *
39071191 ACCAAATTAGGGAAAAAAATGTCAAGTTCAGGTGCCAAATTGGGTCCAAAAAAAATTTATGT
1 ACCAAATTA-GG-AAAAAATGTCAACTTCAGGTACCAAATTGGGTCCAAAAAAAATTTATGT
* * * *
39071253 ACTAAATTAGGAAAAAGTGTCAACTTCTGGTACCAAATTGGGT-CAAAAAAAGTTTATGT
1 ACCAAATTAGGAAAAAATGTCAACTTCAGGTACCAAATTGGGTCCAAAAAAAATTTATGT
* * * *
39071312 ACCAAATTAGAAAAAAATGTTAAGTTCAAGTACCAAAT
1 ACCAAATTAGGAAAAAATGTCAACTTCAGGTACCAAAT
39071350 GTTATATTAA
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
59 46 0.55
60 28 0.33
61 2 0.02
62 8 0.10
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.26
Consensus pattern (60 bp):
ACCAAATTAGGAAAAAATGTCAACTTCAGGTACCAAATTGGGTCCAAAAAAAATTTATGT
Found at i:39077666 original size:46 final size:46
Alignment explanation
Indices: 39077611--39077702 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
39077601 ATCAAATACA
39077611 GGTGATCTGCTCAGACAAATTAGAGCCACTTTTAATCATTGGATGC
1 GGTGATCTGCTCAGACAAATTAGAGCCACTTTTAATCATTGGATGC
39077657 GGTGATCTGCTCAGACAAATTAGAGCCACTTTTAATCATTGGATGC
1 GGTGATCTGCTCAGACAAATTAGAGCCACTTTTAATCATTGGATGC
39077703 CTTCGGAGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (46 bp):
GGTGATCTGCTCAGACAAATTAGAGCCACTTTTAATCATTGGATGC
Found at i:39078447 original size:25 final size:26
Alignment explanation
Indices: 39078400--39078448 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
39078390 AAAATGTTTA
*
39078400 ATTTTTATATAAAATATATTAATCAT
1 ATTTTTATATAAAATATAATAATCAT
39078426 ATTTTTAT-T-AAATATTAATAATC
1 ATTTTTATATAAAATA-TAATAATC
39078449 TTTAAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 8 0.38
26 8 0.38
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (26 bp):
ATTTTTATATAAAATATAATAATCAT
Found at i:39087441 original size:2 final size:2
Alignment explanation
Indices: 39087434--39087460 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39087424 AAGATAATAG
39087434 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
39087461 TTATCCCAAA
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:39091219 original size:23 final size:25
Alignment explanation
Indices: 39091165--39091221 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
39091155 AAACGACAAG
***
39091165 AAATATTGTAATTCAATATTTTCTA
1 AAATATTGTAATTCAATAAAATCTA
39091190 AAATATTGTAATT-AATAAAATC-A
1 AAATATTGTAATTCAATAAAATCTA
39091213 AAATATTGT
1 AAATATTGT
39091222 TAAAATACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 10 0.34
24 6 0.21
25 13 0.45
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (25 bp):
AAATATTGTAATTCAATAAAATCTA
Found at i:39093360 original size:25 final size:25
Alignment explanation
Indices: 39093324--39093377 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 25
39093314 AAGTCAATGA
39093324 TTAAAGTCAAATCAAT-GGTCAAAG
1 TTAAAGTCAAATCAATGGGTCAAAG
*
39093348 TTAAAGTCAAAATCAATGGGTCATAG
1 TTAAAGTC-AAATCAATGGGTCAAAG
39093374 TTAA
1 TTAA
39093378 CGGGTCAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 8 0.30
25 8 0.30
26 11 0.41
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.28
Consensus pattern (25 bp):
TTAAAGTCAAATCAATGGGTCAAAG
Found at i:39093450 original size:27 final size:27
Alignment explanation
Indices: 39093420--39093491 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
39093410 CGAATAAGTT
39093420 AACTCGAGTCAATCG-GTCGGATCGATC
1 AACTCGAGTCAA-CGAGTCGGATCGATC
* * * *
39093447 AACTCAAGTTAACGAGTTGGGTCGATC
1 AACTCGAGTCAACGAGTCGGATCGATC
* *
39093474 AACTCGGGTCAACAAGTC
1 AACTCGAGTCAACGAGTC
39093492 AGGTTTGAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 2 0.06
27 33 0.94
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.22
Consensus pattern (27 bp):
AACTCGAGTCAACGAGTCGGATCGATC
Found at i:39096126 original size:37 final size:37
Alignment explanation
Indices: 39096085--39096158 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
39096075 AAGGCCCAGT
*
39096085 TAGGGAGTATGTGTGCAAGTTTAGTGAACTCATGCTC
1 TAGGGAGTATGTATGCAAGTTTAGTGAACTCATGCTC
*
39096122 TAGGGAGTATGTATGCGAGTTTAGTGAACTCATGCTC
1 TAGGGAGTATGTATGCAAGTTTAGTGAACTCATGCTC
39096159 CAAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (37 bp):
TAGGGAGTATGTATGCAAGTTTAGTGAACTCATGCTC
Found at i:39121931 original size:23 final size:23
Alignment explanation
Indices: 39121901--39121979 Score: 122
Period size: 23 Copynumber: 3.4 Consensus size: 23
39121891 GAATGCTAGC
* *
39121901 GTGCTTACTGTTTCGCACTTTGT
1 GTGCTTACTGTTTCACACTTCGT
39121924 GTGCTTACTGTTTCACACTTCGT
1 GTGCTTACTGTTTCACACTTCGT
*
39121947 GTGCTTACTGTTTCACACCTCGT
1 GTGCTTACTGTTTCACACTTCGT
*
39121970 GTGCCTACTG
1 GTGCTTACTG
39121980 ATTTGCGCTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.11, C:0.27, G:0.20, T:0.42
Consensus pattern (23 bp):
GTGCTTACTGTTTCACACTTCGT
Found at i:39122031 original size:23 final size:22
Alignment explanation
Indices: 39121992--39122038 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
39121982 TTGCGCTATT
*
39121992 TGCCTACTGATTACACTGTGTG
1 TGCCTAATGATTACACTGTGTG
*
39122014 TGCCTAATGGATTGCACTGTGTG
1 TGCCTAAT-GATTACACTGTGTG
39122037 TG
1 TG
39122039 GTTCTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (22 bp):
TGCCTAATGATTACACTGTGTG
Found at i:39129167 original size:23 final size:23
Alignment explanation
Indices: 39129142--39129263 Score: 94
Period size: 23 Copynumber: 5.4 Consensus size: 23
39129132 CTAGTGCGCT
*
39129142 TACT-ATTTCGCACTTTGTGTGCT
1 TACTGATTT-GCACTTTGTGTGCC
* * *
39129165 TACT-ATTTCACACCTCGTGTGCC
1 TACTGATTT-GCACTTTGTGTGCC
*
39129188 TACTGATTTGCACTATGTGTGCC
1 TACTGATTTGCACTTTGTGTGCC
*
39129211 TACTGA-TTGCA-TTGTGTATGCC
1 TACTGATTTGCACTT-TGTGTGCC
* *
39129233 TACTGGA-TTGCACTGTGTGTGCT
1 TACT-GATTTGCACTTTGTGTGCC
39129256 TACT-ATTT
1 TACTGATTT
39129264 CCCCAGCACT
Statistics
Matches: 81, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
21 2 0.02
22 18 0.22
23 56 0.69
24 5 0.06
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.42
Consensus pattern (23 bp):
TACTGATTTGCACTTTGTGTGCC
Found at i:39129232 original size:22 final size:22
Alignment explanation
Indices: 39129181--39129259 Score: 104
Period size: 23 Copynumber: 3.5 Consensus size: 22
39129171 TTCACACCTC
*
39129181 GTGTGCCTACTGATTTGCACTAT
1 GTGTGCCTACTGA-TTGCACTGT
*
39129204 GTGTGCCTACTGATTGCATTGT
1 GTGTGCCTACTGATTGCACTGT
*
39129226 GTATGCCTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTGT
*
39129249 GTGTGCTTACT
1 GTGTGCCTACT
39129260 ATTTCCCCAG
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 17 0.35
23 32 0.65
ACGTcount: A:0.15, C:0.20, G:0.25, T:0.39
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTGT
Found at i:39134795 original size:21 final size:21
Alignment explanation
Indices: 39134769--39134808 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39134759 TATCCTGTAT
*
39134769 TTCTACCGATACAACTATGGG
1 TTCTACCGAAACAACTATGGG
*
39134790 TTCTACCGAAACAAGTATG
1 TTCTACCGAAACAACTATG
39134809 CAAAATTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.28
Consensus pattern (21 bp):
TTCTACCGAAACAACTATGGG
Found at i:39135377 original size:24 final size:24
Alignment explanation
Indices: 39135326--39135400 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
39135316 ACAGACAACA
* * * **
39135326 TTAGCTCTCATGAGCCCAAGATAA
1 TTAGCTCTTACGAGCCCAAAATGG
* *
39135350 TTAGCTCTTACGAGTCCAGAATGG
1 TTAGCTCTTACGAGCCCAAAATGG
39135374 TTAGCTCTTACGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAAAATGG
39135398 TTA
1 TTA
39135401 ACCAGTATAC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAAAATGG
Found at i:39142730 original size:87 final size:87
Alignment explanation
Indices: 39142577--39142997 Score: 514
Period size: 87 Copynumber: 4.9 Consensus size: 87
39142567 TAGTTTAACA
* * * *
39142577 CATGTGTTGCAGACTCGAGTTA-TATGAGATATGATCATTCTGATTCTGATTTGTTGACGATCGT
1 CATGTGTTACAGACTCGAGTTATTATGAGACATGATCATTCTGATTCTGATTTGCTGACGAGCGT
39142641 AAACATTCTGATCGAGCTCCTG
66 AAACATTCTGATCGAGCTCCTG
* * * * *
39142663 CATGTGTTCCAGACTCGAGTTATTATGAGACATGATCATTATGATTTTGATTTGCTGGCGAGTGT
1 CATGTGTTACAGACTCGAGTTATTATGAGACATGATCATTCTGATTCTGATTTGCTGACGAGCGT
*
39142728 AAATGTATTC--A-CGAAGCTCCTG
66 AAA--CATTCTGATCG-AGCTCCTG
* *
39142750 CATGTGTTGCAGACTCGGGTTAATT-TGAGACATGA-CTATTCTGATTCTGATTTGCTGACGAGC
1 CATGTGTTACAGACTCGAGTT-ATTATGAGACATGATC-ATTCTGATTCTGATTTGCTGACGAGC
*
39142813 GTAAACATTCTGATCGAGCTTCTG
64 GTAAACATTCTGATCGAGCTCCTG
* * *
39142837 CATGTGTTACGGACTCGTGTTATTATGAGACATGA-CATTCTGATTTTGATTTGCTGACGAGCGT
1 CATGTGTTACAGACTCGAGTTATTATGAGACATGATCATTCTGATTCTGATTTGCTGACGAGCGT
* * * * *
39142901 AAACGTTTTGACCAAGCTCCTT
66 AAACATTCTGATCGAGCTCCTG
* * * * *
39142923 CATGTGTTACGGACTCGGGTTATTATGAGACATGATCATTTTGATTCTGATTTGCTAATGAGCGT
1 CATGTGTTACAGACTCGAGTTATTATGAGACATGATCATTCTGATTCTGATTTGCTGACGAGCGT
39142988 AAACATTCTG
66 AAACATTCTG
39142998 GAATTACGTA
Statistics
Matches: 290, Mismatches: 34, Indels: 21
0.84 0.10 0.06
Matches are distributed among these distances:
85 4 0.01
86 104 0.36
87 173 0.60
88 5 0.02
89 4 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (87 bp):
CATGTGTTACAGACTCGAGTTATTATGAGACATGATCATTCTGATTCTGATTTGCTGACGAGCGT
AAACATTCTGATCGAGCTCCTG
Found at i:39142929 original size:173 final size:173
Alignment explanation
Indices: 39142577--39142997 Score: 603
Period size: 173 Copynumber: 2.4 Consensus size: 173
39142567 TAGTTTAACA
* * * * *
39142577 CATGTGTTGCAGACTCGAGTTATATGAGATATGATCATTCTGATTCTGATTTGTTGACGATCGTA
1 CATGTGTTGCAGACTCGGGTTATTTGAGACATGATCATTCTGATTCTGATTTGCTGACGAGCGTA
*
39142642 AACATTCTGATCGAGCTCCTGCATGTGTTCCAGACTCGAGTTATTATGAGACATGATCATTATGA
66 AACATTCTGATCGAGCTCCTGCATGTGTTACAGACTCGAGTTATTATGAGACATGATCATTATGA
* * * *
39142707 TTTTGATTTGCTGGCGAGTGTAAATGTATTCACGAAGCTCCTG
131 TTTTGATTTGCTGACGAGCGTAAACGTATTCACCAAGCTCCTG
39142750 CATGTGTTGCAGACTCGGGTTAATTTGAGACATGA-CTATTCTGATTCTGATTTGCTGACGAGCG
1 CATGTGTTGCAGACTCGGGTT-ATTTGAGACATGATC-ATTCTGATTCTGATTTGCTGACGAGCG
* * * *
39142814 TAAACATTCTGATCGAGCTTCTGCATGTGTTACGGACTCGTGTTATTATGAGACATGA-CATTCT
64 TAAACATTCTGATCGAGCTCCTGCATGTGTTACAGACTCGAGTTATTATGAGACATGATCATTAT
* * *
39142878 GATTTTGATTTGCTGACGAGCGTAAACGTTTTGACCAAGCTCCTT
129 GATTTTGATTTGCTGACGAGCGTAAACGTATTCACCAAGCTCCTG
* * * * *
39142923 CATGTGTTACGGACTCGGGTTATTATGAGACATGATCATTTTGATTCTGATTTGCTAATGAGCGT
1 CATGTGTTGCAGACTCGGGTTATT-TGAGACATGATCATTCTGATTCTGATTTGCTGACGAGCGT
39142988 AAACATTCTG
65 AAACATTCTG
39142998 GAATTACGTA
Statistics
Matches: 222, Mismatches: 22, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
172 3 0.01
173 128 0.58
174 91 0.41
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (173 bp):
CATGTGTTGCAGACTCGGGTTATTTGAGACATGATCATTCTGATTCTGATTTGCTGACGAGCGTA
AACATTCTGATCGAGCTCCTGCATGTGTTACAGACTCGAGTTATTATGAGACATGATCATTATGA
TTTTGATTTGCTGACGAGCGTAAACGTATTCACCAAGCTCCTG
Found at i:39149767 original size:43 final size:43
Alignment explanation
Indices: 39149714--39149933 Score: 248
Period size: 43 Copynumber: 5.1 Consensus size: 43
39149704 TTAATGACCT
* * * * *
39149714 TGAGAGGAACACTATTTCCTAATATTGTAAGTATGTGACCAAA
1 TGAGAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAA
* *
39149757 TGAGAGGAACATTGTTTCCTAGTATTGAAAGTATGTGATCGAT
1 TGAGAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAA
* *
39149800 TGTA-TGGAACA-TGTTTCCTAATTTTGAAAGTATGTGATCGAA
1 TG-AGAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAA
* * * * *
39149842 TAAGTGGAGCAATGTTTCCTAGTATTGAAAGTATGTGATCGAA
1 TGAGAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAA
* * *
39149885 TGA-ATGGAACATTGTTTCCTAATATTGATAGTATGTGATTGAT
1 TGAGA-GGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAA
39149928 TGAGAG
1 TGAGAG
39149934 CATGATAAAT
Statistics
Matches: 149, Mismatches: 23, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.01
42 35 0.23
43 111 0.74
44 2 0.01
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (43 bp):
TGAGAGGAACATTGTTTCCTAATATTGAAAGTATGTGATCGAA
Found at i:39149871 original size:85 final size:86
Alignment explanation
Indices: 39149719--39149923 Score: 286
Period size: 85 Copynumber: 2.4 Consensus size: 86
39149709 GACCTTGAGA
* * * * *
39149719 GGAACACTATTTCCTAATATTGTAAGTATGTGACCAAATGAGAGGAACATTGTTTCCTAGTATTG
1 GGAACACTGTTTCCTAATATTGAAAGTATGTGATCAAATAAGAGGAACAATGTTTCCTAGTATTG
* *
39149784 AAAGTATGTGATCGATTGTAT
66 AAAGTATGTGATCGAATGAAT
* * * *
39149805 GGAACA-TGTTTCCTAATTTTGAAAGTATGTGATCGAATAAGTGGAGCAATGTTTCCTAGTATTG
1 GGAACACTGTTTCCTAATATTGAAAGTATGTGATCAAATAAGAGGAACAATGTTTCCTAGTATTG
39149869 AAAGTATGTGATCGAATGAAT
66 AAAGTATGTGATCGAATGAAT
* *
39149890 GGAACATTGTTTCCTAATATTGATAGTATGTGAT
1 GGAACACTGTTTCCTAATATTGAAAGTATGTGAT
39149924 TGATTGAGAG
Statistics
Matches: 105, Mismatches: 13, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
85 74 0.70
86 31 0.30
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.36
Consensus pattern (86 bp):
GGAACACTGTTTCCTAATATTGAAAGTATGTGATCAAATAAGAGGAACAATGTTTCCTAGTATTG
AAAGTATGTGATCGAATGAAT
Found at i:39165479 original size:19 final size:19
Alignment explanation
Indices: 39165440--39165623 Score: 122
Period size: 19 Copynumber: 9.8 Consensus size: 19
39165430 TTAGAGCATT
**
39165440 CTGGCTCATTTGAGC-ATA
1 CTGGCTCATAAGAGCGATA
39165458 CTGGCTCATAAGAGCGATA
1 CTGGCTCATAAGAGCGATA
** *
39165477 CTGGCTTTTAAGAGCAATA
1 CTGGCTCATAAGAGCGATA
* *
39165496 TTGGCTCGTAAGAGCGATA
1 CTGGCTCATAAGAGCGATA
*
39165515 CTGGCTCATTAGAGC-ATA
1 CTGGCTCATAAGAGCGATA
** ** **
39165533 CTGGCTTGTTTGAATGATA
1 CTGGCTCATAAGAGCGATA
* * **
39165552 CTAGCTCGTAAGAATGATA
1 CTGGCTCATAAGAGCGATA
** *
39165571 CTAACTCGTAAGAGCGATA
1 CTGGCTCATAAGAGCGATA
* *
39165590 CTGACTCATAAGAGCAATA
1 CTGGCTCATAAGAGCGATA
*
39165609 CTAGCT-AGTAAGAGC
1 CTGGCTCA-TAAGAGC
39165624 AAATTACTGA
Statistics
Matches: 134, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
18 27 0.20
19 107 0.80
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (19 bp):
CTGGCTCATAAGAGCGATA
Found at i:39165529 original size:38 final size:37
Alignment explanation
Indices: 39165427--39165623 Score: 148
Period size: 38 Copynumber: 5.3 Consensus size: 37
39165417 CTGTATTGGA
* * *
39165427 TCGTTAGAGC-ATTCTGGCTCATTTGAGCATACTGGC
1 TCGTAAGAGCGATACTGGCTCATTAGAGCATACTGGC
* * *
39165463 TCATAAGAGCGATACTGGCT-TTTAAGAGCAATATTGGC
1 TCGTAAGAGCGATACTGGCTCATT-AGAGC-ATACTGGC
39165501 TCGTAAGAGCGATACTGGCTCATTAGAGCATACTGGC
1 TCGTAAGAGCGATACTGGCTCATTAGAGCATACTGGC
* ** ** * * * **
39165538 TTGTTTGAATGATACTAGCTCGTAAGAATG-ATACTAAC
1 TCGTAAGAGCGATACTGGCTCATTAG-A-GCATACTGGC
* * *
39165576 TCGTAAGAGCGATACTGACTCATAAGAGCAATACTAGC
1 TCGTAAGAGCGATACTGGCTCATTAGAGC-ATACTGGC
*
39165614 TAGTAAGAGC
1 TCGTAAGAGC
39165624 AAATTACTGA
Statistics
Matches: 124, Mismatches: 29, Indels: 14
0.74 0.17 0.08
Matches are distributed among these distances:
36 11 0.09
37 38 0.31
38 72 0.58
39 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (37 bp):
TCGTAAGAGCGATACTGGCTCATTAGAGCATACTGGC
Found at i:39165552 original size:75 final size:75
Alignment explanation
Indices: 39165420--39165610 Score: 177
Period size: 75 Copynumber: 2.5 Consensus size: 75
39165410 GAAAGTACTG
* * * * * * *
39165420 TATTGGATCGTTAGAGC-ATTCTGGCTCATTTGAGCATACTGGCTCATAAGAGCGATACTGGCTT
1 TATTGGCTCGTAAGAGCGATACTGGCTCATTAGAGCATACTGGCTCATAAGAACGATACTAGCTC
* *
39165484 TTAAGAGCAA
66 GTAAGAACAA
** ** *
39165494 TATTGGCTCGTAAGAGCGATACTGGCTCATTAGAGCATACTGGCTTGTTTGAATGATACTAGCTC
1 TATTGGCTCGTAAGAGCGATACTGGCTCATTAGAGCATACTGGCTCATAAGAACGATACTAGCTC
**
39165559 GTAAGAATGA
66 GTAAGAACAA
* ** * *
39165569 TACTAACTCGTAAGAGCGATACTGACTCATAAGAGCAATACT
1 TATTGGCTCGTAAGAGCGATACTGGCTCATTAGAGC-ATACT
39165611 AGCTAGTAAG
Statistics
Matches: 94, Mismatches: 21, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
74 15 0.16
75 74 0.79
76 5 0.05
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (75 bp):
TATTGGCTCGTAAGAGCGATACTGGCTCATTAGAGCATACTGGCTCATAAGAACGATACTAGCTC
GTAAGAACAA
Found at i:39165571 original size:56 final size:57
Alignment explanation
Indices: 39165455--39165621 Score: 158
Period size: 57 Copynumber: 2.9 Consensus size: 57
39165445 TCATTTGAGC
* * * *
39165455 ATACTGGCTCATAAGAGCGATACTGGCTTTTAAGAGCAATATTGGCTCGTAAGAGCG
1 ATACTGGCTCATAAGAGCGATACTGGCTTTTAAGAACAATACTAGCTCGTAAGAACG
* * ** *
39165512 ATACTGGCTCATTAGAGC-ATACTGGCTTGTT-TGAATGATACTAGCTCGTAAGAATG
1 ATACTGGCTCATAAGAGCGATACTGGCTT-TTAAGAACAATACTAGCTCGTAAGAACG
** * * ** * *
39165568 ATACTAACTCGTAAGAGCGATACTGACTCATAAGAGCAATACTAGCTAGTAAGA
1 ATACTGGCTCATAAGAGCGATACTGGCTTTTAAGAACAATACTAGCTCGTAAGA
39165622 GCAAATTACT
Statistics
Matches: 86, Mismatches: 21, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
56 42 0.49
57 44 0.51
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (57 bp):
ATACTGGCTCATAAGAGCGATACTGGCTTTTAAGAACAATACTAGCTCGTAAGAACG
Found at i:39171918 original size:42 final size:42
Alignment explanation
Indices: 39171809--39171998 Score: 204
Period size: 42 Copynumber: 4.5 Consensus size: 42
39171799 TGATGTATAA
*** * *
39171809 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAATTTGTAT-
1 AAAGGAAGACTCATGTCTCGAAATGAGAATGAGAATATG-ATC
* * * *
39171851 AAATGGAAGACTCGTGACTCGAAATGAGCATGAAAATATGATC
1 AAA-GGAAGACTCATGTCTCGAAATGAGAATGAGAATATGATC
* * *
39171894 AAAGGAAGACTCATGTCTCAAAATGAGAATGAGATTATGATT
1 AAAGGAAGACTCATGTCTCGAAATGAGAATGAGAATATGATC
*
39171936 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAATATGA-C
1 AAAGGAAGACTCATGTCTCGAAATGAGAATGAGAATATGATC
* *
39171977 TAAAGGAAGACTTATGACTCGA
1 -AAAGGAAGACTCATGTCTCGA
39171999 TAGAGCATAA
Statistics
Matches: 125, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
42 93 0.74
43 32 0.26
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAAATGAGAATGAGAATATGATC
Found at i:39172678 original size:21 final size:21
Alignment explanation
Indices: 39172654--39172709 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
39172644 CTGAAGTTTT
39172654 TAGTATCGGTAGAAGCATA-AC
1 TAGTATCGGTAGAAG-ATACAC
* * *
39172675 TAGTTTCGGTAGATGTTACAC
1 TAGTATCGGTAGAAGATACAC
*
39172696 TTGTATCGGTAGAA
1 TAGTATCGGTAGAA
39172710 CTATCACAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.32
Consensus pattern (21 bp):
TAGTATCGGTAGAAGATACAC
Found at i:39178467 original size:40 final size:38
Alignment explanation
Indices: 39178399--39178533 Score: 96
Period size: 40 Copynumber: 3.4 Consensus size: 38
39178389 ACCAAAATGG
* *
39178399 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAAAGTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAG-AATAAAGTGA
* *
39178439 CACCCAGTGTCTCATCGGCCTAGCCGAAG--TAAAGTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAATAAAGTGA
* * * * *
39178476 TACCCAGTACCTCATCGAATCTATCCGAAGTAA-AATAATGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAG-AATAA-AGTGA
*
39178517 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
39178534 ACTCAAGGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
37 21 0.28
38 9 0.12
40 24 0.32
41 20 0.27
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.21
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAATAAAGTGA
Found at i:39178531 original size:41 final size:38
Alignment explanation
Indices: 39178431--39178534 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
39178421 TTCGAAGCAA
* *
39178431 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
39178468 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
39178506 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
39178535 CTCAAGGTCA
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:39178656 original size:6 final size:6
Alignment explanation
Indices: 39178637--39178675 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
39178627 ACAATTCATA
*
39178637 TCACTT TCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
39178676 ATTTTGATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.49
Consensus pattern (6 bp):
TCACTT
Found at i:39181767 original size:42 final size:42
Alignment explanation
Indices: 39181736--39181845 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
39181726 CATGAAAAGG
* *
39181736 TGATTAAAGGAAGGCTTATGTCTCGAAATGAGAATGAGATTA
1 TGATTAAAGGAAGACTTATGTCTCGAAATGAGAATGAGAATA
* **
39181778 TGATTAAAGGAAGACTCATGTCTCGGGATGAGAATGAGAATA
1 TGATTAAAGGAAGACTTATGTCTCGAAATGAGAATGAGAATA
*
39181820 TGATTAAAGGAAGACTTATGACTCGA
1 TGATTAAAGGAAGACTTATGTCTCGA
39181846 TAGAGCATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.38, C:0.09, G:0.26, T:0.26
Consensus pattern (42 bp):
TGATTAAAGGAAGACTTATGTCTCGAAATGAGAATGAGAATA
Done.