Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 153 of 171
Found at i:45871662 original size:23 final size:23
Alignment explanation
Indices: 45871608--45871739 Score: 167
Period size: 23 Copynumber: 5.7 Consensus size: 23
45871598 ATTAACATTA
* *
45871608 TTCGTGAACGTGTTCAATTATATG
1 TTCGTGAACATGTTCGATTA-ATG
* *
45871632 TTCATGAACATGTTCGTTTAATG
1 TTCGTGAACATGTTCGATTAATG
45871655 TTCGTGAACATGTTCGATTAATG
1 TTCGTGAACATGTTCGATTAATG
* *
45871678 TTCGTGAATATGTTCGATTAATA
1 TTCGTGAACATGTTCGATTAATG
45871701 TTCGTGAACATGTTCGATTAA-G
1 TTCGTGAACATGTTCGATTAATG
**
45871723 TTAAATGAACATGTTCG
1 TT-CGTGAACATGTTCG
45871740 TGAACATTAA
Statistics
Matches: 95, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
22 2 0.02
23 77 0.81
24 16 0.17
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (23 bp):
TTCGTGAACATGTTCGATTAATG
Found at i:45871749 original size:23 final size:23
Alignment explanation
Indices: 45871705--45871750 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
45871695 TTAATATTCG
* *
45871705 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
45871728 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
45871751 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:45874288 original size:13 final size:14
Alignment explanation
Indices: 45874272--45874300 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
45874262 CTAAATAAAT
45874272 AATTAATT-AATTA
1 AATTAATTAAATTA
45874285 AATTAATTAAATTA
1 AATTAATTAAATTA
45874299 AA
1 AA
45874301 ATTTCGTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AATTAATTAAATTA
Found at i:45874290 original size:9 final size:9
Alignment explanation
Indices: 45874267--45874299 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
45874257 ATACCCTAAA
45874267 TAAA-TAAT
1 TAAATTAAT
45874275 T-AATTAAT
1 TAAATTAAT
45874283 TAAATTAAT
1 TAAATTAAT
45874292 TAAATTAA
1 TAAATTAA
45874300 AATTTCGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 2 0.09
8 6 0.26
9 15 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (9 bp):
TAAATTAAT
Found at i:45882969 original size:23 final size:24
Alignment explanation
Indices: 45882942--45883007 Score: 116
Period size: 23 Copynumber: 2.8 Consensus size: 24
45882932 TTGAAACAAA
45882942 TTAAAAAAATAAATTTATACTA-T
1 TTAAAAAAATAAATTTATACTATT
*
45882965 TTAAAAAAATAAACTTATACTATT
1 TTAAAAAAATAAATTTATACTATT
45882989 TTAAAAAAATAAATTTATA
1 TTAAAAAAATAAATTTATA
45883008 TTAAATATAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
23 21 0.52
24 19 0.47
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAAAAATAAATTTATACTATT
Found at i:45883119 original size:22 final size:23
Alignment explanation
Indices: 45883079--45883122 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
45883069 AAAATTTAAT
*
45883079 AAATAAAAAATTATAAAATATTA
1 AAATAAAAAAATATAAAATATTA
*
45883102 AAATAAAAAAATGT-AAATATT
1 AAATAAAAAAATATAAAATATT
45883123 TTTTTAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATAAAAAAATATAAAATATTA
Found at i:45884489 original size:3 final size:3
Alignment explanation
Indices: 45884477--45884505 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
45884467 TAAAATATAA
45884477 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
45884506 AATATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:45885852 original size:24 final size:24
Alignment explanation
Indices: 45885791--45885853 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
45885781 TAGAGTAATA
* *
45885791 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
45885815 AAAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
45885839 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
45885854 GATTATTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:45887843 original size:24 final size:24
Alignment explanation
Indices: 45887782--45887844 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
45887772 TAGAGTAATA
*
45887782 AGAGTTTAACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
* *
45887806 AGAATTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
45887830 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
45887845 AATTATTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.54, C:0.11, G:0.11, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:45892544 original size:26 final size:26
Alignment explanation
Indices: 45892495--45892544 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
45892485 AAATTTTTTA
* * * *
45892495 AAAATATTTTTCAAAATCACTTTTCC
1 AAAATACTTCTCAAAAGCAATTTTCC
45892521 AAAATACTTCTCAAAAGCAATTTT
1 AAAATACTTCTCAAAAGCAATTTT
45892545 AAATTAACCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.42, C:0.18, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAATACTTCTCAAAAGCAATTTTCC
Found at i:45893700 original size:20 final size:21
Alignment explanation
Indices: 45893672--45893725 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
45893662 TTTAGAAAAA
*
45893672 TTTTA-AATTTTTTATA-TAT
1 TTTTAGAATTTTTTATAGAAT
*
45893691 TTTTAGAATTTTTTTTAGAAT
1 TTTTAGAATTTTTTATAGAAT
45893712 TTTTAGAATTTTTT
1 TTTTAGAATTTTTT
45893726 TAAAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 5 0.16
20 10 0.32
21 16 0.52
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTTAGAATTTTTTATAGAAT
Found at i:45893705 original size:12 final size:12
Alignment explanation
Indices: 45893690--45893726 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
45893680 TTTTTATATA
45893690 TTTTTAGAATTT
1 TTTTTAGAATTT
45893702 TTTTTAGAA---
1 TTTTTAGAATTT
45893711 TTTTTAGAATTT
1 TTTTTAGAATTT
45893723 TTTT
1 TTTT
45893727 AAAAATATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 9 0.41
12 13 0.59
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TTTTTAGAATTT
Found at i:45893775 original size:19 final size:20
Alignment explanation
Indices: 45893744--45893781 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
45893734 TAAATTTTGA
45893744 AATTTTTATAAA-TATTTTC
1 AATTTTTATAAATTATTTTC
45893763 AATTTTTGA-AAATTATTTT
1 AATTTTT-ATAAATTATTTT
45893782 TGTAATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.58
Consensus pattern (20 bp):
AATTTTTATAAATTATTTTC
Found at i:45914895 original size:52 final size:52
Alignment explanation
Indices: 45914715--45914901 Score: 185
Period size: 52 Copynumber: 3.6 Consensus size: 52
45914705 ATTACACTTA
* * * * ** * * *
45914715 ATACTCACAATGACGCATAGTCATTGGACCTCTTGTTCCGTAAAGGAATCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAC
* * ** * *
45914767 ACACTCATGATGACACATAGTCATTAGACCTCATAATCCGTAAAGGATTTAC
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAC
* *
45914819 ATACTCACGATGACACGTAGTCATCGGACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAC
* * * *
45914871 ATACTTACGGTGACACAAAGTCATCGAACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
45914902 TTCTCATTTA
Statistics
Matches: 111, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 111 1.00
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCATAAAGGATTCAC
Found at i:45922132 original size:52 final size:52
Alignment explanation
Indices: 45921989--45922139 Score: 167
Period size: 52 Copynumber: 2.9 Consensus size: 52
45921979 GACCTCTTGT
* * * ** * * *
45921989 TCCATAAAGGAATCATACACTCACAATGACATATAGTCACTGGACCTCATAA
1 TCCATAAAGGATTCACATACTCACGGTGACACATAGTCATTGGACCTCAAAA
* * *
45922041 TCCATAAAGGATTTACATACTCATGGTGACACGTAGTCATTGGACCTCAAAA
1 TCCATAAAGGATTCACATACTCACGGTGACACATAGTCATTGGACCTCAAAA
* * * *
45922093 TCCGTAAAGGATTCATATACTTACGGTGACACATAGTCATTAGACCT
1 TCCATAAAGGATTCACATACTCACGGTGACACATAGTCATTGGACCT
45922140 TTCTCATTTA
Statistics
Matches: 81, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (52 bp):
TCCATAAAGGATTCACATACTCACGGTGACACATAGTCATTGGACCTCAAAA
Found at i:45924112 original size:52 final size:52
Alignment explanation
Indices: 45924030--45924323 Score: 405
Period size: 52 Copynumber: 5.6 Consensus size: 52
45924020 TTCTCATTTA
*
45924030 ATACTCACGATGACACATAGTCATCAGACCTCATAATCTGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAAGATTCAT
* * *
45924082 ATAATCACGATGACACATAGTCATCGGACCTCGTAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAAGATTCAT
* *
45924134 ATACTCACGAATGACACATAGTCATCGGGACCTCATAATTCGT-AAAGAATTCAT
1 ATACTCACG-ATGACACATAGTCATC-AGACCTCATAATCCGTAAAAG-ATTCAT
* * *
45924188 ATACTCATGATGACACATAGTCATCAGACTTAATAATCCG-AAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAA-GATTCAT
* *
45924240 ATACTCATGATGACACATAGTCATTAGACCTCGA-AATCCGTAAAAGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTC-ATAATCCGTAAAAGATTCAT
*
45924292 ATAACTCACGATGACACATAGTCATCGGACCT
1 AT-ACTCACGATGACACATAGTCATCAGACCT
45924324 TTTGCATTTA
Statistics
Matches: 216, Mismatches: 18, Indels: 15
0.87 0.07 0.06
Matches are distributed among these distances:
52 120 0.56
53 68 0.31
54 28 0.13
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCGTAAAAGATTCAT
Found at i:45924179 original size:106 final size:104
Alignment explanation
Indices: 45924030--45924323 Score: 407
Period size: 105 Copynumber: 2.8 Consensus size: 104
45924020 TTCTCATTTA
45924030 ATACTCACGATGACACATAGTCATCAGACCTCATAA-TCTGTAAAAGATTCATATAATCACGATG
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATTC-GTAAAAGATTCATATAATCACGATG
**
45924094 ACACATAGTCATCGGACCTCGTAATCCGTAAAA-GATTCAT
65 ACACATAGTCATCGGACCTAATAATCCG-AAAAGGATTCAT
* * *
45924134 ATACTCACGAATGACACATAGTCATCGGGACCTCATAATTCGT-AAAGAATTCATATACTCATGA
1 ATACTCACG-ATGACACATAGTCATC-AGACCTCATAATTCGTAAAAG-ATTCATATAATCACGA
* *
45924198 TGACACATAGTCATCAGACTTAATAATCCGAAAAGGATTCAT
63 TGACACATAGTCATCGGACCTAATAATCCGAAAAGGATTCAT
* * *
45924240 ATACTCATGATGACACATAGTCATTAGACCTCGA-AATCCGTAAAAGATTCATATAACTCACGAT
1 ATACTCACGATGACACATAGTCATCAGACCTC-ATAATTCGTAAAAGATTCATATAA-TCACGAT
45924304 GACACATAGTCATCGGACCT
64 GACACATAGTCATCGGACCT
45924324 TTTGCATTTA
Statistics
Matches: 167, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
104 30 0.18
105 68 0.41
106 67 0.40
107 2 0.01
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (104 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATTCGTAAAAGATTCATATAATCACGATGA
CACATAGTCATCGGACCTAATAATCCGAAAAGGATTCAT
Found at i:45924318 original size:158 final size:157
Alignment explanation
Indices: 45924030--45924323 Score: 466
Period size: 158 Copynumber: 1.9 Consensus size: 157
45924020 TTCTCATTTA
* *
45924030 ATACTCACGATGACACATAGTCATCAGACCTCATAATCTGTAAAAGATTCATATAATCACGATGA
1 ATACTCACGATGACACATAGTCATCAGACCTAATAATCCGTAAAAGATTCATATAATCACGATGA
* *
45924095 CACATAGTCATCGGACCTCGTAATCCGTAAAAGATTCATATACTCACGAATGACACATAGTCATC
66 CACATAGTCATCAGACCTCGAAATCCGTAAAAGATTCATATACTCACGAATGACACATAGTCATC
45924160 GGGACCTCATAATTCGTAAAGAATTCAT
131 -GGACCTCATAATTCGTAAAGAATTCAT
* * * *
45924188 ATACTCATGATGACACATAGTCATCAGACTTAATAATCCG-AAAAGGATTCATATACTCATGATG
1 ATACTCACGATGACACATAGTCATCAGACCTAATAATCCGTAAAA-GATTCATATAATCACGATG
*
45924252 ACACATAGTCATTAGACCTCGAAATCCGTAAAAGATTCATATAACTCACG-ATGACACATAGTCA
65 ACACATAGTCATCAGACCTCGAAATCCGTAAAAGATTCATAT-ACTCACGAATGACACATAGTCA
45924316 TCGGACCT
129 TCGGACCT
45924324 TTTGCATTTA
Statistics
Matches: 125, Mismatches: 9, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
157 10 0.08
158 108 0.86
159 7 0.06
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (157 bp):
ATACTCACGATGACACATAGTCATCAGACCTAATAATCCGTAAAAGATTCATATAATCACGATGA
CACATAGTCATCAGACCTCGAAATCCGTAAAAGATTCATATACTCACGAATGACACATAGTCATC
GGACCTCATAATTCGTAAAGAATTCAT
Found at i:45924811 original size:16 final size:16
Alignment explanation
Indices: 45924787--45924818 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45924777 TCCTTACAAA
*
45924787 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
45924803 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
45924819 AAAAGTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:45931535 original size:15 final size:14
Alignment explanation
Indices: 45931509--45931538 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
45931499 AAAAATTCAA
45931509 TTAATTAAATTTAT
1 TTAATTAAATTTAT
45931523 TTAATTAAAATTTAT
1 TTAATT-AAATTTAT
45931538 T
1 T
45931539 CTCATCTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAATTAAATTTAT
Found at i:45931740 original size:2 final size:2
Alignment explanation
Indices: 45931733--45931758 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45931723 AAATACCTCC
45931733 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
45931759 TAACACGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45938589 original size:3 final size:3
Alignment explanation
Indices: 45938581--45938606 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
45938571 TAGCTATTTT
45938581 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
45938607 GTTGATTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:45939602 original size:2 final size:2
Alignment explanation
Indices: 45939564--45939591 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45939554 TAATTTTATC
45939564 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
45939592 TATTCATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45944099 original size:21 final size:21
Alignment explanation
Indices: 45944075--45944115 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
45944065 ACCTTTTCTA
45944075 AAGTTAAAA-GTCAAAACTACT
1 AAGTTAAAAGGT-AAAACTACT
45944096 AAGTTAAAAGGTAAAACTAC
1 AAGTTAAAAGGTAAAACTAC
45944116 GTCATTTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (21 bp):
AAGTTAAAAGGTAAAACTACT
Found at i:45949491 original size:21 final size:20
Alignment explanation
Indices: 45949467--45949542 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 20
45949457 CATTGAATGA
*
45949467 TAATAATAATAATAAAAGTTT
1 TAATAATAATAATAATA-TTT
*
45949488 TAATAATAATAA-ATGTATTT
1 TAATAATAATAATA-ATATTT
*
45949508 TAATAATGATAATAACTACTTT
1 TAATAATAATAATAA-TA-TTT
45949530 TAA-AATAATAATA
1 TAATAATAATAATA
45949543 TTTAATATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
20 15 0.33
21 25 0.54
22 6 0.13
ACGTcount: A:0.54, C:0.03, G:0.04, T:0.39
Consensus pattern (20 bp):
TAATAATAATAATAATATTT
Found at i:45949493 original size:18 final size:19
Alignment explanation
Indices: 45949470--45949519 Score: 66
Period size: 18 Copynumber: 2.6 Consensus size: 19
45949460 TGAATGATAA
45949470 TAATAATAATAAAAG-TTT
1 TAATAATAATAAAAGATTT
*
45949488 TAATAATAATAAATGTATTT
1 TAATAATAATAAAAG-ATTT
*
45949508 TAATAATGATAA
1 TAATAATAATAA
45949520 TAACTACTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 14 0.50
20 14 0.50
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
TAATAATAATAAAAGATTT
Found at i:45950624 original size:29 final size:30
Alignment explanation
Indices: 45950564--45950794 Score: 103
Period size: 29 Copynumber: 7.9 Consensus size: 30
45950554 TTTTGTAGGT
45950564 CCCTAAACTATCCAAAAATTACCATTTTAC
1 CCCTAAACTATCCAAAAATTACCATTTTAC
* *
45950594 CCCTAAACTTTCC-AAAATT-TCATTTTAAC
1 CCCTAAACTATCCAAAAATTACCATTTT-AC
**
45950623 CCCGGT-TTC-AT-CAAAAATTACCATTTTAC
1 CCC--TAAACTATCCAAAAATTACCATTTTAC
** * * *
45950652 CCCCGAATTTTCC-AAAATT-CCATTTTAA
1 CCCTAAACTATCCAAAAATTACCATTTTAC
* **
45950680 CCCTGATTTCAT-CAAAAATTACCATTTTA-
1 CCCTAAACT-ATCCAAAAATTACCATTTTAC
* *
45950709 CCCTCGAACT-TCCCAAAATT-CCATTTTTAAC
1 CCCT-AAACTATCCAAAAATTACCA-TTTT-AC
* * ** * *
45950740 CTCGATTCCAT-AAAAAATTACCATTTTAC
1 CCCTAAACTATCCAAAAATTACCATTTTAC
* *
45950769 CCCTTAACTTTCC-AAAATT-CCATTTT
1 CCCTAAACTATCCAAAAATTACCATTTT
45950795 TGACCTCGGT
Statistics
Matches: 148, Mismatches: 34, Indels: 40
0.67 0.15 0.18
Matches are distributed among these distances:
28 34 0.23
29 64 0.43
30 43 0.29
31 7 0.05
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.35
Consensus pattern (30 bp):
CCCTAAACTATCCAAAAATTACCATTTTAC
Found at i:45950637 original size:28 final size:28
Alignment explanation
Indices: 45950606--45950943 Score: 158
Period size: 29 Copynumber: 11.5 Consensus size: 28
45950596 CTAAACTTTC
* *
45950606 CAAAATTTCATTTTAACCCCGGTTTCAT
1 CAAAATTCCATTTTAACCCCGATTTCAT
*
45950634 CAAAAATTACCATTTTACCCCCGAATTT--T
1 C-AAAATT-CCATTTTAACCCCG-ATTTCAT
*
45950663 CCAAAATTCCATTTTAACCCTGATTTCAT
1 -CAAAATTCCATTTTAACCCCGATTTCAT
* *
45950692 CAAAAATTACCATTTT-ACCCTCGAACTTC-C
1 C-AAAATT-CCATTTTAACCC-CG-ATTTCAT
* *
45950722 CAAAATTCCATTTTTAACCTCGATTCCAT
1 CAAAATTCCA-TTTTAACCCCGATTTCAT
* *
45950751 AAAAAATTACCATTTT-ACCCCTTAACTTTC--
1 -CAAAATT-CCATTTTAACCCC--GA-TTTCAT
* * * *
45950781 CAAAATTCCATTTTTGACCTCGGTTTCAC
1 CAAAATTCCA-TTTTAACCCCGATTTCAT
*
45950810 CAAAAATTACCATTTTACCCCCGAACTTTC--
1 C-AAAATT-CCATTTTAACCCCG-A-TTTCAT
* * *
45950840 CAAAATTCCATTTTTGACCTCGATTTCAC
1 CAAAATTCCA-TTTTAACCCCGATTTCAT
* **
45950869 CAAAAATTACCATTTTATCCCTAAACTTTC-T
1 C-AAAATT-CCATTTTAACCC-CGA-TTTCAT
*
45950900 -AAAATTCCATTTTTAACCCCGATTTCAC
1 CAAAATTCCA-TTTTAACCCCGATTTCAT
45950928 CAAAAATTACCATTTT
1 C-AAAATT-CCATTTT
45950944 GCCCTCGGGT
Statistics
Matches: 235, Mismatches: 37, Indels: 74
0.68 0.11 0.21
Matches are distributed among these distances:
27 16 0.07
28 31 0.13
29 80 0.34
30 76 0.32
31 21 0.09
32 11 0.05
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (28 bp):
CAAAATTCCATTTTAACCCCGATTTCAT
Found at i:45950647 original size:58 final size:59
Alignment explanation
Indices: 45950575--45950943 Score: 501
Period size: 59 Copynumber: 6.3 Consensus size: 59
45950565 CCTAAACTAT
* * *
45950575 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCA-TTTTAACCCCGGTTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
45950633 TCAAAAATTACCATTTTACCCCCGAATTTTCCAAAATTCCA-TTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
45950691 TCAAAAATTACCATTTTA-CCCTCGAACTTCCCAAAATTCCATTTTTAACCTCGATTCCA
1 CCAAAAATTACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
** * * * *
45950750 TAAAAAATTACCATTTTACCCCTTAACTTTCCAAAATTCCATTTTTGACCTCGGTTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
45950809 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
45950868 CCAAAAATTACCATTTTATCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
45950927 CCAAAAATTACCATTTT
1 CCAAAAATTACCATTTT
45950944 GCCCTCGGGT
Statistics
Matches: 278, Mismatches: 30, Indels: 5
0.89 0.10 0.02
Matches are distributed among these distances:
57 3 0.01
58 85 0.31
59 186 0.67
60 4 0.01
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:45950978 original size:118 final size:118
Alignment explanation
Indices: 45950575--45950987 Score: 521
Period size: 118 Copynumber: 3.5 Consensus size: 118
45950565 CCTAAACTAT
* * * * *
45950575 CCAAAAATTACCATTTTACCC-CTAAACTTTCCAAAATTTCA-TTTTAACCCCGGTTTCATCAAA
1 CCAAAAATTACCATTTTACCCTC-GAACTTCCCAAAATTCCATTTTTAACCTCGATTTCATCAAA
** * *
45950638 AATTACCATTTTACCCCCGAATTTTCCAAAATTCCA-TTTTAACCCTGATTTCA
65 AATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
45950691 TCAAAAATTACCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCTCGATTCCATAAAAA
1 CCAAAAATTACCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCTCGATTTCATCAAAA
* * * *
45950756 ATTACCATTTTACCCCTTAACTTTCCAAAATTCCATTTTTGACCTCGGTTTCA
66 ATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
45950809 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCTCGATTTCATCAAAA
* *
45950874 ATTACCATTTTATCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
66 ATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* ** * *
45950927 CCAAAAATTACCATTTTGCCCTCG-GGTACCCAAAAGTCC-TGTTTTCAACCTCGATTTCATC
1 CCAAAAATTACCATTTTACCCTCGAACTTCCCAAAATTCCAT-TTTT-AACCTCGATTTCATC
45950988 GTTTCTTCTT
Statistics
Matches: 255, Mismatches: 37, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
116 36 0.14
117 66 0.26
118 153 0.60
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (118 bp):
CCAAAAATTACCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCTCGATTTCATCAAAA
ATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:45950982 original size:59 final size:58
Alignment explanation
Indices: 45950575--45950985 Score: 452
Period size: 59 Copynumber: 7.0 Consensus size: 58
45950565 CCTAAACTAT
** * * *
45950575 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTTCA-TTTTAACCCCGGTTTCA
1 CCAAAAATTACCATTTTA-CCCTCGACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* * *
45950633 TCAAAAATTACCATTTTACCCCCGAATTTTCCAAAATTCCA-TTTTAACC-CTGATTTCA
1 CCAAAAATTACCATTTTACCCTCG-ACTTTCCAAAATTCCATTTTTAACCTC-GATTTCA
* * *
45950691 TCAAAAATTACCATTTTACCCTCGAACTTCCCAAAATTCCATTTTTAACCTCGATTCCA
1 CCAAAAATTACCATTTTACCCTCG-ACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
** ** * *
45950750 TAAAAAATTACCATTTTACCCCTTAACTTTCCAAAATTCCATTTTTGACCTCGGTTTCA
1 CCAAAAATTACCATTTTA-CCCTCGACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* *
45950809 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCG-ACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
** * *
45950868 CCAAAAATTACCATTTTATCCCTAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTA-CCCTCGACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
* ** ** *
45950927 CCAAAAATTACCATTTTGCCCTCGGGTACCCAAAAGTCC-TGTTTTCAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCTCGACTTTCCAAAATTCCAT-TTTT-AACCTCGATTTCA
45950986 TCGTTTCTTC
Statistics
Matches: 304, Mismatches: 40, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
57 5 0.02
58 103 0.34
59 188 0.62
60 8 0.03
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCTCGACTTTCCAAAATTCCATTTTTAACCTCGATTTCA
Found at i:45952590 original size:11 final size:11
Alignment explanation
Indices: 45952574--45952598 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
45952564 AAATATATGA
45952574 AAATTTTGAAG
1 AAATTTTGAAG
45952585 AAATTTTGAAG
1 AAATTTTGAAG
45952596 AAA
1 AAA
45952599 AACATACCTT
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (11 bp):
AAATTTTGAAG
Found at i:45952749 original size:22 final size:20
Alignment explanation
Indices: 45952721--45952768 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
45952711 CTTTATATAT
*
45952721 ATATTATTATATTACTTATAAA
1 ATATTATTATATTA--AATAAA
*
45952743 ATATTATTATTTTAAATAAA
1 ATATTATTATATTAAATAAA
45952763 ATATTA
1 ATATTA
45952769 AATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 11 0.46
22 13 0.54
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATTATATTAAATAAA
Found at i:45969400 original size:24 final size:24
Alignment explanation
Indices: 45969368--45969449 Score: 101
Period size: 24 Copynumber: 3.4 Consensus size: 24
45969358 GTTAGGATAT
45969368 GATTCTGTATCTAAAATTGTATCC
1 GATTCTGTATCTAAAATTGTATCC
* * *
45969392 GATTCTGTATATGAAATTGTATTC
1 GATTCTGTATCTAAAATTGTATCC
* * *
45969416 GATTCTGTATCTAAGATTGCATCT
1 GATTCTGTATCTAAAATTGTATCC
*
45969440 GATTTTGTAT
1 GATTCTGTAT
45969450 TTGAACTGCA
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.45
Consensus pattern (24 bp):
GATTCTGTATCTAAAATTGTATCC
Found at i:45971013 original size:30 final size:29
Alignment explanation
Indices: 45970916--45971014 Score: 73
Period size: 30 Copynumber: 3.5 Consensus size: 29
45970906 TTTACGATAA
*
45970916 TAAAAATATAATTTTATT-ATTTTAATAG
1 TAAAAATATAATTTTATTAATTTTAAAAG
** * *
45970944 T--TTATAT-A-TTTATTATTTTTAAAAAA
1 TAAAAATATAATTTTATTAATTTT-AAAAG
* * *
45970970 TTAAATTAAAATTTTATTAATTTTATAAAG
1 TAAAAATATAATTTTATTAATTTTA-AAAG
45971000 TAAAAATATAATTTT
1 TAAAAATATAATTTT
45971015 TACCTGATTC
Statistics
Matches: 50, Mismatches: 14, Indels: 12
0.66 0.18 0.16
Matches are distributed among these distances:
24 6 0.12
25 5 0.10
26 8 0.16
28 3 0.06
29 2 0.04
30 26 0.52
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TAAAAATATAATTTTATTAATTTTAAAAG
Found at i:45973873 original size:42 final size:42
Alignment explanation
Indices: 45973805--45973919 Score: 194
Period size: 42 Copynumber: 2.7 Consensus size: 42
45973795 TTCAAGCCTC
* * * *
45973805 TGCAGTTTTCGGGAACATCTCATTATCGCAGGACCAATCCTT
1 TGCAGTTTCCGGGAAGAGCTCGTTATCGCAGGACCAATCCTT
45973847 TGCAGTTTCCGGGAAGAGCTCGTTATCGCAGGACCAATCCTT
1 TGCAGTTTCCGGGAAGAGCTCGTTATCGCAGGACCAATCCTT
45973889 TGCAGTTTCCGGGAAGAGCTCGTTATCGCAG
1 TGCAGTTTCCGGGAAGAGCTCGTTATCGCAG
45973920 TTGGATAACG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 69 1.00
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (42 bp):
TGCAGTTTCCGGGAAGAGCTCGTTATCGCAGGACCAATCCTT
Found at i:45980915 original size:16 final size:15
Alignment explanation
Indices: 45980892--45980929 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
45980882 GGGGCAAATT
45980892 TGTAATTTTTTACAAG
1 TGTAATTTTTTA-AAG
*
45980908 TTTAA-TTTTTAAAG
1 TGTAATTTTTTAAAG
45980922 TGTAATTT
1 TGTAATTT
45980930 CCCCAAGGGC
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 7 0.37
15 8 0.42
16 4 0.21
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.55
Consensus pattern (15 bp):
TGTAATTTTTTAAAG
Found at i:45980922 original size:14 final size:15
Alignment explanation
Indices: 45980892--45980929 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
45980882 GGGGCAAATT
45980892 TGTAATTTTTTACAAG
1 TGTAA-TTTTTACAAG
*
45980908 TTTAATTTTTA-AAG
1 TGTAATTTTTACAAG
45980922 TGTAATTT
1 TGTAATTT
45980930 CCCCAAGGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 10 0.50
15 6 0.30
16 4 0.20
ACGTcount: A:0.32, C:0.03, G:0.11, T:0.55
Consensus pattern (15 bp):
TGTAATTTTTACAAG
Found at i:45988731 original size:7 final size:7
Alignment explanation
Indices: 45988687--45988730 Score: 79
Period size: 7 Copynumber: 6.3 Consensus size: 7
45988677 AAAAGAAGAG
45988687 AAGTAAA
1 AAGTAAA
45988694 AAGTAAA
1 AAGTAAA
45988701 AAGTAAA
1 AAGTAAA
45988708 AAGTAAA
1 AAGTAAA
45988715 AAGTAAA
1 AAGTAAA
*
45988722 AAATAAA
1 AAGTAAA
45988729 AA
1 AA
45988731 AGAAATTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 36 1.00
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (7 bp):
AAGTAAA
Found at i:45989968 original size:3 final size:3
Alignment explanation
Indices: 45989960--45989997 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
45989950 GTCAATCTGC
45989960 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
45989998 GGCAGGTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:45995464 original size:77 final size:75
Alignment explanation
Indices: 45995361--45995511 Score: 212
Period size: 76 Copynumber: 2.0 Consensus size: 75
45995351 TTTTCTATTA
* ** * **
45995361 CTGTACTTTTTTGGGTTAAATGTAGGGATGATAATTCGGATAGCGGATTTGGATATATCTGATCC
1 CTGTACTTTTTTAGGCCAAATGTAGGGATGATAATTCGGATAGCGGA-TTGAATATATCTGATAA
45995426 AAATTTACTGT
65 AAATTTACTGT
* *
45995437 CTGTACTTTTGTTAGGCCAAATGTAGGGATGATAATTCGGATTGCGGATTGAATATATTTGATAA
1 CTGTACTTTT-TTAGGCCAAATGTAGGGATGATAATTCGGATAGCGGATTGAATATATCTGATAA
45995502 AAATTTACTG
65 AAATTTACTG
45995512 GTTGCAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
76 33 0.50
77 33 0.50
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.38
Consensus pattern (75 bp):
CTGTACTTTTTTAGGCCAAATGTAGGGATGATAATTCGGATAGCGGATTGAATATATCTGATAAA
AATTTACTGT
Found at i:45996032 original size:29 final size:29
Alignment explanation
Indices: 45995997--45996064 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
45995987 TTTATATTGG
45995997 ATAAATATAATTATATTTGTATGTAATAT
1 ATAAATATAATTATATTTGTATGTAATAT
45996026 ATAAATATAATTATATTTGTATGTAATAT
1 ATAAATATAATTATATTTGTATGTAATAT
45996055 ATAAATATAA
1 ATAAATATAA
45996065 AGTTATGTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (29 bp):
ATAAATATAATTATATTTGTATGTAATAT
Found at i:46000763 original size:217 final size:217
Alignment explanation
Indices: 46000377--46000811 Score: 753
Period size: 217 Copynumber: 2.0 Consensus size: 217
46000367 TATAGATCAG
*
46000377 TTCCATGAAGAGGACACAACGAGAGCGTCGCTAGAACAAATGGGGGAGAATGTCATGGGTTGTGC
1 TTCCATGAAGAGGACACAACGAGAGCGTCACTAGAACAAATGGGGGAGAATGTCATGGGTTGTGC
*
46000442 ATTTGAGCCTACAACCATGACTCATTTGAGTGACACGTCATGTTCAAAAGGAGGCATTTGGCCCA
66 ATTTGAACCTACAACCATGACTCATTTGAGTGACACGTCATGTTCAAAAGGAGGCATTTGGCCCA
*
46000507 ATCAAACTAGTCCACTGCTTGGAATGAGTGAAAGCTTATCTACAAAGCTTGGAAAACATGAAAGG
131 ATCAAACTAGTCCACTGCTTGGAATCAGTGAAAGCTTATCTACAAAGCTTGGAAAACATGAAAGG
*
46000572 TGATCTTAAAAGATTGATGATA
196 TGATCTTAAAAGATTGACGATA
* * * * *
46000594 TTCCATGAGGAGGACATAACGAGGGCGTCACTAGAACAGATGGGGGAGAATGTCATGGGTTGTGT
1 TTCCATGAAGAGGACACAACGAGAGCGTCACTAGAACAAATGGGGGAGAATGTCATGGGTTGTGC
* *
46000659 TTTTGAACCTACAACCATGACTCATTTGAGTGACCCGTCATGTTCAAAAGGAGGCATTTGGCCCA
66 ATTTGAACCTACAACCATGACTCATTTGAGTGACACGTCATGTTCAAAAGGAGGCATTTGGCCCA
* *
46000724 ATCAAACTAGTCCACTGCTTGGAATCAGTGAAGGCTTATCTACAAAGCTTGGCAAACATGAAAGG
131 ATCAAACTAGTCCACTGCTTGGAATCAGTGAAAGCTTATCTACAAAGCTTGGAAAACATGAAAGG
46000789 TGATCTTAAAAGATTGACGATA
196 TGATCTTAAAAGATTGACGATA
46000811 T
1 T
46000812 CAGATTTGAA
Statistics
Matches: 205, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 205 1.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (217 bp):
TTCCATGAAGAGGACACAACGAGAGCGTCACTAGAACAAATGGGGGAGAATGTCATGGGTTGTGC
ATTTGAACCTACAACCATGACTCATTTGAGTGACACGTCATGTTCAAAAGGAGGCATTTGGCCCA
ATCAAACTAGTCCACTGCTTGGAATCAGTGAAAGCTTATCTACAAAGCTTGGAAAACATGAAAGG
TGATCTTAAAAGATTGACGATA
Found at i:46002911 original size:87 final size:87
Alignment explanation
Indices: 46002735--46002912 Score: 205
Period size: 87 Copynumber: 2.0 Consensus size: 87
46002725 GTTTTGCTTT
* * * * *
46002735 TGTTTTAAATTCCACTTGAGCTTTACAATGTAATTTTTCAATTTTCCACACCAATAAACCTTTGA
1 TGTTTTAAATTCCACTCGAGCTTTAAAATATAATTTTTCAATTTTCCACACCAACAAACCTTTAA
* *
46002800 ACACCATTAAATTAATTTTTTG
66 ACACCATTAAATTAACTTTCTG
** * * *
46002822 TGTTTTAAATTTTACTCGAGTTTTAAAATATATTTTTTTAATTTTCCACACCAACAAACCTTTAA
1 TGTTTTAAATTCCACTCGAGCTTTAAAATATAATTTTTCAATTTTCCACACCAACAAACCTTTAA
** *
46002887 ACATGATTATACTT-ACTTTCTG
66 ACACCATTA-AATTAACTTTCTG
46002909 TGTT
1 TGTT
46002913 AATAATGTAA
Statistics
Matches: 75, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
87 72 0.96
88 3 0.04
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (87 bp):
TGTTTTAAATTCCACTCGAGCTTTAAAATATAATTTTTCAATTTTCCACACCAACAAACCTTTAA
ACACCATTAAATTAACTTTCTG
Found at i:46014785 original size:61 final size:61
Alignment explanation
Indices: 46014710--46014856 Score: 285
Period size: 61 Copynumber: 2.4 Consensus size: 61
46014700 AACTCTTACT
46014710 TGACATCGTAATCATGAAATATGAAGCAAGAGCAAATGAAACTGTGTTTTGCTGTTTCATA
1 TGACATCGTAATCATGAAATATGAAGCAAGAGCAAATGAAACTGTGTTTTGCTGTTTCATA
46014771 TGACATCGTAATCATGAAATATGAAGCAAGAGCAAATGAAACTGTGTTTTGCTGTTTCATA
1 TGACATCGTAATCATGAAATATGAAGCAAGAGCAAATGAAACTGTGTTTTGCTGTTTCATA
*
46014832 TGACATCGTAATCATGGAATATGAA
1 TGACATCGTAATCATGAAATATGAA
46014857 CATTCATAGT
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
61 85 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (61 bp):
TGACATCGTAATCATGAAATATGAAGCAAGAGCAAATGAAACTGTGTTTTGCTGTTTCATA
Found at i:46015779 original size:52 final size:54
Alignment explanation
Indices: 46015683--46015794 Score: 149
Period size: 52 Copynumber: 2.1 Consensus size: 54
46015673 CTTTAATGAT
*
46015683 TTTCCACACCAATGAACCTTTAAACACGACTACACTTATTTCTTGTG-TTTAAA
1 TTTCCACACCAATGAACCTTTAAACACGACTACACTTACTTCTTGTGTTTTAAA
* * * * *
46015736 TTTCCACATCAATTAACC-TTAAGCACGACTAGATTTACTTCTTGTGTTTTAAA
1 TTTCCACACCAATGAACCTTTAAACACGACTACACTTACTTCTTGTGTTTTAAA
46015789 -TTCCAC
1 TTTCCAC
46015795 TTCAGTTTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
52 30 0.58
53 22 0.42
ACGTcount: A:0.30, C:0.24, G:0.08, T:0.38
Consensus pattern (54 bp):
TTTCCACACCAATGAACCTTTAAACACGACTACACTTACTTCTTGTGTTTTAAA
Found at i:46021424 original size:173 final size:173
Alignment explanation
Indices: 46021135--46021482 Score: 597
Period size: 173 Copynumber: 2.0 Consensus size: 173
46021125 AAATTGCATA
* *
46021135 TTAACTTACCTTTTGTTGAAGCTCTTTCGCAAATGTCGGAGTATGTAAAATTCTTAAAGGAGCTG
1 TTAACTTACCTTTTGTTGAAACTCTTTCGCAAATGCCGGAGTATGTAAAATTCTTAAAGGAGCTG
* *
46021200 TTAAAAAATAAGAGGAAGTTAGATGACTTGTCGACTATGGAGCTTAATGCAGTTTGCTCGACCAT
66 CTAAAAAATAAGAGGAAGTTAGACGACTTGTCGACTATGGAGCTTAATGCAGTTTGCTCGACCAT
46021265 TCTCCAAAACAAACTACCCAACAAACTTAAAGATCTAGGGAGT
131 TCTCCAAAACAAACTACCCAACAAACTTAAAGATCTAGGGAGT
* *
46021308 TTAACTTACCTTTTGTTGAAACTCTTTCGTAGATGCCGGAGTATGTAAAATTCTTAAAGGAGCTG
1 TTAACTTACCTTTTGTTGAAACTCTTTCGCAAATGCCGGAGTATGTAAAATTCTTAAAGGAGCTG
* *
46021373 CTAACAAATAAGAGGAAGTTAGACGACTTGTTGACTATGGAGCTTAATGCAGTTTGCTCGACCAT
66 CTAAAAAATAAGAGGAAGTTAGACGACTTGTCGACTATGGAGCTTAATGCAGTTTGCTCGACCAT
* * *
46021438 TCTCCAAAACAAATTATCCAACAAACTTAAAGATTTAGGGAGT
131 TCTCCAAAACAAACTACCCAACAAACTTAAAGATCTAGGGAGT
46021481 TT
1 TT
46021483 TACTATTCCT
Statistics
Matches: 164, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
173 164 1.00
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (173 bp):
TTAACTTACCTTTTGTTGAAACTCTTTCGCAAATGCCGGAGTATGTAAAATTCTTAAAGGAGCTG
CTAAAAAATAAGAGGAAGTTAGACGACTTGTCGACTATGGAGCTTAATGCAGTTTGCTCGACCAT
TCTCCAAAACAAACTACCCAACAAACTTAAAGATCTAGGGAGT
Found at i:46022542 original size:17 final size:17
Alignment explanation
Indices: 46022513--46022553 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
46022503 AAATAGTATA
46022513 TTTATTTTCATTTCATT
1 TTTATTTTCATTTCATT
*
46022530 TTTAGTTTT-ATTTTA-T
1 TTTA-TTTTCATTTCATT
46022546 TTTATTTT
1 TTTATTTT
46022554 TAATTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 4 0.18
16 5 0.23
17 9 0.41
18 4 0.18
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTATTTTCATTTCATT
Found at i:46022543 original size:5 final size:5
Alignment explanation
Indices: 46022513--46022566 Score: 54
Period size: 6 Copynumber: 9.8 Consensus size: 5
46022503 AAATAGTATA
*
46022513 TTTAT TTTCAT TTCATT TTTAGT TTTAT TTTAT TTTATT TTTAAT TTTAT
1 TTTAT TTT-AT TTTA-T TTTA-T TTTAT TTTAT TTTA-T TTT-AT TTTAT
46022563 TTTA
1 TTTA
46022567 ATTATGCAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
5 20 0.48
6 21 0.50
7 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (5 bp):
TTTAT
Found at i:46022552 original size:22 final size:22
Alignment explanation
Indices: 46022513--46022566 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
46022503 AAATAGTATA
*
46022513 TTTATTTTCATTTCATTTTTAGT
1 TTTATTTT-ATTTCATTTTTAAT
*
46022536 TTTATTTTATTTTATTTTTAAT
1 TTTATTTTATTTCATTTTTAAT
46022558 TTTATTTTA
1 TTTATTTTA
46022567 ATTATGCAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTATTTTATTTCATTTTTAAT
Found at i:46022559 original size:17 final size:16
Alignment explanation
Indices: 46022529--46022566 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
46022519 TTCATTTCAT
46022529 TTTTAGTTTTATTTTA
1 TTTTAGTTTTATTTTA
*
46022545 TTTTATTTTTAATTTTA
1 TTTTAGTTTT-ATTTTA
46022562 TTTTA
1 TTTTA
46022567 ATTATGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (16 bp):
TTTTAGTTTTATTTTA
Found at i:46023521 original size:15 final size:16
Alignment explanation
Indices: 46023503--46023543 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
46023493 AAAAAAGTCG
46023503 AAAAGAAAAATT-AAA
1 AAAAGAAAAATTAAAA
46023518 AAAAG-AAAATTGAAAA
1 AAAAGAAAAATT-AAAA
46023534 AAAAGAAAAA
1 AAAAGAAAAA
46023544 AAAAGACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 6 0.26
15 5 0.22
16 8 0.35
17 4 0.17
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAAGAAAAATTAAAA
Found at i:46026179 original size:21 final size:20
Alignment explanation
Indices: 46026155--46026195 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
46026145 AAAAGATAAT
*
46026155 TAATATTAAATCTAAACAATA
1 TAATAATAAATCT-AACAATA
*
46026176 TAATAATAATTCTAACAATA
1 TAATAATAAATCTAACAATA
46026196 ATCCTTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (20 bp):
TAATAATAAATCTAACAATA
Found at i:46027820 original size:13 final size:13
Alignment explanation
Indices: 46027802--46027826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46027792 AACAAAAATC
46027802 AAACCAAATATAG
1 AAACCAAATATAG
46027815 AAACCAAATATA
1 AAACCAAATATA
46027827 AGATTAACCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAACCAAATATAG
Found at i:46039816 original size:127 final size:127
Alignment explanation
Indices: 46039619--46039865 Score: 422
Period size: 127 Copynumber: 1.9 Consensus size: 127
46039609 TCGAGCATTT
* *
46039619 ATGTATGTGCGTTGTCAAAAAATTAAAAAAGTATGAACAGATCCTACCATGTAATAACATCAATT
1 ATGTATGTGCGTTGCCAAAAAATTAAAAAAGTATGAACAGATCCTACCATGTAATAACATAAATT
* *
46039684 GCATTAATATAGTTTATACTAGACAATATTATTTTTTTAAAAATATTTATGTTGTGTGAAAG
66 ACATTAATATAGTTTATACTAGACAATATTATTTTTTAAAAAATATTTATGTTGTGTGAAAG
* * *
46039746 ATGTGTGTGCGTTGCCAAAAAGTTAAAAAAGTATGAACAGATCCTACCATGTAATCACATAAATT
1 ATGTATGTGCGTTGCCAAAAAATTAAAAAAGTATGAACAGATCCTACCATGTAATAACATAAATT
*
46039811 ACATTATTATAGTTTATACTAGACAATATTATTTTTTAAAAAATATTTATGTTGT
66 ACATTAATATAGTTTATACTAGACAATATTATTTTTTAAAAAATATTTATGTTGT
46039866 TTTATTTTAA
Statistics
Matches: 112, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
127 112 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (127 bp):
ATGTATGTGCGTTGCCAAAAAATTAAAAAAGTATGAACAGATCCTACCATGTAATAACATAAATT
ACATTAATATAGTTTATACTAGACAATATTATTTTTTAAAAAATATTTATGTTGTGTGAAAG
Found at i:46040532 original size:27 final size:26
Alignment explanation
Indices: 46040471--46040542 Score: 76
Period size: 29 Copynumber: 2.7 Consensus size: 26
46040461 ATTACAAAAA
46040471 ATTAAAA--TTAATAAAATCTATAAAT
1 ATTAAAATTTTAATAAAAT-TATAAAT
*
46040496 ATTAAGAAATTTTAATGAAAATTTTAAAT
1 ATT-A-AAATTTTAAT-AAAATTATAAAT
*
46040525 ATTAAAATTTTATTAAAA
1 ATTAAAATTTTAATAAAA
46040543 ATTAGAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 12 0.30
28 1 0.03
29 14 0.35
30 5 0.12
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (26 bp):
ATTAAAATTTTAATAAAATTATAAAT
Found at i:46040543 original size:27 final size:29
Alignment explanation
Indices: 46040478--46040545 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 29
46040468 AAAATTAAAA
*
46040478 TTAAT-AAAATCTATAAATATTAAGAAATT
1 TTAATAAAAAT-TTTAAATATTAAGAAATT
*
46040507 TTAATGAAAATTTTAAATATT-A-AAATT
1 TTAATAAAAATTTTAAATATTAAGAAATT
*
46040534 TTATTAAAAATT
1 TTAATAAAAATT
46040546 AGAAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 15 0.43
28 1 0.03
29 14 0.40
30 5 0.14
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (29 bp):
TTAATAAAAATTTTAAATATTAAGAAATT
Found at i:46040601 original size:45 final size:46
Alignment explanation
Indices: 46040552--46040639 Score: 126
Period size: 46 Copynumber: 1.9 Consensus size: 46
46040542 AATTAGAAAA
**
46040552 AAAATA-AAAATTTTGTAAAATTTTATAAAAATCGTAA-AAAATAAT
1 AAAATATAAAATTTAATAAAATTTTAT-AAAATCGTAAGAAAATAAT
*
46040597 AAAATATAAAATTTAATAAAATTTTATAAAGTCGTAAGAAAAT
1 AAAATATAAAATTTAATAAAATTTTATAAAATCGTAAGAAAAT
46040640 TATACAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
45 15 0.39
46 23 0.61
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (46 bp):
AAAATATAAAATTTAATAAAATTTTATAAAATCGTAAGAAAATAAT
Found at i:46057983 original size:15 final size:16
Alignment explanation
Indices: 46057948--46057985 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
46057938 TTTTTAAATA
* *
46057948 TTTATATTATATTATT
1 TTTATATTATAATAAT
46057964 TTTATATT-TAATAAT
1 TTTATATTATAATAAT
46057979 TTTATAT
1 TTTATAT
46057986 ATTTTTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 12 0.60
16 8 0.40
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATATTATAATAAT
Found at i:46057995 original size:15 final size:15
Alignment explanation
Indices: 46057948--46057995 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
46057938 TTTTTAAATA
46057948 TTTATATTATATTATT
1 TTTATATT-TATTATT
*
46057964 TTTATATTTAATAATT
1 TTTATATTT-ATTATT
46057980 TTATATATTT-TTATT
1 TT-TATATTTATTATT
46057995 T
1 T
46057996 ATCAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
15 6 0.21
16 15 0.54
17 7 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATATTTATTATT
Found at i:46066992 original size:13 final size:13
Alignment explanation
Indices: 46066958--46066995 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
46066948 AACAAATATC
46066958 AAACCAAATATAG
1 AAACCAAATATAG
**
46066971 AAAAGAAATATAG
1 AAACCAAATATAG
46066984 AAACCAAATATA
1 AAACCAAATATA
46066996 AGATTAACCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.66, C:0.11, G:0.08, T:0.16
Consensus pattern (13 bp):
AAACCAAATATAG
Found at i:46080357 original size:13 final size:13
Alignment explanation
Indices: 46080320--46080367 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
46080310 AGGAAGAAAA
*
46080320 AAAAGAAAAGA-G
1 AAAAGAAGAGAGG
46080332 AAAAGAA-AGAGG
1 AAAAGAAGAGAGG
46080344 AAAAGAAGAGAGG
1 AAAAGAAGAGAGG
46080357 AACAAG-AGAGA
1 AA-AAGAAGAGA
46080368 TGCGAAGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
11 3 0.09
12 15 0.45
13 12 0.36
14 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAGAGG
Found at i:46080523 original size:192 final size:191
Alignment explanation
Indices: 46080308--46080691 Score: 653
Period size: 192 Copynumber: 2.0 Consensus size: 191
46080298 CAGGGAAAAG
*
46080308 AGAGGAAGAAAAAAAAGAAAAGAGAAAAGAAAGAGGAAAAGAAGAGAGGAACAAGAGAGATGCGA
1 AGAGGAAGAAAAAAAAGAAAAGAGAAAAGAAAGAGGAAAAGAAGAGAGGAACAAGAGAGATGCAA
*
46080373 AGCAAGGGAAGAAAATAGAGAAAGCATAGAGCAAGGTTAAGGGGTGAGAGTAGAAATAAGAGGAG
66 AGCAAGGGAAGAAAATAGAGAAAGCATAGAGCAAGGTTAAGGGGTGAGAGTAGAAACAAGAGGAG
*
46080438 TGAAAAGAGAGGGGTCGATCG-AAAAAATATGCTTAAATACTTAAGGTTGTAAGGCATACT
131 TGAAAAGAGAGGGGTCGATCGAAAAAAACATGCTTAAATACTTAAGGTTGTAAGGCATACT
*
46080498 AGAGGAAGAAAAAAAAAAGAAAAGAGGAAAGAAAGAGGAAAAGAAGAGAGGAACAAGAGAGATGC
1 AGAGGAAG--AAAAAAAAGAAAAGAGAAAAGAAAGAGGAAAAGAAGAGAGGAACAAGAGAGATGC
* * *
46080563 AAAGCAAGGGAAGAAAATAGAGAAGGCATAGAGCTAGGTTAAGGGGTGAGAGTAGGAACAAGAGG
64 AAAGCAAGGGAAGAAAATAGAGAAAGCATAGAGCAAGGTTAAGGGGTGAGAGTAGAAACAAGAGG
* * *
46080628 AGTGAAAAGAGAGGGGTCGATCGAAAAAAACATGCTTAATTACTTAGGGTTGTGAGGCATACT
129 AGTGAAAAGAGAGGGGTCGATCGAAAAAAACATGCTTAAATACTTAAGGTTGTAAGGCATACT
46080691 A
1 A
46080692 AGGTTACAAC
Statistics
Matches: 181, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
190 8 0.04
192 137 0.76
193 36 0.20
ACGTcount: A:0.49, C:0.06, G:0.32, T:0.12
Consensus pattern (191 bp):
AGAGGAAGAAAAAAAAGAAAAGAGAAAAGAAAGAGGAAAAGAAGAGAGGAACAAGAGAGATGCAA
AGCAAGGGAAGAAAATAGAGAAAGCATAGAGCAAGGTTAAGGGGTGAGAGTAGAAACAAGAGGAG
TGAAAAGAGAGGGGTCGATCGAAAAAAACATGCTTAAATACTTAAGGTTGTAAGGCATACT
Found at i:46080549 original size:13 final size:13
Alignment explanation
Indices: 46080512--46080559 Score: 57
Period size: 12 Copynumber: 3.8 Consensus size: 13
46080502 GAAGAAAAAA
*
46080512 AAAAGAAAAGAGG
1 AAAAGAAGAGAGG
46080525 -AAAGAA-AGAGG
1 AAAAGAAGAGAGG
46080536 AAAAGAAGAGAGG
1 AAAAGAAGAGAGG
46080549 AACAAG-AGAGA
1 AA-AAGAAGAGA
46080560 TGCAAAGCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 5 0.16
12 12 0.38
13 12 0.38
14 3 0.09
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAGAGG
Found at i:46086211 original size:15 final size:15
Alignment explanation
Indices: 46086191--46086219 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
46086181 CAGGCAAATT
46086191 GAAACTTGTCTTAGA
1 GAAACTTGTCTTAGA
46086206 GAAACTTGTCTTAG
1 GAAACTTGTCTTAG
46086220 TAAGTTCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (15 bp):
GAAACTTGTCTTAGA
Found at i:46088511 original size:36 final size:36
Alignment explanation
Indices: 46088399--46088500 Score: 168
Period size: 36 Copynumber: 2.8 Consensus size: 36
46088389 GGCCTTATGT
**
46088399 TCTAACCGAGACATAAGTTCTTCCTTAGCATTACGC
1 TCTAACCGAGACATAAGCACTTCCTTAGCATTACGC
46088435 TCTAACCGAGACATAAGCACTTCCTTAGCATTACGC
1 TCTAACCGAGACATAAGCACTTCCTTAGCATTACGC
* *
46088471 TCTAACCGAGACGTAAGCACTTCCATAGCA
1 TCTAACCGAGACATAAGCACTTCCTTAGCA
46088501 ATATTCTCTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.30, C:0.29, G:0.15, T:0.25
Consensus pattern (36 bp):
TCTAACCGAGACATAAGCACTTCCTTAGCATTACGC
Found at i:46088565 original size:36 final size:36
Alignment explanation
Indices: 46088525--46088595 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
46088515 TGACATACGC
* * *
46088525 AATCACACAACATTTCGCTTTAATCGAGATGTAAGT
1 AATCACACAACATTTCGCTCTAACCGAAATGTAAGT
46088561 AATCACACAACATTTCGCTCTAACCGAAATGTAAG
1 AATCACACAACATTTCGCTCTAACCGAAATGTAAG
46088596 CTCTTTCATT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.27
Consensus pattern (36 bp):
AATCACACAACATTTCGCTCTAACCGAAATGTAAGT
Found at i:46090451 original size:18 final size:19
Alignment explanation
Indices: 46090411--46090451 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
46090401 TGGTCAACTA
*
46090411 TCAAAGTCAACATATCTGG
1 TCAAAGTCAACAGATCTGG
*
46090430 TCAAAGTCAACAGGTC-GG
1 TCAAAGTCAACAGATCTGG
46090448 TCAA
1 TCAA
46090452 CGGGTCAACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (19 bp):
TCAAAGTCAACAGATCTGG
Found at i:46091865 original size:14 final size:14
Alignment explanation
Indices: 46091846--46091879 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
46091836 TTATTTCGTC
*
46091846 ATTCTAATTAAATA
1 ATTCTAATTAAACA
46091860 ATTCTAATTAAACA
1 ATTCTAATTAAACA
46091874 ATTCTA
1 ATTCTA
46091880 CTTTTGCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTCTAATTAAACA
Found at i:46101743 original size:20 final size:19
Alignment explanation
Indices: 46101688--46101744 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 19
46101678 TTACAAAAGG
46101688 AAAAA-TCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
46101706 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
46101725 AAAAATTCTAAAATTTTTAT
1 AAAAATTC-AAAATATTTAT
46101745 TTTTAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 8 0.24
19 15 0.45
20 10 0.30
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:46101762 original size:23 final size:24
Alignment explanation
Indices: 46101718--46101765 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
46101708 AAATTCAAAA
46101718 TATTTATAAAAATTCTAAAATTTT
1 TATTTATAAAAATTCTAAAATTTT
* *
46101742 TATTTTTAAAAATT-TATAATTTT
1 TATTTATAAAAATTCTAAAATTTT
46101765 T
1 T
46101766 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (24 bp):
TATTTATAAAAATTCTAAAATTTT
Found at i:46101835 original size:56 final size:55
Alignment explanation
Indices: 46101714--46101855 Score: 239
Period size: 56 Copynumber: 2.6 Consensus size: 55
46101704 TTTAAAATTC
* *
46101714 AAAATATTTATAAAAATTCTAAAATTTTTATTTTTAAAAATTTATAATTTTTTTA
1 AAAATATATATAAAAATTCTAAAATTTTTATTTTTAAAAATTTATAATTTTTTAA
46101769 AAAATATATATAAAAATTCTAAAATTTTTATTTTTAAAAAATTTATAATTTTTTAA
1 AAAATATATATAAAAATTCTAAAATTTTTATTTTT-AAAAATTTATAATTTTTTAA
* *
46101825 AAAATATATATTAAAATTTTAAAATTTTTAT
1 AAAATATATATAAAAATTCTAAAATTTTTAT
46101856 AAAATAATAA
Statistics
Matches: 82, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
55 34 0.41
56 48 0.59
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (55 bp):
AAAATATATATAAAAATTCTAAAATTTTTATTTTTAAAAATTTATAATTTTTTAA
Found at i:46102740 original size:23 final size:23
Alignment explanation
Indices: 46102714--46102774 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
46102704 TAAAATATTA
*
46102714 CAATAAATATGATTTAAATGTAT
1 CAATTAATATGATTTAAATGTAT
* *
46102737 CAATTCATATGGTTTAAATGTAT
1 CAATTAATATGATTTAAATGTAT
*
46102760 CAATTAGTATGATTT
1 CAATTAATATGATTT
46102775 TAATTATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (23 bp):
CAATTAATATGATTTAAATGTAT
Found at i:46103045 original size:19 final size:21
Alignment explanation
Indices: 46103015--46103060 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
46103005 AAAAAAAAAA
* *
46103015 TCAAAATGATTT-TCAAAAGT
1 TCAAAATGATTTATAAAAACT
46103035 TCAAAAT-ATTTATAAAAACT
1 TCAAAATGATTTATAAAAACT
46103055 TCAAAA
1 TCAAAA
46103061 CTTATATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.52, C:0.11, G:0.04, T:0.33
Consensus pattern (21 bp):
TCAAAATGATTTATAAAAACT
Found at i:46103431 original size:22 final size:23
Alignment explanation
Indices: 46103405--46103473 Score: 60
Period size: 21 Copynumber: 3.3 Consensus size: 23
46103395 TACTATGGTG
* *
46103405 TTATTTTATTGTAATATTATTAA
1 TTATTTTAATGCAATATTATTAA
*
46103428 -TA-TTTAATGCAATATTTTTAA
1 TTATTTTAATGCAATATTATTAA
46103449 TTA-TTT-AT-CAATA-TATTAA
1 TTATTTTAATGCAATATTATTAA
*
46103468 TCATTT
1 TTATTT
46103474 AACATGTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 7 0.18
20 7 0.18
21 18 0.46
22 7 0.18
ACGTcount: A:0.36, C:0.04, G:0.03, T:0.57
Consensus pattern (23 bp):
TTATTTTAATGCAATATTATTAA
Found at i:46104705 original size:92 final size:90
Alignment explanation
Indices: 46104524--46104754 Score: 272
Period size: 90 Copynumber: 2.6 Consensus size: 90
46104514 TTAAAGGTGT
* * ** **
46104524 AAAAAAACCCTCAAACTTTTTCAAAAAAAACAATTAAACCCCT-CTTT-TTTTTGCACTCAATTA
1 AAAAAAACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTATCCTCCCACTCAATTA
*
46104587 AGCACTTGAACTTTCAAAATGTATA
66 AGCACTTGAACTTTCAAAATGCATA
*
46104612 AAAAAAATGCCCTCAAACTTCTTCAAAAAAAGCAATTAAGCCCCTGCTTTATCCTCCCACTCAAT
1 AAAAAAA--CCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTATCCTCCCACTCAAT
* * *
46104677 T-GGATAGTTGAACTTTCAAAATGCATAA
64 TAAG-CACTTGAACTTTCAAAATGCAT-A
* *
46104705 AAAAAAACCCTCAAAATTTTTC-AAAAAAGCAATTAAGCCCTTGCTCTTAT
1 AAAAAAACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCT-TTAT
46104755 TAAAAATTAG
Statistics
Matches: 122, Mismatches: 14, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
88 7 0.06
90 55 0.45
91 22 0.18
92 30 0.25
93 8 0.07
ACGTcount: A:0.41, C:0.23, G:0.07, T:0.29
Consensus pattern (90 bp):
AAAAAAACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTGCTTTATCCTCCCACTCAATTA
AGCACTTGAACTTTCAAAATGCATA
Found at i:46104899 original size:19 final size:19
Alignment explanation
Indices: 46104851--46104908 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
46104841 AATTCAAACT
46104851 ATTTTATAAAAATCGTAAA
1 ATTTTATAAAAATCGTAAA
** * * *
46104870 AAATAAAAAAAATTGTAAA
1 ATTTTATAAAAATCGTAAA
*
46104889 ATTTTATAAAAATCATAAA
1 ATTTTATAAAAATCGTAAA
46104908 A
1 A
46104909 AAATTATAAA
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (19 bp):
ATTTTATAAAAATCGTAAA
Found at i:46105085 original size:19 final size:19
Alignment explanation
Indices: 46105035--46105087 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
46105025 GACATGTGAC
* *
46105035 GAAAAATGATAAAA-AATA
1 GAAAAATTATAAAATTATA
*
46105053 GAAAACAATA-AAAATTATA
1 GAAAA-ATTATAAAATTATA
46105072 GAAAAATTATAAAATT
1 GAAAAATTATAAAATT
46105088 CTTCTTTTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 12 0.43
19 16 0.57
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (19 bp):
GAAAAATTATAAAATTATA
Found at i:46105226 original size:56 final size:58
Alignment explanation
Indices: 46105117--46105249 Score: 166
Period size: 56 Copynumber: 2.3 Consensus size: 58
46105107 TTTATAATTT
* * * *
46105117 TTTTACAA-ATTTTATATTTCTTTATATTTTGTATGATTTTCTTACGAATTTATAAAA
1 TTTTACAATTTTTTATATTTCTATATATTTTGTATAATATTCTTACGAATTTATAAAA
* *
46105174 TTTTATAATTTTTTATATTTCTATATA-TTT-TATAATATT-TTACGATGTTTATAAAA
1 TTTTACAATTTTTTATATTTCTATATATTTTGTATAATATTCTTACGA-ATTTATAAAA
*
46105230 TTTTACAATTTTTTTTATTT
1 TTTTACAATTTTTTATATTT
46105250 TTTTTGAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
55 6 0.09
56 34 0.52
57 10 0.15
58 16 0.24
ACGTcount: A:0.31, C:0.05, G:0.04, T:0.60
Consensus pattern (58 bp):
TTTTACAATTTTTTATATTTCTATATATTTTGTATAATATTCTTACGAATTTATAAAA
Found at i:46105436 original size:89 final size:89
Alignment explanation
Indices: 46105343--46105556 Score: 285
Period size: 89 Copynumber: 2.4 Consensus size: 89
46105333 AAGCAAAATT
* *
46105343 TTAATTTTTTTTTTTGAAAAAGTTTGAGGTTTCTTTTT-ATGCATTTTAAAAGTTCAAGTA-CTC
1 TTAATTGTTTTTTTTGAAAAAGTTTGAGG-GTCTTTTTGATGCATTTTAAAAGTTCAAGTATC-C
*
46105406 AATTGAGTGC-AAAAAAAAGTATGAG-C
64 AAATGAGTGCAAAAAAAAAG-A-GAGAC
* *
46105432 TTAATTGTTTTTTTTGAAAAGGTTTGAGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTATCCAA
1 TTAATTGTTTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTATCCAA
*
46105497 ATGAGTGCAAAAAAAAAGAGGGAC
66 ATGAGTGCAAAAAAAAAGAGAGAC
* *
46105521 TTAATTGCTTTTTTTGAGAAAGTTTGAGGG-CTTTTT
1 TTAATTGTTTTTTTTGAAAAAGTTTGAGGGTCTTTTT
46105557 CCCCTTTGAA
Statistics
Matches: 112, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
88 15 0.13
89 87 0.78
90 10 0.09
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.42
Consensus pattern (89 bp):
TTAATTGTTTTTTTTGAAAAAGTTTGAGGGTCTTTTTGATGCATTTTAAAAGTTCAAGTATCCAA
ATGAGTGCAAAAAAAAAGAGAGAC
Found at i:46107405 original size:31 final size:32
Alignment explanation
Indices: 46107368--46107436 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
46107358 TGATCACTTA
* *
46107368 ATTTAAAAAGTTATAATTTGA-TCTTTGAGTT
1 ATTTAAAAAGTTATAATTTAAGTCTTTGAGCT
* *
46107399 ATTT-AAAAGTTTTCATTTAAGTCTTTGAGCT
1 ATTTAAAAAGTTATAATTTAAGTCTTTGAGCT
46107430 A-TTAAAA
1 ATTTAAAA
46107437 CCAATGTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 15 0.47
31 17 0.53
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (32 bp):
ATTTAAAAAGTTATAATTTAAGTCTTTGAGCT
Found at i:46107409 original size:30 final size:31
Alignment explanation
Indices: 46107368--46107436 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
46107358 TGATCACTTA
* *
46107368 ATTTAAAAAGTTATAATTTGA-TCTTTGAGTT
1 ATTT-AAAAGTTATAATTTAAGTCTTTGAGCT
* *
46107399 ATTTAAAAGTTTTCATTTAAGTCTTTGAGCT
1 ATTTAAAAGTTATAATTTAAGTCTTTGAGCT
46107430 A-TTAAAA
1 ATTTAAAA
46107437 CCAATGTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 19 0.58
31 14 0.42
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (31 bp):
ATTTAAAAGTTATAATTTAAGTCTTTGAGCT
Found at i:46112525 original size:10 final size:10
Alignment explanation
Indices: 46112510--46112537 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
46112500 CTGGTTGTTT
46112510 GGAAAGTGAA
1 GGAAAGTGAA
46112520 GGAAAGTGAA
1 GGAAAGTGAA
46112530 GGAAAGTG
1 GGAAAGTG
46112538 GAAAGGATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.43, T:0.11
Consensus pattern (10 bp):
GGAAAGTGAA
Found at i:46117764 original size:71 final size:71
Alignment explanation
Indices: 46117648--46117791 Score: 288
Period size: 71 Copynumber: 2.0 Consensus size: 71
46117638 AAAAAAATCC
46117648 GATGATTTTTTCACCATTGATCATAATTCAACATCGAAACAATACCTAAAAAGAAAAAGGGGTTG
1 GATGATTTTTTCACCATTGATCATAATTCAACATCGAAACAATACCTAAAAAGAAAAAGGGGTTG
46117713 ATACTT
66 ATACTT
46117719 GATGATTTTTTCACCATTGATCATAATTCAACATCGAAACAATACCTAAAAAGAAAAAGGGGTTG
1 GATGATTTTTTCACCATTGATCATAATTCAACATCGAAACAATACCTAAAAAGAAAAAGGGGTTG
46117784 ATACTT
66 ATACTT
46117790 GA
1 GA
46117792 CTGTTCAAGA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 73 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (71 bp):
GATGATTTTTTCACCATTGATCATAATTCAACATCGAAACAATACCTAAAAAGAAAAAGGGGTTG
ATACTT
Found at i:46118230 original size:19 final size:20
Alignment explanation
Indices: 46118206--46118246 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
46118196 TTTAAAATCA
46118206 TTTT-AAAAATAT-TATAATT
1 TTTTAAAAAATATATA-AATT
46118225 TTTTAAAAAATATATAAATT
1 TTTTAAAAAATATATAAATT
46118245 TT
1 TT
46118247 AGAATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 4 0.20
20 14 0.70
21 2 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAAAAATATATAAATT
Found at i:46126010 original size:15 final size:15
Alignment explanation
Indices: 46125975--46126028 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
46125965 ATTCGGAGGA
* *
46125975 GGAGAGGAGGAGGAG
1 GGAGAGGAAGAGAAG
*
46125990 GAAGAGGAAGAGAAG
1 GGAGAGGAAGAGAAG
46126005 GGAGAGAGAAGA-AAG
1 GGAGAG-GAAGAGAAG
*
46126020 GGAAAGGAA
1 GGAGAGGAA
46126029 AAGGAGGAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
14 3 0.09
15 25 0.76
16 5 0.15
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (15 bp):
GGAGAGGAAGAGAAG
Found at i:46126043 original size:27 final size:26
Alignment explanation
Indices: 46126013--46126072 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
46126003 AGGGAGAGAG
*
46126013 AAGAAAGGGAAAGGAAAAGGAGGAA-GA
1 AAGAAA-GGAAAAGAAAAGGA-GAAGGA
46126040 AAGAGAAGGAAAAGAAAAGGAGAAGGA
1 AAGA-AAGGAAAAGAAAAGGAGAAGGA
46126067 AAGAAA
1 AAGAAA
46126073 AAGAGAGAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
27 23 0.77
28 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (26 bp):
AAGAAAGGAAAAGAAAAGGAGAAGGA
Found at i:46126064 original size:17 final size:16
Alignment explanation
Indices: 46126039--46126078 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 16
46126029 AAGGAGGAAG
46126039 AAAGAGAAGGAAAAGAA
1 AAAGAGAAGG-AAAGAA
*
46126056 AAGGAGAAGGAAAGAA
1 AAAGAGAAGGAAAGAA
46126072 AAAGAGA
1 AAAGAGA
46126079 GAGGCGAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.57
17 9 0.43
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (16 bp):
AAAGAGAAGGAAAGAA
Found at i:46126119 original size:20 final size:20
Alignment explanation
Indices: 46126093--46126139 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
46126083 CGAAGAGAGG
46126093 AAAAGAAA-GAAGAGAAAAGA
1 AAAAGAAAGGAA-AGAAAAGA
* *
46126113 GAAAGAAAGGAAAGCAAAGA
1 AAAAGAAAGGAAAGAAAAGA
46126133 AAAAGAA
1 AAAAGAA
46126140 GGATAAGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGGAAAGAAAAGA
Found at i:46133995 original size:13 final size:14
Alignment explanation
Indices: 46133967--46133999 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
46133957 ATTAAAGGTT
46133967 ATTATATTTAAGTA
1 ATTATATTTAAGTA
*
46133981 ATTATA-TTAATTA
1 ATTATATTTAAGTA
46133994 ATTATA
1 ATTATA
46134000 AAATATTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (14 bp):
ATTATATTTAAGTA
Found at i:46147803 original size:17 final size:17
Alignment explanation
Indices: 46147781--46147813 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
46147771 ACTTTTTGCC
*
46147781 TTTATTTTTTTATTTTG
1 TTTATTCTTTTATTTTG
46147798 TTTATTCTTTTATTTT
1 TTTATTCTTTTATTTT
46147814 ATGCTCTTTA
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:0.12, C:0.03, G:0.03, T:0.82
Consensus pattern (17 bp):
TTTATTCTTTTATTTTG
Found at i:46155991 original size:8 final size:7
Alignment explanation
Indices: 46155978--46156026 Score: 55
Period size: 7 Copynumber: 6.6 Consensus size: 7
46155968 AGCAATATCT
46155978 TTTTCTTC
1 TTTTC-TC
46155986 TTTTCTTC
1 TTTTC-TC
46155994 TTTTCTC
1 TTTTCTC
46156001 TTTTCTC
1 TTTTCTC
46156008 TTTTCATC
1 TTTTC-TC
46156016 TTCTTC-C
1 TT-TTCTC
46156023 TTTT
1 TTTT
46156027 TATTTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
6 2 0.05
7 17 0.44
8 17 0.44
9 3 0.08
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCTC
Found at i:46156004 original size:7 final size:8
Alignment explanation
Indices: 46155978--46156017 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
46155968 AGCAATATCT
46155978 TTTTCTTC
1 TTTTCTTC
46155986 TTTTCTTC
1 TTTTCTTC
46155994 TTTTC-TC
1 TTTTCTTC
46156001 TTTTC-TC
1 TTTTCTTC
*
46156008 TTTTCATC
1 TTTTCTTC
46156016 TT
1 TT
46156018 CTTCCTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 14 0.45
8 17 0.55
ACGTcount: A:0.03, C:0.25, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTCTTC
Found at i:46156004 original size:15 final size:14
Alignment explanation
Indices: 46155978--46156026 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 14
46155968 AGCAATATCT
46155978 TTTTCTTCTTTTCTTC
1 TTTTC-TCTTTTC-TC
46155994 TTTTCTCTTTTCTC
1 TTTTCTCTTTTCTC
46156008 TTTTCATCTTCTTC-C
1 TTTTC-TCTT-TTCTC
46156023 TTTT
1 TTTT
46156027 TATTTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.23
15 16 0.52
16 8 0.26
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTCTTTTCTC
Found at i:46156649 original size:18 final size:17
Alignment explanation
Indices: 46156611--46156654 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
46156601 AGATAAACTA
*
46156611 ACAAATAAAATACAGTG
1 ACAAATAAAATACAATG
*
46156628 ACAAATAAAGATGCAATG
1 ACAAATAAA-ATACAATG
*
46156646 ACAACTAAA
1 ACAAATAAA
46156655 TAAAATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (17 bp):
ACAAATAAAATACAATG
Found at i:46170664 original size:2 final size:2
Alignment explanation
Indices: 46170657--46170687 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
46170647 ATTGCTTTCT
46170657 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46170688 GGACTTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:46174349 original size:72 final size:71
Alignment explanation
Indices: 46174226--46174361 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 71
46174216 ATGCTCCATA
* * *
46174226 AACTCTTCCTTCAACTTATCCAAGCTTGTTTGGGAGACTTACATGGGTGAGTTTCTGTTGCCTTA
1 AACTCCTCCTTCAACTTATCCAAGCTTGTTTGGGAGACTTACATGGGTGAGTTGCTGCTGCCTTA
46174291 CCTTGG
66 CCTTGG
* * *
46174297 AACTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTC-T-CATAGAGTTGAGTTGCTGCTGCC
1 AACTCCTCCTTCAACTTAT-CCAAGCTTGTTTGGGAGACTTACAT-G-GGTGAGTTGCTGCTGCC
46174360 TT
63 TT
46174362 CTCGATAAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
70 3 0.05
71 19 0.34
72 34 0.61
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (71 bp):
AACTCCTCCTTCAACTTATCCAAGCTTGTTTGGGAGACTTACATGGGTGAGTTGCTGCTGCCTTA
CCTTGG
Found at i:46176447 original size:72 final size:71
Alignment explanation
Indices: 46176324--46176459 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 71
46176314 ATGCTCCATA
* * *
46176324 AACTCTTCCTTCAACTTATCCAAGCTTGTTTGGGAGACTTACATGGGTGAGTTTCTGTTGCCTTA
1 AACTCCTCCTTCAACTTATCCAAGCTTGTTTGGGAGACTTACATGGGTGAGTTGCTGCTGCCTTA
46176389 CCTTGG
66 CCTTGG
* * *
46176395 AACTCCTCCTTCAGCTTATCCCAAGCTTGTTTGGGAGTC-T-CATAGAGTTGAGTTGCTGCTGCC
1 AACTCCTCCTTCAACTTAT-CCAAGCTTGTTTGGGAGACTTACAT-G-GGTGAGTTGCTGCTGCC
46176458 TT
63 TT
46176460 CTCGATAAGC
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
70 3 0.05
71 19 0.34
72 34 0.61
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (71 bp):
AACTCCTCCTTCAACTTATCCAAGCTTGTTTGGGAGACTTACATGGGTGAGTTGCTGCTGCCTTA
CCTTGG
Found at i:46180646 original size:72 final size:71
Alignment explanation
Indices: 46180523--46180658 Score: 193
Period size: 72 Copynumber: 1.9 Consensus size: 71
46180513 ATGCTTCATA
* * * *
46180523 AACTCCTCCTTCGACTTATCCAAGCTTGTTTGGGAGTCTTAAAGGGGTGAGTTTCTGCTGCCTTA
1 AACTCATCCTTCGACTTATCCAAGCTTGTTTGGGAGTCTCAAAGAGGTGAGTTGCTGCTGCCTTA
46180588 CCTTGG
66 CCTTGG
* *
46180594 AACTCATCCTTC-AGCTTATCCCAAGCTTGTTTGGGAGTCTCATAGAGTTGAGTTGCTGCTGCCT
1 AACTCATCCTTCGA-CTTAT-CCAAGCTTGTTTGGGAGTCTCAAAGAGGTGAGTTGCTGCTGCCT
46180658 T
64 T
46180659 CTCGACAAGC
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
70 1 0.02
71 16 0.28
72 40 0.70
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (71 bp):
AACTCATCCTTCGACTTATCCAAGCTTGTTTGGGAGTCTCAAAGAGGTGAGTTGCTGCTGCCTTA
CCTTGG
Found at i:46185926 original size:72 final size:71
Alignment explanation
Indices: 46185796--46185928 Score: 173
Period size: 72 Copynumber: 1.9 Consensus size: 71
46185786 ATGCGCCATA
* * *
46185796 AACTCTTCCTTTGACTTATCCAAACTTGTTTGGGAGTCTTACAAGGGTGAGTTGCTGTTGCTTTA
1 AACTCCTCCTTTGACTTATCCAAACTTCTTTGGGAGTCTTACAAGGGTGAGTTACTGTTGCTTTA
46185861 CCTTGG
66 CCTTGG
*
46185867 AACTCCTCCTTT-AGCTTATCCAAAGCTTCTTTGGGAGTC-T-CATAGAGTTGAGTTACTGTTGC
1 AACTCCTCCTTTGA-CTTATCCAAA-CTTCTTTGGGAGTCTTACA-AG-GGTGAGTTACTGTTGC
46185929 CTTCTCGACA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
70 3 0.06
71 24 0.44
72 27 0.50
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (71 bp):
AACTCCTCCTTTGACTTATCCAAACTTCTTTGGGAGTCTTACAAGGGTGAGTTACTGTTGCTTTA
CCTTGG
Found at i:46188040 original size:72 final size:71
Alignment explanation
Indices: 46187906--46188041 Score: 166
Period size: 72 Copynumber: 1.9 Consensus size: 71
46187896 ATGCGCCATA
* * * * *
46187906 AACTCCTCCTTTGACTTATCCAAGCTTGTTTAGGAGTCTTACAGGGGCGAGTTACTATTGCCTTA
1 AACTCCTCCTTTGACTTATCCAAGCTTGTTTAGGAGTCTCAAAGAGGCGAGTTACCACTGCCTTA
46187971 CCTTGC
66 CCTTGC
* ** *
46187977 AACTCCTCCTTT-AGCTTATCCCAAGCTTGTTTGGGAGTCTCAAAGAGTTGAGTTACCGCTGCCT
1 AACTCCTCCTTTGA-CTTAT-CCAAGCTTGTTTAGGAGTCTCAAAGAGGCGAGTTACCACTGCCT
46188041 T
64 T
46188042 CTCGACAAGC
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
70 1 0.02
71 17 0.31
72 36 0.67
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.35
Consensus pattern (71 bp):
AACTCCTCCTTTGACTTATCCAAGCTTGTTTAGGAGTCTCAAAGAGGCGAGTTACCACTGCCTTA
CCTTGC
Found at i:46189096 original size:72 final size:71
Alignment explanation
Indices: 46188961--46189097 Score: 159
Period size: 72 Copynumber: 1.9 Consensus size: 71
46188951 CATGCGCCAT
* * * * * *
46188961 AAACTCCTCCTTTGACTTATCCAAGCTTGTTTAAAAGTCTTACAGGGGTGAGTTGCTGTTGCCTT
1 AAACTCCTCCTTTGACTTATCCAAGCTTGTTTAAAACTCTCAAAGAGGTGAGTTACTGCTGCCTT
46189026 ACCTTG
66 ACCTTG
*** *
46189032 AAACTCCTCCTTT-AGCTTATCCTAAGCTTGTTTGGGACTCTCAAAGAGTTGAGTTACTGCTGCC
1 AAACTCCTCCTTTGA-CTTATCC-AAGCTTGTTTAAAACTCTCAAAGAGGTGAGTTACTGCTGCC
46189096 TT
64 TT
46189098 CTCGACAAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
70 1 0.02
71 20 0.37
72 33 0.61
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.36
Consensus pattern (71 bp):
AAACTCCTCCTTTGACTTATCCAAGCTTGTTTAAAACTCTCAAAGAGGTGAGTTACTGCTGCCTT
ACCTTG
Found at i:46190141 original size:72 final size:71
Alignment explanation
Indices: 46190018--46190153 Score: 175
Period size: 72 Copynumber: 1.9 Consensus size: 71
46190008 ATGCGCCATA
* * * * *
46190018 AACTCCTCCTTTGACTTATCAAAGCTTGTTTAGGAGTCTTACAGGGGTGAGTTGCTGTTGCCTTA
1 AACTCCTCCTTTGACTTATCAAAGCTTGTTTAGGAGTCTCAAAGAGGTGAGTTACTGCTGCCTTA
46190083 CCTTGC
66 CCTTGC
* * *
46190089 AACTCCTCCTTT-AGCTTATCCCAAGCTTGTTTGGGAGTCTCAAAGAGTTGAGTTACTGCTGCCT
1 AACTCCTCCTTTGA-CTTAT-CAAAGCTTGTTTAGGAGTCTCAAAGAGGTGAGTTACTGCTGCCT
46190153 T
64 T
46190154 CTCGACAAGC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
70 1 0.02
71 17 0.31
72 37 0.67
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (71 bp):
AACTCCTCCTTTGACTTATCAAAGCTTGTTTAGGAGTCTCAAAGAGGTGAGTTACTGCTGCCTTA
CCTTGC
Found at i:46191155 original size:71 final size:72
Alignment explanation
Indices: 46191074--46191209 Score: 204
Period size: 72 Copynumber: 1.9 Consensus size: 72
46191064 ATGCCCCATT
* * * *
46191074 AACTCCTCCTTT-GACTTAT-CCAAGCTTGTTTGGGAGTCTTACAGGGGTGAGTTGCTGTTGCCT
1 AACTCCTCCTTTAG-CTTATCCCAAGCTTGTTTCGGAGTCTCACAGAGGTGAGTTGCTGCTGCCT
46191137 TACCTTGG
65 TACCTTGG
*
46191145 AACTCCTCCTTTAGCTTATCCCAAGCTTGTTTCGGAGTCTCACAGAGTTGAGTTGCTGCTGCCTT
1 AACTCCTCCTTTAGCTTATCCCAAGCTTGTTTCGGAGTCTCACAGAGGTGAGTTGCTGCTGCCTT
46191210 CTCGACAAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 17 0.29
72 41 0.71
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (72 bp):
AACTCCTCCTTTAGCTTATCCCAAGCTTGTTTCGGAGTCTCACAGAGGTGAGTTGCTGCTGCCTT
ACCTTGG
Found at i:46193308 original size:72 final size:71
Alignment explanation
Indices: 46193185--46193320 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 71
46193175 ATGCGCCATA
* * * * * *
46193185 AACTCCTCCTTTGACTTATGCAAGCTTGTTTGGGAGTCTTACAGGGGTGAGTTGTTGTTGCCTTA
1 AACTCCTCCTTTGACTTATCCAAGCTTGTTTGGGAGTCTCAAAGAGGTGAGTTGCTGCTGCCTTA
46193250 CCTTGG
66 CCTTGG
*
46193256 AACTCCTCCTTT-AGCTTATCCAAAGCTTGTTTGGGAGTCTCAAAGAGTTGAGTTGCTGCTGCCT
1 AACTCCTCCTTTGA-CTTATCC-AAGCTTGTTTGGGAGTCTCAAAGAGGTGAGTTGCTGCTGCCT
46193320 T
64 T
46193321 CTCGACAAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
70 1 0.02
71 18 0.32
72 37 0.66
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (71 bp):
AACTCCTCCTTTGACTTATCCAAGCTTGTTTGGGAGTCTCAAAGAGGTGAGTTGCTGCTGCCTTA
CCTTGG
Found at i:46194361 original size:72 final size:71
Alignment explanation
Indices: 46194238--46194373 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 71
46194228 ATGCTCCATA
* * * *
46194238 AACTCCTCCTTCGACTTATCCAAGCTTGTTTGTGAGTCTTACAGGGGTGAGTTGCTACTGCCTTA
1 AACTCCTCCTTCGACTTATCCAAGATTGTTTGGGAGTCTCACAGAGGTGAGTTGCTACTGCCTTA
46194303 CCTTGG
66 CCTTGG
* * *
46194309 AACTCCTCCTTC-AGCTTATCCCAAGATTGTTTGGGAGTCTCATAGAGTTGAGTTGCTGCTGCCT
1 AACTCCTCCTTCGA-CTTAT-CCAAGATTGTTTGGGAGTCTCACAGAGGTGAGTTGCTACTGCCT
46194373 T
64 T
46194374 CTCGACAAGC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
70 1 0.02
71 17 0.30
72 38 0.68
ACGTcount: A:0.18, C:0.25, G:0.22, T:0.35
Consensus pattern (71 bp):
AACTCCTCCTTCGACTTATCCAAGATTGTTTGGGAGTCTCACAGAGGTGAGTTGCTACTGCCTTA
CCTTGG
Found at i:46197829 original size:19 final size:18
Alignment explanation
Indices: 46197789--46197836 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
46197779 ACTTGAAGGG
* *
46197789 GAAGGGGAAGGGGAAGGG
1 GAAGGGGAAGGGGAAAGA
46197807 GAAGGGGAAAGGGGAAAGA
1 GAAGGGG-AAGGGGAAAGA
*
46197826 GAAGGAGAAGG
1 GAAGGGGAAGG
46197837 AGAATGAGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 11 0.42
19 15 0.58
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (18 bp):
GAAGGGGAAGGGGAAAGA
Found at i:46197840 original size:6 final size:6
Alignment explanation
Indices: 46197783--46197836 Score: 72
Period size: 6 Copynumber: 8.8 Consensus size: 6
46197773 GGTTGAACTT
* * *
46197783 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG GAAAGGG GAAAGA GAAGGA
1 GAAGGG GAAGGG GAAGGG GAAGGG GAAGGG G-AAGGG GAAGGG GAAGGG
46197832 GAAGG
1 GAAGG
46197837 AGAATGAGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
6 38 0.86
7 6 0.14
ACGTcount: A:0.41, C:0.00, G:0.59, T:0.00
Consensus pattern (6 bp):
GAAGGG
Found at i:46197940 original size:11 final size:11
Alignment explanation
Indices: 46197899--46197939 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
46197889 ATAATTTTAT
*
46197899 ATTTAAAAATA
1 ATTTTAAAATA
*
46197910 ATTTTAAATTA
1 ATTTTAAAATA
46197921 ATTTTAAAAT-
1 ATTTTAAAATA
46197931 ATTTTAAAA
1 ATTTTAAAA
46197940 AATAATTAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTTTAAAATA
Found at i:46198758 original size:6 final size:6
Alignment explanation
Indices: 46198747--46198774 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
46198737 ATTTATTATT
46198747 AATTTA AATTTA AATTTA AATTTA AATT
1 AATTTA AATTTA AATTTA AATTTA AATT
46198775 AATTAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
AATTTA
Found at i:46199137 original size:198 final size:202
Alignment explanation
Indices: 46198760--46199138 Score: 477
Period size: 202 Copynumber: 1.9 Consensus size: 202
46198750 TTAAATTTAA
** *
46198760 ATTTAAATTTAAATTAATTAATATTTAAAAATAGAATTTACAATATATATTAATGTACTTCAAAA
1 ATTTAAACATAAATTAATTAATATTTAAAAATAGAATTTACAATATATATTAATCTACTTCAAAA
* * *
46198825 TTAATAAATTTAAATATGAAATTTTAATTATATTTTTCAAAAATTTCAAACTTAATAAATTTGAT
66 TTAATAAATTTAAATA-GAAA-TTTAATTAAATTTATCAAAAATTTCAAAATTAATAAATTTGAT
* *** * *
46198890 CTATTTAAGTATGTAAAAATAATTCTGTTTAATTTAATTAAAATATAGTTCTAAGTAATTAATTT
129 CTATTTAAGTATGTAAAAATAAATCAAATCAATTTAACTAAAATATAGTTCTAAGTAATTAATTT
46198955 TATTATTTT
194 TATTATTTT
* * *
46198964 ATTTAAACATAAATTAATTAATATTTAAAATTAGAA-TT-CACTTTATATTAATCTACTTCAAAA
1 ATTTAAACATAAATTAATTAATATTTAAAAATAGAATTTACAATATATATTAATCTACTTCAAAA
* **
46199027 TTAATAAATTTAAATA-AACA-TTAA-TAAATTTAT-AAAAATTT-AAAATTAATTAATTTTTCT
66 TTAATAAATTTAAATAGAA-ATTTAATTAAATTTATCAAAAATTTCAAAATTAA-TAAATTTGAT
*
46199087 CTATTTAAGTATATTAAAAATAAAAT-AAATCAATTTAACTAAAATATAGTTC
129 CTATTTAAGTAT-GTAAAAAT-AAATCAAATCAATTTAACTAAAATATAGTTC
46199139 GTTAATTTAT
Statistics
Matches: 152, Mismatches: 19, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
196 7 0.05
197 27 0.18
198 35 0.23
199 7 0.05
200 2 0.01
201 1 0.01
202 38 0.25
203 2 0.01
204 33 0.22
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (202 bp):
ATTTAAACATAAATTAATTAATATTTAAAAATAGAATTTACAATATATATTAATCTACTTCAAAA
TTAATAAATTTAAATAGAAATTTAATTAAATTTATCAAAAATTTCAAAATTAATAAATTTGATCT
ATTTAAGTATGTAAAAATAAATCAAATCAATTTAACTAAAATATAGTTCTAAGTAATTAATTTTA
TTATTTT
Found at i:46201605 original size:39 final size:39
Alignment explanation
Indices: 46201562--46201746 Score: 185
Period size: 39 Copynumber: 4.7 Consensus size: 39
46201552 AGTATTGCGA
* *
46201562 TGTTTAAAGTGTCACCGCCAGTTCAATATAGCATCGCAG
1 TGTTTAAAGTGTCACTGCCAGTTCAGTATAGCATCGCAG
* * * *
46201601 TGTTTACAGTGTCACTACCAGTTCAGTATAGTATCGTAG
1 TGTTTAAAGTGTCACTGCCAGTTCAGTATAGCATCGCAG
* * *
46201640 TGTTTACAA-CGTCACTGCAAGTTCAGTATAGCACCGCAG
1 TGTTTA-AAGTGTCACTGCCAGTTCAGTATAGCATCGCAG
* * * * *
46201679 TGTTTACAGTGTCATTGCCAGTTTAGTAGAGTTATCGCAG
1 TGTTTAAAGTGTCACTGCCAGTTCAGTATAG-CATCGCAG
* *
46201719 TGTTTTCAA-TGTCACTGCCAGTTTAGTA
1 TG-TTTAAAGTGTCACTGCCAGTTCAGTA
46201747 GGGATATCTT
Statistics
Matches: 118, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
38 1 0.01
39 86 0.73
40 27 0.23
41 4 0.03
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (39 bp):
TGTTTAAAGTGTCACTGCCAGTTCAGTATAGCATCGCAG
Found at i:46201654 original size:78 final size:77
Alignment explanation
Indices: 46201522--46201741 Score: 248
Period size: 78 Copynumber: 2.8 Consensus size: 77
46201512 AACATTTAGT
* * * *
46201522 AGTGTTTATAGTGGCACTACTA-TTTAGTATAGTATTGCGA-TGTTTA-AAGTGTCACCGCCAGT
1 AGTGTTTACAGTGTCACTACCAGTTTAGTATAGTA-T-CGAGTGTTTACAA-TGTCACTGCCAGT
*
46201584 TCAATATAGCATCGC
63 TCAATATAGCACCGC
* * *
46201599 AGTGTTTACAGTGTCACTACCAGTTCAGTATAGTATCGTAGTGTTTACAACGTCACTGCAAGTTC
1 AGTGTTTACAGTGTCACTACCAGTTTAGTATAGTATCG-AGTGTTTACAATGTCACTGCCAGTTC
*
46201664 AGTATAGCACCGC
65 AATATAGCACCGC
* * * *
46201677 AGTGTTTACAGTGTCATTGCCAGTTTAGTAGAGTTATCGCAGTGTTTTCAATGTCACTGCCAGTT
1 AGTGTTTACAGTGTCACTACCAGTTTAGTATAG-TATCG-AGTGTTTACAATGTCACTGCCAGTT
46201742 TAGTAGGGAT
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
76 2 0.02
77 21 0.17
78 69 0.57
79 29 0.24
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (77 bp):
AGTGTTTACAGTGTCACTACCAGTTTAGTATAGTATCGAGTGTTTACAATGTCACTGCCAGTTCA
ATATAGCACCGC
Found at i:46202110 original size:73 final size:73
Alignment explanation
Indices: 46201991--46202149 Score: 237
Period size: 73 Copynumber: 2.2 Consensus size: 73
46201981 TGTATTTTTC
* *
46201991 CCCGTGTAATTCAGTGTATCTGAATTCACAAAACAGAATATCCACACAGTCTAACACACGCCCGT
1 CCCGTGTAACTCAGTGTATCTGAATTCACAAAACAGAATATCCACACAGTCTAACACACGCCAGT
46202056 GTGTCCAG
66 GTGTCCAG
* * * ** *
46202064 CCCGTGTAACTCATTGTATCTTAATTCATATGACAGAATATCCACACGGTCTAACACACGCCAGT
1 CCCGTGTAACTCAGTGTATCTGAATTCACAAAACAGAATATCCACACAGTCTAACACACGCCAGT
46202129 GTGTCCAG
66 GTGTCCAG
*
46202137 CCCATGTAACTCA
1 CCCGTGTAACTCA
46202150 CTATATACCA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.25
Consensus pattern (73 bp):
CCCGTGTAACTCAGTGTATCTGAATTCACAAAACAGAATATCCACACAGTCTAACACACGCCAGT
GTGTCCAG
Found at i:46202787 original size:37 final size:37
Alignment explanation
Indices: 46202709--46202787 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
46202699 TTTCACCGTT
***
46202709 ATAATTCAACAGTTCTCCAAAACTTACCGCAACTGCT
1 ATAATTCAACAGTTCTCCAAAACTTACCGCAACTAAG
* *
46202746 ATAATTCAACAGTTCTCCAAAACTTACTGCAATTAAG
1 ATAATTCAACAGTTCTCCAAAACTTACCGCAACTAAG
46202783 ATAAT
1 ATAAT
46202788 ACAGTTTGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (37 bp):
ATAATTCAACAGTTCTCCAAAACTTACCGCAACTAAG
Found at i:46206475 original size:42 final size:42
Alignment explanation
Indices: 46206349--46206497 Score: 167
Period size: 42 Copynumber: 3.5 Consensus size: 42
46206339 GGATATGGCG
* *
46206349 TTGGATATGGCATT-GAAGATGGGAACCAGTTAGGTACAGGCG
1 TTGGATAAGGCATTGGAA-ATGGGAACCAGTTAGGTACAGGCA
* *
46206391 TTGGATATGGCATTGGAGAA-GGGAACCAGGTAGGTACAGGCA
1 TTGGATAAGGCATTGGA-AATGGGAACCAGTTAGGTACAGGCA
* * * **
46206433 TTGGACAAGGCATGGGAAATGGGAACCAGTTAGGAATGGGCA
1 TTGGATAAGGCATTGGAAATGGGAACCAGTTAGGTACAGGCA
* *
46206475 TTGGGTACGGCATTGGAAATGGG
1 TTGGATAAGGCATTGGAAATGGG
46206498 GGTCAATCAG
Statistics
Matches: 91, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
41 2 0.02
42 85 0.93
43 3 0.03
44 1 0.01
ACGTcount: A:0.30, C:0.11, G:0.38, T:0.21
Consensus pattern (42 bp):
TTGGATAAGGCATTGGAAATGGGAACCAGTTAGGTACAGGCA
Found at i:46206535 original size:84 final size:84
Alignment explanation
Indices: 46206447--46206606 Score: 230
Period size: 84 Copynumber: 1.9 Consensus size: 84
46206437 ACAAGGCATG
* * * *
46206447 GGAAATGGGAACCAGTTAGGAATGGGCATTGGGTACGGCATTGGAAATGGGGGTCAATCAGGAAA
1 GGAAATGGGAACCAGATAGGAATGGGCATCGGGTACGGCATTGGAAATGGGGCTCAAGCAGGAAA
46206512 TAACATGGGATTTGGTAAT
66 TAACATGGGATTTGGTAAT
* * * * *
46206531 GGAAATGGGAACCAGATGGGAATGGGTATCGGGTATGGCATTGGAAATGGGGCTCAGGCCGGAAA
1 GGAAATGGGAACCAGATAGGAATGGGCATCGGGTACGGCATTGGAAATGGGGCTCAAGCAGGAAA
*
46206596 TAGCATGGGAT
66 TAACATGGGAT
46206607 ATGGAATTGG
Statistics
Matches: 66, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
84 66 1.00
ACGTcount: A:0.31, C:0.11, G:0.38, T:0.21
Consensus pattern (84 bp):
GGAAATGGGAACCAGATAGGAATGGGCATCGGGTACGGCATTGGAAATGGGGCTCAAGCAGGAAA
TAACATGGGATTTGGTAAT
Found at i:46206661 original size:30 final size:30
Alignment explanation
Indices: 46206626--46206689 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
46206616 GCTTTGGCAG
* *
46206626 TGGAAATGGGAACCAGTTAGGGACTGGTAT
1 TGGAAATGGGAACCAGTTAGGAACCGGTAT
46206656 TGGAAATGGGAACCAGTTAGGAACCGGTAT
1 TGGAAATGGGAACCAGTTAGGAACCGGTAT
46206686 TGGA
1 TGGA
46206690 TTTGGTATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.11, G:0.36, T:0.22
Consensus pattern (30 bp):
TGGAAATGGGAACCAGTTAGGAACCGGTAT
Found at i:46211075 original size:16 final size:17
Alignment explanation
Indices: 46211056--46211121 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 17
46211046 CTACAAACTA
46211056 CGAGCTC-TGCAAAGTG
1 CGAGCTCATGCAAAGTG
*
46211072 CGAGC-CAT-CAAGGTG
1 CGAGCTCATGCAAAGTG
* **
46211087 CAAGCTCAATAAAAAGTG
1 CGAGCTC-ATGCAAAGTG
*
46211105 CGAGC-CCTGCAAAGTG
1 CGAGCTCATGCAAAGTG
46211121 C
1 C
46211122 AAGCCCATCA
Statistics
Matches: 38, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
15 11 0.29
16 15 0.39
17 3 0.08
18 9 0.24
ACGTcount: A:0.32, C:0.26, G:0.27, T:0.15
Consensus pattern (17 bp):
CGAGCTCATGCAAAGTG
Found at i:46211198 original size:18 final size:18
Alignment explanation
Indices: 46211150--46211198 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
46211140 CGAGCTCAGT
* * *
46211150 AAAAAGTGTGTGCGCTGC
1 AAAAAGTGAGAGCTCTGC
*
46211168 AAAAAGTGCGAGCTCTGC
1 AAAAAGTGAGAGCTCTGC
*
46211186 AAAAGGTGAGAGC
1 AAAAAGTGAGAGC
46211199 CATTAAATTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.33, T:0.16
Consensus pattern (18 bp):
AAAAAGTGAGAGCTCTGC
Done.