Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019747.1 Corchorus olitorius cultivar O-4 contig19780, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 138122
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:45 original size:17 final size:16
Alignment explanation
Indices: 23--66 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
13 ATGAGGCCCA
23 CGCGCTGGCCTGGGCC
1 CGCGCTGGCCTGGGCC
*
39 GCGCGCTGGCCTAGGCC
1 -CGCGCTGGCCTGGGCC
56 CGC-CTGGCCTG
1 CGCGCTGGCCTG
67 CTGGCTGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.28
16 3 0.12
17 15 0.60
ACGTcount: A:0.02, C:0.43, G:0.41, T:0.14
Consensus pattern (16 bp):
CGCGCTGGCCTGGGCC
Found at i:1694 original size:150 final size:150
Alignment explanation
Indices: 1507--1812 Score: 578
Period size: 150 Copynumber: 2.0 Consensus size: 150
1497 CTTTAGTATT
1507 AGTTTGAAGTATGGTGACTTTGTTGGTGTTAACCTCTATAGATATTTTTGTAACCTTAGAGTATT
1 AGTTTGAAGTATGGTGACTTTGTTGGTGTTAACCTCTATAGATATTTTTGTAACCTTAGAGTATT
1572 TTACACTCATAAATTTATATCTATGAAGTAATGAGTTTTTATGTACATATATATTAAAAAAAATT
66 TTACACTCATAAATTTATATCTATGAAGTAATGAGTTTTTATGTACATATATATT-AAAAAAATT
1637 T-AATTTAATTATTATTACAA
130 TAAATTTAATTATTATTACAA
1657 AGTTTGAAGTATGGTGACTTTGTTGGTGTTAACCTCTATAGATATTTTTGTAACCTTAGAGTATT
1 AGTTTGAAGTATGGTGACTTTGTTGGTGTTAACCTCTATAGATATTTTTGTAACCTTAGAGTATT
*
1722 TTACACTCATAAATTTATATTTATGAAGTAATGAGTTTTTATGTACATATATATTAAAAAAATTT
66 TTACACTCATAAATTTATATCTATGAAGTAATGAGTTTTTATGTACATATATATTAAAAAAATTT
1787 AAAATTTAATTATTATTACAA
131 -AAATTTAATTATTATTACAA
1808 AGTTT
1 AGTTT
1813 ATACCTAAAA
Statistics
Matches: 153, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
149 10 0.07
150 119 0.78
151 24 0.16
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (150 bp):
AGTTTGAAGTATGGTGACTTTGTTGGTGTTAACCTCTATAGATATTTTTGTAACCTTAGAGTATT
TTACACTCATAAATTTATATCTATGAAGTAATGAGTTTTTATGTACATATATATTAAAAAAATTT
AAATTTAATTATTATTACAA
Found at i:2234 original size:2 final size:2
Alignment explanation
Indices: 2227--2251 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2217 CATAATAATT
2227 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 T
2252 TTAGATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3549 original size:37 final size:37
Alignment explanation
Indices: 3479--3549 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 37
3469 TATATATTAT
* * *
3479 AATTAATATATTAATTAATTAATGAATATTATAAGAA
1 AATTAAAATATTAATTAATTAATGAAAAATATAAGAA
*
3516 AATTAAAATATTAATT-GTATAATGAAAAATATAA
1 AATTAAAATATTAATTAAT-TAATGAAAAATATAA
3550 AGCTGTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.03
37 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (37 bp):
AATTAAAATATTAATTAATTAATGAAAAATATAAGAA
Found at i:4624 original size:26 final size:26
Alignment explanation
Indices: 4590--4650 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
4580 AGACCAGCGT
*
4590 GGCCCAGCGTGCCAGGCCAGGCACGC
1 GGCCCAGCGTGCCAAGCCAGGCACGC
4616 GGCCCAGCGTGCCAAGCCAGGCACGC
1 GGCCCAGCGTGCCAAGCCAGGCACGC
4642 GGCCCAGCG
1 GGCCCAGCG
4651 ACCCGGGCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.16, C:0.43, G:0.38, T:0.03
Consensus pattern (26 bp):
GGCCCAGCGTGCCAAGCCAGGCACGC
Found at i:5755 original size:28 final size:28
Alignment explanation
Indices: 5695--5747 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
5685 CCTATCATGA
* *
5695 AAAATTACCGTTTTGCCCTTTGTCGAAT
1 AAAATTACCGTTTTGCCCTCTGTAGAAT
*
5723 AAAATTATCGTTTTGCCC-CTGTAGA
1 AAAATTACCGTTTTGCCCTCTGTAGA
5748 CCTAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (28 bp):
AAAATTACCGTTTTGCCCTCTGTAGAAT
Found at i:11357 original size:11 final size:11
Alignment explanation
Indices: 11341--11371 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
11331 TAGTCTTCAA
11341 ATCTTCAAATT
1 ATCTTCAAATT
11352 ATCTTCAAATT
1 ATCTTCAAATT
11363 ATCTTCAAA
1 ATCTTCAAA
11372 CACGAATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (11 bp):
ATCTTCAAATT
Found at i:11741 original size:8 final size:8
Alignment explanation
Indices: 11728--11753 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11718 GACGCCGGTT
11728 TTGGTCGG
1 TTGGTCGG
11736 TTGGTCGG
1 TTGGTCGG
11744 TTGGTCGG
1 TTGGTCGG
11752 TT
1 TT
11754 TTAGGGGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.46, T:0.42
Consensus pattern (8 bp):
TTGGTCGG
Found at i:12722 original size:14 final size:15
Alignment explanation
Indices: 12703--12731 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12693 TTAAAATATA
12703 TAAATATA-TATAAT
1 TAAATATATTATAAT
12717 TAAATATATTATAAT
1 TAAATATATTATAAT
12732 ATATGGGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATATATTATAAT
Found at i:14216 original size:22 final size:22
Alignment explanation
Indices: 14191--14626 Score: 242
Period size: 22 Copynumber: 19.9 Consensus size: 22
14181 AATAATGACT
*
14191 GGTTAACAAAATTTCATAAGTA
1 GGTTATCAAAATTTCATAAGTA
* * *
14213 GGTTAACAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGTA
* *
14235 TGG-TAACAAAATTTCAT-AGAAA
1 -GGTTATCAAAATTTCATAAG-TA
* * *
14257 GGTTCTCAAAATTTCATAGGGA
1 GGTTATCAAAATTTCATAAGTA
* * *
14279 GGTTCTCGAAATTCCAT-AGT-
1 GGTTATCAAAATTTCATAAGTA
* *
14299 GTCATTATCAAAATTTCATAGGGT-
1 G--GTTATCAAAATTTCATA-AGTA
14323 GGTTATCAAAATTTCAT--GT-
1 GGTTATCAAAATTTCATAAGTA
* * * *
14342 GATTATCAAAATTTCTTAGGGA
1 GGTTATCAAAATTTCATAAGTA
14364 GGTTATCAAAATTTCATATA-TA
1 GGTTATCAAAATTTCATA-AGTA
* * *
14386 GGGAGATTATCCAAATTACAT-AGTGT
1 --G-G-TTATCAAAATTTCATAAGT-A
*
14412 GGTTATCAAAATTTCATAAGGA
1 GGTTATCAAAATTTCATAAGTA
* *
14434 GGTTATCAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGTA
14456 GGTTATCAAAATTTCATAATGT-
1 GGTTATCAAAATTTCATAA-GTA
* * * *
14478 GTTTATCAAGATTTCATATGAA
1 GGTTATCAAAATTTCATAAGTA
*
14500 GGTTATCAAAATTTCAT-ATTGA
1 GGTTATCAAAATTTCATAAGT-A
* *
14522 GATTATCAAAATTTAAT-AGT-
1 GGTTATCAAAATTTCATAAGTA
* * *
14542 GTGTTTATCAAAATTTGATAGGGA
1 G-G-TTATCAAAATTTCATAAGTA
* * *
14566 GATCA-CTAAAATTCCATAATGT-
1 GGTTATC-AAAATTTCATAA-GTA
*
14588 GATTATCAAAATTTCAT-AG-A
1 GGTTATCAAAATTTCATAAGTA
*
14608 GGTTAACAAAATTTCATAA
1 GGTTATCAAAATTTCATAA
14627 AGATGTTTCT
Statistics
Matches: 322, Mismatches: 61, Indels: 63
0.72 0.14 0.14
Matches are distributed among these distances:
19 17 0.05
20 18 0.06
21 9 0.03
22 246 0.76
23 10 0.03
24 7 0.02
25 2 0.01
26 13 0.04
ACGTcount: A:0.39, C:0.10, G:0.16, T:0.35
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAAGTA
Found at i:14244 original size:44 final size:44
Alignment explanation
Indices: 14191--15054 Score: 301
Period size: 44 Copynumber: 19.9 Consensus size: 44
14181 AATAATGACT
* *
14191 GGTTAACAAAATTTCATAAGTAGGTTAACAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCATAGGAA
* * * *
14235 TGG-TAACAAAATTTCAT-AGAAAGGTTCTCAAAATTTCATAGGGA
1 -GGTTATCAAAATTTCATAAG-TAGGTTATCAAAATTTCATAGGAA
* * * * **
14279 GGTTCTCGAAATTCCAT-AGT-GTCATTATCAAAATTTCATAGGGT
1 GGTTATCAAAATTTCATAAGTAG--GTTATCAAAATTTCATAGGAA
* * *
14323 GGTTATCAAAATTTCAT--GT-GATTATCAAAATTTCTTAGGGA
1 GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCATAGGAA
* * *
14364 GGTTATCAAAATTTCATATA-TAGGGAGATTATCCAAATTACATAGTG-T
1 GGTTATCAAAATTTCATA-AGTA--G-G-TTATCAAAATTTCATAG-GAA
*
14412 GGTTATCAAAATTTCATAAGGAGGTTATCAAAATTTCATAGGAA
1 GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCATAGGAA
* * *
14456 GGTTATCAAAATTTCATAATGT-GTTTATCAAGATTTCATATGAA
1 GGTTATCAAAATTTCATAA-GTAGGTTATCAAAATTTCATAGGAA
* * * *
14500 GGTTATCAAAATTTCAT-ATTGAGATTATCAAAATTTAATAGTG-T
1 GGTTATCAAAATTTCATAAGT-AGGTTATCAAAATTTCATAG-GAA
* * * * * * * *
14544 GTTTATCAAAATTTGATAGGGAGATCA-CTAAAATTCCATA--AT
1 GGTTATCAAAATTTCATAAGTAGGTTATC-AAAATTTCATAGGAA
*
14586 GTGATTATCAAAATTTCAT-AG-AGGTTAACAAAATTTCATA--AA
1 G-G-TTATCAAAATTTCATAAGTAGGTTATCAAAATTTCATAGGAA
* * *
14628 GATGTT-TCTAAAATTTTAT-AGTGTGGTTA-CAAAAATTTCATAGTGTTA
1 G--GTTATC-AAAATTTCATAAGT-AGGTTATC-AAAATTTCATAG-G-AA
* * * *** * *
14676 --TTATCAAAATTTTATAGGGAGAACAGT-AAAATTTCATAGTAT
1 GGTTATCAAAATTTCATAAGTAGGTTA-TCAAAATTTCATAGGAA
* * * *
14718 GATTATAAAAATTTCAT-AG-AGCTTAACAAAATTTCATAAGGATA
1 GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCAT-AGGA-A
** * * *
14762 TATTGCA-AAAAATTT-TTAATGT-GATTATCAAAATTTCATAGAGAA
1 GGTT--ATCAAAATTTCATAA-GTAGGTTATCAAAATTTCATAG-GAA
* * * * * * *
14807 -ATTATC-AAATTTCATAGGGATGTTATCGAAATTTCATGGGGA
1 GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCATAGGAA
* *
14849 GGTTATCAAAA-TTC--------CTTACCAAAATTTCATAGGGAA
1 GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCATA-GGAA
* * *
14885 -ATTATC-AAATTTCCAT-AGTGTGGTTATCAAGATTTCATAGAGATA
1 GGTTATCAAAATTT-CATAAGT-AGGTTATCAAAATTTCATAG-GA-A
** * * * * * * *
14930 --TTATTGAAATTTCATAGGGATGTTATCAAACTTCCATATTG-T
1 GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCATA-GGAA
* * * * * *
14972 GGTTATCAAATTTTCAAAAGGAAGTTATCAAATTTTCATAGGGA
1 GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCATAGGAA
* * * *
15016 GGTTATCGAAATTTCATAAGGAGGTTGTCAAATTTTCAT
1 GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCAT
15055 TAGAATCAAA
Statistics
Matches: 626, Mismatches: 120, Indels: 147
0.70 0.13 0.16
Matches are distributed among these distances:
34 3 0.00
35 20 0.03
36 4 0.01
41 38 0.06
42 56 0.09
43 47 0.08
44 373 0.60
45 28 0.04
46 21 0.03
47 1 0.00
48 34 0.05
49 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAAGTAGGTTATCAAAATTTCATAGGAA
Found at i:14282 original size:66 final size:66
Alignment explanation
Indices: 14191--14755 Score: 324
Period size: 66 Copynumber: 8.6 Consensus size: 66
14181 AATAATGACT
* * *
14191 GGTTAACAAAATTTCATAAGT-AGGTTAACAAAATTTCATAGGAATGG-TAACAAAATTTCATAG
1 GGTTATCAAAATTTCAT-AGTGAGGTTATCAAAATTTCATAGGAA-GGTTATCAAAATTTCATAG
14254 AAA
64 AAA
* * * * * *
14257 GGTTCTCAAAATTTCATAGGGAGGTTCTCGAAATTCCATAGTGTCA--TTATCAAAATTTCATAG
1 GGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAG-G-AAGGTTATCAAAATTTCATAG
***
14320 GGT
64 AAA
* * *
14323 GGTTATCAAAATTTCAT-GTGA--TTATCAAAATTTCTTAGGGAGGTTATCAAAATTTCATATAT
1 GGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGA-
14385 AGGGA
65 A---A
* * * * *
14390 GATTATCCAAATTACATAGTGTGGTTATCAAAATTTCATAAGG-AGGTTATCAAAATTTCATAGG
1 GGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCAT-AGGAAGGTTATCAAAATTTCATAGA
14454 AA
65 AA
* * * * * ***
14456 GGTTATCAAAATTTCATAATGTGTTTATCAAGATTTCATATGAAGGTTATCAAAATTTCATATTG
1 GGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGAA
14521 A
66 A
* * * * * * * * *
14522 GATTATCAAAATTTAATAGTGTGTTTATCAAAATTTGATAGGGAGATCA-CTAAAATTCCAT--A
1 GGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAGGTTATC-AAAATTTCATAGA
*
14584 AT
65 AA
* *
14586 GTGATTATCAAAATTTCATA--GAGGTTAACAAAATTTCATA--AAGATGTT-TCTAAAATTTTA
1 G-G-TTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAG--GTTATC-AAAATTTCA
***
14646 TAGTGT
61 TAGAAA
*** * * ***
14652 GGTTA-CAAAAATTTCATAGTGTTATTATCAAAATTTTATAGGGAGAACAGT-AAAATTTCATAG
1 GGTTATC-AAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAGGTTA-TCAAAATTTCATAG
* *
14715 TAT
64 AAA
* * * *
14718 GATTATAAAAATTTCATA--GAGCTTAACAAAATTTCATA
1 GGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATA
14756 AGGATATATT
Statistics
Matches: 384, Mismatches: 84, Indels: 64
0.72 0.16 0.12
Matches are distributed among these distances:
61 1 0.00
62 3 0.01
63 30 0.08
64 57 0.15
65 9 0.02
66 225 0.59
67 15 0.04
68 7 0.02
69 1 0.00
70 33 0.09
71 3 0.01
ACGTcount: A:0.39, C:0.10, G:0.15, T:0.36
Consensus pattern (66 bp):
GGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTCATAGGAAGGTTATCAAAATTTCATAGAA
A
Found at i:14662 original size:22 final size:22
Alignment explanation
Indices: 14294--14736 Score: 167
Period size: 22 Copynumber: 20.2 Consensus size: 22
14284 TCGAAATTCC
* *
14294 ATAGTGTCATTATCAAAATTTC
1 ATAGTGTGATTATCAAAATTTT
* *
14316 ATAGGGTGGTTATCAAAA-TTT
1 ATAGTGTGATTATCAAAATTTT
*
14337 -CA-TGTGATTATCAAAATTTCT
1 ATAGTGTGATTATCAAAATTT-T
* * *
14358 -TAGGGAGGTTATCAAAATTTCATAT
1 ATAGTGTGATTATCAAAA-TT--T-T
* * * **
14383 ATAGGGAGATTATCCAAATTAC
1 ATAGTGTGATTATCAAAATTTT
* *
14405 ATAGTGTGGTTATCAAAATTTC
1 ATAGTGTGATTATCAAAATTTT
* * *
14427 ATAAG-GAGGTTATCAAAATTTC
1 AT-AGTGTGATTATCAAAATTTT
* * *
14449 ATAG-GAAGGTTATCAAAATTTC
1 ATAGTG-TGATTATCAAAATTTT
* * * *
14471 ATAATGTGTTTATCAAGATTTC
1 ATAGTGTGATTATCAAAATTTT
* * *
14493 ATA-TGAAGGTTATCAAAATTTC
1 ATAGTG-TGATTATCAAAATTTT
* * *
14515 ATATTGAGATTATCAAAATTTA
1 ATAGTGTGATTATCAAAATTTT
* *
14537 ATAGTGTGTTTATCAAAATTTG
1 ATAGTGTGATTATCAAAATTTT
* * * **
14559 ATAGGGAGATCA-CTAAAATTCC
1 ATAGTGTGATTATC-AAAATTTT
* *
14581 ATAATGTGATTATCAAAATTTC
1 ATAGTGTGATTATCAAAATTTT
* * *
14603 ATAGAG-G-TTAACAAAATTTC
1 ATAGTGTGATTATCAAAATTTT
**
14623 ATAAAGATG-TT-TCTAAAATTTT
1 ATAGTG-TGATTATC-AAAATTTT
* *
14645 ATAGTGTGGTTA-CAAAAATTTC
1 ATAGTGTGATTATC-AAAATTTT
*
14667 ATAGTGTTATTATCAAAATTTT
1 ATAGTGTGATTATCAAAATTTT
* * ** *
14689 ATAGGGAGAACAGT-AAAATTTC
1 ATAGTGTGATTA-TCAAAATTTT
* * *
14711 ATAGTATGATTATAAAAATTTC
1 ATAGTGTGATTATCAAAATTTT
14733 ATAG
1 ATAG
14737 AGCTTAACAA
Statistics
Matches: 329, Mismatches: 70, Indels: 44
0.74 0.16 0.10
Matches are distributed among these distances:
19 12 0.04
20 20 0.06
21 15 0.05
22 253 0.77
23 10 0.03
25 4 0.01
26 15 0.05
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (22 bp):
ATAGTGTGATTATCAAAATTTT
Found at i:14680 original size:130 final size:132
Alignment explanation
Indices: 14522--14826 Score: 379
Period size: 130 Copynumber: 2.3 Consensus size: 132
14512 TTCATATTGA
* * *
14522 GATTATCAAAATTTAATAGTGTGT-TTATCAAAATTTGATAGGGAGATCACTAAAATTCCATAAT
1 GATTATCAAAATTTCATAGTGT-TATTATCAAAATTTCATAGGGAGAACACTAAAATTCCATAAT
* * * * *
14586 GTGATTATCAAAATTTCATAGAGGTTAACAAAATTTCATAAAGATGT-TT-C-TAAAATTTTATA
65 ATGATTATAAAAATTTCATAGAGCTTAACAAAATTTCATAAAGATATATTGCAAAAAATTTT-TA
*
14648 GTGT
129 ATGT
* * * * *
14652 GGTTA-CAAAAATTTCATAGTGTTATTATCAAAATTTTATAGGGAGAACAGTAAAATTTCATAGT
1 GATTATC-AAAATTTCATAGTGTTATTATCAAAATTTCATAGGGAGAACACTAAAATTCCATAAT
*
14716 ATGATTATAAAAATTTCATAGAGCTTAACAAAATTTCATAAGGATATATTGCAAAAAATTTTTAA
65 ATGATTATAAAAATTTCATAGAGCTTAACAAAATTTCATAAAGATATATTGCAAAAAATTTTTAA
14781 TGT
130 TGT
* **
14784 GATTATCAAAATTTCATAGAGAAATTATC-AAATTTCATAGGGA
1 GATTATCAAAATTTCATAGTGTTATTATCAAAATTTCATAGGGA
14827 TGTTATCGAA
Statistics
Matches: 150, Mismatches: 19, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
129 2 0.01
130 95 0.63
131 15 0.10
132 29 0.19
133 9 0.06
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.36
Consensus pattern (132 bp):
GATTATCAAAATTTCATAGTGTTATTATCAAAATTTCATAGGGAGAACACTAAAATTCCATAATA
TGATTATAAAAATTTCATAGAGCTTAACAAAATTTCATAAAGATATATTGCAAAAAATTTTTAAT
GT
Found at i:14787 original size:66 final size:64
Alignment explanation
Indices: 14582--14804 Score: 195
Period size: 66 Copynumber: 3.4 Consensus size: 64
14572 TAAAATTCCA
* * *
14582 TAATGTGATTATCAAAATTTCATAGAGGTTAACAAAATTTCATAAAGATGT-TTC-TAAAATTTT
1 TAATGTGATTATAAAAATTTCATAGA-GTTAACAAAATTTCATAAGGATATATTCATAAAATTTT
* * * * * * *
14645 ATAGTGTGGTTACAAAAATTTCATAGTGTTATTATCAAAATTTTATAGGGAGA-A--CAGTAAAA
1 -TAATGTGATTATAAAAATTTCATAGAGTTA--A-CAAAATTTCATAAGGATATATTCA-TAAAA
*
14707 TTTCA
61 TTT-T
* * *
14712 TAGTATGATTATAAAAATTTCATAGAGCTTAACAAAATTTCATAAGGATATATTGCAAAAAATTT
1 TAATGTGATTATAAAAATTTCATAGAG-TTAACAAAATTTCATAAGGATATATT-CATAAAATTT
14777 T
64 T
*
14778 TAATGTGATTATCAAAATTTCATAGAG
1 TAATGTGATTATAAAAATTTCATAGAG
14805 AAATTATCAA
Statistics
Matches: 124, Mismatches: 23, Indels: 22
0.73 0.14 0.13
Matches are distributed among these distances:
63 4 0.03
64 37 0.30
65 3 0.02
66 68 0.55
67 10 0.08
68 2 0.02
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (64 bp):
TAATGTGATTATAAAAATTTCATAGAGTTAACAAAATTTCATAAGGATATATTCATAAAATTTT
Found at i:14810 original size:22 final size:22
Alignment explanation
Indices: 14785--14861 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
14775 TTTTAATGTG
*
14785 ATTATCAAAATTTCATAGAGAA
1 ATTATCAAAATTTCATAGGGAA
*
14807 ATTATC-AAATTTCATAGGGAT
1 ATTATCAAAATTTCATAGGGAA
* * * *
14828 GTTATCGAAATTTCATGGGGAG
1 ATTATCAAAATTTCATAGGGAA
*
14850 GTTATCAAAATT
1 ATTATCAAAATT
14862 CCTTACCAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 18 0.38
22 30 0.62
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (22 bp):
ATTATCAAAATTTCATAGGGAA
Found at i:14901 original size:22 final size:21
Alignment explanation
Indices: 14870--15050 Score: 137
Period size: 22 Copynumber: 8.3 Consensus size: 21
14860 TTCCTTACCA
**
14870 AAATTTCATAGGGAAATTATC
1 AAATTTCATAGGGAGGTTATC
* *
14891 AAATTTCCATAGTGTGGTTATC
1 AAATTT-CATAGGGAGGTTATC
* ** *
14913 AAGATTTCATAGAGATATTATTG
1 AA-ATTTCATAGGGAGGTTA-TC
*
14936 AAATTTCATAGGGATGTTATC
1 AAATTTCATAGGGAGGTTATC
* ** *
14957 AAACTTCCATATTGTGGTTATC
1 AAA-TTTCATAGGGAGGTTATC
* * *
14979 AAATTTTCAAAAGGAAGTTATC
1 AAA-TTTCATAGGGAGGTTATC
15001 AAATTTTCATAGGGAGGTTATC
1 AAA-TTTCATAGGGAGGTTATC
* *
15023 GAAATTTCATAAGGAGGTTGTC
1 -AAATTTCATAGGGAGGTTATC
15045 AAATTT
1 AAATTT
15051 TCATTAGAAT
Statistics
Matches: 126, Mismatches: 29, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
21 16 0.13
22 100 0.79
23 10 0.08
ACGTcount: A:0.35, C:0.10, G:0.18, T:0.37
Consensus pattern (21 bp):
AAATTTCATAGGGAGGTTATC
Found at i:15009 original size:66 final size:66
Alignment explanation
Indices: 14870--15053 Score: 180
Period size: 66 Copynumber: 2.8 Consensus size: 66
14860 TTCCTTACCA
* * *
14870 AAATTTCATAGGGAAATTATCAAATTTCCATAGTGTGGTTATCAAGA-TTTC-ATAGAGATATTA
1 AAATTTCATAGGGAAGTTATCAAA-TTCCATAATGTGGTTATCAA-ATTTTCAAAAGAGATATTA
*
14933 TTG
64 TTC
* *
14936 AAATTTCATAGGGATGTTATCAAACTTCCATATTGTGGTTATCAAATTTTCAAAAG-GA-AGTTA
1 AAATTTCATAGGGAAGTTATCAAA-TTCCATAATGTGGTTATCAAATTTTCAAAAGAGATA-TTA
14999 -TC
64 TTC
* * * * *
15001 AAATTTTCATAGGGAGGTTATCGAAATTTCATAAGGAGGTTGTCAAATTTTCA
1 AAA-TTTCATAGGGAAGTTATC-AAATTCCATAATGTGGTTATCAAATTTTCA
15054 TTAGAATCAA
Statistics
Matches: 101, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
65 6 0.06
66 89 0.88
67 6 0.06
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.37
Consensus pattern (66 bp):
AAATTTCATAGGGAAGTTATCAAATTCCATAATGTGGTTATCAAATTTTCAAAAGAGATATTATT
C
Found at i:15433 original size:28 final size:29
Alignment explanation
Indices: 15382--15438 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
15372 GAACCAGGAC
* * *
15382 ATTTTCATTAGGGGGCCAATCGGTGTATA
1 ATTTTCAATAGGGGGCCAACCGGTATATA
15411 ATTTTCAAT-GGGGGCCAACCGGTATATA
1 ATTTTCAATAGGGGGCCAACCGGTATATA
15439 TATACATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 17 0.68
29 8 0.32
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (29 bp):
ATTTTCAATAGGGGGCCAACCGGTATATA
Found at i:17777 original size:27 final size:27
Alignment explanation
Indices: 17639--17781 Score: 117
Period size: 27 Copynumber: 5.1 Consensus size: 27
17629 ACAACACAAA
** **
17639 TCCCAACTGCGGGAGCTTCAGCAAAAG
1 TCCCAACTGCGGGAGCTTTGGCATGAG
* *
17666 TCCCAACTAC-AGAGGCTTTGGCATGAG
1 TCCCAACTGCGGGA-GCTTTGGCATGAG
* *
17693 TCCCAACTGCGGGGCGAGAATTTCGGCGTGAG
1 TCCCAACTGC--GG-GAG-CTTT-GGCATGAG
***
17725 TCCCAACTGCGGGAGCTTCAACATGAG
1 TCCCAACTGCGGGAGCTTTGGCATGAG
*
17752 TCCCAACTGCGGGAGCTTTGGTATGAG
1 TCCCAACTGCGGGAGCTTTGGCATGAG
17779 TCC
1 TCC
17782 TTTGGCATAA
Statistics
Matches: 90, Mismatches: 19, Indels: 14
0.73 0.15 0.11
Matches are distributed among these distances:
26 2 0.02
27 58 0.64
28 2 0.02
29 3 0.03
30 3 0.03
31 5 0.06
32 17 0.19
ACGTcount: A:0.23, C:0.27, G:0.29, T:0.20
Consensus pattern (27 bp):
TCCCAACTGCGGGAGCTTTGGCATGAG
Found at i:17844 original size:27 final size:27
Alignment explanation
Indices: 17814--17892 Score: 86
Period size: 30 Copynumber: 2.8 Consensus size: 27
17804 GAGGCTTTGA
17814 CATGAGTCCCAACTGCGGGAGCTTCAG
1 CATGAGTCCCAACTGCGGGAGCTTCAG
**
17841 CATGAGTCCCACCAACTGCGGGAATTTCAG
1 CATGAGT--C-CCAACTGCGGGAGCTTCAG
* * *
17871 CGTGAGTGCCAACTACGGGAGC
1 CATGAGTCCCAACTGCGGGAGC
17893 ATCTTTCTCT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
27 18 0.43
29 1 0.02
30 23 0.55
ACGTcount: A:0.24, C:0.29, G:0.29, T:0.18
Consensus pattern (27 bp):
CATGAGTCCCAACTGCGGGAGCTTCAG
Found at i:19161 original size:24 final size:24
Alignment explanation
Indices: 19131--19207 Score: 64
Period size: 24 Copynumber: 3.1 Consensus size: 24
19121 CCATTTTGCG
*
19131 GCAGAAGCCAACCACAATTCTACC
1 GCAGAAGCCAACCACAATTATACC
* * * * * *
19155 GCGGAAGTCAAGCACCATATTTTGCG
1 GCAGAAGCCAACCA-CA-ATTATACC
*
19181 GTAGAAGCCAACCACAATTATACC
1 GCAGAAGCCAACCACAATTATACC
19205 GCA
1 GCA
19208 AAAGTCAAGT
Statistics
Matches: 37, Mismatches: 14, Indels: 4
0.67 0.25 0.07
Matches are distributed among these distances:
24 18 0.49
25 4 0.11
26 15 0.41
ACGTcount: A:0.35, C:0.30, G:0.18, T:0.17
Consensus pattern (24 bp):
GCAGAAGCCAACCACAATTATACC
Found at i:19189 original size:50 final size:48
Alignment explanation
Indices: 19116--19216 Score: 148
Period size: 50 Copynumber: 2.1 Consensus size: 48
19106 CACCAATCTT
* **
19116 AAGCACCATTTTGCGGCAGAAGCCAACCACAATTCTACCGCGGAAGTC
1 AAGCACCATTTTGCGGCAGAAGCCAACCACAATTATACCGCAAAAGTC
*
19164 AAGCACCATATTTTGCGGTAGAAGCCAACCACAATTATACCGCAAAAGTC
1 AAGCACC--ATTTTGCGGCAGAAGCCAACCACAATTATACCGCAAAAGTC
19214 AAG
1 AAG
19217 TATCATCCTA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
48 7 0.15
50 40 0.85
ACGTcount: A:0.36, C:0.28, G:0.19, T:0.18
Consensus pattern (48 bp):
AAGCACCATTTTGCGGCAGAAGCCAACCACAATTATACCGCAAAAGTC
Found at i:27010 original size:130 final size:130
Alignment explanation
Indices: 26856--27118 Score: 388
Period size: 130 Copynumber: 2.0 Consensus size: 130
26846 GTCATTTAAG
* *
26856 AAATATATTTTAAAAATTCTAATATATCTAAG-TTTTTTAATTAAATTAGTAAAATGGTAAAAAT
1 AAATATATTTAAAAAATTCTAATATA--TAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAAT
* * * * *
26920 AAAATAGGTATAAAGATATTAGATTTTA-TACAATAGAAATAGAGTTTTTAGTTGAGTAAAATTA
64 AAAAGAGGTATAAAGATATTAGATTTAATTA-AATAAAAATAGAGTTTTTAGTTGAATAAAACTA
26984 TAA
128 TAA
26987 AAATATA-TTAAAAAATTCTAATATATAAGTTTTTTTTAATTAAAATAGTAAAATGGTAAAAATA
1 AAATATATTTAAAAAATTCTAATATATAAG-TTTTTTTAATTAAAATAGTAAAATGGTAAAAATA
* *
27051 AAAGAGTTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATA
65 AAAGAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATA
27116 A
130 A
27117 AA
1 AA
27119 GTTTAAATAA
Statistics
Matches: 120, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
128 4 0.03
130 107 0.89
131 9 0.08
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (130 bp):
AAATATATTTAAAAAATTCTAATATATAAGTTTTTTTAATTAAAATAGTAAAATGGTAAAAATAA
AAGAGGTATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAATAAAACTATAA
Found at i:31943 original size:14 final size:14
Alignment explanation
Indices: 31919--31953 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
31909 TTTATCTAAT
31919 TATAT-TATATATC
1 TATATCTATATATC
31932 TATATCTATATATC
1 TATATCTATATATC
31946 TATATCTA
1 TATATCTA
31954 GTCTAGGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATCTATATATC
Found at i:32923 original size:40 final size:41
Alignment explanation
Indices: 32874--32965 Score: 168
Period size: 40 Copynumber: 2.3 Consensus size: 41
32864 TCCTCCATTG
32874 TTGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTT
*
32915 TTG-AGGATATTTAAGAATGTATTTTTTAAAGGATTTATTT
1 TTGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTT
32955 TTGAAGGATAT
1 TTGAAGGATAT
32966 ATTATGATGA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 39 0.80
41 10 0.20
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (41 bp):
TTGAAGGATATTTAAGAATATATTTTTTAAAGGATTTATTT
Found at i:33660 original size:22 final size:22
Alignment explanation
Indices: 33629--33884 Score: 81
Period size: 22 Copynumber: 11.5 Consensus size: 22
33619 GAGATTAACG
* *
33629 AAATTCCATAGGGAAGTTATCA
1 AAATTTCATAGCGAAGTTATCA
* *
33651 ACATTTCATAGCGAGGTTATCA
1 AAATTTCATAGCGAAGTTATCA
* * *
33673 AAATTTCATAG-TATATTTATCC
1 AAATTTCATAGCGA-AGTTATCA
* * ***
33695 AAATGTCATAGTGTACCATATCA
1 AAATTTCATAGCG-AAGTTATCA
** * **
33718 ACAA-TTCGCAGTGTGGTTATCA
1 A-AATTTCATAGCGAAGTTATCA
* *
33740 AAATTTCATAGTG-AGCTCATCAA
1 AAATTTCATAGCGAAG-TTATC-A
*
33763 ATTAATTTCATA-CAGAGGTTATCA
1 A--AATTTCATAGC-GAAGTTATCA
* * * ** *
33787 CAATTTTATAGTGTGGTTATCC
1 AAATTTCATAGCGAAGTTATCA
* *
33809 AAATTTCATAGTGAAGTTATCC
1 AAATTTCATAGCGAAGTTATCA
* ** *
33831 AAATTTCATAGTGTGGCTATCA
1 AAATTTCATAGCGAAGTTATCA
* * *
33853 AAATTTGATAG-TATAATTATCA
1 AAATTTCATAGCGA-AGTTATCA
33875 AAATTTCATA
1 AAATTTCATA
33885 AATAGTTTAT
Statistics
Matches: 172, Mismatches: 49, Indels: 26
0.70 0.20 0.11
Matches are distributed among these distances:
21 4 0.02
22 136 0.79
23 13 0.08
24 4 0.02
25 14 0.08
26 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (22 bp):
AAATTTCATAGCGAAGTTATCA
Found at i:33829 original size:44 final size:44
Alignment explanation
Indices: 33629--33884 Score: 164
Period size: 44 Copynumber: 5.7 Consensus size: 44
33619 GAGATTAACG
* * * * *
33629 AAATTCCATAGGGAAGTTAT-CAACATTTCATAGCGAGGTTATCA
1 AAATTTCATAGTGAAGTTATCCAA-ATTTCATAGTGTGGCTATCA
* * **
33673 AAATTTCATAGT-ATATTTATCCAAATGTCATAGTGTACCATATCA
1 AAATTTCATAGTGA-AGTTATCCAAATTTCATAGTGTGGC-TATCA
** ** * *
33718 ACAA-TTCGCAGTGTGGTTATCAAAATTTCATAGTG-AGCTCATCAA
1 A-AATTTCATAGTGAAGTTATCCAAATTTCATAGTGTGGCT-ATC-A
** * * * *
33763 ATTAATTTCATACAGAGGTTAT-CACAATTTTATAGTGTGGTTATCC
1 A--AATTTCATAGTGAAGTTATCCA-AATTTCATAGTGTGGCTATCA
33809 AAATTTCATAGTGAAGTTATCCAAATTTCATAGTGTGGCTATCA
1 AAATTTCATAGTGAAGTTATCCAAATTTCATAGTGTGGCTATCA
* * *
33853 AAATTTGATAGT-ATAATTATCAAAATTTCATA
1 AAATTTCATAGTGA-AGTTATCCAAATTTCATA
33885 AATAGTTTAT
Statistics
Matches: 162, Mismatches: 37, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
43 3 0.02
44 90 0.56
45 36 0.22
46 6 0.04
47 25 0.15
48 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (44 bp):
AAATTTCATAGTGAAGTTATCCAAATTTCATAGTGTGGCTATCA
Found at i:41718 original size:47 final size:47
Alignment explanation
Indices: 41645--42640 Score: 1532
Period size: 47 Copynumber: 22.0 Consensus size: 47
41635 AACCTCTTCT
* *
41645 TTAGTTTAATTACCTAGAATTGAACTAATCT-TTCCTTCTTCTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTT-CTTCTTTTACTAC
41692 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
41739 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTC-TTT--TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
41783 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTC-TTT--TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
41827 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTC-TTT--TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
41871 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
41918 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
*
41965 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTC-TCCTTT--TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
42009 TTAGTTTAATTACCTAGAATTAAACTAA-----TC-TC---T--T-C
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
*
42044 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTC-TCCTTT--TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
42088 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
*
42135 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTC-TCCTTT--TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
42179 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTC-TTT--TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
42223 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
*
42270 TTAGTTTAATTACCTAGAATTAAAGTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
42317 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
* *
42364 TTAGTTTAATTACCTAGAATTGAACTAATCTCTTCTTGTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
* *
42411 TTAGTTTAATTACCTAGAATTAAACTAATATCTTCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
* *
42458 TTAGTTTAATTACCTAGAATTAAA-TCAAGCTCTTCTTCTTTTACTAT
1 TTAGTTTAATTACCTAGAATTAAACT-AATCTCTTCTTCTTTTACTAC
*
42505 TTAGTTTAATTATCTAGAATTAAA-TCAAGT-TCTTCTTCTTTTACTAC
1 TTAGTTTAATTACCTAGAATTAAACT-AA-TCTCTTCTTCTTTTACTAC
*
42552 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTC-TCCTTT--TAC
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
* *
42596 TTAGTTTAATTACCTGGAATTAAACTAATCTTTTCTTCTTTTACT
1 TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACT
42641 GTTCAGTTTG
Statistics
Matches: 899, Mismatches: 23, Indels: 54
0.92 0.02 0.06
Matches are distributed among these distances:
35 29 0.03
36 2 0.00
39 4 0.00
40 4 0.00
43 2 0.00
44 314 0.35
45 18 0.02
46 20 0.02
47 503 0.56
48 3 0.00
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.47
Consensus pattern (47 bp):
TTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTTCTTTTACTAC
Found at i:42047 original size:35 final size:35
Alignment explanation
Indices: 42008--42124 Score: 153
Period size: 35 Copynumber: 3.1 Consensus size: 35
41998 TCTCCTTTTA
42008 CTTAGTTTAATTACCTAGAATTAAACTAATCTCTT
1 CTTAGTTTAATTACCTAGAATTAAACTAATCTCTT
42043 CTTAGTTTAATTACCTAGAATTAAACTAATCTCTTCTCCTTTT
1 CTTAGTTTAATTACCTAGAATTAAACTAA-----TCT-C--TT
42086 ACTTAGTTTAATTACCTAGAATTAAACTAATCTCTT
1 -CTTAGTTTAATTACCTAGAATTAAACTAATCTCTT
42122 CTT
1 CTT
42125 CTTTTACTAC
Statistics
Matches: 73, Mismatches: 0, Indels: 18
0.80 0.00 0.20
Matches are distributed among these distances:
35 32 0.44
36 2 0.03
38 1 0.01
39 3 0.04
40 3 0.04
41 1 0.01
43 2 0.03
44 29 0.40
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (35 bp):
CTTAGTTTAATTACCTAGAATTAAACTAATCTCTT
Found at i:51673 original size:28 final size:28
Alignment explanation
Indices: 51599--51696 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 28
51589 AGTGAGCTCA
* * *
51599 AAATGACCAAAACGCCCCCTGGATGTGC
1 AAATGACCAAAATGCCCCTTGAATGTGC
* *
51627 AAAATGACTAAAAT-ACCCTTGAATGTGC
1 -AAATGACCAAAATGCCCCTTGAATGTGC
* * * *
51655 AAATGACCAAAATGCCCCTAGATTTTGA
1 AAATGACCAAAATGCCCCTTGAATGTGC
51683 AAATGACCCAAAAT
1 AAATGA-CCAAAAT
51697 TCCCTTAGAT
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
27 12 0.21
28 26 0.46
29 18 0.32
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.20
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTTGAATGTGC
Found at i:55168 original size:380 final size:380
Alignment explanation
Indices: 54467--55177 Score: 1278
Period size: 380 Copynumber: 1.9 Consensus size: 380
54457 TATCTGTTGA
54467 TTTCTTTTATTTCCTTTTGGATTTGGATTTGCCCTTGTTAGTAATACGTGTTTATGCTTCCGCTG
1 TTTCTTTTATTTCCTTTTGGATTTGGATTTGCCCTTGTTAGTAATACGTGTTTATGCTTCCGCTG
54532 AGAGGAAATTCTTGACTTAAATGTTTATTCCCTTGGATTTGAGCCTGAGGCTCTAATGTTAATGT
66 AGAGGAAATTCTTGACTTAAATGTTTATTCCCTTGGATTTGAGCCTGAGGCTCTAATGTTAATGT
*
54597 TTGGATTTCGGAACTATGTTTTACATCTTATCTGCATTTGAATTGTCTTTATTTTTGTTTTGTTT
131 TTGGATTTCGGAACTATGTCTTACATCTTATCTGCATTTGAATTGTCTTTATTTTTGTTTTGTTT
*
54662 TGGCCTTGATACTGACGCTTCACGAGACCTCATGTGCATGTGACACACGGCACGTATTACGAGGT
196 TGGCCTTGATACTGACGCTTCACGAGACCTCATGTGCATGTGACACACGGCACGTATTACGAGAT
* * *
54727 ATCGTGGCGGTTGTCTGTGCTCGATCCCGAGTTGGGGCGTGACATGGTAACTAATCATCATCATC
261 ATCGTGGCGGTTGTCCGTGCTCGATCCCGAATCGGGGCGTGACATGGTAACTAATCATCATCATC
54792 ACTTGTTATTTCCTTGTTAGTAATACTTGTTTATGCTTCCGCTGGGAGGAAATTC
326 ACTTGTTATTTCCTTGTTAGTAATACTTGTTTATGCTTCCGCTGGGAGGAAATTC
* *
54847 TTTCTTTTATTTCCTTTTGGATTTGGATTTGCCCTTGTTAGTAATACTTGTTTATGCTTTCGCTG
1 TTTCTTTTATTTCCTTTTGGATTTGGATTTGCCCTTGTTAGTAATACGTGTTTATGCTTCCGCTG
54912 AGAGGAAATTCTTGACTTAAATGTTTATTCCCTTGGATTTGAGCCTGAGGCTCTAATGTTAATGT
66 AGAGGAAATTCTTGACTTAAATGTTTATTCCCTTGGATTTGAGCCTGAGGCTCTAATGTTAATGT
*
54977 TTGGATTTCGGAACTATGTCTTACATCTTATCTGCATTTGAATTTTCTTTATTTTTGTTTTGTTT
131 TTGGATTTCGGAACTATGTCTTACATCTTATCTGCATTTGAATTGTCTTTATTTTTGTTTTGTTT
* * * * * **
55042 TGGCCTTGATAGTGACGCTTCGCGAGACCTCGTGTGCGTGTGACGCGTGGCACGTATTACGAGAT
196 TGGCCTTGATACTGACGCTTCACGAGACCTCATGTGCATGTGACACACGGCACGTATTACGAGAT
*
55107 ATTGTGGCGGTTGTCCGTGCTCGATCCCGAATCGGGGCGTGACATGGTAACTAATCATCATCATC
261 ATCGTGGCGGTTGTCCGTGCTCGATCCCGAATCGGGGCGTGACATGGTAACTAATCATCATCATC
55172 ACTTGT
326 ACTTGT
55178 CGCCACATCC
Statistics
Matches: 315, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
380 315 1.00
ACGTcount: A:0.19, C:0.18, G:0.22, T:0.41
Consensus pattern (380 bp):
TTTCTTTTATTTCCTTTTGGATTTGGATTTGCCCTTGTTAGTAATACGTGTTTATGCTTCCGCTG
AGAGGAAATTCTTGACTTAAATGTTTATTCCCTTGGATTTGAGCCTGAGGCTCTAATGTTAATGT
TTGGATTTCGGAACTATGTCTTACATCTTATCTGCATTTGAATTGTCTTTATTTTTGTTTTGTTT
TGGCCTTGATACTGACGCTTCACGAGACCTCATGTGCATGTGACACACGGCACGTATTACGAGAT
ATCGTGGCGGTTGTCCGTGCTCGATCCCGAATCGGGGCGTGACATGGTAACTAATCATCATCATC
ACTTGTTATTTCCTTGTTAGTAATACTTGTTTATGCTTCCGCTGGGAGGAAATTC
Found at i:61721 original size:26 final size:26
Alignment explanation
Indices: 61692--61744 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
61682 TATATAAGGG
*
61692 TTTGATCATCTCTTGTAAACAGAAGT
1 TTTGATCATCACTTGTAAACAGAAGT
61718 TTTGATCATCACTTGTAAACAGAAGT
1 TTTGATCATCACTTGTAAACAGAAGT
61744 T
1 T
61745 AAGTTCATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (26 bp):
TTTGATCATCACTTGTAAACAGAAGT
Found at i:61752 original size:26 final size:26
Alignment explanation
Indices: 61695--61754 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
61685 ATAAGGGTTT
* **
61695 GATCATCTCTTGTAAACAGAAGTTTT
1 GATCATCACTTGTAAACAGAAGTTAA
61721 GATCATCACTTGTAAACAGAAGTTAA
1 GATCATCACTTGTAAACAGAAGTTAA
*
61747 GTTCATCA
1 GATCATCA
61755 ATCAAATTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (26 bp):
GATCATCACTTGTAAACAGAAGTTAA
Found at i:64803 original size:17 final size:17
Alignment explanation
Indices: 64781--64813 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
64771 TTTTCTGGAT
64781 ATTTAT-ATTATTAATTA
1 ATTTATAATT-TTAATTA
64798 ATTTATAATTTTAATT
1 ATTTATAATTTTAATT
64814 GATGTAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATAATTTTAATTA
Found at i:66791 original size:30 final size:30
Alignment explanation
Indices: 66757--66820 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
66747 TAATTAAATA
66757 AAAATAGAGTTTTTAGTTGAGTAAAATAGT
1 AAAATAGAGTTTTTAGTTGAGTAAAATAGT
66787 AAAATAGAGTTTTTAGTTGAGTAAAATAGT
1 AAAATAGAGTTTTTAGTTGAGTAAAATAGT
66817 AAAA
1 AAAA
66821 AGGTAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (30 bp):
AAAATAGAGTTTTTAGTTGAGTAAAATAGT
Found at i:67206 original size:9 final size:9
Alignment explanation
Indices: 67192--67261 Score: 58
Period size: 9 Copynumber: 8.2 Consensus size: 9
67182 CCAACAAACA
67192 AACCCAGTG
1 AACCCAGTG
67201 AACCCAGTG
1 AACCCAGTG
** *
67210 AAATC--TC
1 AACCCAGTG
67217 AACCCAGTG
1 AACCCAGTG
67226 AACCCAGTG
1 AACCCAGTG
** *
67235 AAATC--TC
1 AACCCAGTG
67242 AACCCAGTG
1 AACCCAGTG
67251 AACCCAGTG
1 AACCCAGTG
67260 AA
1 AA
67262 ATCTCATTAC
Statistics
Matches: 45, Mismatches: 12, Indels: 8
0.69 0.18 0.12
Matches are distributed among these distances:
7 8 0.18
9 37 0.82
ACGTcount: A:0.37, C:0.31, G:0.17, T:0.14
Consensus pattern (9 bp):
AACCCAGTG
Found at i:67220 original size:25 final size:25
Alignment explanation
Indices: 67192--67267 Score: 152
Period size: 25 Copynumber: 3.0 Consensus size: 25
67182 CCAACAAACA
67192 AACCCAGTGAACCCAGTGAAATCTC
1 AACCCAGTGAACCCAGTGAAATCTC
67217 AACCCAGTGAACCCAGTGAAATCTC
1 AACCCAGTGAACCCAGTGAAATCTC
67242 AACCCAGTGAACCCAGTGAAATCTC
1 AACCCAGTGAACCCAGTGAAATCTC
67267 A
1 A
67268 TTACATTTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 51 1.00
ACGTcount: A:0.37, C:0.32, G:0.16, T:0.16
Consensus pattern (25 bp):
AACCCAGTGAACCCAGTGAAATCTC
Found at i:67222 original size:16 final size:16
Alignment explanation
Indices: 67201--67252 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 16
67191 AAACCCAGTG
67201 AACCCAGTGAAATCTC
1 AACCCAGTGAAATCTC
67217 AACCCAGTG-------
1 AACCCAGTGAAATCTC
67226 AACCCAGTGAAATCTC
1 AACCCAGTGAAATCTC
67242 AACCCAGTGAA
1 AACCCAGTGAA
67253 CCCAGTGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 14
0.67 0.00 0.33
Matches are distributed among these distances:
9 9 0.31
16 20 0.69
ACGTcount: A:0.38, C:0.31, G:0.15, T:0.15
Consensus pattern (16 bp):
AACCCAGTGAAATCTC
Found at i:69247 original size:62 final size:62
Alignment explanation
Indices: 69181--69364 Score: 359
Period size: 62 Copynumber: 3.0 Consensus size: 62
69171 TTGAGCGTGG
69181 GCCATTTGGGCTAGGCCCGAAATATATCTGGATTCCTGGGAATTGGTAAATCTGATTCTGCC
1 GCCATTTGGGCTAGGCCCGAAATATATCTGGATTCCTGGGAATTGGTAAATCTGATTCTGCC
*
69243 GCCATTTGGGCTAGGCCCGAAATATATCTGGATTCCTGGGAATCGGTAAATCTGATTCTGCC
1 GCCATTTGGGCTAGGCCCGAAATATATCTGGATTCCTGGGAATTGGTAAATCTGATTCTGCC
69305 GCCATTTGGGCTAGGCCCGAAATATATCTGGATTCCTGGGAATTGGTAAATCTGATTCTG
1 GCCATTTGGGCTAGGCCCGAAATATATCTGGATTCCTGGGAATTGGTAAATCTGATTCTG
69365 ACGCATGAAC
Statistics
Matches: 120, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 120 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (62 bp):
GCCATTTGGGCTAGGCCCGAAATATATCTGGATTCCTGGGAATTGGTAAATCTGATTCTGCC
Found at i:76622 original size:17 final size:17
Alignment explanation
Indices: 76600--76652 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
76590 CCATGTAAAA
76600 TTATTAATTTAGAGAGG
1 TTATTAATTTAGAGAGG
**
76617 TTATTAATTTATCGA-G
1 TTATTAATTTAGAGAGG
76633 -TATTAATTTATGAG-GG
1 TTATTAATTTA-GAGAGG
76649 TTAT
1 TTAT
76653 ACTGGTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
15 10 0.34
16 3 0.10
17 16 0.55
ACGTcount: A:0.32, C:0.02, G:0.19, T:0.47
Consensus pattern (17 bp):
TTATTAATTTAGAGAGG
Found at i:76622 original size:76 final size:76
Alignment explanation
Indices: 76496--76643 Score: 251
Period size: 76 Copynumber: 1.9 Consensus size: 76
76486 AAACCTCTAT
* * *
76496 AAATTAATAATGTTAGGACCGTGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTGTT
1 AAATTAATAATATTAGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
76561 AATTTATATGG
66 AATTTATATGG
* *
76572 AAATTAATAATATTGGGACCATGTAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
1 AAATTAATAATATTAGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
76637 AATTTAT
66 AATTTAT
76644 GAGGGTTATA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.39, C:0.04, G:0.16, T:0.41
Consensus pattern (76 bp):
AAATTAATAATATTAGGACCATGAAAAATTATTAATTTAGAGAGGTTATTAATTTATCGAGTATT
AATTTATATGG
Found at i:80874 original size:46 final size:46
Alignment explanation
Indices: 80807--80898 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
80797 TACTAGAAGT
**
80807 CTAGAATGAACCAAAGTAGGTCAAATTTTCAGATTATTTAAAAAAG
1 CTAGAATGAACCAAAGTAGGTCAAATCCTCAGATTATTTAAAAAAG
*
80853 CTAGAATGAACCAAAGTAGGTCAAATCCTCAGGTTATTTAAAAAAG
1 CTAGAATGAACCAAAGTAGGTCAAATCCTCAGATTATTTAAAAAAG
80899 AAAGACAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (46 bp):
CTAGAATGAACCAAAGTAGGTCAAATCCTCAGATTATTTAAAAAAG
Found at i:97318 original size:4 final size:4
Alignment explanation
Indices: 97309--97333 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
97299 TTAGAGACTC
97309 CAAT CAAT CAAT CAAT CAAT CAAT C
1 CAAT CAAT CAAT CAAT CAAT CAAT C
97334 TAGACAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (4 bp):
CAAT
Found at i:103692 original size:2 final size:2
Alignment explanation
Indices: 103687--103723 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
103677 AGACACACAT
103687 TA TA TA -A TA TA TA -A 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 TA TA TA TA T
103724 CTCCAATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:104586 original size:40 final size:40
Alignment explanation
Indices: 104515--104593 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
104505 AAATCCTAAG
*
104515 GATTTTTCAAAACCTTGTACGGTGACGGATTTTCAAGAGA
1 GATTTTTCAAAACCTTGTACGGTAACGGATTTTCAAGAGA
*
104555 GATTTTTCAAAAACCTTTTAC-GTAATC-GATTTTCAAGAG
1 GATTTTTC-AAAACCTTGTACGGTAA-CGGATTTTCAAGAG
104594 GGTTTTGGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 23 0.66
41 12 0.34
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (40 bp):
GATTTTTCAAAACCTTGTACGGTAACGGATTTTCAAGAGA
Found at i:104731 original size:3 final size:3
Alignment explanation
Indices: 104723--104787 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
104713 AATATTTAAA
104723 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
104771 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
104788 GTTCATTTAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:105388 original size:2 final size:2
Alignment explanation
Indices: 105381--105407 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
105371 CTATTAATAG
105381 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
105408 TTCTCTAACA
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:108629 original size:16 final size:16
Alignment explanation
Indices: 108608--108639 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
108598 ATTGAATTAT
108608 AGATCTTGGACTAAAC
1 AGATCTTGGACTAAAC
108624 AGATCTTGGACTAAAC
1 AGATCTTGGACTAAAC
108640 GCATAACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (16 bp):
AGATCTTGGACTAAAC
Found at i:109623 original size:54 final size:54
Alignment explanation
Indices: 109499--110100 Score: 566
Period size: 54 Copynumber: 11.2 Consensus size: 54
109489 ACGGAAACCT
* * *
109499 TTCTTGGAGTGACCATACTGGATCAAAT-TGGAGATCAACTCTGATCATCGAAAAC
1 TTCTTGGAATGACCACACTGGATC--ATCTGGAGATCAACTCTGATCTTCGAAAAC
* * *
109554 TTCTT-GAAGGACCACACTGGATCATCTGGAGATCAACTCTAATTTTCGAAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAAC
* * * * * * *
109607 TTCTTGAAACGACCACACCGGATCATCTGAAGATCAACTTTGATCTTCTAGAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAAC
* * *
109661 TTCTTGAAACGACCACACCGGATCATCTGGAGATCAACTCTGATCTTCGAAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAAC
** * * * * *
109715 TTCTCAGAA-GAAACGCACTGGAACATCTGGACATCAACTCTGAT-TATCAAAAAC
1 TTCTTGGAATG-ACCACACTGGATCATCTGGAGATCAACTCTGATCT-TCGAAAAC
* * *
109769 TTCTTGGAATGACCACACCGGATCATCT-GAGGATCAACTCTGACCGTT-AAAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGA-GATCAACTCTGATC-TTCGAAAAC
* *
109823 TTCTTGGAATGACCGCACTGGATCATCT-GAGGATCAACTCTGACCATT-GAAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGA-GATCAACTCTGATC-TTCGAAAAC
* * * *
109877 TTCTTGAAATGACCGCACTGGATCATCT-GAGGATCAAATCTGATCATT-AAAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGA-GATCAACTCTGATC-TTCGAAAAC
* * * * *
109931 TTTTTGGAATGACCGCACTAGATCAATCTGG-GATCAACTCTAATCATCGAAAAC
1 TTCTTGGAATGACCACACTGGATC-ATCTGGAGATCAACTCTGATCTTCGAAAAC
* * * * * *
109985 TTCTTGGAATGACCGCACCGGACCATTTGG-GATCAACTTTGGTCATT-GAAAAC
1 TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATC-TTCGAAAAC
* * * *
110038 TTCTTGGAATGACTACACTAGATCAATCT-GAGATCAACTCTGATCATCAAAAAC
1 TTCTTGGAATGACCACACTGGATC-ATCTGGAGATCAACTCTGATCTTCGAAAAC
110092 TTCTTGGAA
1 TTCTTGGAA
110101 CTTCCACACA
Statistics
Matches: 462, Mismatches: 70, Indels: 31
0.82 0.12 0.06
Matches are distributed among these distances:
52 2 0.00
53 77 0.17
54 370 0.80
55 11 0.02
56 2 0.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (54 bp):
TTCTTGGAATGACCACACTGGATCATCTGGAGATCAACTCTGATCTTCGAAAAC
Found at i:111605 original size:20 final size:22
Alignment explanation
Indices: 111573--111618 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
111563 CTTTCCTCCG
111573 TCTTTTGCTTTTTCAACT-TTT
1 TCTTTTGCTTTTTCAACTCTTT
*
111594 TCTTTT-CTTTTTCAATTCTTT
1 TCTTTTGCTTTTTCAACTCTTT
111615 TCTT
1 TCTT
111619 CATTTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.09, C:0.20, G:0.02, T:0.70
Consensus pattern (22 bp):
TCTTTTGCTTTTTCAACTCTTT
Found at i:115167 original size:16 final size:16
Alignment explanation
Indices: 115146--115177 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
115136 ATTGAATTAT
115146 AGATCTTGGACTAAAC
1 AGATCTTGGACTAAAC
115162 AGATCTTGGACTAAAC
1 AGATCTTGGACTAAAC
115178 GCATAACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (16 bp):
AGATCTTGGACTAAAC
Found at i:118878 original size:15 final size:15
Alignment explanation
Indices: 118858--118887 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
118848 ATTAGGCTGC
*
118858 CACGATACACGATAT
1 CACGATACACAATAT
118873 CACGATACACAATAT
1 CACGATACACAATAT
118888 TTCAACCGTA
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:0.43, C:0.27, G:0.10, T:0.20
Consensus pattern (15 bp):
CACGATACACAATAT
Found at i:120689 original size:5 final size:5
Alignment explanation
Indices: 120685--120718 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
120675 AAAAAACTTC
*
120685 CCTTC CCTTT CCTTT CCTTT CCTTT CCTTT CCTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT CCTT
120719 CAATGATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (5 bp):
CCTTT
Found at i:121817 original size:24 final size:24
Alignment explanation
Indices: 121785--121834 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
121775 GCTATTAATC
121785 GGAGATGGGGTGGTAGAAAAAAGA
1 GGAGATGGGGTGGTAGAAAAAAGA
*
121809 GGAGATGGGGTGGTAGAAAAAGGA
1 GGAGATGGGGTGGTAGAAAAAAGA
121833 GG
1 GG
121835 CTGCAAATGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.00, G:0.50, T:0.12
Consensus pattern (24 bp):
GGAGATGGGGTGGTAGAAAAAAGA
Found at i:122879 original size:2 final size:2
Alignment explanation
Indices: 122872--122909 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
122862 AACTAAAAGG
122872 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
122910 CACACACATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.