Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 105 of 182
Found at i:34168227 original size:20 final size:20
Alignment explanation
Indices: 34168084--34168214 Score: 63
Period size: 20 Copynumber: 6.2 Consensus size: 20
34168074 GACCTCTCCC
*
34168084 TTTTCAATTTTTTTATTTTTA
1 TTTT-AATTATTTTATTTTTA
*
34168105 TTTCAATT-TCTTTATTTTTA
1 TTTTAATTAT-TTTATTTTTA
34168125 TTAGTATTAATTATTTGTATTTTTA
1 -T--T-TTAATTATTT-TATTTTTA
* **
34168150 TTTTATGTTATTTTATTATTCC
1 TTTTA-ATTATTTTATT-TTTA
* *
34168172 TTGTT--TTATTTTATTATCA
1 TT-TTAATTATTTTATTTTTA
*
34168191 TTATTATTTATTTTA-TTTTA
1 TT-TTAATTATTTTATTTTTA
34168211 TTTT
1 TTTT
34168215 TATTTTAGTT
Statistics
Matches: 88, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.10
20 29 0.33
21 19 0.22
22 11 0.12
23 3 0.03
24 8 0.09
25 9 0.10
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTAATTATTTTATTTTTA
Found at i:34177650 original size:16 final size:16
Alignment explanation
Indices: 34177631--34177677 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
34177621 AAAATTCAAT
34177631 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
34177647 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
34177663 AAATAAAATAATATA
1 AAATAAAA-AATATA
34177678 AATGCTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:34184191 original size:18 final size:18
Alignment explanation
Indices: 34184141--34184191 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 18
34184131 ATGTGCTTTA
*
34184141 TTTATTTGTTAATTTTATGT
1 TTTATTT-TT-ATTTAATGT
34184161 TTTATTTTCTATTTAAT-T
1 TTTATTTT-TATTTAATGT
34184179 TTTATTTATTATT
1 TTTATTT-TTATT
34184192 ATTATCTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 12 0.43
19 8 0.29
20 8 0.29
ACGTcount: A:0.22, C:0.02, G:0.04, T:0.73
Consensus pattern (18 bp):
TTTATTTTTATTTAATGT
Found at i:34192741 original size:13 final size:13
Alignment explanation
Indices: 34192723--34192747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34192713 AATTCCTCAT
34192723 TAAATCATGTAAA
1 TAAATCATGTAAA
34192736 TAAATCATGTAA
1 TAAATCATGTAA
34192748 TACAATTTTA
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:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
TAAATCATGTAAA
Found at i:34194800 original size:20 final size:20
Alignment explanation
Indices: 34194754--34194800 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
34194744 TTTTTTATTG
*
34194754 ATGTTTGCTATTTTTTACCA
1 ATGTTTGCTATTTTTGACCA
**
34194774 ACATTTGCTATTTTTGACCA
1 ATGTTTGCTATTTTTGACCA
34194794 ATGTTTG
1 ATGTTTG
34194801 TAATCTTTGG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.15, G:0.13, T:0.51
Consensus pattern (20 bp):
ATGTTTGCTATTTTTGACCA
Found at i:34198189 original size:15 final size:15
Alignment explanation
Indices: 34198169--34198197 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
34198159 GAAGTTATTG
34198169 GTTGGATTTGAATTA
1 GTTGGATTTGAATTA
34198184 GTTGGATTTGAATT
1 GTTGGATTTGAATT
34198198 TACAGGACAA
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:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (15 bp):
GTTGGATTTGAATTA
Found at i:34204132 original size:24 final size:26
Alignment explanation
Indices: 34204100--34204148 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 26
34204090 TGGATCTAAT
34204100 ATTATTAAATA-AAAAATA-TATAAA
1 ATTATTAAATATAAAAATAGTATAAA
*
34204124 ATTATTAAATATTAAAATAGTATAA
1 ATTATTAAATATAAAAATAGTATAA
34204149 TATAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.50
25 6 0.27
26 5 0.23
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
ATTATTAAATATAAAAATAGTATAAA
Found at i:34213035 original size:20 final size:20
Alignment explanation
Indices: 34213010--34213051 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
34213000 TGCCAGCTAC
*
34213010 AACAAGAAGGAA-ATGAAAGA
1 AACAAGAA-GAAGAAGAAAGA
34213030 AACAAGAAGAAGAAGAAAGA
1 AACAAGAAGAAGAAGAAAGA
34213050 AA
1 AA
34213052 GGCGTGTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.69, C:0.05, G:0.24, T:0.02
Consensus pattern (20 bp):
AACAAGAAGAAGAAGAAAGA
Found at i:34213876 original size:15 final size:16
Alignment explanation
Indices: 34213858--34213895 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
34213848 AAATAAAAAT
*
34213858 ATATAAAAATATTA-A
1 ATATAAAAATAATATA
*
34213873 ATATTAAAATAATATA
1 ATATAAAAATAATATA
34213889 ATATAAA
1 ATATAAA
34213896 TATTTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAAAATAATATA
Found at i:34213891 original size:16 final size:15
Alignment explanation
Indices: 34213848--34213895 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
34213838 AAAATTCAAT
*
34213848 AAATAAAAATATATAA
1 AAATAATAA-ATATAA
* *
34213864 AAATATTAAATATTA
1 AAATAATAAATATAA
34213879 AAATAATATAATATAA
1 AAATAATA-AATATAA
34213895 A
1 A
34213896 TATTTTTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 12 0.46
16 14 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAATAAATATAA
Found at i:34214626 original size:21 final size:22
Alignment explanation
Indices: 34214602--34214647 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
34214592 CGCACGATCC
34214602 TGTATCT-CAAACACACGCCCG
1 TGTATCTACAAACACACGCCCG
** *
34214623 TGTATCTACATCCACACGCCTG
1 TGTATCTACAAACACACGCCCG
34214645 TGT
1 TGT
34214648 CTTTGACAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (22 bp):
TGTATCTACAAACACACGCCCG
Found at i:34217375 original size:24 final size:24
Alignment explanation
Indices: 34217314--34217376 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
34217304 TAGAGTAATA
* *
34217314 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
34217338 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
34217362 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
34217377 GATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:34225549 original size:16 final size:16
Alignment explanation
Indices: 34225528--34225562 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
34225518 AGTCCTCGTA
34225528 ATTTTA-TCACTTTAAC
1 ATTTTAGTC-CTTTAAC
34225544 ATTTTAGTCCTTTAAC
1 ATTTTAGTCCTTTAAC
34225560 ATT
1 ATT
34225563 AAAATTACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 16 0.89
17 2 0.11
ACGTcount: A:0.29, C:0.17, G:0.03, T:0.51
Consensus pattern (16 bp):
ATTTTAGTCCTTTAAC
Found at i:34226005 original size:21 final size:21
Alignment explanation
Indices: 34225963--34226006 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
34225953 CTATGTACTT
* *
34225963 CTACCGATACATGCATGAAAA
1 CTACCGAAACAAGCATGAAAA
* *
34225984 CTACCGAAACAAGTATGCAAA
1 CTACCGAAACAAGCATGAAAA
34226005 CT
1 CT
34226007 TCTAAAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.25, G:0.14, T:0.18
Consensus pattern (21 bp):
CTACCGAAACAAGCATGAAAA
Found at i:34226550 original size:24 final size:24
Alignment explanation
Indices: 34226517--34226580 Score: 110
Period size: 24 Copynumber: 2.7 Consensus size: 24
34226507 CCAAACAAAT
*
34226517 TTAGCTCTTACGAGCCTGGAGAGG
1 TTAGCCCTTACGAGCCTGGAGAGG
*
34226541 TTAGCCCTTACGAGCCTGGATAGG
1 TTAGCCCTTACGAGCCTGGAGAGG
34226565 TTAGCCCTTACGAGCC
1 TTAGCCCTTACGAGCC
34226581 AAAAAAAAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (24 bp):
TTAGCCCTTACGAGCCTGGAGAGG
Found at i:34227667 original size:21 final size:21
Alignment explanation
Indices: 34227638--34227687 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
34227628 TTAAAACTTT
* *
34227638 CATTATTAAGTTTAATTAATC
1 CATTTTTAACTTTAATTAATC
*
34227659 CCTTTTTAACTTTAATTAATC
1 CATTTTTAACTTTAATTAATC
34227680 CATTTTTA
1 CATTTTTA
34227688 TAATTCACTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (21 bp):
CATTTTTAACTTTAATTAATC
Found at i:34230572 original size:19 final size:19
Alignment explanation
Indices: 34230548--34230606 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
34230538 GGAATAAACG
*
34230548 ATATTGGCTCGTAGGAGCA
1 ATATTGGCTCGTAAGAGCA
* *
34230567 ATATTGGCTCCTAAGAGCG
1 ATATTGGCTCGTAAGAGCA
*
34230586 ATACTGGCTCGTAAGAGCA
1 ATATTGGCTCGTAAGAGCA
34230605 AT
1 AT
34230607 TTACTAACTG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (19 bp):
ATATTGGCTCGTAAGAGCA
Found at i:34230623 original size:26 final size:26
Alignment explanation
Indices: 34230588--34230640 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
34230578 TAAGAGCGAT
34230588 ACTGGCTCGTAAGAGC-AATTTACTA
1 ACTGGCTCGTAAGAGCAAATTTACTA
*
34230613 ACTGAGCTCGTATGAGCTAAATTTACTA
1 ACTG-GCTCGTAAGAGC-AAATTTACTA
34230641 GGAGAGTCGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 4 0.17
26 11 0.46
28 9 0.38
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (26 bp):
ACTGGCTCGTAAGAGCAAATTTACTA
Found at i:34233925 original size:140 final size:142
Alignment explanation
Indices: 34233592--34234226 Score: 601
Period size: 140 Copynumber: 4.4 Consensus size: 142
34233582 TGATTTAAAC
* * * *
34233592 AAAATCACTATTTTACTTTAAAGTCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCTAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * * *
34233657 GTTTAAAAATTTAAACTTTTCACTTTAAAATCACTAAAAACAAATTTTTATTTTTTAAAAATCTA
66 ATTTAAAAATTTAAACTTTT-TCTTT-AAA--A-T---AACTAATTTTTA-TTTTT-AAAATATA
*
34233722 AA----CTTTCTTTTTCTAATG
121 AACTTTCTTTCTTTTTTTAATG
* *
34233740 AAAATCACTA-CTTATCTTAAAAATCTAAACTTTTATTTCGAAATAGTGTAAAAAAATCAAAACT
1 AAAATCACTATTTTA-CTTAAAAATCTAAATTTTTATTTCGAAATAGT-TAAAAAAATCAAAACT
34233804 TTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAA-TTTT-TTTTT-AAATATAAACTTTCT
64 TTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAATTTTTATTTTTAAAATATAAACTTTCT
34233866 TTCTTTTTTTAATG
129 TTCTTTTTTTAATG
* * * *
34233880 AAAATCACTATTTTACTTAAAAATCCAAATTTTTTTTTCAAAATAGTTAAAAAAAATCAAAACCT
1 AAAATCACTATTTTACTTAAAAATCTAAATTTTTATTTCGAAATAGTT-AAAAAAATCAAAACTT
* *
34233945 TATTTAAAAGTTT-AATTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTAAAAATATA
65 TATTTAAAAATTTAAACTTTTTCTTTAAAATAACT--------AATTTTTATTTTT-AAAATATA
*
34234009 AACTTTC--TCCTTTTTTAATG
121 AACTTTCTTTCTTTTTTTAATG
* *
34234029 AAAATCACTACTTT-CTTAAAAATCTAAATTTTTATTTCGAAATAATTAAAAAAATCAAAACTTT
1 AAAATCACTATTTTACTTAAAAATCTAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * * *
34234093 GTTTAAAAAATTAAAC-TTTTC--TAAAA-AACAAATTTTTATTTTTAAAAATCTAAA---T-TT
66 ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAATTTTTATTTTT-AAAATATAAACTTTCTT
*
34234150 TCTATTTTTTAAAG
130 TCT-TTTTTTAATG
* * ** * *
34234164 CAAGTCACTATTTTACTTAAAAATC-AAGGCTATTATTTCGAAATTGTTTAAAAAAAATCAAAA
1 AAAATCACTATTTTACTTAAAAATCTAA-ATTTTTATTTCGAAATAG-TT-AAAAAAATCAAAA
34234227 TTTTTCCCAA
Statistics
Matches: 419, Mismatches: 40, Indels: 66
0.80 0.08 0.13
Matches are distributed among these distances:
133 1 0.00
134 2 0.00
135 22 0.05
136 54 0.13
137 2 0.00
138 18 0.04
139 21 0.05
140 84 0.20
141 8 0.02
144 4 0.01
145 6 0.01
147 38 0.09
148 78 0.19
149 67 0.16
151 14 0.03
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (142 bp):
AAAATCACTATTTTACTTAAAAATCTAAATTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
ATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAATTTTTATTTTTAAAATATAAACTTTCTTT
CTTTTTTTAATG
Found at i:34233986 original size:288 final size:282
Alignment explanation
Indices: 34233585--34234226 Score: 821
Period size: 288 Copynumber: 2.2 Consensus size: 282
34233575 ATACTTTTGA
* * * *
34233585 TTTAAACAAAATCACTATTTTACTTTAAAGTCAAAACTTTTATTTCGAAATAGTTAAAAAAATCA
1 TTTAAAGAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCAAAATAGTTAAAAAAATCA
* * *
34233650 AAACTTTGTTTAAAAATTTAAACTTTTCACTTTAAAATCACTAAAAACAAATTTTTATTTTTTAA
66 AAACCTTATTTAAAAATTTAAACTTTTCACTTTAAAATAACTAAAAACAAATTTTTA-TTTTTAA
*
34233715 AAATCTAAACTTTCT-TTTTCTAATGAAAATCACTACTTATCTTAAAAATCTAAACTTTTATTTC
130 AAATATAAACTTTCTCTTTTCTAATGAAAATCACTACTT-TCTTAAAAATCTAAACTTTTATTTC
* * *
34233779 GAAATAGTGTAAAAAAATCAAAACTTTATTTAAAAATTTAAACTTTTTCTTTAAAATAACTAA-T
194 GAAATAAT-TAAAAAAATCAAAACTTTATTTAAAAAATTAAAC-TTTTC--TAAAA-AACAAATT
34233843 TTT-TTTTT-AAATATAAACTTTCTTTCT-TTT
254 TTTATTTTTAAAATATAAA---T-TTTCTATTT
* * * *
34233873 TTTAATGAAAATCACTATTTTACTTAAAAATCCAAATTTTTTTTTCAAAATAGTTAAAAAAAATC
1 TTTAAAGAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCAAAATAGTT-AAAAAAATC
* **
34233938 AAAACCTTATTTAAAAGTTT-AA-TTTTTTCTTTAAAATAACTAAAAAACAAATTTTTATTTTTA
65 AAAACCTTATTTAAAAATTTAAACTTTTCACTTTAAAATAACT-AAAAACAAATTTTTATTTTTA
* *
34234001 AAAATATAAACTTTCTCCTTTTTTAATGAAAATCACTACTTTCTTAAAAATCTAAATTTTTATTT
129 AAAATATAAACTTTCT-CTTTTCTAATGAAAATCACTACTTTCTTAAAAATCTAAACTTTTATTT
*
34234066 CGAAATAATTAAAAAAATCAAAACTTTGTTTAAAAAATTAAACTTTTCTAAAAAACAAATTTTTA
193 CGAAATAATTAAAAAAATCAAAACTTTATTTAAAAAATTAAACTTTTCTAAAAAACAAATTTTTA
*
34234131 TTTTTAAAAATCTAAATTTTCTATTT
258 TTTTT-AAAATATAAATTTTCTATTT
* * ** * * *
34234157 TTTAAAGCAAGTCACTATTTTACTTAAAAATCAAGGCTATTATTTCGAAATTGTTTAAAAAAAAT
1 TTTAAAGAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCAAAATAG-TT-AAAAAAAT
34234222 CAAAA
64 CAAAA
34234227 TTTTTCCCAA
Statistics
Matches: 311, Mismatches: 33, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
283 10 0.03
284 55 0.18
285 21 0.07
286 5 0.02
287 77 0.25
288 95 0.31
289 48 0.15
ACGTcount: A:0.44, C:0.11, G:0.03, T:0.42
Consensus pattern (282 bp):
TTTAAAGAAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCAAAATAGTTAAAAAAATCA
AAACCTTATTTAAAAATTTAAACTTTTCACTTTAAAATAACTAAAAACAAATTTTTATTTTTAAA
AATATAAACTTTCTCTTTTCTAATGAAAATCACTACTTTCTTAAAAATCTAAACTTTTATTTCGA
AATAATTAAAAAAATCAAAACTTTATTTAAAAAATTAAACTTTTCTAAAAAACAAATTTTTATTT
TTAAAATATAAATTTTCTATTT
Found at i:34234102 original size:20 final size:19
Alignment explanation
Indices: 34234077--34234124 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
34234067 GAAATAATTA
*
34234077 AAAAAATCAAAACTTTGTTT
1 AAAAAATCAAAACTTT-TCT
*
34234097 AAAAAAT-TAAACTTTTCT
1 AAAAAATCAAAACTTTTCT
34234115 AAAAAA-CAAA
1 AAAAAATCAAA
34234125 TTTTTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 10 0.42
19 7 0.29
20 7 0.29
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAAATCAAAACTTTTCT
Found at i:34234134 original size:22 final size:23
Alignment explanation
Indices: 34234109--34234158 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
34234099 AAAATTAAAC
34234109 TTTTCTAAAAAAC-AAATTTT-TA
1 TTTT-TAAAAAACTAAATTTTCTA
*
34234131 TTTTTAAAAATCTAAATTTTCTA
1 TTTTTAAAAAACTAAATTTTCTA
34234154 TTTTT
1 TTTTT
34234159 TAAAGCAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 7 0.28
22 11 0.44
23 7 0.28
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTTAAAAAACTAAATTTTCTA
Found at i:34234239 original size:136 final size:136
Alignment explanation
Indices: 34233977--34234226 Score: 333
Period size: 136 Copynumber: 1.8 Consensus size: 136
34233967 TTTAAAATAA
* *
34233977 CTAAAAAACAAATTTTTATTTTTAAAAATATAAACTTTCTCCTTTTTTAATGAAAATCACTACTT
1 CTAAAAAACAAATTTTTATTTTTAAAAATATAAACTTTCTCATTTTTTAAAGAAAATCACTACTT
* * *
34234042 TCTTAAAAATCTAAATTTTTATTTCGAAATAATTAAAAAAATCAAAACTTTGTTTAAAAAATTAA
66 TCTTAAAAATCTAAACTATTATTTCGAAATAATTAAAAAAATCAAAACTTTGTTCAAAAAATTAA
34234107 ACTTTT
131 ACTTTT
* * * * *
34234113 CTAAAAAACAAATTTTTATTTTTAAAAATCTAAATTTTCT-ATTTTTTAAAGCAAGTCACTATTT
1 CTAAAAAACAAATTTTTATTTTTAAAAATATAAACTTTCTCATTTTTTAAAGAAAATCACTACTT
* **
34234177 TACTTAAAAATC-AAGGCTATTATTTCGAAATTGTTTAAAAAAAATCAAAA
66 T-CTTAAAAATCTAA-ACTATTATTTCGAAA-TAATT-AAAAAAATCAAAA
34234227 TTTTTCCCAA
Statistics
Matches: 98, Mismatches: 12, Indels: 6
0.84 0.10 0.05
Matches are distributed among these distances:
135 22 0.22
136 60 0.61
137 3 0.03
138 13 0.13
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.41
Consensus pattern (136 bp):
CTAAAAAACAAATTTTTATTTTTAAAAATATAAACTTTCTCATTTTTTAAAGAAAATCACTACTT
TCTTAAAAATCTAAACTATTATTTCGAAATAATTAAAAAAATCAAAACTTTGTTCAAAAAATTAA
ACTTTT
Found at i:34234655 original size:3 final size:3
Alignment explanation
Indices: 34234647--34234712 Score: 107
Period size: 3 Copynumber: 22.0 Consensus size: 3
34234637 GAAACCCAAA
34234647 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
34234695 AGT AA- AGAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT
34234713 TTGGGTCTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
2 1 0.02
3 57 0.97
4 1 0.02
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:34234751 original size:11 final size:11
Alignment explanation
Indices: 34234735--34234759 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
34234725 CAAGCCCAAA
34234735 AAAGAAAAGAG
1 AAAGAAAAGAG
34234746 AAAGAAAAGAG
1 AAAGAAAAGAG
34234757 AAA
1 AAA
34234760 CAATGATCTT
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAG
Found at i:34235224 original size:42 final size:42
Alignment explanation
Indices: 34235155--34235319 Score: 195
Period size: 42 Copynumber: 3.9 Consensus size: 42
34235145 AAAAAATGAA
* * * * * * *
34235155 TAAATGGACCTCTACGCCTAGGTCTCTAAATGCAATAAAAAA
1 TAAATGGGCCTCTACACTTGGGCCTCTAAATGCAATGAAAAG
*
34235197 TAAATGGGCCTTTACACTTGGGCCTCTAAATGCAATGAAAAG
1 TAAATGGGCCTCTACACTTGGGCCTCTAAATGCAATGAAAAG
* * * ***
34235239 TAAATGGGTCTCCACACCTAAACCTCTAAATGCAATGAAAAG
1 TAAATGGGCCTCTACACTTGGGCCTCTAAATGCAATGAAAAG
*
34235281 TAAATGGACCTCTACACTTGGGCCTCTAAATGCAATGAA
1 TAAATGGGCCTCTACACTTGGGCCTCTAAATGCAATGAA
34235320 TGATTTCCAT
Statistics
Matches: 101, Mismatches: 22, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 101 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (42 bp):
TAAATGGGCCTCTACACTTGGGCCTCTAAATGCAATGAAAAG
Found at i:34235732 original size:10 final size:10
Alignment explanation
Indices: 34235719--34235771 Score: 60
Period size: 9 Copynumber: 5.5 Consensus size: 10
34235709 TTGCTCTCTC
34235719 TTTCTATTTT
1 TTTCTATTTT
34235729 TTTCTATATTT
1 TTTCTAT-TTT
34235740 TTT-T-TCTTT
1 TTTCTAT-TTT
34235749 TTTCT-TTTT
1 TTTCTATTTT
34235758 TTT-TATTTT
1 TTTCTATTTT
34235767 TTTCT
1 TTTCT
34235772 TGATTCAAAC
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
8 1 0.03
9 20 0.53
10 11 0.29
11 6 0.16
ACGTcount: A:0.08, C:0.09, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTCTATTTT
Found at i:34245126 original size:51 final size:51
Alignment explanation
Indices: 34245012--34245385 Score: 129
Period size: 51 Copynumber: 7.5 Consensus size: 51
34245002 AAAATCATTA
* *
34245012 TTTACTTAAAAATCTAAACTTTTATTTTGAAATAGTATAAAAAAATCAAAAT
1 TTTATTTAAAAATATAAACTTTTATTTTGAAATAG-ATAAAAAAATCAAAAT
* * *
34245064 TTTATTT-AAAATTTAAACTTTT-TCTTTGAAATA-ACT-AAAAAA-CATATT
1 TTTATTTAAAAATATAAACTTTTAT-TTTGAAATAGA-TAAAAAAATCAAAAT
*** *** * ** *
34245112 TTTATTTTTAAAAATATAAACTTTCT-TTCTT-TTTTTCTTAATGAAAATCATTAC
1 TTTA--TTTAAAAATATAAACTTT-TATT-TTGAAATAGATAA-AAAAATCAAAAT
* ** * ** * *
34245166 TTTACTTAAAAATCCAAATTTTTATTTCAAAATAGTTAAAAAAAATTAAAAT
1 TTTATTTAAAAATATAAACTTTTATTTTGAAATAGAT-AAAAAAATCAAAAT
* * * *
34245218 TTTATTTAAAAATTTAAACTTTT-TATTTAAAATA-ACT-AAAAAA-CAGATT
1 TTTATTTAAAAATATAAACTTTTAT-TTTGAAATAGA-TAAAAAAATCAAAAT
* ** * ** *
34245267 TTTATTTTTAAAAATATAAACTCTCCTTTT----TA-AT--GAAAATCACCAC
1 TTTA--TTTAAAAATATAAACTTTTATTTTGAAATAGATAAAAAAATCAAAAT
* * * * *
34245313 TTT-CTTAAAAATCTAAACTTTTATTTAGAAATAGTTAAAAAAATCAAAAC
1 TTTATTTAAAAATATAAACTTTTATTTTGAAATAGATAAAAAAATCAAAAT
* *
34245363 TTTATTTAAAAATTTAAATTTTT
1 TTTATTTAAAAATATAAACTTTT
34245386 CTAAAAAAAA
Statistics
Matches: 235, Mismatches: 59, Indels: 57
0.67 0.17 0.16
Matches are distributed among these distances:
43 18 0.08
45 4 0.02
46 6 0.03
47 5 0.02
48 9 0.04
49 14 0.06
50 23 0.10
51 77 0.33
52 66 0.28
53 6 0.03
54 7 0.03
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (51 bp):
TTTATTTAAAAATATAAACTTTTATTTTGAAATAGATAAAAAAATCAAAAT
Found at i:34245234 original size:20 final size:21
Alignment explanation
Indices: 34245205--34245249 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
34245195 AAATAGTTAA
34245205 AAAAAATTAAA-ATTTTATTT
1 AAAAAATTAAACATTTTATTT
* *
34245225 AAAAATTTAAACTTTTTATTT
1 AAAAAATTAAACATTTTATTT
34245246 AAAA
1 AAAA
34245250 TAACTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AAAAAATTAAACATTTTATTT
Found at i:34245283 original size:155 final size:147
Alignment explanation
Indices: 34244868--34245497 Score: 658
Period size: 155 Copynumber: 4.3 Consensus size: 147
34244858 AGCCACCTCC
* * *
34244868 CTTTATTTCAAAATCAAAACTTTTATTTCAAAATAGTT-AAAAAAATCAAAATTTTATTTAAAAT
1 CTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAAATCAAAATTTTATTTAAAAT
* * * * * *
34244932 TTAAACATTTCACTTTAAAATCACTAAAAAATAGATTTTTATTTTTTTAAAATCTAAA----CTT
66 TTAAACTTTTTA-TTTAAAATAACTAAAAAACAGATTTTTA-TTTTTAAAAATATAAACTCTCTT
*
34244993 TTTTTAATGAAAATCATTA
129 TTTTTAATGAAAATCACTA
* **
34245012 -TTTACTTAAAAATCTAAACTTTTATTTTGAAATAG-TATAAAAAAATCAAAATTTTATTTAAAA
1 CTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTA-AAAAAAATCAAAATTTTATTTAAAA
* * *
34245075 TTTAAACTTTTTCTTTGAAATAACTAAAAAACATATTTTTATTTTTAAAAATATAAACTTTCTTT
65 TTTAAACTTTTTATTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAAC--TC--T
*
34245140 CTTTTTTTCTTAATGAAAATCATTA
126 C--TTTTT-TTAATGAAAATCACTA
* *
34245165 CTTTACTTAAAAATCCAAATTTTTATTTCAAAATAGTTAAAAAAAATTAAAATTTTATTTAAAAA
1 CTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAAATCAAAATTTTATTT-AAAA
*
34245230 TTTAAACTTTTTATTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAACTCTC-CT
65 TTTAAACTTTTTATTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAACTCTCTTT
*
34245294 TTTTAATGAAAATCACCA
130 TTTTAATGAAAATCACTA
* *
34245312 CTTT-CTTAAAAATCTAAACTTTTATTT-AGAAATAGTT-AAAAAAATCAAAACTTTATTTAAAA
1 CTTTACTTAAAAATCCAAACTTTTATTTCA-AAATAGTTAAAAAAAATCAAAATTTTATTT-AAA
* *
34245374 ATTTAAA----TT-TTT---CTAA--AAAAAATAGA-TTTTATTTTTAAAAATATAAACTTTCTC
64 ATTTAAACTTTTTATTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAAC--TCTC
*
34245428 TTTTTTTTAAAGAAAATCACTA
127 -TTTTTTTAATGAAAATCACTA
* * * *
34245450 TTTTACTTAAAAAT-CAAGGCTTTTTATTTCGAAATTATTTAAAAAAAA
1 CTTTACTTAAAAATCCAA-AC-TTTTATTTC-AAAATAGTTAAAAAAAA
34245498 AATAAAACTT
Statistics
Matches: 420, Mismatches: 39, Indels: 56
0.82 0.08 0.11
Matches are distributed among these distances:
134 22 0.05
135 9 0.02
136 4 0.01
137 3 0.01
138 22 0.05
139 10 0.02
140 11 0.03
141 8 0.02
142 23 0.05
143 54 0.13
144 35 0.08
145 31 0.07
146 29 0.07
147 18 0.04
148 3 0.01
150 1 0.00
151 2 0.00
152 5 0.01
153 18 0.04
154 51 0.12
155 61 0.15
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (147 bp):
CTTTACTTAAAAATCCAAACTTTTATTTCAAAATAGTTAAAAAAAATCAAAATTTTATTTAAAAT
TTAAACTTTTTATTTAAAATAACTAAAAAACAGATTTTTATTTTTAAAAATATAAACTCTCTTTT
TTTAATGAAAATCACTA
Found at i:34245929 original size:3 final size:3
Alignment explanation
Indices: 34245921--34245951 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
34245911 CTTGAAACCT
34245921 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
34245952 TTGGGTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:34249009 original size:28 final size:28
Alignment explanation
Indices: 34248973--34249036 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
34248963 TATGCACTTC
*
34248973 GGTGATTACTATTACAAGATTGCACTTTT
1 GGTGCTTACTATTACAAGATTGCA-TTTT
* * *
34249002 -GTGCTTACTGTTACATGGTTGCATTTT
1 GGTGCTTACTATTACAAGATTGCATTTT
34249029 GGTGCTTA
1 GGTGCTTA
34249037 TAGCTATTGC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 4 0.13
28 26 0.87
ACGTcount: A:0.20, C:0.14, G:0.22, T:0.44
Consensus pattern (28 bp):
GGTGCTTACTATTACAAGATTGCATTTT
Found at i:34249119 original size:22 final size:22
Alignment explanation
Indices: 34249071--34249127 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
34249061 CCTACGTGAA
* * *
34249071 TGCACTACGGAGCCTACTGTTC
1 TGCACTTCGGTGCTTACTGTTC
34249093 TGCACTTCGGTGCTTACTGTT-
1 TGCACTTCGGTGCTTACTGTTC
34249114 TAGCACTTCGGTGC
1 T-GCACTTCGGTGC
34249128 CCTTTGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.14, C:0.28, G:0.25, T:0.33
Consensus pattern (22 bp):
TGCACTTCGGTGCTTACTGTTC
Found at i:34251052 original size:72 final size:72
Alignment explanation
Indices: 34250957--34251101 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
34250947 GAATGAAGAA
34250957 AGATTTGATTTGTTATGTTTACTTGATAAATTCTTTGGTTAACTTGAGTTAGTAAATTAGAAGTA
1 AGATTTGATTTGTTATGTTTACTTGATAAATTCTTTGGTTAACTTGAGTTAGTAAATTAGAAGTA
34251022 GAAATAT
66 GAAATAT
34251029 AGATTTGATTTGTTATGTTTACTTGATAAATTCTTTGGTTAACTTGAGTTAGTAAATTAGAAGTA
1 AGATTTGATTTGTTATGTTTACTTGATAAATTCTTTGGTTAACTTGAGTTAGTAAATTAGAAGTA
34251094 GAAATAT
66 GAAATAT
34251101 A
1 A
34251102 TTATTAAGTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.34, C:0.04, G:0.18, T:0.44
Consensus pattern (72 bp):
AGATTTGATTTGTTATGTTTACTTGATAAATTCTTTGGTTAACTTGAGTTAGTAAATTAGAAGTA
GAAATAT
Found at i:34252204 original size:11 final size:12
Alignment explanation
Indices: 34252169--34252219 Score: 61
Period size: 11 Copynumber: 4.4 Consensus size: 12
34252159 GGGCCCAATA
34252169 AAATTTAAATTT
1 AAATTTAAATTT
* *
34252181 -ATTTTAAAGTT
1 AAATTTAAATTT
*
34252192 AAATTT-ATTTT
1 AAATTTAAATTT
34252203 AAATTTAAATTT
1 AAATTTAAATTT
34252215 AAATT
1 AAATT
34252220 AATGTCCAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
11 18 0.58
12 13 0.42
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (12 bp):
AAATTTAAATTT
Found at i:34252221 original size:5 final size:6
Alignment explanation
Indices: 34252169--34252219 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
34252159 GGGCCCAATA
* * *
34252169 AAATTT AAATTT -ATTTT AAAGTT AAATTT -ATTTT AAATTT AAATTT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT
34252215 AAATT
1 AAATT
34252220 AATGTCCAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
5 8 0.22
6 29 0.78
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (6 bp):
AAATTT
Found at i:34252221 original size:17 final size:17
Alignment explanation
Indices: 34252169--34252215 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
34252159 GGGCCCAATA
34252169 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
*
34252186 AAAGTTAAATTTATTTT
1 AAATTTAAATTTATTTT
34252203 AAATTTAAATTTA
1 AAATTTAAATTTA
34252216 AATTAATGTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:34252239 original size:14 final size:14
Alignment explanation
Indices: 34252220--34252249 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
34252210 AATTTAAATT
34252220 AATGTCCAAATACA
1 AATGTCCAAATACA
*
34252234 AATGTCCAATTACA
1 AATGTCCAAATACA
34252248 AA
1 AA
34252250 AGCCCAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (14 bp):
AATGTCCAAATACA
Found at i:34254068 original size:30 final size:29
Alignment explanation
Indices: 34254002--34254207 Score: 152
Period size: 29 Copynumber: 7.0 Consensus size: 29
34253992 TTTTAATCCC
* *
34254002 AAAACTTTCT-AAAATTACATTTTTACCCT
1 AAAAC-TTCTAAAAATTCCATTTTTACCCA
*
34254031 TAAACTTCTAAAAATTCCATTTTTGACCCA
1 AAAACTTCTAAAAATTCCATTTTT-ACCCA
* *
34254061 AAAACTTCTTAAAATTACATTTTTAACCC-
1 AAAACTTCTAAAAATTCCATTTTT-ACCCA
* * * *
34254090 TAAACTTCCAAAAATTCTATTTTTAACCCC
1 AAAACTTCTAAAAATTCCATTTTT-ACCCA
* * * *
34254120 AAAATTTCTAAAAACTACATTTTTACCCC
1 AAAACTTCTAAAAATTCCATTTTTACCCA
* * *
34254149 TAAATTTCCAAATAA-TCCATTTTTGACCCCA
1 AAAACTTCTAAA-AATTCCATTTTT-A-CCCA
34254180 AAAACTT-TCAAAAATTACCA-TTTTACCC
1 AAAACTTCT-AAAAATT-CCATTTTTACCC
34254208 TCGAAACCTC
Statistics
Matches: 143, Mismatches: 25, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
28 4 0.03
29 67 0.47
30 53 0.37
31 16 0.11
32 3 0.02
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (29 bp):
AAAACTTCTAAAAATTCCATTTTTACCCA
Found at i:34254081 original size:59 final size:59
Alignment explanation
Indices: 34254002--34254208 Score: 244
Period size: 59 Copynumber: 3.5 Consensus size: 59
34253992 TTTTAATCCC
* *
34254002 AAAACTTTCTAAAATTACATTTTTACCCTTAAACTTCTAAAAATTCCATTTTTGACCCA
1 AAAACTTTCAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCA
* * * *
34254061 AAAAC-TTCTTAAAATTACATTTTTAACCC-TAAACTTCCAAAAATTCTATTTTTAACCCC
1 AAAACTTTC-AAAAATTACATTTTT-ACCCTTAAACTTCCAAAAATTCCATTTTTGACCCA
* * *
34254120 AAAA-TTTCTAAAAACTACATTTTTACCCCTAAATTTCCAAATAA-TCCATTTTTGACCCCA
1 AAAACTTTC-AAAAATTACATTTTTACCCTTAAACTTCCAAA-AATTCCATTTTTGA-CCCA
34254180 AAAACTTTCAAAAATTACCA-TTTTACCCT
1 AAAACTTTCAAAAATTA-CATTTTTACCCT
34254209 CGAAACCTCG
Statistics
Matches: 128, Mismatches: 12, Indels: 15
0.83 0.08 0.10
Matches are distributed among these distances:
58 7 0.05
59 87 0.68
60 28 0.22
61 6 0.05
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.37
Consensus pattern (59 bp):
AAAACTTTCAAAAATTACATTTTTACCCTTAAACTTCCAAAAATTCCATTTTTGACCCA
Found at i:34254718 original size:96 final size:97
Alignment explanation
Indices: 34254575--34254764 Score: 244
Period size: 96 Copynumber: 2.0 Consensus size: 97
34254565 ACTTTAAAAC
* * ***
34254575 CGAGGCAATATTCTTTTATTTCGAGTTTCGAAATTTTGTGCCTTAACTTACTAGGTGCATGTTTT
1 CGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACCTTT
* *
34254640 CTTCAAATCGAAATAATCGAATA-CCTTTAAT
66 CGTCAAATCGAAATAATCAAATATCCTTTAAT
*
34254671 CGAGGCAATGTT-TCTTTATCTTCGA--TTCTGAAAATTTGCGCCTTAACTTACTAGGTGCAACC
1 CGAGGCAATATTCT-TTTAT-TTCGAGTTTC-GAAAATTTGCGCCTTAACTTACTAGGTGCAACC
*
34254733 TTTCGTCAAATCGAGATAATCAAATATCCTTT
63 TTTCGTCAAATCGAAATAATCAAATATCCTTT
34254765 TCTAAAATTT
Statistics
Matches: 81, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
95 4 0.05
96 67 0.83
97 10 0.12
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (97 bp):
CGAGGCAATATTCTTTTATTTCGAGTTTCGAAAATTTGCGCCTTAACTTACTAGGTGCAACCTTT
CGTCAAATCGAAATAATCAAATATCCTTTAAT
Found at i:34258770 original size:25 final size:25
Alignment explanation
Indices: 34258736--34258784 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
34258726 GTAATTATTG
34258736 TCGATTTTTATTTATAAAAAAATGC
1 TCGATTTTTATTTATAAAAAAATGC
34258761 TCGATTTTTATTTATAAAAAAATG
1 TCGATTTTTATTTATAAAAAAATG
34258785 TACTTTGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (25 bp):
TCGATTTTTATTTATAAAAAAATGC
Found at i:34263407 original size:13 final size:13
Alignment explanation
Indices: 34263389--34263447 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 13
34263379 ATTGGTAAAA
34263389 AAAGTCAATGGTC
1 AAAGTCAATGGTC
*
34263402 AAAGTCAA-AGTC
1 AAAGTCAATGGTC
* *
34263414 AGAGGTC-ATGATC
1 A-AAGTCAATGGTC
*
34263427 AAAGTCAACGGTC
1 AAAGTCAATGGTC
34263440 AAAGTCAA
1 AAAGTCAA
34263448 CAAGTCAATC
Statistics
Matches: 36, Mismatches: 7, Indels: 6
0.73 0.14 0.12
Matches are distributed among these distances:
12 9 0.25
13 27 0.75
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (13 bp):
AAAGTCAATGGTC
Found at i:34263413 original size:19 final size:18
Alignment explanation
Indices: 34263389--34263447 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 18
34263379 ATTGGTAAAA
34263389 AAAGTCAATGGTCAAAGTC
1 AAAGTCAA-GGTCAAAGTC
*
34263408 AAAGTCAGAGGTC-ATGATC
1 AAAGTCA-AGGTCAAAG-TC
34263427 AAAGTCAACGGTCAAAGTC
1 AAAGTCAA-GGTCAAAGTC
34263446 AA
1 AA
34263448 CAAGTCAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
18 3 0.09
19 28 0.82
20 3 0.09
ACGTcount: A:0.42, C:0.17, G:0.22, T:0.19
Consensus pattern (18 bp):
AAAGTCAAGGTCAAAGTC
Found at i:34263549 original size:8 final size:8
Alignment explanation
Indices: 34263538--34263572 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
34263528 TCATGGTTTT
34263538 GGGTTATA
1 GGGTTATA
34263546 GGGTTAT-
1 GGGTTATA
*
34263553 GGGTTATT
1 GGGTTATA
34263561 GGGTTATA
1 GGGTTATA
34263569 GGGT
1 GGGT
34263573 CAAGAGTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (8 bp):
GGGTTATA
Found at i:34263549 original size:23 final size:24
Alignment explanation
Indices: 34263523--34263572 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
34263513 TATTAGGTTT
34263523 GGGTTTCAT-GGTT-TTGGGTTATA
1 GGGTTT-ATGGGTTATTGGGTTATA
34263546 GGG-TTATGGGTTATTGGGTTATA
1 GGGTTTATGGGTTATTGGGTTATA
34263569 GGGT
1 GGGT
34263573 CAAGAGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 2 0.08
22 6 0.25
23 16 0.67
ACGTcount: A:0.14, C:0.02, G:0.40, T:0.44
Consensus pattern (24 bp):
GGGTTTATGGGTTATTGGGTTATA
Found at i:34263550 original size:15 final size:15
Alignment explanation
Indices: 34263532--34263572 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
34263522 TGGGTTTCAT
*
34263532 GGTTTTGGGTTATAG
1 GGTTATGGGTTATAG
*
34263547 GGTTATGGGTTATTG
1 GGTTATGGGTTATAG
34263562 GGTTATAGGGT
1 GGTTAT-GGGT
34263573 CAAGAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.15, C:0.00, G:0.41, T:0.44
Consensus pattern (15 bp):
GGTTATGGGTTATAG
Found at i:34263581 original size:23 final size:23
Alignment explanation
Indices: 34263536--34263587 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
34263526 TTTCATGGTT
* * *
34263536 TTGGGTTATAGGGTTATGGGTTA
1 TTGGGTTATAGGGTCAAGAGTTA
34263559 TTGGGTTATAGGGTCAAGAGTTA
1 TTGGGTTATAGGGTCAAGAGTTA
34263582 TTGGGT
1 TTGGGT
34263588 CTCTTCTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.19, C:0.02, G:0.38, T:0.40
Consensus pattern (23 bp):
TTGGGTTATAGGGTCAAGAGTTA
Found at i:34267732 original size:40 final size:40
Alignment explanation
Indices: 34267676--34267782 Score: 171
Period size: 40 Copynumber: 2.7 Consensus size: 40
34267666 AGCCCGTTAA
** *
34267676 ATACACCAGCGGGAAGCCTGCTAGGCATTGAGCCTGATAG
1 ATACACCAGCACGAAGCCTGCTAGGCATTGAGCCTAATAG
34267716 ATACACC-GACACGAAGCCTGCTAGGCATTGAGCCTAATAG
1 ATACACCAG-CACGAAGCCTGCTAGGCATTGAGCCTAATAG
34267756 ATACACCAGCACGAAGCCTGCTAGGCA
1 ATACACCAGCACGAAGCCTGCTAGGCA
34267783 AAAGGCCCTT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
39 1 0.02
40 60 0.97
41 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.16
Consensus pattern (40 bp):
ATACACCAGCACGAAGCCTGCTAGGCATTGAGCCTAATAG
Found at i:34267866 original size:47 final size:47
Alignment explanation
Indices: 34267815--34268023 Score: 177
Period size: 47 Copynumber: 4.4 Consensus size: 47
34267805 CACCAGTATC
***
34267815 AAAGCCTGCTAGGCCCAAGGGTTGATACGGTACAGTAAATCGACATT
1 AAAGCCTGCTAGGCCCAAGGCCCGATACGGTACAGTAAATCGACATT
* * * * *
34267862 AAAGCTTGCTAGGCCCGAGGCCCGATATGGTATAGTACATCGACATT
1 AAAGCCTGCTAGGCCCAAGGCCCGATACGGTACAGTAAATCGACATT
* ** * ** * * *
34267909 AAAGCCTTCTAGGCCTTAGGCCCAATACGGTTGAATACA-CTGGCATT
1 AAAGCCTGCTAGGCCCAAGGCCCGATACGGTACAGTAAATC-GACATT
*** * * * *
34267956 AAAGCCTGCTAGGCTTGAGGCCCGATACAGTACAATACACCGACATT
1 AAAGCCTGCTAGGCCCAAGGCCCGATACGGTACAGTAAATCGACATT
*
34268003 AAAGCCTGCTAGGCACAAGGC
1 AAAGCCTGCTAGGCCCAAGGC
34268024 TCGCGTCATT
Statistics
Matches: 131, Mismatches: 29, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
46 1 0.01
47 129 0.98
48 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (47 bp):
AAAGCCTGCTAGGCCCAAGGCCCGATACGGTACAGTAAATCGACATT
Found at i:34267913 original size:94 final size:94
Alignment explanation
Indices: 34267815--34268023 Score: 213
Period size: 94 Copynumber: 2.2 Consensus size: 94
34267805 CACCAGTATC
**** * *
34267815 AAAGCCTGCTAGGCCCAAGGGTTGATACGGTACAGTAAA-TCGACATTAAAGCTTGCTAGGCCCG
1 AAAGCCTGCTAGGCCCAAGGCCCAATACGGTACAATAAACT-GACATTAAAGCCTGCTAGGCCCG
** * * *
34267879 AGGCCCGATATGGTATAGTACATCGACATT
65 AGGCCCGATACAGTACAATACACCGACATT
* ** ** * * **
34267909 AAAGCCTTCTAGGCCTTAGGCCCAATACGGTTGAATACACTGGCATTAAAGCCTGCTAGGCTTGA
1 AAAGCCTGCTAGGCCCAAGGCCCAATACGGTACAATAAACTGACATTAAAGCCTGCTAGGCCCGA
34267974 GGCCCGATACAGTACAATACACCGACATT
66 GGCCCGATACAGTACAATACACCGACATT
*
34268003 AAAGCCTGCTAGGCACAAGGC
1 AAAGCCTGCTAGGCCCAAGGC
34268024 TCGCGTCATT
Statistics
Matches: 90, Mismatches: 24, Indels: 2
0.78 0.21 0.02
Matches are distributed among these distances:
94 89 0.99
95 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.24, T:0.21
Consensus pattern (94 bp):
AAAGCCTGCTAGGCCCAAGGCCCAATACGGTACAATAAACTGACATTAAAGCCTGCTAGGCCCGA
GGCCCGATACAGTACAATACACCGACATT
Found at i:34270479 original size:13 final size:13
Alignment explanation
Indices: 34270461--34270487 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34270451 CTCGTACAAA
34270461 GTTGAAATAATGC
1 GTTGAAATAATGC
34270474 GTTGAAATAATGC
1 GTTGAAATAATGC
34270487 G
1 G
34270488 GGATACCCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (13 bp):
GTTGAAATAATGC
Found at i:34271096 original size:24 final size:24
Alignment explanation
Indices: 34271069--34271137 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
34271059 AATTTTCTAG
*
34271069 AAATGTTACTAGGGTAAAATCGTC-
1 AAATTTTACTAGGGTAAAATC-TCA
* **
34271093 AAATTTTACCAGAATAAAATTCTCA
1 AAATTTTACTAGGGTAAAA-TCTCA
34271118 AAATTTTACTAGGGTAAAAT
1 AAATTTTACTAGGGTAAAAT
34271138 TAGGATGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (24 bp):
AAATTTTACTAGGGTAAAATCTCA
Found at i:34271135 original size:25 final size:25
Alignment explanation
Indices: 34271069--34271138 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 25
34271059 AATTTTCTAG
*
34271069 AAATGTTACTAGGGTAAAA-TCGTC
1 AAATTTTACTAGGGTAAAATTCGTC
* **
34271093 AAATTTTACCAGAATAAAATTC-TC
1 AAATTTTACTAGGGTAAAATTCGTC
34271117 AAAATTTTACTAGGGTAAAATT
1 -AAATTTTACTAGGGTAAAATT
34271139 AGGATGAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
24 17 0.46
25 20 0.54
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (25 bp):
AAATTTTACTAGGGTAAAATTCGTC
Found at i:34274880 original size:28 final size:26
Alignment explanation
Indices: 34274834--34274886 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
34274824 GACATGTGTC
34274834 AAAAATGAAAAAAAATTAAAAAATAT
1 AAAAATGAAAAAAAATTAAAAAATAT
*
34274860 AAAAATCGTAAAAATAATTAAAAAATA
1 AAAAAT-G-AAAAAAAATTAAAAAATA
34274887 CATAGAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.25
27 1 0.04
28 17 0.71
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (26 bp):
AAAAATGAAAAAAAATTAAAAAATAT
Found at i:34275255 original size:9 final size:9
Alignment explanation
Indices: 34275144--34275283 Score: 60
Period size: 9 Copynumber: 15.6 Consensus size: 9
34275134 GGTTAAAGTT
*
34275144 TTTTTATAT
1 TTTTTATAA
34275153 TTTTTATAAA
1 TTTTTAT-AA
* * *
34275163 ATTTTACAG
1 TTTTTATAA
34275172 TTTTT-TATA
1 TTTTTATA-A
*
34275181 TTTTTATGA
1 TTTTTATAA
*
34275190 CTTTTAT--
1 TTTTTATAA
*
34275197 TTTTAATAAA
1 TTTTTAT-AA
34275207 TTTTTA-ATA
1 TTTTTATA-A
* *
34275216 CTTTTATAT
1 TTTTTATAA
34275225 TTTTTATTAAA
1 TTTTTA-T-AA
* *
34275236 ATTTAATAA
1 TTTTTATAA
34275245 TTTTTATAA
1 TTTTTATAA
*
34275254 -TTTTATTGA
1 TTTTTA-TAA
34275263 -TTTT-TAA
1 TTTTTATAA
34275270 TTTTTATAA
1 TTTTTATAA
34275279 TTTTT
1 TTTTT
34275284 CTCACATGCC
Statistics
Matches: 96, Mismatches: 22, Indels: 26
0.67 0.15 0.18
Matches are distributed among these distances:
7 7 0.07
8 11 0.11
9 58 0.60
10 15 0.16
11 5 0.05
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (9 bp):
TTTTTATAA
Found at i:34275258 original size:28 final size:26
Alignment explanation
Indices: 34275209--34275282 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 26
34275199 TTAATAAATT
* *
34275209 TTTAAT-ACTTTTATATTTTTTATTAAAA
1 TTTAATAATTTTTATA-ATTTTATT--AA
*
34275237 TTTAATAATTTTTATAATTTTATTGA
1 TTTAATAATTTTTATAATTTTATTAA
*
34275263 TTT-TTAATTTTTATAATTTT
1 TTTAATAATTTTTATAATTTT
34275283 TCTCACATGC
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 16 0.39
26 4 0.10
28 13 0.32
29 8 0.20
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (26 bp):
TTTAATAATTTTTATAATTTTATTAA
Found at i:34275281 original size:72 final size:72
Alignment explanation
Indices: 34275145--34275283 Score: 185
Period size: 72 Copynumber: 1.9 Consensus size: 72
34275135 GTTAAAGTTT
* * *
34275145 TTTTATATTTTTTATAAAATTTTACAGTTTTTTATATTTTTATGACTTTTATTTTTAATAAATTT
1 TTTTATATTTTTTATAAAATTTAACAGATTTTTATAATTTTATGACTTTTATTTTTAATAAATTT
34275210 TTAATAC
66 TTAATAC
* *
34275217 TTTTATATTTTTTATTAAAATTTAATA-ATTTTTATAATTTTATTGATTTTTAATTTTT-AT-AA
1 TTTTATATTTTTTA-TAAAATTTAACAGATTTTTATAATTTTA-TGACTTTT-ATTTTTAATAAA
34275279 TTTTT
63 TTTTT
34275284 CTCACATGCC
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
72 34 0.58
73 19 0.32
74 6 0.10
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (72 bp):
TTTTATATTTTTTATAAAATTTAACAGATTTTTATAATTTTATGACTTTTATTTTTAATAAATTT
TTAATAC
Found at i:34279963 original size:10 final size:10
Alignment explanation
Indices: 34279948--34279974 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
34279938 CAACATAAAT
34279948 CTTGGTAAGA
1 CTTGGTAAGA
34279958 CTTGGTAAGA
1 CTTGGTAAGA
34279968 CTTGGTA
1 CTTGGTA
34279975 TATTTCTACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.26, C:0.11, G:0.30, T:0.33
Consensus pattern (10 bp):
CTTGGTAAGA
Found at i:34293059 original size:23 final size:23
Alignment explanation
Indices: 34293011--34293074 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
34293001 GTATTTTCAC
*
34293011 TTTCTTTAAATTT-TTTTATATA
1 TTTCTTTAACTTTATTTTATATA
*
34293033 TTTTCTTTAACTTTATTTTATA-C
1 -TTTCTTTAACTTTATTTTATATA
34293056 TTT-TTTATACTTTATTTTA
1 TTTCTTTA-ACTTTATTTTA
34293075 AATAAGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
21 4 0.11
22 14 0.38
23 12 0.32
24 7 0.19
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTCTTTAACTTTATTTTATATA
Found at i:34293073 original size:12 final size:12
Alignment explanation
Indices: 34293038--34293074 Score: 53
Period size: 10 Copynumber: 3.3 Consensus size: 12
34293028 ATATATTTTC
34293038 TTTA-ACTTTAT
1 TTTATACTTTAT
34293049 TTTATAC-TT-T
1 TTTATACTTTAT
34293059 TTTATACTTTAT
1 TTTATACTTTAT
34293071 TTTA
1 TTTA
34293075 AATAAGTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 8 0.35
11 8 0.35
12 7 0.30
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATACTTTAT
Found at i:34294500 original size:9 final size:8
Alignment explanation
Indices: 34294488--34294669 Score: 89
Period size: 9 Copynumber: 20.8 Consensus size: 8
34294478 AAAACGGTTA
34294488 AAAACATAT
1 AAAA-ATAT
34294497 AAAAATTACT
1 AAAAA-TA-T
34294507 AAAAATAT
1 AAAAATAT
34294515 -AAAATAT
1 AAAAATAT
* *
34294522 AGAAATAG
1 AAAAATAT
*
34294530 AAAAGTATTT
1 AAAA--ATAT
*
34294540 AAAATTTAT
1 AAAA-ATAT
*
34294549 AAAAATAG
1 AAAAATAT
* *
34294557 AAAAGTTT
1 AAAAATAT
*
34294565 TAAAATAT
1 AAAAATAT
34294573 AAAAAATGAT
1 -AAAAAT-AT
34294583 AAAAATTATT
1 AAAAA-TA-T
34294593 ATAAAATAT
1 A-AAAATAT
34294602 AAAGAATAT
1 AAA-AATAT
*
34294611 AGAAAT-T
1 AAAAATAT
*
34294618 TAAAATAT
1 AAAAATAT
34294626 AAAAAATGAT
1 -AAAAAT-AT
34294636 AAAAAGTATT
1 AAAAA-TA-T
34294646 ATAAAATAT
1 A-AAAATAT
34294655 AAAGAATAT
1 AAA-AATAT
*
34294664 AGAAAT
1 AAAAAT
34294670 TTATTAATAA
Statistics
Matches: 134, Mismatches: 21, Indels: 37
0.70 0.11 0.19
Matches are distributed among these distances:
7 12 0.09
8 33 0.25
9 55 0.41
10 26 0.19
11 8 0.06
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.29
Consensus pattern (8 bp):
AAAAATAT
Found at i:34294586 original size:10 final size:9
Alignment explanation
Indices: 34294566--34294664 Score: 69
Period size: 10 Copynumber: 10.9 Consensus size: 9
34294556 GAAAAGTTTT
34294566 AAAATATAA
1 AAAATATAA
34294575 AAAATGATAA
1 AAAAT-ATAA
* *
34294585 AAATTATTAT
1 AAAATA-TAA
34294595 AAAATATAA
1 AAAATATAA
*
34294604 AGAATAT-A
1 AAAATATAA
* *
34294612 GAAAT-T-T
1 AAAATATAA
34294619 AAAATATAA
1 AAAATATAA
34294628 AAAATGATAA
1 AAAAT-ATAA
* *
34294638 AAAGTATTAT
1 AAAATA-TAA
34294648 AAAATATAA
1 AAAATATAA
*
34294657 AGAATATA
1 AAAATATA
34294665 GAAATTTATT
Statistics
Matches: 69, Mismatches: 15, Indels: 12
0.72 0.16 0.12
Matches are distributed among these distances:
7 5 0.07
8 5 0.07
9 29 0.42
10 30 0.43
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (9 bp):
AAAATATAA
Found at i:34294601 original size:29 final size:28
Alignment explanation
Indices: 34294512--34294696 Score: 131
Period size: 29 Copynumber: 6.8 Consensus size: 28
34294502 TTACTAAAAA
* * *
34294512 TATAAAATAT-AGAAATA-GAAAAGTAT
1 TATAAAATATAAAAAATATAAAAATTAT
* * *
34294538 T-TAAAATTTATAAAAATA-GAAAAGT-T
1 TATAAAATATA-AAAAATATAAAAATTAT
34294564 T-TAAAATATAAAAAATGATAAAAATTAT
1 TATAAAATATAAAAAAT-ATAAAAATTAT
* *
34294592 TATAAAATATAAAGAATAT-AGAA--AT
1 TATAAAATATAAAAAATATAAAAATTAT
*
34294617 T-TAAAATATAAAAAATGATAAAAAGTAT
1 TATAAAATATAAAAAAT-ATAAAAATTAT
* *
34294645 TATAAAATATAAAGAATATAGAAATTTAT
1 TATAAAATATAAAAAATATA-AAAATTAT
**
34294674 TAATAATTTATAAAAAAT-TAAAA
1 T-ATAAAATATAAAAAATATAAAA
34294697 TTTAAAAACA
Statistics
Matches: 131, Mismatches: 15, Indels: 24
0.77 0.09 0.14
Matches are distributed among these distances:
24 14 0.11
25 18 0.14
26 15 0.11
27 21 0.16
28 13 0.10
29 37 0.28
30 13 0.10
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (28 bp):
TATAAAATATAAAAAATATAAAAATTAT
Found at i:34294620 original size:53 final size:53
Alignment explanation
Indices: 34294530--34294672 Score: 211
Period size: 53 Copynumber: 2.7 Consensus size: 53
34294520 ATAGAAATAG
*
34294530 AAAAGTATT-TAAAATTTATAA-AA-ATAGAAAAGTTTTAAAATATAAAAAATGATA
1 AAAAGTATTATAAAATATA-AAGAATATAG-AAA--TTTAAAATATAAAAAATGATA
*
34294584 AAAATTATTATAAAATATAAAGAATATAGAAATTTAAAATATAAAAAATGATA
1 AAAAGTATTATAAAATATAAAGAATATAGAAATTTAAAATATAAAAAATGATA
34294637 AAAAGTATTATAAAATATAAAGAATATAGAAATTTA
1 AAAAGTATTATAAAATATAAAGAATATAGAAATTTA
34294673 TTAATAATTT
Statistics
Matches: 83, Mismatches: 3, Indels: 7
0.89 0.03 0.08
Matches are distributed among these distances:
53 56 0.67
54 10 0.12
55 13 0.16
56 4 0.05
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (53 bp):
AAAAGTATTATAAAATATAAAGAATATAGAAATTTAAAATATAAAAAATGATA
Found at i:34294658 original size:17 final size:17
Alignment explanation
Indices: 34294589--34294658 Score: 54
Period size: 17 Copynumber: 4.0 Consensus size: 17
34294579 TGATAAAAAT
34294589 TATTATAAAATATAAAG
1 TATTATAAAATATAAAG
* * *
34294606 -AATATAGAAATTTAAAA
1 TATTATA-AAATATAAAG
*
34294623 TA-TAAAAAATGATAAAAAG
1 TATTATAAAAT-AT--AAAG
34294642 TATTATAAAATATAAAG
1 TATTATAAAATATAAAG
34294659 AATATAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
16 9 0.22
17 16 0.40
18 1 0.03
19 7 0.17
20 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (17 bp):
TATTATAAAATATAAAG
Found at i:34294669 original size:17 final size:16
Alignment explanation
Indices: 34294488--34294669 Score: 89
Period size: 19 Copynumber: 10.4 Consensus size: 16
34294478 AAAACGGTTA
34294488 AAAACATATAAAAATTACT
1 AAAA-ATATAAAAA-TA-T
34294507 AAAAATAT-AAAATAT
1 AAAAATATAAAAATAT
* * *
34294522 AGAAATAGAAAAGTATTT
1 AAAAATATAAAA--ATAT
* *
34294540 AAAATTTATAAAAATAG
1 AAAA-ATATAAAAATAT
* * *
34294557 AAAAGTTTTAAAATAT
1 AAAAATATAAAAATAT
34294573 AAAAAATGATAAAAATTATT
1 -AAAAAT-ATAAAAA-TA-T
34294593 ATAAAATATAAAGAATAT
1 A-AAAATATAAA-AATAT
* *
34294611 AGAAAT-TTAAAATAT
1 AAAAATATAAAAATAT
34294626 AAAAAATGATAAAAAGTATT
1 -AAAAAT-ATAAAAA-TA-T
34294646 ATAAAATATAAAGAATAT
1 A-AAAATATAAA-AATAT
*
34294664 AGAAAT
1 AAAAAT
34294670 TTATTAATAA
Statistics
Matches: 126, Mismatches: 20, Indels: 36
0.69 0.11 0.20
Matches are distributed among these distances:
15 12 0.10
16 21 0.17
17 23 0.18
18 24 0.19
19 30 0.24
20 16 0.13
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.29
Consensus pattern (16 bp):
AAAAATATAAAAATAT
Found at i:34294700 original size:17 final size:17
Alignment explanation
Indices: 34294672--34294704 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
34294662 ATAGAAATTT
34294672 ATTAATAATTTATAAAAA
1 ATTAATAATTTA-AAAAA
34294690 ATTAA-AATTTAAAAA
1 ATTAATAATTTAAAAA
34294705 CATATAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
ATTAATAATTTAAAAAA
Found at i:34295523 original size:25 final size:25
Alignment explanation
Indices: 34295485--34295538 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
34295475 TTATAATTTT
* *
34295485 ATAATTTTAATATTTTATTTTA-TA
1 ATAAATTTAATATTTTATGTTATTA
34295509 ATAAATTTAATTATTTTATGTTATTA
1 ATAAATTTAA-TATTTTATGTTATTA
34295535 ATAA
1 ATAA
34295539 TTTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 9 0.35
25 11 0.42
26 6 0.23
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
ATAAATTTAATATTTTATGTTATTA
Found at i:34295560 original size:9 final size:9
Alignment explanation
Indices: 34295548--34295616 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
34295538 ATTTTTAAAA
*
34295548 ATTTTCTAT
1 ATTTTATAT
34295557 ATTTTATAT
1 ATTTTATAT
* *
34295566 TTTTTCTAT
1 ATTTTATAT
*
34295575 -TTTTCATAA
1 ATTTT-ATAT
*
34295584 ATTTTAAAT
1 ATTTTATAT
*
34295593 AGTTTTATGT
1 A-TTTTATAT
34295603 ATTTT-TAT
1 ATTTTATAT
34295611 ATTTTA
1 ATTTTA
34295617 AAATAATATT
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
8 11 0.24
9 24 0.52
10 11 0.24
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (9 bp):
ATTTTATAT
Found at i:34295561 original size:18 final size:18
Alignment explanation
Indices: 34295540--34295620 Score: 60
Period size: 18 Copynumber: 4.6 Consensus size: 18
34295530 TATTAATAAT
*
34295540 TTTTAAAAATTTTCTATA
1 TTTTATAAATTTTCTATA
**
34295558 TTTTATATTTTTTCTAT-
1 TTTTATAAATTTTCTATA
**
34295575 TTTTCATAAATTTTAAATA
1 TTTT-ATAAATTTTCTATA
**
34295594 GTTTTATGTATTTT-TATA
1 -TTTTATAAATTTTCTATA
34295612 TTTTA-AAAT
1 TTTTATAAAT
34295621 AATATTATGA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
16 2 0.04
17 9 0.19
18 26 0.54
19 7 0.15
20 4 0.08
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTTATAAATTTTCTATA
Found at i:34296173 original size:27 final size:27
Alignment explanation
Indices: 34296139--34296192 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
34296129 TTAATGAAAT
*
34296139 TTTTGGCTTAAAAGTTAAAAAGATTTA
1 TTTTGGCTTAAAAGTTAAAAAAATTTA
34296166 TTTTGGCTTAAAAGTTAAAAAAATTTA
1 TTTTGGCTTAAAAGTTAAAAAAATTTA
34296193 CTTTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.04, G:0.13, T:0.41
Consensus pattern (27 bp):
TTTTGGCTTAAAAGTTAAAAAAATTTA
Found at i:34304746 original size:21 final size:21
Alignment explanation
Indices: 34304721--34304765 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
34304711 CGATCTGAGG
34304721 AAAATAAAAGAAACAGAATTA
1 AAAATAAAAGAAACAGAATTA
34304742 AAAATAAAAGAAACAGAATTA
1 AAAATAAAAGAAACAGAATTA
34304763 AAA
1 AAA
34304766 GAAATAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.13
Consensus pattern (21 bp):
AAAATAAAAGAAACAGAATTA
Found at i:34304774 original size:21 final size:19
Alignment explanation
Indices: 34304721--34304775 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 19
34304711 CGATCTGAGG
34304721 AAAATAAAAGAAACAGAATT
1 AAAA-AAAAGAAACAGAATT
34304741 AAAAATAAAAGAAACAGAATT
1 -AAAA-AAAAGAAACAGAATT
34304762 AAAAGAAATAGAAA
1 AAAA-AAA-AGAAA
34304776 ATAGAGGTGT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.22
21 25 0.78
ACGTcount: A:0.73, C:0.04, G:0.11, T:0.13
Consensus pattern (19 bp):
AAAAAAAAGAAACAGAATT
Found at i:34305602 original size:19 final size:19
Alignment explanation
Indices: 34305578--34305620 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
34305568 AAACATAAAT
34305578 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
34305597 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
34305616 TAAAT
1 TAAAT
34305621 CCTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:34307145 original size:22 final size:21
Alignment explanation
Indices: 34307101--34307145 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
34307091 AGTATTAGTT
* *
34307101 AGTGAAATGGCATGAGTATTA
1 AGTGAAATAGCATGAGTAATA
*
34307122 AGTGAATATAGCATGATTAATA
1 AGTGAA-ATAGCATGAGTAATA
34307144 AG
1 AG
34307146 GTTAACAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.29
Consensus pattern (21 bp):
AGTGAAATAGCATGAGTAATA
Found at i:34308085 original size:51 final size:50
Alignment explanation
Indices: 34307971--34308145 Score: 251
Period size: 51 Copynumber: 3.5 Consensus size: 50
34307961 AAAGGGTCTG
* ** *
34307971 ATGACTAAGTGTCATCGTGAGTAAATCAATCCTTGCGAATTAAAGGTCCA
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTATGGATTAAAGGTCCA
34308021 ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATTAAAGGTCCA
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCC-TTATGGATTAAAGGTCCA
* * *
34308072 ATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTTCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCC-TTATGGATTAAAGGTCCA
* *
34308123 ATGACTCAGTGTCATCATGAGTA
1 ATGACTAAGTGTCATCGTGAGTA
34308146 TGAATTCCTA
Statistics
Matches: 114, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 31 0.27
51 83 0.73
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (50 bp):
ATGACTAAGTGTCATCGTGAGTAAATGAATCCTTATGGATTAAAGGTCCA
Found at i:34308178 original size:102 final size:100
Alignment explanation
Indices: 34307965--34308196 Score: 261
Period size: 102 Copynumber: 2.3 Consensus size: 100
34307955 TAAATGAAAG
* *
34307965 GGTCTGATGACTAAGTGTCATCGTGAGTAAATCAATCCTTGCGAATTAAAGGTCCAATGACTAAG
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATCAATCCATGCGAATTAAAGGTCCAATGACTAAG
* * * **
34308030 TGTCATCGTGAGTAAATGAATCCTTTATGGATTAAA
66 TGTCATCATGAGT-AATGAATCCTATACGGAACAAA
* * * * * * *
34308066 GGTCCAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATTAAAGGTTCGATGACTCA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATCAATCCATG-CGAATTAAAGGTCCAATGACTAA
34308131 GTGTCATCATGAGT-ATGAATTCCTATACGGAACAAGA
65 GTGTCATCATGAGTAATGAA-TCCTATACGGAACAA-A
* *
34308168 GGTTCGATGAC-AATATGTCATCGTGAGTA
1 GGTCCGATGACTAA-GTGTCATCGTGAGTA
34308197 TCAAATGAAT
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
100 5 0.05
101 50 0.45
102 55 0.50
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.29
Consensus pattern (100 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATCAATCCATGCGAATTAAAGGTCCAATGACTAAG
TGTCATCATGAGTAATGAATCCTATACGGAACAAA
Found at i:34308801 original size:21 final size:24
Alignment explanation
Indices: 34308776--34308832 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 24
34308766 GACTTGAGTT
34308776 GTATCGGTAGTTAAAT-TAT-G-A
1 GTATCGGTAGTTAAATGTATAGAA
**
34308797 GTATCGGTAGTTGTATGTATAGAA
1 GTATCGGTAGTTAAATGTATAGAA
34308821 GTATCGGTAGTT
1 GTATCGGTAGTT
34308833 TGCATGCTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 14 0.45
22 3 0.10
23 1 0.03
24 13 0.42
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.39
Consensus pattern (24 bp):
GTATCGGTAGTTAAATGTATAGAA
Found at i:34314146 original size:66 final size:66
Alignment explanation
Indices: 34314040--34314177 Score: 269
Period size: 66 Copynumber: 2.1 Consensus size: 66
34314030 TGTTCAATGG
34314040 TAAGAAATTTCGTGATGAAATTTCCTTAAGGGGGGAGAGTTGTAATAGCCCGATTTTCAGTGGTG
1 TAAGAAATTTCGTGATGAAATTTCCTTAAGGGGGGAGAGTTGTAATAGCCCGATTTTCAGTGGTG
34314105 T
66 T
34314106 TAAGAAATTTCGTGATGAAATTTCCTTAAGGGGGGAGAGTTGTAATAGCCCGATTTTCAGTGGTG
1 TAAGAAATTTCGTGATGAAATTTCCTTAAGGGGGGAGAGTTGTAATAGCCCGATTTTCAGTGGTG
34314171 T
66 T
34314172 T-AGAAA
1 TAAGAAA
34314178 CCGTGGTTTC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
65 5 0.07
66 67 0.93
ACGTcount: A:0.29, C:0.10, G:0.28, T:0.33
Consensus pattern (66 bp):
TAAGAAATTTCGTGATGAAATTTCCTTAAGGGGGGAGAGTTGTAATAGCCCGATTTTCAGTGGTG
T
Found at i:34315519 original size:101 final size:98
Alignment explanation
Indices: 34315321--34315526 Score: 220
Period size: 101 Copynumber: 2.1 Consensus size: 98
34315311 CGAAAGGGTT
* * * * * *
34315321 GATGACTAAGTGTCATCGTGAGTAAATGAATCCTTGCGGATTAAAGTCCGATGACTAAGTGTCAT
1 GATGACTAAGTATCATAGTAAATAAATGAATCCATGCAGATTAAAGTCCGATGACTAAGTGTCAT
* * **
34315386 GTGAGTAATATCTTTTTTAATGGATTAAAGGTCC
66 GTGAGTAATATC-TTTATAACGGAACAAAGGTCC
* *
34315420 GATGACTAAGTATCATAGTAAATAAATGAATCCATGATAGATTAAAGGTCCGATGACTCAGTGTC
1 GATGACTAAGTATCATAGTAAATAAATGAATCCATG-CAGATTAAA-GTCCGATGACTAAGTGTC
34315485 ATCGTGAGT-ATGAATC-TTAT-ACGGAACAAGAGGTCC
64 AT-GTGAGTAAT--ATCTTTATAACGGAACAA-AGGTCC
34315521 GATGAC
1 GATGAC
34315527 ATATGTCATC
Statistics
Matches: 89, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
99 31 0.35
100 13 0.15
101 36 0.40
102 6 0.07
103 3 0.03
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.30
Consensus pattern (98 bp):
GATGACTAAGTATCATAGTAAATAAATGAATCCATGCAGATTAAAGTCCGATGACTAAGTGTCAT
GTGAGTAATATCTTTATAACGGAACAAAGGTCC
Found at i:34315608 original size:58 final size:58
Alignment explanation
Indices: 34315494--34315608 Score: 126
Period size: 58 Copynumber: 2.0 Consensus size: 58
34315484 CATCGTGAGT
* * ***
34315494 ATGAATCTTATACGGAACAAGAGGTCCGATGACATATGTCATCGTGAGTTTTAAATGA
1 ATGAATCTAATACGGAAAAAGAGGTCCGATGACATATGTCATCGTGAGTAACAAATGA
* * *
34315552 ATGAATTCTAATAC-GAAAAAG-GGTCCGATGACTTTGTGTCATTGTGAGTAACAAATG
1 ATGAA-TCTAATACGGAAAAAGAGGTCCGATGAC-ATATGTCATCGTGAGTAACAAATG
34315609 CGAGTGAAAC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
57 11 0.23
58 29 0.62
59 7 0.15
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (58 bp):
ATGAATCTAATACGGAAAAAGAGGTCCGATGACATATGTCATCGTGAGTAACAAATGA
Found at i:34317871 original size:21 final size:21
Alignment explanation
Indices: 34317847--34317888 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
34317837 TCTAATATTG
34317847 TAAAAATAATT-TTTAAATGTT
1 TAAAAATAATTATTT-AATGTT
* *
34317868 TAAATATGATTATTTAATGTT
1 TAAAAATAATTATTTAATGTT
34317889 GTGAAAGAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (21 bp):
TAAAAATAATTATTTAATGTT
Found at i:34338013 original size:25 final size:26
Alignment explanation
Indices: 34337985--34338043 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
34337975 TATTTGGCTT
* *
34337985 GTAAGAGCGATATTTTGTCT-AGTTC
1 GTAAGAGCGATATTCTGTCTGAGCTC
*
34338010 GTAAGAGCGATATTCTGTCTGGGCTC
1 GTAAGAGCGATATTCTGTCTGAGCTC
34338036 GTAAGAGC
1 GTAAGAGC
34338044 TAAACTCTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 19 0.63
26 11 0.37
ACGTcount: A:0.24, C:0.15, G:0.29, T:0.32
Consensus pattern (26 bp):
GTAAGAGCGATATTCTGTCTGAGCTC
Found at i:34338060 original size:26 final size:26
Alignment explanation
Indices: 34338008--34338061 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
34337998 TTTGTCTAGT
* * * *
34338008 TCGTAAGAGCGATATTCTGTCTGGGC
1 TCGTAAGAGCGAAACTCTATCTAGGC
*
34338034 TCGTAAGAGCTAAACTCTATCTAGGC
1 TCGTAAGAGCGAAACTCTATCTAGGC
34338060 TC
1 TC
34338062 ATTTGAGCTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (26 bp):
TCGTAAGAGCGAAACTCTATCTAGGC
Found at i:34348899 original size:5 final size:6
Alignment explanation
Indices: 34348870--34348897 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34348860 TGAATTCATA
34348870 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
34348898 GATTATGTAC
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:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:34349039 original size:29 final size:29
Alignment explanation
Indices: 34349006--34349063 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
34348996 CTAAATCTAT
34349006 ACCAAGCATCCACACTTTTTAAATTTTAA
1 ACCAAGCATCCACACTTTTTAAATTTTAA
34349035 ACCAAGCATCCACACTTTTTAAATTTTAA
1 ACCAAGCATCCACACTTTTTAAATTTTAA
34349064 CTTTAAAGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.34
Consensus pattern (29 bp):
ACCAAGCATCCACACTTTTTAAATTTTAA
Found at i:34356079 original size:29 final size:29
Alignment explanation
Indices: 34356021--34356079 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
34356011 AAAATTAGTA
* **
34356021 CCAGATTAGTACCTAAAGTTTTTTTTGTC
1 CCAGATTAGTACCTAAACTTTTTTCCGTC
*
34356050 CCAGATTAGTACCTGAACTTTTTTCCGTC
1 CCAGATTAGTACCTAAACTTTTTTCCGTC
34356079 C
1 C
34356080 ATTGATTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.41
Consensus pattern (29 bp):
CCAGATTAGTACCTAAACTTTTTTCCGTC
Found at i:34356505 original size:38 final size:37
Alignment explanation
Indices: 34356463--34356570 Score: 137
Period size: 37 Copynumber: 2.9 Consensus size: 37
34356453 ACCCGTTCAC
*
34356463 ATTACCTCTTTTGTTTGCTTAAAAAGAACCCATTTAAA
1 ATTACCTCTTTTGTTTGCTTAAAAAGAACCCAATT-AA
* *
34356501 ATTACCTCTTTTGTTTGCTT-AAAAGAACTCAATTCA
1 ATTACCTCTTTTGTTTGCTTAAAAAGAACCCAATTAA
* ** *
34356537 CTTTGCTCTTTTGTTTGCTTAAAATGAACCCAAT
1 ATTACCTCTTTTGTTTGCTTAAAAAGAACCCAAT
34356571 GTTTTGTTTG
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
36 18 0.30
37 23 0.38
38 20 0.33
ACGTcount: A:0.30, C:0.19, G:0.09, T:0.42
Consensus pattern (37 bp):
ATTACCTCTTTTGTTTGCTTAAAAAGAACCCAATTAA
Found at i:34360434 original size:80 final size:79
Alignment explanation
Indices: 34360104--34360475 Score: 451
Period size: 79 Copynumber: 4.7 Consensus size: 79
34360094 AGTTTAACTG
* * * * *
34360104 ACTAGAGTTGGGATCACAATTGTGGTTTATCTGCTAGGCACTGGGTGCCAGGATTTAACGGATAT
1 ACTAGAGTTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACAGATAT
34360169 TGTTGGTTAATCCA
66 TGTTGGTTAATCCA
* * ** *
34360183 ACTATA-TCTGGACTCA-AATTTGTTGTTTACCCGCTAGGCACTGGGTGCCAGGATTTGACAGAT
1 ACTAGAGT-TGGGCTCACAA-TTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACAGAT
*
34360246 ATTGTTGGTTAATCAA
64 ATTGTTGGTTAATCCA
* * ** * *
34360262 ACTAGAGCTGGTCTCACAATTGAAGTTTATCCGCTAGGCACTAGGTGTCAGGATTTGACAGATAT
1 ACTAGAGTTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACAGATAT
34360327 TGTTGGTTAATCCA
66 TGTTGGTTAATCCA
* * * * * * *
34360341 ACTAAAGTTGGGCTCACAATTGCGGTTTATCCACTACGTACTGGGTGCTAGGATTTGACGGTTAT
1 ACTAGAGTTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACAGATA-
34360406 TTGTTGGTTAATCCA
65 TTGTTGGTTAATCCA
** * *
34360421 ACTAGAGTTGGGCTCACTTTTGCGATTTATCTGCTAGGCACTGGGTGCCAGGATT
1 ACTAGAGTTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATT
34360476 GTCGGTTTAT
Statistics
Matches: 248, Mismatches: 40, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
78 3 0.01
79 182 0.73
80 63 0.25
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (79 bp):
ACTAGAGTTGGGCTCACAATTGCGGTTTATCCGCTAGGCACTGGGTGCCAGGATTTGACAGATAT
TGTTGGTTAATCCA
Found at i:34371885 original size:25 final size:25
Alignment explanation
Indices: 34371851--34371921 Score: 106
Period size: 26 Copynumber: 2.8 Consensus size: 25
34371841 AGATTTGACC
*
34371851 CTTGACCTTTCACCTACTAAAAACT
1 CTTGATCTTTCACCTACTAAAAACT
* *
34371876 CTTGATCTTTCATCTACAAAAAAACT
1 CTTGATCTTTCACCTAC-TAAAAACT
34371902 CTTGATCTTTCACCTACTAA
1 CTTGATCTTTCACCTACTAA
34371922 CTACTAAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 17 0.43
26 23 0.57
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.35
Consensus pattern (25 bp):
CTTGATCTTTCACCTACTAAAAACT
Found at i:34377654 original size:177 final size:179
Alignment explanation
Indices: 34377347--34377756 Score: 567
Period size: 177 Copynumber: 2.3 Consensus size: 179
34377337 TTTAAAAAAA
* *
34377347 TCTCTCATTTTCTCTCTTGCCAAACACCATATTTCTTCTTCAAAACACATGATTGGCTCATTTCA
1 TCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGATTGGATCATTTCA
34377412 TCTACAAGAATTCCCATTTCCATAGTTATAATCATGCTTTCGTGTAATTTTTGTAAACTCACACC
66 TCTACAAGAATTCCCATTTCCATAGTTATAATCATGCTTTCGTGTAATTTTTGTAAACTCACACC
* * * *
34377477 ACACTTTTAATTTACAATC-TTTCCCCCACTATCGGCTGCCA-TTATTT
131 ACACTTTCAACTTAAAATCTTTTCCCCCACTATCGACTGCCATTTATTT
* * * *
34377524 TCTCTTATTTTCTCTCTTACCAAACACCATTTTTCTTTTTCAAAACACATGGTTGGATCATTTCA
1 TCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGATTGGATCATTTCA
* *
34377589 TCTACAAGAATAT-CCATTTCCATGGTTATAATCATGCTTTTGTGTAATTTTTGTAAA-TCCACA
66 TCTACAAGAAT-TCCCATTTCCATAGTTATAATCATGCTTTCGTGTAATTTTTGTAAACT-CACA
* * * *
34377652 CCACACTTTCAACTTAAAATCATTGTTTTTTCCCCACTATTGACTGCTATTTTTTT
129 CCACACTTTCAACTTAAAATC-----TTTTCCCCCACTATCGACTGCCATTTATTT
* *
34377708 TCTCTCATTTTCTCTCTTGCCAAGCACTATTTTTCTTCTTCAAAACACA
1 TCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACA
34377757 ACATCTAGTT
Statistics
Matches: 203, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
176 1 0.00
177 134 0.66
178 1 0.00
183 18 0.09
184 49 0.24
ACGTcount: A:0.26, C:0.25, G:0.07, T:0.42
Consensus pattern (179 bp):
TCTCTCATTTTCTCTCTTGCCAAACACCATTTTTCTTCTTCAAAACACATGATTGGATCATTTCA
TCTACAAGAATTCCCATTTCCATAGTTATAATCATGCTTTCGTGTAATTTTTGTAAACTCACACC
ACACTTTCAACTTAAAATCTTTTCCCCCACTATCGACTGCCATTTATTT
Found at i:34392216 original size:23 final size:23
Alignment explanation
Indices: 34392180--34392234 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
34392170 TGGATTACAA
34392180 GTATCGATAATTTTAACATTGAT
1 GTATCGATAATTTTAACATTGAT
* *
34392203 GTATCGGTAGTTTTAACATTGAT
1 GTATCGATAATTTTAACATTGAT
34392226 GTATCGATA
1 GTATCGATA
34392235 GGTTGTATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (23 bp):
GTATCGATAATTTTAACATTGAT
Found at i:34392325 original size:21 final size:19
Alignment explanation
Indices: 34392295--34392347 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
34392285 GGAGTTTTTG
*
34392295 GTATCAGTAGATGCATGACTT
1 GTATCGGTAGAT-CAT-ACTT
34392316 GTATCGGTAGAAATCATACTT
1 GTATCGGTAG--ATCATACTT
*
34392337 GTATTGGTAGA
1 GTATCGGTAGA
34392348 GCTAGCACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 1 0.04
21 22 0.79
22 3 0.11
23 2 0.07
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:34393696 original size:25 final size:25
Alignment explanation
Indices: 34393667--34393772 Score: 140
Period size: 25 Copynumber: 4.2 Consensus size: 25
34393657 CAAAATTTCA
34393667 CTCTTACGAGCTAGATAGAATATCG
1 CTCTTACGAGCTAGATAGAATATCG
* *
34393692 CTCTTACAAGCTAGACAGAATATCG
1 CTCTTACGAGCTAGATAGAATATCG
* * * *
34393717 TTCTTATGAGCCAGATAGAATATCA
1 CTCTTACGAGCTAGATAGAATATCG
* *
34393742 CTCTTATGAGCTAGATAGAATATAG
1 CTCTTACGAGCTAGATAGAATATCG
34393767 CTCTTA
1 CTCTTA
34393773 TAAGCCAGAG
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 69 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (25 bp):
CTCTTACGAGCTAGATAGAATATCG
Found at i:34395803 original size:19 final size:18
Alignment explanation
Indices: 34395757--34395803 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
34395747 CGGAAGGACT
**
34395757 AGCATACTGGCTTGTTTG
1 AGCATACTGGCTTGTAAG
34395775 AGCATACTGGCTTGTAAG
1 AGCATACTGGCTTGTAAG
34395793 AGCATTACTGG
1 AGCA-TACTGG
34395804 ATCACAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.32
Consensus pattern (18 bp):
AGCATACTGGCTTGTAAG
Found at i:34396540 original size:21 final size:21
Alignment explanation
Indices: 34396501--34396540 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
34396491 TTTTTAGTAT
*
34396501 CGGTAGAAGTATAATTTGTTC
1 CGGTAGAAGTATAACTTGTTC
* *
34396522 CGGTAGAAGTGTCACTTGT
1 CGGTAGAAGTATAACTTGT
34396541 ATCGATAGAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.12, G:0.28, T:0.35
Consensus pattern (21 bp):
CGGTAGAAGTATAACTTGTTC
Found at i:34396549 original size:21 final size:21
Alignment explanation
Indices: 34396525--34396573 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
34396515 TTTGTTCCGG
* *
34396525 TAGAAGTGTCACTTGTATCGA
1 TAGAAGTATCACTAGTATCGA
** *
34396546 TAGAACCATCACTAGTATCGG
1 TAGAAGTATCACTAGTATCGA
34396567 TAGAAGT
1 TAGAAGT
34396574 CTGCTACTGT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (21 bp):
TAGAAGTATCACTAGTATCGA
Found at i:34401372 original size:19 final size:20
Alignment explanation
Indices: 34401348--34401388 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
34401338 AGGAGATAGA
34401348 ATATCCT-AGAACTTTTTCT
1 ATATCCTCAGAACTTTTTCT
34401367 ATATCCTCAGAACTTTTTCT
1 ATATCCTCAGAACTTTTTCT
34401387 AT
1 AT
34401389 GCCGCCACCG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (20 bp):
ATATCCTCAGAACTTTTTCT
Found at i:34410266 original size:21 final size:22
Alignment explanation
Indices: 34410228--34410284 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
34410218 CTCTGCAACT
* *
34410228 TCTACCGATACAAGCACA-CAA
1 TCTACCGATACTACCACAGCAA
*
34410249 TCTACCGATACTTCCACATGCAA
1 TCTACCGATACTACCACA-GCAA
34410272 TACTACCGATACT
1 T-CTACCGATACT
34410285 CACAATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 15 0.50
23 4 0.13
24 11 0.37
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.23
Consensus pattern (22 bp):
TCTACCGATACTACCACAGCAA
Found at i:34410965 original size:52 final size:52
Alignment explanation
Indices: 34410861--34411206 Score: 412
Period size: 52 Copynumber: 6.7 Consensus size: 52
34410851 TTCGCGTATG
* **
34410861 ATACTCACGATGACACA-ACTTCATCGGACC-CTTAATCCACAATA-GATTCAT
1 ATACTCACGATGACACATA-GTCATCGGACCTCTTAATCCGTAA-AGGATTCAT
* * *
34410912 ATACTCACGATGACACATAGTCAACGAACCTCTTAATCCGCAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
* ** * * *
34410964 ATATTCATAATGACACTTAGTCATTGGACCTCTTAATCCGTAAAGGTTTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
* * * *
34411016 ATACTCACGATGACACGTAGTCTTTGGACCACTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
** * *
34411068 ATACTCACGATGACATGTAGTCATTGGACCTCTTAATCCGTAAAGGATACAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
* * * *
34411120 ATACTCACAATGACACGTGGTCAT-GGAACCTCTTAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGG-ACCTCTTAATCCGTAAAGGATTCAT
*
34411172 ATACTCACGATGACACATAGTCATCGAACCTCTTA
1 ATACTCACGATGACACATAGTCATCGGACCTCTTA
34411207 CATTTACTAC
Statistics
Matches: 257, Mismatches: 33, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
51 28 0.11
52 228 0.89
53 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
Found at i:34411371 original size:17 final size:16
Alignment explanation
Indices: 34411333--34411372 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
34411323 ATTTCTAAGT
*
34411333 TTAAATTTAAATTTGT
1 TTAAATTTAAATTTGC
34411349 TCTAAATTTAAATTTAGC
1 T-TAAATTTAAATTT-GC
34411367 TTAAAT
1 TTAAAT
34411373 ATGAAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 18 0.86
18 2 0.10
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (16 bp):
TTAAATTTAAATTTGC
Found at i:34412143 original size:19 final size:18
Alignment explanation
Indices: 34412103--34412154 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
34412093 ATATTAATAA
*
34412103 TAATTATAATAAATGCTT
1 TAATAATAATAAATGCTT
*
34412121 TAATAATAATAAGATGTTT
1 TAATAATAATAA-ATGCTT
34412140 TAATAATAAGTAAAT
1 TAATAATAA-TAAAT
34412155 ATTATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 11 0.37
19 16 0.53
20 3 0.10
ACGTcount: A:0.50, C:0.02, G:0.08, T:0.40
Consensus pattern (18 bp):
TAATAATAATAAATGCTT
Found at i:34413335 original size:29 final size:28
Alignment explanation
Indices: 34413283--34413417 Score: 94
Period size: 29 Copynumber: 4.7 Consensus size: 28
34413273 AATTATCCAA
* * *
34413283 AAAACTACATTTTGACCCAAAACTTCCT
1 AAAATTACATTTTTACCCCAAACTTCCT
*
34413311 AAAATTACATTTTTACCCACGAACTTTCC-
1 AAAATTACATTTTTACCC-CAAAC-TTCCT
** * * *
34413340 AAAATCCCATTTTAACCCC-AATTTCACCA
1 AAAATTACATTTTTACCCCAAACTT--CCT
* *
34413369 AAAATTACATTTTTGCCCCTAAACTTTCT
1 AAAATTACATTTTTACCCC-AAACTTCCT
*
34413398 AAAATTCCATTTTTCACCCC
1 AAAATTACATTTTT-ACCCC
34413418 GATTTCACCA
Statistics
Matches: 82, Mismatches: 17, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 19 0.23
29 47 0.57
30 8 0.10
31 4 0.05
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (28 bp):
AAAATTACATTTTTACCCCAAACTTCCT
Found at i:34413430 original size:29 final size:29
Alignment explanation
Indices: 34413398--34413499 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 29
34413388 TAAACTTTCT
34413398 AAAATTCCATTTTTCACCCCGATTTCACCA
1 AAAATTCCATTTTTCACCCCGATTT-ACCA
* ***
34413428 AAAATTACATTTTATC-CCTAAACTTT-CC-
1 AAAATTCCATTTT-TCACCCCGA-TTTACCA
* *
34413456 AAAATCCCATTTTTAACCCCGATTTTACCA
1 AAAATTCCATTTTTCACCCCGA-TTTACCA
34413486 AAAATTACCATTTT
1 AAAATT-CCATTTT
34413500 ATTTCTCGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
27 1 0.02
28 17 0.31
29 4 0.07
30 20 0.37
31 12 0.22
ACGTcount: A:0.34, C:0.27, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTCACCCCGATTTACCA
Found at i:34413440 original size:59 final size:60
Alignment explanation
Indices: 34413311--34413676 Score: 378
Period size: 58 Copynumber: 6.2 Consensus size: 60
34413301 AAAACTTCCT
* * *
34413311 AAAATTA-CATTTTTACCCAC-GAACTTTCCAAAATCCCA-TTTTAACCCCAATTTCACCA
1 AAAATTACCATTTTTACCC-CTGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
34413369 AAAATTA-CATTTTTGCCCCTAAACTTTCTAAAATTCCATTTTTCACCCCGATTTCACCA
1 AAAATTACCATTTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * * * *
34413428 AAAATTA-CA-TTTTATCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTTACCA
1 AAAATTACCATTTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
*** * * * * * *
34413486 AAAATTACCA-TTTTATTTCTCGAACTTTTTAAAATTTCATTTTTGACCTCGATTTTACCC
1 AAAATTACCATTTTTACCCCT-GAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
34413546 AAAATTACCA-TTTTACCCCCTGAACTTTCTAAAATTCCATTTTAAACCTCAATTTCACC-
1 AAAATTACCATTTTTA-CCCCTGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
* * *
34413605 AAAATTACCA-TTTTACCCCT-AATTTTCTAAAATTTCATTTTAAACCCCGA-TTCACCCA
1 AAAATTACCATTTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCA-CCA
34413663 AAAATTACCATTTT
1 AAAATTACCATTTT
34413677 GCCCCCGAAA
Statistics
Matches: 265, Mismatches: 35, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
56 4 0.02
57 29 0.11
58 97 0.37
59 55 0.21
60 78 0.29
61 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.37
Consensus pattern (60 bp):
AAAATTACCATTTTTACCCCTGAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCA
Found at i:34413587 original size:29 final size:27
Alignment explanation
Indices: 34413546--34413646 Score: 89
Period size: 30 Copynumber: 3.6 Consensus size: 27
34413536 GATTTTACCC
34413546 AAAATTACCATTTTACCCCCTGAACTTTCT
1 AAAATTACCATTTTA-CCCCT-AA-TTTCT
** *
34413576 AAAATT-CCATTTTAAACCTCAATTTCACC
1 AAAATTACCATTTTACCCCT-AATTT--CT
34413605 AAAATTACCATTTTACCCCTAATTTTCT
1 AAAATTACCATTTTACCCCTAA-TTTCT
*
34413633 AAAATT-TCATTTTA
1 AAAATTACCATTTTA
34413647 AACCCCGATT
Statistics
Matches: 59, Mismatches: 8, Indels: 11
0.76 0.10 0.14
Matches are distributed among these distances:
27 10 0.17
28 12 0.20
29 17 0.29
30 20 0.34
ACGTcount: A:0.35, C:0.25, G:0.01, T:0.40
Consensus pattern (27 bp):
AAAATTACCATTTTACCCCTAATTTCT
Found at i:34413651 original size:29 final size:28
Alignment explanation
Indices: 34413546--34413652 Score: 92
Period size: 29 Copynumber: 3.7 Consensus size: 28
34413536 GATTTTACCC
* *
34413546 AAAATTACCATTTTACCCCCTGAACTTTCT
1 AAAATT-CCATTTTAACCCCT-AATTTTCT
* * *
34413576 AAAATTCCATTTTAA-ACCTCAATTTCACC
1 AAAATTCCATTTTAACCCCT-AATTT-TCT
34413605 AAAATTACCATTTT-ACCCCTAATTTTCT
1 AAAATT-CCATTTTAACCCCTAATTTTCT
*
34413633 AAAATTTCATTTTAAACCCC
1 AAAATTCCATTTT-AACCCC
34413653 GATTCACCCA
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
27 6 0.10
28 14 0.23
29 26 0.42
30 16 0.26
ACGTcount: A:0.35, C:0.27, G:0.01, T:0.37
Consensus pattern (28 bp):
AAAATTCCATTTTAACCCCTAATTTTCT
Found at i:34417032 original size:15 final size:16
Alignment explanation
Indices: 34417012--34417043 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
34417002 AAAATTTCGA
34417012 AGTAATAAT-AATAAT
1 AGTAATAATAAATAAT
34417027 AGTAATAATAAATAAT
1 AGTAATAATAAATAAT
34417043 A
1 A
34417044 AATTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
AGTAATAATAAATAAT
Found at i:34418132 original size:7 final size:7
Alignment explanation
Indices: 34418107--34418171 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
34418097 TGAAAAAAAT
34418107 TCAACGG
1 TCAACGG
*
34418114 TCAA-AG
1 TCAACGG
34418120 TCAACGG
1 TCAACGG
*
34418127 TTAACGG
1 TCAACGG
34418134 TCAAC-G
1 TCAACGG
*
34418140 TCAACTG
1 TCAACGG
*
34418147 TCAATGG
1 TCAACGG
*
34418154 TCAATGG
1 TCAACGG
34418161 TCAACGG
1 TCAACGG
34418168 TCAA
1 TCAA
34418172 AGTCAATAGC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
6 11 0.22
7 38 0.78
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (7 bp):
TCAACGG
Found at i:34418134 original size:20 final size:20
Alignment explanation
Indices: 34418107--34418171 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
34418097 TGAAAAAAAT
34418107 TCAACGGTCAAAGTCAACGG
1 TCAACGGTCAAAGTCAACGG
* * *
34418127 TTAACGGTCAACGTCAACTG
1 TCAACGGTCAAAGTCAACGG
* *
34418147 TCAATGGTCAATGGTCAACGG
1 TCAACGGTCAA-AGTCAACGG
34418168 TCAA
1 TCAA
34418172 AGTCAATAGC
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 26 0.70
21 11 0.30
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (20 bp):
TCAACGGTCAAAGTCAACGG
Found at i:34418176 original size:27 final size:27
Alignment explanation
Indices: 34418107--34418178 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
34418097 TGAAAAAAAT
* *
34418107 TCAACGGTCAAAGTCAACGGTTAACGG
1 TCAACGGTCAAAGTCAATGGTCAACGG
* *
34418134 TCAAC-GTCAACTGTCAATGGTCAATGG
1 TCAACGGTCAA-AGTCAATGGTCAACGG
34418161 TCAACGGTCAAAGTCAAT
1 TCAACGGTCAAAGTCAAT
34418179 AGCCGGTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 5 0.13
27 28 0.74
28 5 0.13
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.22
Consensus pattern (27 bp):
TCAACGGTCAAAGTCAATGGTCAACGG
Found at i:34424039 original size:51 final size:52
Alignment explanation
Indices: 34423807--34424047 Score: 337
Period size: 52 Copynumber: 4.7 Consensus size: 52
34423797 TTTGCGTTTG
* * * * * *
34423807 ATACTCATGATGACATAG-AGTCATCGAACC-CTTAATTCGCAATGGATTCAT
1 ATACTCACGATGACA-CGTAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
* * *
34423858 ATACTCACGATGACACGCAGTCATCAGACCTCTTAATCCGTAAAAGATTCAT
1 ATACTCACGATGACACGTAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
*
34423910 ATACTCA-GAATGACACGTAGTCATCGGACCTCTTAATCCTTAAAGGATTCAT
1 ATACTCACG-ATGACACGTAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
*
34423962 ATACTCACGATGACACGTAGTAATCGGACCTCTTAATCCGTAAAGGATT-AT
1 ATACTCACGATGACACGTAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
34424013 ATACTCACGATGACACGTAGTCATCGGACCTCTTA
1 ATACTCACGATGACACGTAGTCATCGGACCTCTTA
34424048 CATTTACGGC
Statistics
Matches: 171, Mismatches: 15, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
50 1 0.01
51 61 0.36
52 108 0.63
53 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACGTAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
Found at i:34425434 original size:21 final size:21
Alignment explanation
Indices: 34425386--34425437 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
34425376 GGAGTTTTTA
*
34425386 GTATCGGTAGAAGCATGACAT
1 GTATCGGTAAAAGCATGACAT
* *
34425407 GTTTCGGTAAAAGTCATG-CTT
1 GTATCGGTAAAAG-CATGACAT
34425428 GTATCGGTAA
1 GTATCGGTAA
34425438 TATTATCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (21 bp):
GTATCGGTAAAAGCATGACAT
Found at i:34431974 original size:21 final size:21
Alignment explanation
Indices: 34431899--34431976 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
34431889 CTGGAGTTTT
34431899 TAGTATCGGTAGAAGCATCAC
1 TAGTATCGGTAGAAGCATCAC
** * **
34431920 TTTTTTCGGTAGAAGTGTCAC
1 TAGTATCGGTAGAAGCATCAC
* ** *
34431941 TTGTATCAATAGAACCATCAC
1 TAGTATCGGTAGAAGCATCAC
34431962 TAGTATCGGTAGAAG
1 TAGTATCGGTAGAAG
34431977 TCTGCTATTA
Statistics
Matches: 41, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.31
Consensus pattern (21 bp):
TAGTATCGGTAGAAGCATCAC
Found at i:34434496 original size:19 final size:19
Alignment explanation
Indices: 34434474--34434512 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
34434464 CTTTTATATC
34434474 ATCCTT-GAAAATCAATTAA
1 ATCCTTAGAAAAT-AATTAA
*
34434493 ATCCTTATAAAATAATTAA
1 ATCCTTAGAAAATAATTAA
34434512 A
1 A
34434513 AAAATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.51, C:0.13, G:0.03, T:0.33
Consensus pattern (19 bp):
ATCCTTAGAAAATAATTAA
Found at i:34440681 original size:19 final size:19
Alignment explanation
Indices: 34440657--34440707 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
34440647 TACATGTTAA
34440657 AATATTATAAAAATAAAAT
1 AATATTATAAAAATAAAAT
*
34440676 AATATT-TAAAATATATAAT
1 AATATTATAAAA-ATAAAAT
*
34440695 -TTATTA-AAAAATA
1 AATATTATAAAAATA
34440708 TAATTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
17 3 0.11
18 13 0.46
19 12 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
AATATTATAAAAATAAAAT
Found at i:34440701 original size:17 final size:17
Alignment explanation
Indices: 34440681--34440713 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
34440671 AAAATAATAT
*
34440681 TTAAAATATATAATTTA
1 TTAAAAAATATAATTTA
34440698 TTAAAAAATATAATTT
1 TTAAAAAATATAATTT
34440714 TTTTTACACA
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TTAAAAAATATAATTTA
Found at i:34441238 original size:79 final size:79
Alignment explanation
Indices: 34441147--34441304 Score: 280
Period size: 79 Copynumber: 2.0 Consensus size: 79
34441137 TACTCAACTT
*
34441147 CATATGAATGGCAATACCATTCAAACCATATTCAACGTGATCCCTCCATTAAGTGGTTTGGTTGT
1 CATATGAATGGCAATACCATTCAAACCATATTCAACGTGACCCCTCCATTAAGTGGTTTGGTTGT
*
34441212 TGTTAATACTATTA
66 TGGTAATACTATTA
* *
34441226 CATATGAATGGCAATGCCATTCAAGCCATATTCAACGTGACCCCTCCATTAAGTGGTTTGGTTGT
1 CATATGAATGGCAATACCATTCAAACCATATTCAACGTGACCCCTCCATTAAGTGGTTTGGTTGT
34441291 TGGTAATACTATTA
66 TGGTAATACTATTA
34441305 AGACGAATAG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
79 75 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (79 bp):
CATATGAATGGCAATACCATTCAAACCATATTCAACGTGACCCCTCCATTAAGTGGTTTGGTTGT
TGGTAATACTATTA
Found at i:34443444 original size:30 final size:29
Alignment explanation
Indices: 34443376--34443613 Score: 215
Period size: 30 Copynumber: 7.9 Consensus size: 29
34443366 GTTCGAAGGT
* * *
34443376 AAAATCTAATTTTGGAAAAAGTTTGGGGGTC
1 AAAATGTAATTTT-TAAAAAGTTT-AGGGTC
*
34443407 AAAAATGTAATTTTTAAAAAGTTTAGGGATT
1 -AAAATGTAATTTTTAAAAAGTTTAGGG-TC
* * *
34443438 AAAATGTAATTTTTAGAAAGTTTTGGGCC
1 AAAATGTAATTTTTAAAAAGTTTAGGGTC
* *
34443467 AAAATGTAATGTTTAGAAAGTTTAAGGGTC
1 AAAATGTAATTTTTAAAAAGTTT-AGGGTC
*
34443497 AAAATGTAATTTTTAAAAAGTTTTAGGGTT
1 AAAATGTAATTTTTAAAAAG-TTTAGGGTC
* *
34443527 AAAATATAATTTTTAAAAAGTTTTGGGGTC
1 AAAATGTAATTTTTAAAAAG-TTTAGGGTC
* ** * *
34443557 AAAATATAATTTTGGAAATGTTCAGGGGTC
1 AAAATGTAATTTTTAAAAAGTTTA-GGGTC
* * * *
34443587 AAAATATAATTTCTAGATAGTTTAGGG
1 AAAATGTAATTTTTAAAAAGTTTAGGG
34443614 ACCTATAAGC
Statistics
Matches: 173, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
29 27 0.16
30 121 0.70
31 13 0.08
32 12 0.07
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTAAAAAGTTTAGGGTC
Done.