Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 181 of 295
Found at i:57252651 original size:20 final size:20
Alignment explanation
Indices: 57252588--57252652 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
57252578 AGTTTTTCCC
* * * *
57252588 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
57252608 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
57252627 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
57252648 AGCTC
1 AGCTC
57252653 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:57253887 original size:10 final size:10
Alignment explanation
Indices: 57253872--57253909 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
57253862 GCTCGTTTCC
*
57253872 AGCTCACTCG
1 AGCTCAATCG
57253882 AGCTCAAGTC-
1 AGCTCAA-TCG
57253892 AGCTCAATCG
1 AGCTCAATCG
57253902 AGCTCAAT
1 AGCTCAAT
57253910 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:57253896 original size:20 final size:20
Alignment explanation
Indices: 57253871--57253908 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
57253861 AGCTCGTTTC
*
57253871 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
57253891 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
57253909 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:57253915 original size:20 final size:20
Alignment explanation
Indices: 57253872--57253932 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
57253862 GCTCGTTTCC
* * *
57253872 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
57253892 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
57253912 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
57253932 A
1 A
57253933 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:57253926 original size:11 final size:10
Alignment explanation
Indices: 57253882--57253928 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
57253872 AGCTCACTCG
*
57253882 AGCTCAAGTC
1 AGCTCAATTC
57253892 AGCTCAA-TC
1 AGCTCAATTC
*
57253901 GAGCTCAATTT
1 -AGCTCAATTC
57253912 AGCTACAATTC
1 AGCT-CAATTC
57253923 AGCTCA
1 AGCTCA
57253929 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:57265302 original size:21 final size:21
Alignment explanation
Indices: 57265276--57265315 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
57265266 TTGAGCTCGT
*
57265276 TTTAGCTCGTTTGAGCTCAAA
1 TTTAGCTCGTTTCAGCTCAAA
57265297 TTTAGCTCGTTTCAGCTCA
1 TTTAGCTCGTTTCAGCTCA
57265316 TTCCTTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TTTAGCTCGTTTCAGCTCAAA
Found at i:57267454 original size:19 final size:20
Alignment explanation
Indices: 57267422--57267462 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
57267412 GAATGAAATC
57267422 GAGAGAAGAAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
57267442 GAGAGAA-AAACAAAGAAAA
1 GAGAGAAGAAACAAAGAAAA
57267461 GA
1 GA
57267463 AAATGAGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.71, C:0.05, G:0.24, T:0.00
Consensus pattern (20 bp):
GAGAGAAGAAACAAAGAAAA
Found at i:57275320 original size:15 final size:14
Alignment explanation
Indices: 57275284--57275338 Score: 65
Period size: 15 Copynumber: 3.8 Consensus size: 14
57275274 TCTATTGATC
57275284 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
57275298 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
*
57275312 GAGTGAAAAGAAAAA
1 GAG-AAAAAGAAAAA
*
57275327 GAAAGAAAAGAA
1 GAGA-AAAAGAA
57275339 TGAGGAGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
14 16 0.47
15 18 0.53
ACGTcount: A:0.75, C:0.02, G:0.22, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:57288105 original size:11 final size:12
Alignment explanation
Indices: 57288079--57288109 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
57288069 TTCTTTTTGG
57288079 TTTTCAAAGGCT
1 TTTTCAAAGGCT
57288091 TTTTCAAAGGCT
1 TTTTCAAAGGCT
57288103 TTTTCAA
1 TTTTCAA
57288110 TTTCTCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.13, T:0.45
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:57288167 original size:5 final size:5
Alignment explanation
Indices: 57288157--57288213 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57288147 CTCTTGCCTC
*
57288157 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCTCTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T-CT-TT TCTTT
57288204 TCTTT TCTTT
1 TCTTT TCTTT
57288214 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 28 0.64
6 8 0.18
7 4 0.09
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:57290833 original size:30 final size:30
Alignment explanation
Indices: 57290748--57290844 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
57290738 TAAACTAAAA
* *
57290748 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCCTGAGCTGAAGT
* * * * *
57290778 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCCTGAGCTGAAGT
*
57290808 TGAGCTAAGGTTTAGCTCTTGAGCTGAA-T
1 TGAGCTAAGGTTTAGCTCCTGAGCTGAAGT
57290837 ATGAGCTA
1 -TGAGCTA
57290845 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCCTGAGCTGAAGT
Found at i:57299195 original size:21 final size:21
Alignment explanation
Indices: 57299169--57299231 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
57299159 TTGGTATTTG
57299169 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
57299190 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
57299211 GGTATTTGGTACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
57299232 ACGGTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 22 0.59
22 15 0.41
ACGTcount: A:0.30, C:0.03, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:57301740 original size:12 final size:12
Alignment explanation
Indices: 57301725--57301792 Score: 68
Period size: 12 Copynumber: 5.5 Consensus size: 12
57301715 TTTTGCTCGA
*
57301725 TTTTTTTTCACT
1 TTTTTTTTCAAT
*
57301737 TTTTTTTTGAAT
1 TTTTTTTTCAAT
57301749 TTTTTTTCAATCAAT
1 TTTTTTT---TCAAT
57301764 TTTTTTTTCGAAT
1 TTTTTTTTC-AAT
57301777 TTTTTTTT--AT
1 TTTTTTTTCAAT
57301787 TTTTTT
1 TTTTTT
57301793 GTTACTCCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
10 8 0.16
12 19 0.39
13 11 0.22
15 11 0.22
ACGTcount: A:0.15, C:0.07, G:0.03, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:57301752 original size:13 final size:13
Alignment explanation
Indices: 57301736--57301784 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
57301726 TTTTTTTCAC
57301736 TTTTTTTTTGAAT
1 TTTTTTTTTGAAT
* *
57301749 TTTTTTTCAATCAAT
1 TTTTTTT--TTGAAT
*
57301764 TTTTTTTTCGAAT
1 TTTTTTTTTGAAT
57301777 TTTTTTTT
1 TTTTTTTT
57301785 ATTTTTTTGT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
13 18 0.62
15 11 0.38
ACGTcount: A:0.16, C:0.06, G:0.04, T:0.73
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:57312197 original size:21 final size:21
Alignment explanation
Indices: 57312168--57312223 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
57312158 CAAGCTCTCT
*
57312168 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
57312189 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
57312210 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
57312224 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:57312216 original size:14 final size:14
Alignment explanation
Indices: 57312167--57312223 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
57312157 TCAAGCTCTC
57312167 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
57312180 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
57312194 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
57312208 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
57312222 TT
1 TT
57312224 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:57312280 original size:21 final size:23
Alignment explanation
Indices: 57312244--57312286 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
57312234 TTTGATTTCT
57312244 TTTTCTTTTGCAATTTCTTTTTG
1 TTTTCTTTTGCAATTTCTTTTTG
57312267 TTTTC-TTT-CAATTTCTTTTT
1 TTTTCTTTTGCAATTTCTTTTT
57312287 CAATCTCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
22 3 0.15
23 5 0.25
ACGTcount: A:0.09, C:0.14, G:0.05, T:0.72
Consensus pattern (23 bp):
TTTTCTTTTGCAATTTCTTTTTG
Found at i:57313371 original size:12 final size:12
Alignment explanation
Indices: 57313356--57313424 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 12
57313346 TTTTGCTCGA
*
57313356 TTTTTTTC-ACT
1 TTTTTTTCAATT
*
57313367 TTTTTTTGAATTT
1 TTTTTTTCAA-TT
57313380 TTTTTTCAATCAATT
1 TTTTTT---TCAATT
57313395 TTTTTTTCGAATT
1 TTTTTTTC-AATT
*
57313408 TTTTTTT-GATT
1 TTTTTTTCAATT
57313419 TTTTTT
1 TTTTTT
57313425 GTTACTCCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
11 16 0.33
12 3 0.06
13 18 0.38
15 8 0.17
16 3 0.06
ACGTcount: A:0.14, C:0.07, G:0.04, T:0.74
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:57313382 original size:13 final size:13
Alignment explanation
Indices: 57313366--57313424 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 13
57313356 TTTTTTTCAC
57313366 TTTTTTTTGAATT
1 TTTTTTTTGAATT
*
57313379 TTTTTTTCAATCAATT
1 TTTTTTT---TGAATT
*
57313395 TTTTTTTCGAA-T
1 TTTTTTTTGAATT
57313407 TTTTTTTTG-ATT
1 TTTTTTTTGAATT
57313419 TTTTTT
1 TTTTTT
57313425 GTTACTCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
11 1 0.03
12 16 0.42
13 9 0.24
16 12 0.32
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTTTTTTGAATT
Found at i:57315041 original size:20 final size:19
Alignment explanation
Indices: 57315018--57315082 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
57315008 AAGCTCAAAC
57315018 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
57315038 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
57315058 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
57315078 GAGCT
1 GAGCT
57315083 GGGAAAAAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:57319569 original size:29 final size:29
Alignment explanation
Indices: 57319506--57319573 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
57319496 TAATCAACCG
57319506 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
57319535 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
57319564 CGCACACTTA
1 CGCACACTTA
57319574 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:57319686 original size:174 final size:174
Alignment explanation
Indices: 57319395--57319722 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
57319385 AACTCAAGGT
* *
57319395 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
57319460 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
57319525 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
*
57319569 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
57319634 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
57319699 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
57319723 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:57319714 original size:29 final size:30
Alignment explanation
Indices: 57319675--57319753 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
57319665 CTTAATAATC
57319675 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
57319705 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
57319734 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
57319754 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:57321818 original size:11 final size:11
Alignment explanation
Indices: 57321802--57321844 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
57321792 TGCAGATTCA
57321802 AAAAAAAATCG
1 AAAAAAAATCG
*
57321813 AAAAAAAAAATCA
1 --AAAAAAAATCG
*
57321826 AAAAAAAATTG
1 AAAAAAAATCG
57321837 AAAAAAAA
1 AAAAAAAA
57321845 ATTTGAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.81, C:0.05, G:0.05, T:0.09
Consensus pattern (11 bp):
AAAAAAAATCG
Found at i:57321819 original size:13 final size:13
Alignment explanation
Indices: 57321801--57321860 Score: 79
Period size: 13 Copynumber: 4.8 Consensus size: 13
57321791 TTGCAGATTC
57321801 AAAAAAAAATCGA
1 AAAAAAAAATCGA
57321814 AAAAAAAAATC--
1 AAAAAAAAATCGA
*
57321825 AAAAAAAAATTGA
1 AAAAAAAAATCGA
* *
57321838 AAAAAAAATTTGA
1 AAAAAAAAATCGA
57321851 AAAAAAAAAT
1 AAAAAAAAAT
57321861 TGCATACGGT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
11 10 0.24
13 32 0.76
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.13
Consensus pattern (13 bp):
AAAAAAAAATCGA
Found at i:57321831 original size:24 final size:24
Alignment explanation
Indices: 57321799--57321845 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
57321789 AATTGCAGAT
57321799 TCAAAAAAAAATCGAAAAAAAAAA
1 TCAAAAAAAAATCGAAAAAAAAAA
*
57321823 TCAAAAAAAAATTGAAAAAAAAA
1 TCAAAAAAAAATCGAAAAAAAAA
57321846 TTTGAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.79, C:0.06, G:0.04, T:0.11
Consensus pattern (24 bp):
TCAAAAAAAAATCGAAAAAAAAAA
Found at i:57328459 original size:29 final size:27
Alignment explanation
Indices: 57328418--57328483 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 27
57328408 TTTTTCGCTT
*
57328418 TTTCTTTTCCAATTTT-TTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
57328447 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
57328474 TTTCTTTTTC
1 TTTCTTTTTC
57328484 TCTCACTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 13 0.38
28 1 0.03
29 15 0.44
30 5 0.15
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:57328467 original size:12 final size:12
Alignment explanation
Indices: 57328443--57328573 Score: 54
Period size: 12 Copynumber: 10.9 Consensus size: 12
57328433 TTTTTCATTC
57328443 TCAATTTCTTTT
1 TCAATTTCTTTT
57328455 TCAATTTTCTTTTCT
1 TCAA-TTTC-TTT-T
*
57328470 TCATTTTCTTTT
1 TCAATTTCTTTT
** **
57328482 TCTCTCACTTTT
1 TCAATTTCTTTT
*
57328494 TCGATTTCTTTT
1 TCAATTTCTTTT
* **
57328506 TC-TTTTGCAATT
1 TCAATTT-CTTTT
**
57328518 TCTTTTTCTTTT
1 TCAATTTCTTTT
**
57328530 TCGTTTTCTTTT
1 TCAATTTCTTTT
* *
57328542 T--GTTT-TCTT
1 TCAATTTCTTTT
57328551 TCAATTTCTTTT
1 TCAATTTCTTTT
*
57328563 TCAATCTCTTT
1 TCAATTTCTTT
57328574 CTCCTTTTCT
Statistics
Matches: 91, Mismatches: 20, Indels: 16
0.72 0.16 0.13
Matches are distributed among these distances:
9 4 0.04
10 3 0.03
11 6 0.07
12 56 0.62
13 11 0.12
14 7 0.08
15 4 0.04
ACGTcount: A:0.10, C:0.19, G:0.03, T:0.68
Consensus pattern (12 bp):
TCAATTTCTTTT
Found at i:57328542 original size:18 final size:18
Alignment explanation
Indices: 57328433--57328547 Score: 79
Period size: 18 Copynumber: 6.2 Consensus size: 18
57328423 TTTCCAATTT
* **
57328433 TTTTTCATTCTCAATTTC
1 TTTTTCATTTTCTTTTTC
57328451 TTTTTCAATTTTCTTTTCTTC
1 TTTTTC-ATTTTC-TTT-TTC
* * * **
57328472 ATTTTCTTTTTCTCTCAC
1 TTTTTCATTTTCTTTTTC
57328490 TTTTTCGA-TTTCTTTTTC
1 TTTTTC-ATTTTCTTTTTC
* *
57328508 TTTTGCAATTTCTTTTTC
1 TTTTTCATTTTCTTTTTC
* *
57328526 TTTTTCGTTTTCTTTTTG
1 TTTTTCATTTTCTTTTTC
57328544 TTTT
1 TTTT
57328548 CTTTCAATTT
Statistics
Matches: 74, Mismatches: 18, Indels: 10
0.73 0.18 0.10
Matches are distributed among these distances:
17 1 0.01
18 52 0.70
19 7 0.09
20 6 0.08
21 8 0.11
ACGTcount: A:0.09, C:0.18, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTTTCATTTTCTTTTTC
Found at i:57328564 original size:6 final size:6
Alignment explanation
Indices: 57328447--57328551 Score: 68
Period size: 6 Copynumber: 17.2 Consensus size: 6
57328437 TCATTCTCAA
* * * ** **
57328447 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** * *
57328498 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
57328545 TTTCTT T
1 TTTCTT T
57328552 CAATTTCTTT
Statistics
Matches: 71, Mismatches: 25, Indels: 6
0.70 0.25 0.06
Matches are distributed among these distances:
5 4 0.06
6 55 0.77
7 9 0.13
8 3 0.04
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:57329638 original size:10 final size:10
Alignment explanation
Indices: 57329610--57329648 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
57329600 TTGTCACTTC
**
57329610 TTTTTTTTCC
1 TTTTTTTTGA
57329620 TTTTTTTTGA
1 TTTTTTTTGA
57329630 TTTTTTTTGAA
1 TTTTTTTTG-A
57329641 TTTTTTTT
1 TTTTTTTT
57329649 TGAATTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (10 bp):
TTTTTTTTGA
Found at i:57329649 original size:12 final size:12
Alignment explanation
Indices: 57329620--57329655 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
57329610 TTTTTTTTCC
57329620 TTTTTTTTG-A-
1 TTTTTTTTGAAT
57329630 TTTTTTTTGAAT
1 TTTTTTTTGAAT
57329642 TTTTTTTTGAAT
1 TTTTTTTTGAAT
57329654 TT
1 TT
57329656 CTTCTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.38
11 1 0.04
12 14 0.58
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:57331219 original size:30 final size:30
Alignment explanation
Indices: 57331185--57331281 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
57331175 TAAACTAAAA
57331185 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
57331215 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
57331245 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
57331275 TGAGCTA
1 TGAGCTA
57331282 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:57333119 original size:20 final size:20
Alignment explanation
Indices: 57333063--57333119 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
57333053 AGCTCCGTTT
* *
57333063 AGCTCATTTCCAGCTCACTCG
1 AGCTCAATT-CAGCTCACTCA
* *
57333084 AGCTCAAGTCAACTCACTCA
1 AGCTCAATTCAGCTCACTCA
57333104 AGCTCAATTCAGCTCA
1 AGCTCAATTCAGCTCA
57333120 ATCTTAACCC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.28, C:0.35, G:0.12, T:0.25
Consensus pattern (20 bp):
AGCTCAATTCAGCTCACTCA
Found at i:57334558 original size:28 final size:28
Alignment explanation
Indices: 57334494--57334558 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
57334484 TGGAGTAACA
* *
57334494 AAAAAATAAAAAAATTCGAAAAAAAATTG
1 AAAAAA-AAAAAAATTCAAAAAAAAAGTG
***
57334523 ATTGAAAAAAAAATTCAAAAAAAAAGTG
1 AAAAAAAAAAAAATTCAAAAAAAAAGTG
57334551 AAAAAAAA
1 AAAAAAAA
57334559 TCGAGCAAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
28 25 0.89
29 3 0.11
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (28 bp):
AAAAAAAAAAAAATTCAAAAAAAAAGTG
Found at i:57336747 original size:48 final size:48
Alignment explanation
Indices: 57336646--57336751 Score: 128
Period size: 48 Copynumber: 2.2 Consensus size: 48
57336636 GAGTGTCATG
*
57336646 GAAAAAGAAATTGAGATTGAAAAAGGATGTGAAAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAAAAAGAGAAAGAAATC
* * *
57336694 AAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAA-AGAGA-AAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA--AAAAGAGAAAGAAATC
57336742 GAAAAAGAAA
1 GAAAAAGAAA
57336752 GAAAAGACAA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
48 38 0.76
49 8 0.16
50 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.24, T:0.14
Consensus pattern (48 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAAAAAGAGAAAGAAATC
Found at i:57338468 original size:20 final size:20
Alignment explanation
Indices: 57338422--57338459 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57338412 AGCTCATTTC
*
57338422 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
*
57338442 CAACTCACTCAAGCTCAA
1 CAGCTCACTCAAGCTCAA
57338460 TTTAGCTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.37, G:0.13, T:0.18
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:57341908 original size:10 final size:10
Alignment explanation
Indices: 57341893--57341942 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
57341883 AACTCCGACC
57341893 AGCTCAATTG
1 AGCTCAATTG
* *
57341903 AGCTCATTTC
1 AGCTCAATTG
*
57341913 AGCTCAATCG
1 AGCTCAATTG
*
57341923 AGCTCAATTT
1 AGCTCAATTG
57341933 AGCTACAATT
1 AGCT-CAATT
57341943 CAGATCATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
10 27 0.84
11 5 0.16
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (10 bp):
AGCTCAATTG
Found at i:57341915 original size:20 final size:20
Alignment explanation
Indices: 57341892--57341952 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
57341882 CAACTCCGAC
57341892 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
57341912 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
* *
57341933 -AGCTACAATTCAGATCATTT
1 CAGCT-CAATTGAGCTCATTT
57341953 ATTTTATTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 23 0.66
21 12 0.34
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:57343331 original size:12 final size:13
Alignment explanation
Indices: 57343301--57343334 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
57343291 TTGGATTTAA
57343301 AAAAAAAGAAATTC
1 AAAAAAA-AAATTC
57343315 AAAAAAAAAATTC
1 AAAAAAAAAATTC
57343328 AAAAAAA
1 AAAAAAA
57343335 TCGAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (13 bp):
AAAAAAAAAATTC
Found at i:57344413 original size:12 final size:12
Alignment explanation
Indices: 57344392--57344498 Score: 53
Period size: 12 Copynumber: 8.9 Consensus size: 12
57344382 AGAAAAGGAG
*
57344392 AAAGAGATTGAA
1 AAAGAAATTGAA
57344404 AAAGAAATTGAA
1 AAAGAAATTGAA
57344416 AGAA-AAA---AA
1 A-AAGAAATTGAA
**
57344425 AAAGAAAACGAA
1 AAAGAAATTGAA
*
57344437 AAAGAAA-TCAA
1 AAAGAAATTGAA
** **
57344448 AATAGTGAGAGAA
1 AA-AGAAATTGAA
*
57344461 AAAGAAAATGAAGA
1 AAAGAAATTG-A-A
57344475 AAAGAAAATTGAA
1 AAAG-AAATTGAA
57344488 AAAGAAATTGA
1 AAAGAAATTGA
57344499 GATTGAGAAA
Statistics
Matches: 73, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
8 2 0.03
9 6 0.08
11 4 0.05
12 38 0.52
13 12 0.16
14 6 0.08
15 5 0.07
ACGTcount: A:0.68, C:0.02, G:0.19, T:0.11
Consensus pattern (12 bp):
AAAGAAATTGAA
Found at i:57344503 original size:18 final size:18
Alignment explanation
Indices: 57344482--57344516 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57344472 AGAAAAGAAA
57344482 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
57344500 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
57344517 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:57346815 original size:22 final size:22
Alignment explanation
Indices: 57346787--57346830 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
57346777 TTTTGAACCA
*
57346787 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCATACCAAATCCC
*
57346809 TTACCATTTCATACCAATTCCC
1 TTACCATTTCATACCAAATCCC
57346831 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.36, G:0.02, T:0.34
Consensus pattern (22 bp):
TTACCATTTCATACCAAATCCC
Found at i:57349363 original size:22 final size:22
Alignment explanation
Indices: 57349336--57349383 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
57349326 CAATCTTTGG
*
57349336 AGAATTTGAAAGA-ACTGAAAA
1 AGAAATTGAAAGAGACTGAAAA
* *
57349357 AGAAATTGAGAGAGAGTGAAAA
1 AGAAATTGAAAGAGACTGAAAA
57349379 AGAAA
1 AGAAA
57349384 AGAAAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (22 bp):
AGAAATTGAAAGAGACTGAAAA
Found at i:57351714 original size:22 final size:22
Alignment explanation
Indices: 57351686--57351729 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
57351676 TTTTGAACCA
*
57351686 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCATACCAAATCCC
*
57351708 TTACCATTTCATACCAATTCCC
1 TTACCATTTCATACCAAATCCC
57351730 AAATACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.27, C:0.36, G:0.02, T:0.34
Consensus pattern (22 bp):
TTACCATTTCATACCAAATCCC
Found at i:57353077 original size:10 final size:10
Alignment explanation
Indices: 57353061--57353118 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
57353051 CAACTCCTAC
57353061 CAGCTCAATT
1 CAGCTCAATT
* *
57353071 GAGCTCATTT
1 CAGCTCAATT
57353081 CAGCTCAA-T
1 CAGCTCAATT
57353090 CGAGCTCAATT
1 C-AGCTCAATT
*
57353101 TAGCTACAATT
1 CAGCT-CAATT
57353112 CAGCTCA
1 CAGCTCA
57353119 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:57353084 original size:20 final size:20
Alignment explanation
Indices: 57353061--57353121 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
57353051 CAACTCCTAC
57353061 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
57353081 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
57353102 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
57353122 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:57354496 original size:11 final size:11
Alignment explanation
Indices: 57354480--57354514 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
57354470 AAAAAAGAAG
57354480 AAATTCAAAAA
1 AAATTCAAAAA
57354491 AAATTC-AAAA
1 AAATTCAAAAA
*
57354501 AAATTGAAAAA
1 AAATTCAAAAA
57354512 AAA
1 AAA
57354515 AGAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.17
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:57354502 original size:10 final size:10
Alignment explanation
Indices: 57354480--57354513 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
57354470 AAAAAAGAAG
57354480 AAATTCAAAAA
1 AAATTC-AAAA
57354491 AAATTCAAAA
1 AAATTCAAAA
*
57354501 AAATTGAAAA
1 AAATTCAAAA
57354511 AAA
1 AAA
57354514 AAGAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.74, C:0.06, G:0.03, T:0.18
Consensus pattern (10 bp):
AAATTCAAAA
Found at i:57354573 original size:12 final size:12
Alignment explanation
Indices: 57354497--57354574 Score: 52
Period size: 12 Copynumber: 6.2 Consensus size: 12
57354487 AAAAAAATTC
*
57354497 AAAAAAATTGAA
1 AAAAAAAGTGAA
*
57354509 AAAAAAAG-AAA
1 AAAAAAAGTGAA
57354520 AAAAAGAAGTGACA
1 AAAAA-AAGTGA-A
*
57354534 AAAAAAA-TCGAGTT
1 AAAAAAAGT-GA--A
*
57354548 AAAAAAAGAAGAA
1 AAAAAAAG-TGAA
57354561 AAAAAAAGTGAA
1 AAAAAAAGTGAA
57354573 AA
1 AA
57354575 GTCTTGCGAG
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
11 7 0.14
12 16 0.31
13 13 0.25
14 13 0.25
15 2 0.04
ACGTcount: A:0.74, C:0.03, G:0.14, T:0.09
Consensus pattern (12 bp):
AAAAAAAGTGAA
Found at i:57355557 original size:18 final size:18
Alignment explanation
Indices: 57355536--57355570 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57355526 AGAAAAGAAA
57355536 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
57355554 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
57355571 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:57357652 original size:10 final size:10
Alignment explanation
Indices: 57357636--57357693 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
57357626 CAACTCCGAC
57357636 CAGCTCAATT
1 CAGCTCAATT
* *
57357646 GAGCTCATTT
1 CAGCTCAATT
57357656 CAGCTCAA-T
1 CAGCTCAATT
57357665 CGAGCTCAATT
1 C-AGCTCAATT
*
57357676 TAGCTACAATT
1 CAGCT-CAATT
57357687 CAGCTCA
1 CAGCTCA
57357694 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:57357659 original size:20 final size:20
Alignment explanation
Indices: 57357636--57357696 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
57357626 CAACTCCGAC
57357636 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
57357656 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
57357677 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
57357697 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:57362920 original size:30 final size:30
Alignment explanation
Indices: 57362866--57362950 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
57362856 TTCTTTTGTT
*
57362866 TCAATTTCTTTTTCATCTTCTTTTTCACTC
1 TCAATTTCTTTTTCATCTTCTTTTTCAATC
**
57362896 TCAAATTTCTTTTTGTTC-TCTTTTTCAATC
1 TC-AATTTCTTTTTCATCTTCTTTTTCAATC
* *
57362926 TCATTTTCTTTTTCATTTTCTTTTT
1 TCAATTTCTTTTTCATCTTCTTTTT
57362951 GGTTTTCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 11 0.24
30 22 0.48
31 13 0.28
ACGTcount: A:0.13, C:0.21, G:0.01, T:0.65
Consensus pattern (30 bp):
TCAATTTCTTTTTCATCTTCTTTTTCAATC
Found at i:57362957 original size:12 final size:12
Alignment explanation
Indices: 57362926--57362950 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
57362916 TTTTTCAATC
57362926 TCATTTTCTTTT
1 TCATTTTCTTTT
57362938 TCATTTTCTTTT
1 TCATTTTCTTTT
57362950 T
1 T
57362951 GGTTTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TCATTTTCTTTT
Found at i:57362968 original size:12 final size:12
Alignment explanation
Indices: 57362953--57362983 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
57362943 TTCTTTTTGG
*
57362953 TTTTCAAATGCT
1 TTTTCAAAGGCT
57362965 TTTTCAAAGGCT
1 TTTTCAAAGGCT
57362977 TTTTCAA
1 TTTTCAA
57362984 GTTCTCTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (12 bp):
TTTTCAAAGGCT
Found at i:57363041 original size:5 final size:5
Alignment explanation
Indices: 57363031--57363087 Score: 55
Period size: 5 Copynumber: 11.0 Consensus size: 5
57363021 CTCTTGCCTC
*
57363031 TCTTT TCTTT T-TATT TCATTT TCTTT T-TCT TCTTT TGCCTTT TCTTT
1 TCTTT TCTTT TCT-TT TC-TTT TCTTT TCTTT TCTTT T--CTTT TCTTT
57363078 TCTTT TCTTT
1 TCTTT TCTTT
57363088 ATTTTCTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
4 4 0.09
5 30 0.68
6 4 0.09
7 6 0.14
ACGTcount: A:0.04, C:0.19, G:0.02, T:0.75
Consensus pattern (5 bp):
TCTTT
Found at i:57363087 original size:15 final size:14
Alignment explanation
Indices: 57363031--57363094 Score: 65
Period size: 16 Copynumber: 4.2 Consensus size: 14
57363021 CTCTTGCCTC
57363031 TCTTTTCTTTTTATT
1 TCTTTTCTTTTT-TT
*
57363046 TCATTTTCTTTTTCT
1 TC-TTTTCTTTTTTT
57363061 TCTTTTGCCTTTTCTTT
1 TCTTTT--CTTTT-TTT
*
57363078 TCTTTTCTTTATTT
1 TCTTTTCTTTTTTT
57363092 TCT
1 TCT
57363095 CTTTACAAGA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
14 10 0.24
15 9 0.21
16 15 0.36
17 8 0.19
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.75
Consensus pattern (14 bp):
TCTTTTCTTTTTTT
Found at i:57363097 original size:21 final size:20
Alignment explanation
Indices: 57363029--57363098 Score: 54
Period size: 20 Copynumber: 3.4 Consensus size: 20
57363019 GCCTCTTGCC
57363029 TCTCTTTTCTTTTTATTTCATTT
1 TCTCTTTTC-TTTT-TTT-ATTT
***
57363052 TCT-TTTTCTTCTTTTGCCTT
1 TCTCTTTTCTT-TTTTTATTT
57363072 T-TCTTTTCTTTTCTTTATTT
1 TCTCTTTTCTTTT-TTTATTT
57363092 TCTCTTT
1 TCTCTTT
57363099 ACAAGAATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 3 0.08
20 15 0.41
21 9 0.24
22 7 0.19
23 3 0.08
ACGTcount: A:0.04, C:0.20, G:0.01, T:0.74
Consensus pattern (20 bp):
TCTCTTTTCTTTTTTTATTT
Found at i:57369125 original size:12 final size:12
Alignment explanation
Indices: 57369110--57369166 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 12
57369100 TTTTTTTCAC
57369110 TTTTTTTGAATTT
1 TTTTTTTGAA-TT
*
57369123 TTTTTTCAATCAATT
1 TTTTTT---TGAATT
57369138 TTTTTTTCGAATT
1 TTTTTTT-GAATT
*
57369151 TTTTTTCGAATT
1 TTTTTTTGAATT
57369163 TTTT
1 TTTT
57369167 GTTACTCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 10 0.27
13 16 0.43
15 8 0.22
16 3 0.08
ACGTcount: A:0.18, C:0.07, G:0.05, T:0.70
Consensus pattern (12 bp):
TTTTTTTGAATT
Found at i:57369152 original size:11 final size:12
Alignment explanation
Indices: 57369137--57369166 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
57369127 TTCAATCAAT
57369137 TTTTTTTTCGAA
1 TTTTTTTTCGAA
57369149 TTTTTTTTCGAA
1 TTTTTTTTCGAA
57369161 TTTTTT
1 TTTTTT
57369167 GTTACTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.07, G:0.07, T:0.73
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:57370785 original size:20 final size:19
Alignment explanation
Indices: 57370762--57370826 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
57370752 AAGCTCAAAC
57370762 GAGCTAAAGTAAGCTAAATT
1 GAGCTAAAGT-AGCTAAATT
57370782 GAGCTCAAACG-AGCTAAATT
1 GAGCT-AAA-GTAGCTAAATT
* * * *
57370802 AAGCTCATGTGAGCTAAATC
1 GAGCTAAAGT-AGCTAAATT
57370822 GAGCT
1 GAGCT
57370827 GGGAAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.83
21 3 0.08
22 1 0.03
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (19 bp):
GAGCTAAAGTAGCTAAATT
Found at i:57372640 original size:32 final size:32
Alignment explanation
Indices: 57372603--57372664 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
57372593 GATTACTCAC
57372603 TTCACTCG-TTTCTTTT-ACAGACTCTCTTTCTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTT
*
57372635 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
57372665 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 16 0.59
33 10 0.37
34 1 0.04
ACGTcount: A:0.13, C:0.27, G:0.06, T:0.53
Consensus pattern (32 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTT
Found at i:57372703 original size:18 final size:18
Alignment explanation
Indices: 57372679--57372722 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
57372669 TCTTTTTTCG
* *
57372679 CTTTTTCTTTTTCAATTT
1 CTTTTTCATTCTCAATTT
*
57372697 TTTTTTCATTCTCAATTT
1 CTTTTTCATTCTCAATTT
57372715 CTTTTTCA
1 CTTTTTCA
57372723 ATTTTCTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.14, C:0.18, G:0.00, T:0.68
Consensus pattern (18 bp):
CTTTTTCATTCTCAATTT
Found at i:57372718 original size:30 final size:27
Alignment explanation
Indices: 57372682--57372748 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 27
57372672 TTTTTCGCTT
*
57372682 TTTCTTTTTCAATTTTTTTTTCATTCTCAA
1 TTTCTTTTTCAATTTTCTTTTC--T-TCAA
*
57372712 TTTCTTTTTCAATTTTCTTTTCTTCAT
1 TTTCTTTTTCAATTTTCTTTTCTTCAA
57372739 TTTCTTTTTC
1 TTTCTTTTTC
57372749 TCTCACTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
27 13 0.37
28 1 0.03
30 21 0.60
ACGTcount: A:0.12, C:0.18, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTCTTTTTCAATTTTCTTTTCTTCAA
Found at i:57372722 original size:57 final size:52
Alignment explanation
Indices: 57372661--57372838 Score: 164
Period size: 57 Copynumber: 3.2 Consensus size: 52
57372651 TCAAGCTCTC
57372661 TTTCAATTTCTTTTTTCGCTTTTTCTTTTTCAATTTTTTTTTCATTCTCAATTTCTT
1 TTTCAATTTCTTTTTT--CTTTTTCTTTTTC--TTTTTTTTTCATT-TCAATTTCTT
* ** **
57372718 TTTCAATTTTCTTTTCTTCATTTTCTTTTTCTCTCACTTTTTCGATTTCTTTTTCTT
1 TTTCAA-TTTCTTTT-TTCTTTTTCTTTTTCT-T-TTTTTTTC-ATTTCAATTTCTT
*
57372775 TTGCAATTTC-TTTTTCTTTTT-TGTTTTCTTTTTGTTTTC-TTTCAATTTCTT
1 TTTCAATTTCTTTTTTCTTTTTCT-TTTTCTTTTT-TTTTCATTTCAATTTCTT
*
57372826 TTTCAATCTCTTT
1 TTTCAATTTCTTT
57372839 CTCCTTTTCT
Statistics
Matches: 100, Mismatches: 13, Indels: 21
0.75 0.10 0.16
Matches are distributed among these distances:
51 18 0.18
52 3 0.03
53 7 0.07
54 13 0.13
55 4 0.04
56 5 0.05
57 37 0.37
58 11 0.11
59 2 0.02
ACGTcount: A:0.10, C:0.18, G:0.03, T:0.69
Consensus pattern (52 bp):
TTTCAATTTCTTTTTTCTTTTTCTTTTTCTTTTTTTTTCATTTCAATTTCTT
Found at i:57372732 original size:12 final size:12
Alignment explanation
Indices: 57372682--57372772 Score: 50
Period size: 12 Copynumber: 7.8 Consensus size: 12
57372672 TTTTTCGCTT
57372682 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
57372694 TTTTTTTTTC-A
1 TTTCTTTTTCAA
57372705 -TTC----TCAA
1 TTTCTTTTTCAA
57372712 TTTCTTTTTCAA
1 TTTCTTTTTCAA
*
57372724 TTTTCTTTTCTTCAT
1 -TTTC-TTT-TTCAA
**
57372739 TTTCTTTTTCTC
1 TTTCTTTTTCAA
** *
57372751 TCACTTTTTCGA
1 TTTCTTTTTCAA
57372763 TTTCTTTTTC
1 TTTCTTTTTC
57372773 TTTTGCAATT
Statistics
Matches: 59, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
6 2 0.03
7 1 0.02
8 3 0.05
10 2 0.03
11 1 0.02
12 32 0.54
13 7 0.12
14 7 0.12
15 4 0.07
ACGTcount: A:0.11, C:0.20, G:0.01, T:0.68
Consensus pattern (12 bp):
TTTCTTTTTCAA
Found at i:57372775 original size:18 final size:18
Alignment explanation
Indices: 57372754--57372812 Score: 73
Period size: 18 Copynumber: 3.3 Consensus size: 18
57372744 TTTTCTCTCA
57372754 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
57372772 CTTTTGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
57372790 CTTTTTTGTTTTCTTTTT
1 CTTTTTCGATTTCTTTTT
*
57372808 GTTTT
1 CTTTT
57372813 CTTTCAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.75
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:57372801 original size:12 final size:12
Alignment explanation
Indices: 57372786--57372816 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
57372776 TGCAATTTCT
57372786 TTTTCTTTTTTG
1 TTTTCTTTTTTG
57372798 TTTTC-TTTTTG
1 TTTTCTTTTTTG
57372809 TTTTCTTT
1 TTTTCTTT
57372817 CAATTTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (12 bp):
TTTTCTTTTTTG
Found at i:57373900 original size:11 final size:11
Alignment explanation
Indices: 57373886--57373920 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
57373876 TTTTTTTTCC
*
57373886 TTTTTTTCG-A
1 TTTTTTTTGAA
57373896 TTTTTTTTGAA
1 TTTTTTTTGAA
57373907 TTTTTTTTGAA
1 TTTTTTTTGAA
57373918 TTT
1 TTT
57373921 CTTCTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:57375483 original size:30 final size:30
Alignment explanation
Indices: 57375449--57375545 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
57375439 TAAACTAAAA
57375449 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
57375479 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* * *
57375509 TGAGCTAAGGTTTAGCTTGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
57375539 TGAGCTA
1 TGAGCTA
57375546 GGAGTGAGCT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 2 0.04
30 41 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.14, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:57379431 original size:10 final size:10
Alignment explanation
Indices: 57379415--57379472 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
57379405 CAACTCCGAC
57379415 CAGCTCAATT
1 CAGCTCAATT
* *
57379425 GAGCTCATTT
1 CAGCTCAATT
57379435 CAGCTCAA-T
1 CAGCTCAATT
*
57379444 CGAGCTTAATT
1 C-AGCTCAATT
*
57379455 TAGCTACAATT
1 CAGCT-CAATT
57379466 CAGCTCA
1 CAGCTCA
57379473 TTTATTTTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 2 0.05
10 26 0.70
11 9 0.24
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:57379438 original size:20 final size:20
Alignment explanation
Indices: 57379415--57379475 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
57379405 CAACTCCGAC
57379415 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
* *
57379435 CAGCTCAATCGAGCTTAATTT
1 CAGCTCAATTGAGC-TCATTT
*
57379456 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
57379476 ATTTTATTGG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 22 0.65
21 12 0.35
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:57380748 original size:11 final size:10
Alignment explanation
Indices: 57380732--57380761 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
57380722 TTCGTAATGT
57380732 AAAAAAAAGTC
1 AAAAAAAA-TC
57380743 AAAAAAAATC
1 AAAAAAAATC
57380753 AAAAAAAAT
1 AAAAAAAAT
57380762 TTGAGTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.58
11 8 0.42
ACGTcount: A:0.80, C:0.07, G:0.03, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:57380847 original size:12 final size:13
Alignment explanation
Indices: 57380819--57380857 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
57380809 ATTGTATTGG
*
57380819 ATTTAAAAAAAAGA
1 ATTTCAAAAAAA-A
*
57380833 AATTCAAAAAAAA
1 ATTTCAAAAAAAA
57380846 ATTTCAAAAAAA
1 ATTTCAAAAAAA
57380858 TCGAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.72, C:0.05, G:0.03, T:0.21
Consensus pattern (13 bp):
ATTTCAAAAAAAA
Found at i:57381965 original size:18 final size:18
Alignment explanation
Indices: 57381939--57381988 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
57381929 AAATTGAAAG
*
57381939 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
57381957 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
57381975 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
57381989 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:57381967 original size:6 final size:6
Alignment explanation
Indices: 57381935--57381988 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
57381925 AAAGAAATTG
* * ** *
57381935 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
57381982 AAAGAA A
1 AAAGAA A
57381989 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:57382048 original size:18 final size:18
Alignment explanation
Indices: 57382027--57382061 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57382017 AGAAAAGAAA
57382027 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
57382045 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
57382062 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:57394339 original size:30 final size:30
Alignment explanation
Indices: 57394303--57394364 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
57394293 CAAATAGCTG
*
57394303 AAGCTAGTTTAAATCACATACTTAGTGCCA
1 AAGCTAGTTTAAATCACACACTTAGTGCCA
*
57394333 AAGCTAGTTTAAATCGCACACTTAGTGCCA
1 AAGCTAGTTTAAATCACACACTTAGTGCCA
57394363 AA
1 AA
57394365 ACTTCCGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (30 bp):
AAGCTAGTTTAAATCACACACTTAGTGCCA
Found at i:57396223 original size:40 final size:40
Alignment explanation
Indices: 57396041--57396263 Score: 236
Period size: 40 Copynumber: 5.6 Consensus size: 40
57396031 TCCTCGTTCA
* * * * *
57396041 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
57396080 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
57396120 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
57396160 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* ** * * * *
57396200 AAGGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
57396240 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
57396264 CAGCATTCAA
Statistics
Matches: 160, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 37 0.23
40 115 0.72
41 8 0.05
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:57396272 original size:41 final size:41
Alignment explanation
Indices: 57396195--57396272 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
57396185 TTAGTATCTC
* * *
57396195 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
57396236 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
57396273 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:57398144 original size:23 final size:23
Alignment explanation
Indices: 57398111--57398154 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
57398101 AGGATAGACA
*
57398111 CATTTTTTTTCT-TTTGTTTTCAT
1 CATTTTCTTTCTCTTT-TTTTCAT
57398134 CATTTTCTTTCTCTTTTTTTC
1 CATTTTCTTTCTCTTTTTTTC
57398155 CCATTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.07, C:0.18, G:0.02, T:0.73
Consensus pattern (23 bp):
CATTTTCTTTCTCTTTTTTTCAT
Found at i:57399311 original size:46 final size:47
Alignment explanation
Indices: 57399114--57399423 Score: 271
Period size: 46 Copynumber: 6.6 Consensus size: 47
57399104 GGGTTATTGT
* * *
57399114 GAGCTAGTGTAAGA-CATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGA-GATGA
* *
57399160 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCATCGAGACT-A
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGA-TGA
* * * *
57399208 GTGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCATTGAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGA
* * * * *
57399256 GTGCTAGTGTAAGA-CATTTCTGGGATATGCATCGGCCTCGAGACGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATG-A
* *
57399303 -AGCCAGTGTAAGA-CATGTCTGGGAAATGCATCGG-CTACAAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCT-CGAGATGA
* * * *
57399348 -AGTCAGTGTAAGACCATGTCTGGGGCATGGCATC-GACTTGAGAT-A
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCCTCGAGATGA
* * *
57399393 TGAGCCAGTGTAAAACTATGTCTGCGACATG
1 -GAGCCAGTGTAAGACCATGTCTGGGACATG
57399424 GCATTGGCAC
Statistics
Matches: 222, Mismatches: 30, Indels: 24
0.80 0.11 0.09
Matches are distributed among these distances:
45 16 0.07
46 80 0.36
47 57 0.26
48 67 0.30
49 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCCTCGAGATGA
Found at i:57400610 original size:21 final size:21
Alignment explanation
Indices: 57400569--57400608 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
57400559 TGTCAAAATG
57400569 TTCACACGGGCGTGTTGCCCT
1 TTCACACGGGCGTGTTGCCCT
57400590 TTCACACGGGCGTG-TGCCC
1 TTCACACGGGCGTGTTGCCC
57400609 CTGTGTTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.10, C:0.35, G:0.30, T:0.25
Consensus pattern (21 bp):
TTCACACGGGCGTGTTGCCCT
Found at i:57407869 original size:29 final size:28
Alignment explanation
Indices: 57407833--57407910 Score: 104
Period size: 29 Copynumber: 2.7 Consensus size: 28
57407823 TCATGAGATT
57407833 GGCACTAAGTGTGCGGGTTTAAATTGTACA
1 GGCACTAAGTGTGCGGGTTTAAA--GTACA
*
57407863 -GCACTAAGTGTGCGAGTTTAAAGTACA
1 GGCACTAAGTGTGCGGGTTTAAAGTACA
57407890 TGGCACTAAGTGTGCGCGGTT
1 -GGCACTAAGTGTGCG-GGTT
57407911 GATTATTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
29 35 0.81
30 3 0.07
ACGTcount: A:0.26, C:0.15, G:0.31, T:0.28
Consensus pattern (28 bp):
GGCACTAAGTGTGCGGGTTTAAAGTACA
Found at i:57408128 original size:174 final size:174
Alignment explanation
Indices: 57407863--57408364 Score: 932
Period size: 174 Copynumber: 2.9 Consensus size: 174
57407853 AAATTGTACA
*
57407863 GCACTAAGTGTGCGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
57407928 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
57407993 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
* * *
57408037 GCACTAAGTGTGTGAGTTTAAAGTGCATGACACTAAGTGTGCGCGGTTGATTATTGAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
57408102 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
57408167 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
131 TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
*
57408211 ACACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
1 GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
* * *
57408276 TGTGCGAACTCAATATATATTTTCTATAAATTATTTACATGAAGGGTGCGACTTTACCGAGTCAA
66 TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
57408341 TTTTGGACAGCGGAAAAGGTAAGT
131 TTTTGGACAGCGGAAAAGGTAAGT
57408365 ACCTTGAGTT
Statistics
Matches: 317, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
174 317 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (174 bp):
GCACTAAGTGTGTGAGTTTAAAGTACATGGCACTAAGTGTGCGCGGTTGATTATTAAGCACTATG
TGTGCGAACCCAATATATATTTTCTATAAATTATTTACATTAAGGGTGCGACTTTACCGAGTCGA
TTTTGGACAGCGGAAAAGGTAAGTGTGCGAACTTGAAATGCATG
Found at i:57421112 original size:29 final size:29
Alignment explanation
Indices: 57421049--57421116 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
57421039 TAATCAACCG
57421049 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
57421078 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
57421107 CGCACACTTA
1 CGCACACTTA
57421117 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:57421257 original size:29 final size:30
Alignment explanation
Indices: 57421218--57421296 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
57421208 CTTAATAATC
57421218 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
57421248 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
57421277 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
57421297 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:57424172 original size:18 final size:18
Alignment explanation
Indices: 57424149--57424230 Score: 114
Period size: 18 Copynumber: 4.6 Consensus size: 18
57424139 TGTGGGTAGG
57424149 CCGTGTGG-TAACACACGC
1 CCGTGTGGCT-ACACACGC
57424167 CCGTGTGG-TAACACACGC
1 CCGTGTGGCT-ACACACGC
*
57424185 CCGTGTGGCTACACAAGC
1 CCGTGTGGCTACACACGC
*
57424203 CCGTGTGGCTATACACGC
1 CCGTGTGGCTACACACGC
57424221 CCGTGTGGCT
1 CCGTGTGGCT
57424231 TGGGACACGT
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
18 59 0.98
19 1 0.02
ACGTcount: A:0.18, C:0.33, G:0.29, T:0.20
Consensus pattern (18 bp):
CCGTGTGGCTACACACGC
Found at i:57424874 original size:20 final size:19
Alignment explanation
Indices: 57424839--57424877 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
57424829 GTCGTACTTA
57424839 TTAGCCATGATTCATTCAT
1 TTAGCCATGATTCATTCAT
57424858 TTAGCACATG-TTCCATTCAT
1 TTAGC-CATGATT-CATTCAT
57424878 CACACATCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (19 bp):
TTAGCCATGATTCATTCAT
Found at i:57428676 original size:75 final size:75
Alignment explanation
Indices: 57428552--57428690 Score: 172
Period size: 75 Copynumber: 1.9 Consensus size: 75
57428542 TTGTAAACAG
* * * * *
57428552 AAATCAATTGAACAAATCTGTTTCAAGATTTTATTCCTGTCATTTAACAGGATTTGTTTGATTTT
1 AAATCAATTGAACAAATCTGTTTCAAGATTTTATTCCTGACATTCAACAGAATTTATTCGATTTT
57428617 TTTTAAATAA
66 TTTTAAATAA
* * * * *
57428627 AAATCAATTGAATAATTCTGTTTCAATATTCTT-TTCTTGACGTTCAACAGAATTTATTCGATTT
1 AAATCAATTGAACAAATCTGTTTCAAGATT-TTATTCCTGACATTCAACAGAATTTATTCGATTT
57428691 CTGTTTTTAA
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
75 51 0.96
76 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.45
Consensus pattern (75 bp):
AAATCAATTGAACAAATCTGTTTCAAGATTTTATTCCTGACATTCAACAGAATTTATTCGATTTT
TTTTAAATAA
Found at i:57436122 original size:31 final size:31
Alignment explanation
Indices: 57436087--57436151 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
57436077 TCGCATACAG
57436087 ATAAATACATACTTAAACAGTACAGTCAGAC
1 ATAAATACATACTTAAACAGTACAGTCAGAC
57436118 ATAAATACATACTTAAACAGTACAGTCAGAC
1 ATAAATACATACTTAAACAGTACAGTCAGAC
57436149 ATA
1 ATA
57436152 CATATCAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.49, C:0.18, G:0.09, T:0.23
Consensus pattern (31 bp):
ATAAATACATACTTAAACAGTACAGTCAGAC
Found at i:57436347 original size:31 final size:31
Alignment explanation
Indices: 57436312--57436426 Score: 97
Period size: 31 Copynumber: 3.7 Consensus size: 31
57436302 TGCCCATGTA
57436312 GCTTGCCCGTATGAGCCCACATACCCGTGTG
1 GCTTGCCCGTATGAGCCCACATACCCGTGTG
* * **
57436343 GCTTGCCCGTATGGGCCCACATGCTTGTGTG
1 GCTTGCCCGTATGAGCCCACATACCCGTGTG
* * * * * * *
57436374 GCATGCCTGTATTAGCGCACACACCCAATCTG
1 GCTTGCCCGTATGAGCCCACATACCC-GTGTG
*
57436406 GCTTAGCCCGTGTG-GCCCACA
1 GCTT-GCCCGTATGAGCCCACA
57436427 CGGCCACACT
Statistics
Matches: 62, Mismatches: 20, Indels: 3
0.73 0.24 0.04
Matches are distributed among these distances:
31 44 0.71
32 12 0.19
33 6 0.10
ACGTcount: A:0.17, C:0.34, G:0.26, T:0.23
Consensus pattern (31 bp):
GCTTGCCCGTATGAGCCCACATACCCGTGTG
Found at i:57446893 original size:14 final size:14
Alignment explanation
Indices: 57446874--57446921 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
57446864 TTTCTCTGTA
57446874 TTTCTTTTTCTTTC
1 TTTCTTTTTCTTTC
*
57446888 TTTCTTCTTC-TTC
1 TTTCTTTTTCTTTC
*
57446901 TTT-TTTTCCTTT-
1 TTTCTTTTTCTTTC
57446913 TTTCTTTTT
1 TTTCTTTTT
57446922 TTTTTTTTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 7 0.25
13 12 0.43
14 9 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTTTCTTTC
Found at i:57446901 original size:17 final size:17
Alignment explanation
Indices: 57446875--57446908 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
57446865 TTCTCTGTAT
*
57446875 TTCTTTTTCTTTCTTTC
1 TTCTTCTTCTTTCTTTC
*
57446892 TTCTTCTTCTTTTTTTC
1 TTCTTCTTCTTTCTTTC
57446909 CTTTTTTCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TTCTTCTTCTTTCTTTC
Found at i:57446916 original size:25 final size:23
Alignment explanation
Indices: 57446878--57446930 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 23
57446868 TCTGTATTTC
57446878 TTTTTCTTTCTTTCTTCTTCTTCTT
1 TTTTTCTTTCTTTCTT-TT-TTCTT
*
57446903 TTTTTCCTTT-TTTCTTTTTTTTT
1 TTTTT-CTTTCTTTCTTTTTTCTT
57446926 TTTTT
1 TTTTT
57446931 GTGTGTGTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 9 0.35
24 2 0.08
25 11 0.42
26 4 0.15
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTTCTTTCTTTCTTTTTTCTT
Found at i:57446926 original size:22 final size:21
Alignment explanation
Indices: 57446878--57446929 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
57446868 TCTGTATTTC
*
57446878 TTTTTCTTTCTTTCTTCTTCT
1 TTTTTTTTTCTTTCTTCTTCT
* * *
57446899 TCTTTTTTTCCTTTTTTCTTTT
1 T-TTTTTTTTCTTTCTTCTTCT
57446921 TTTTTTTTT
1 TTTTTTTTT
57446930 TGTGTGTGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (21 bp):
TTTTTTTTTCTTTCTTCTTCT
Found at i:57446930 original size:17 final size:17
Alignment explanation
Indices: 57446874--57446930 Score: 51
Period size: 20 Copynumber: 3.1 Consensus size: 17
57446864 TTTCTCTGTA
57446874 TTTCTTTTTCTTTCTTTCTT
1 TTTCTTTTT-TTT-TTT-TT
* *
57446894 CTTCTTCTTTTTTTCCTTT
1 TTTCTT-TTTTTTT-TTTT
57446913 TTTCTTTTTTTTTTTTT
1 TTTCTTTTTTTTTTTTT
57446930 T
1 T
57446931 GTGTGTGTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 4 0.13
18 7 0.23
19 8 0.26
20 9 0.29
21 3 0.10
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTCTTTTTTTTTTTTT
Found at i:57448908 original size:5 final size:5
Alignment explanation
Indices: 57448892--57448933 Score: 75
Period size: 5 Copynumber: 8.2 Consensus size: 5
57448882 ATCTATCTAT
57448892 ATATA TATATA ATATA ATATA ATATA ATATA ATATA ATATA A
1 ATATA -ATATA ATATA ATATA ATATA ATATA ATATA ATATA A
57448934 ATAGTTCTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 31 0.86
6 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:57454100 original size:25 final size:24
Alignment explanation
Indices: 57454068--57454114 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
57454058 GCCGGAAAGC
* *
57454068 AAAAAAAATAAA-AATTTAGATTT
1 AAAAAAAAAAAAGAAATTAGATTT
57454091 AAAAAAAAAAAAGAAATTAGATTT
1 AAAAAAAAAAAAGAAATTAGATTT
57454115 TACTATACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (24 bp):
AAAAAAAAAAAAGAAATTAGATTT
Found at i:57454688 original size:16 final size:16
Alignment explanation
Indices: 57454667--57454703 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
57454657 CCCGTGATAA
57454667 ATGTGCACAAAACTTC
1 ATGTGCACAAAACTTC
57454683 ATGTGCACAAAACTTC
1 ATGTGCACAAAACTTC
57454699 ATGTG
1 ATGTG
57454704 AAGGTCAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (16 bp):
ATGTGCACAAAACTTC
Found at i:57461741 original size:42 final size:42
Alignment explanation
Indices: 57461682--57461844 Score: 175
Period size: 42 Copynumber: 3.9 Consensus size: 42
57461672 GACATTATGA
* *
57461682 TTATGAG-TTTACGTGTAAAACCATATCTGGGATATGGCATCG
1 TTATGAGATTT-CGTGTAAGACCATATCTAGGATATGGCATCG
* * * *
57461724 TTATGAGATTTCGTGTAAGACCATGTCTGGGACATGGCATCA
1 TTATGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCG
* **
57461766 TTATGAGATTTCGTGTAAGACCATAGCTAGCCTATTGGCATCG
1 TTATGAGATTTCGTGTAAGACCATATCTAGGATA-TGGCATCG
* ** * *
57461809 ATATGAGATCCCATGTAAGACCAAATCTAGGATATG
1 TTATGAGATTTCGTGTAAGACCATATCTAGGATATG
57461845 ACATTGGTAT
Statistics
Matches: 100, Mismatches: 19, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
42 64 0.64
43 36 0.36
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (42 bp):
TTATGAGATTTCGTGTAAGACCATATCTAGGATATGGCATCG
Found at i:57466670 original size:21 final size:20
Alignment explanation
Indices: 57466626--57466674 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
57466616 TCAACTCCCA
* *
57466626 TCAGCTCACTTGAGCTCGAT
1 TCAGCTCGCTTGAGCTAGAT
*
57466646 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCGCTTGAGCTAG-AT
57466667 TCAGCTCG
1 TCAGCTCG
57466675 ATCTAGCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (20 bp):
TCAGCTCGCTTGAGCTAGAT
Found at i:57468977 original size:29 final size:28
Alignment explanation
Indices: 57468884--57468982 Score: 110
Period size: 27 Copynumber: 3.5 Consensus size: 28
57468874 TATATTAAGT
* *
57468884 CCGCACACTCAGTGCTATATAATC-AAC
1 CCGCACACTTAGTGCTATACAATCAAAC
* *
57468911 TCGCACACTTAGTGCTATATAATCAAAC
1 CCGCACACTTAGTGCTATACAATCAAAC
** * *
57468939 TTGCACACTTAGTGCTGTACAATTTAAAC
1 CCGCACACTTAGTGCTATACAA-TCAAAC
57468968 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
57468983 CAATCTCATG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
27 22 0.35
28 22 0.35
29 18 0.29
ACGTcount: A:0.31, C:0.28, G:0.13, T:0.27
Consensus pattern (28 bp):
CCGCACACTTAGTGCTATACAATCAAAC
Found at i:57471547 original size:19 final size:19
Alignment explanation
Indices: 57471523--57471567 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
57471513 TAAAAAAAAG
*
57471523 AAAAAAATATACGAAATTA
1 AAAAAAATATACAAAATTA
57471542 AAAAAAATATACAAAATTA
1 AAAAAAATATACAAAATTA
57471561 AAAAAAA
1 AAAAAAA
57471568 AGTGTGTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (19 bp):
AAAAAAATATACAAAATTA
Found at i:57473635 original size:63 final size:64
Alignment explanation
Indices: 57473489--57473635 Score: 156
Period size: 67 Copynumber: 2.3 Consensus size: 64
57473479 GGGTGCACAT
* * * *
57473489 CATGTGTACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGAC
1 CATGTGTACAAGAGAGCTACGAGATAAATG-AGCTAGGTCACATGCGTGGTACCAAGT--AGGAC
57473554 AC
63 AC
* * **
57473556 CATGTAG-ACAAGAGAGCTACGAGATAAACTG-GCTAGGTCACATGGGTGGTACTAAGT-GTTCA
1 CATGT-GTACAAGAGAGCTACGAGATAAA-TGAGCTAGGTCACATGCGTGGTACCAAGTAGGACA
57473618 C
64 C
57473619 CATGTGTACAAGAGAGC
1 CATGTGTACAAGAGAGC
57473636 CGAACTATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
62 1 0.01
63 19 0.28
66 22 0.32
67 24 0.35
68 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.30, T:0.22
Consensus pattern (64 bp):
CATGTGTACAAGAGAGCTACGAGATAAATGAGCTAGGTCACATGCGTGGTACCAAGTAGGACAC
Found at i:57476036 original size:30 final size:29
Alignment explanation
Indices: 57475994--57476059 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 29
57475984 GAGAAGAAAC
* *
57475994 AAAGAAAAGAAAATGAGA-TTGAGATTGAA
1 AAAGAAAAGAAAA-GAAATTTGAGAGTGAA
*
57476023 AAAGAGAACGAAAAGAAATTTGAGAGTGAA
1 AAAGA-AAAGAAAAGAAATTTGAGAGTGAA
57476053 AAAGAAA
1 AAAGAAA
57476060 TTGAAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 10 0.31
30 22 0.69
ACGTcount: A:0.61, C:0.02, G:0.24, T:0.14
Consensus pattern (29 bp):
AAAGAAAAGAAAAGAAATTTGAGAGTGAA
Found at i:57478331 original size:20 final size:21
Alignment explanation
Indices: 57478308--57478353 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
57478298 TCAGCTCCCA
*
57478308 TCAGCTCACTTGAGCTCG-AT
1 TCAGCTCACTTGAGCTAGAAT
**
57478328 TCAGCTCGTTTGAGCTAGAAT
1 TCAGCTCACTTGAGCTAGAAT
57478349 TCAGC
1 TCAGC
57478354 ATGATCTAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (21 bp):
TCAGCTCACTTGAGCTAGAAT
Found at i:57481003 original size:7 final size:7
Alignment explanation
Indices: 57480991--57481015 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
57480981 CCATCTCTTA
57480991 ATTTAAT
1 ATTTAAT
57480998 ATTTAAT
1 ATTTAAT
57481005 ATTTAAT
1 ATTTAAT
57481012 ATTT
1 ATTT
57481016 CTATTTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (7 bp):
ATTTAAT
Found at i:57483689 original size:40 final size:40
Alignment explanation
Indices: 57483584--57483673 Score: 126
Period size: 40 Copynumber: 2.2 Consensus size: 40
57483574 CCAGGTTTTT
* * ** *
57483584 GGACACAGGCGAGGACACGGGCGTGTCTAGGCCATGTGAG
1 GGACACGGGCGAGAACATAGGCGTGTCTAAGCCATGTGAG
*
57483624 GGACACGGGCGAGAACATAGGCGTGTCTAAGCCGTGTGAG
1 GGACACGGGCGAGAACATAGGCGTGTCTAAGCCATGTGAG
57483664 GGACACGGGC
1 GGACACGGGC
57483674 ATGTGCTTGG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 44 1.00
ACGTcount: A:0.23, C:0.22, G:0.42, T:0.12
Consensus pattern (40 bp):
GGACACGGGCGAGAACATAGGCGTGTCTAAGCCATGTGAG
Found at i:57483696 original size:29 final size:29
Alignment explanation
Indices: 57483654--57483718 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
57483644 GCGTGTCTAA
*
57483654 GCCGTGTGAGGGACACGGGCATGTGCTTG
1 GCCGTGTAAGGGACACGGGCATGTGCTTG
57483683 GCCGTGTAAGGGACACGGGCATGTGCTTG
1 GCCGTGTAAGGGACACGGGCATGTGCTTG
57483712 GCCGTGT
1 GCCGTGT
57483719 GAAAACCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.14, C:0.22, G:0.43, T:0.22
Consensus pattern (29 bp):
GCCGTGTAAGGGACACGGGCATGTGCTTG
Found at i:57483827 original size:23 final size:23
Alignment explanation
Indices: 57483797--57483856 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
57483787 CGTCCCAAAG
*
57483797 CACACGGGAGTGTGCATTGCCTC
1 CACACGGGCGTGTGCATTGCCTC
*
57483820 CACGCGGGCGTGTGCATTGCCTC
1 CACACGGGCGTGTGCATTGCCTC
57483843 CACACGGGCGTGTG
1 CACACGGGCGTGTG
57483857 AGGCTCAACC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.13, C:0.32, G:0.35, T:0.20
Consensus pattern (23 bp):
CACACGGGCGTGTGCATTGCCTC
Found at i:57485370 original size:39 final size:39
Alignment explanation
Indices: 57485316--57485393 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
57485306 GTGCATCCTA
57485316 GCCTCGTTTTTAATGCTCATTACATATTTGAAGTCGTAT
1 GCCTCGTTTTTAATGCTCATTACATATTTGAAGTCGTAT
*
57485355 GCCTCGTTTTTAATGCTCTTTACATATTTGAAGTCGTAT
1 GCCTCGTTTTTAATGCTCATTACATATTTGAAGTCGTAT
57485394 TCACCTGATC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.18, G:0.15, T:0.45
Consensus pattern (39 bp):
GCCTCGTTTTTAATGCTCATTACATATTTGAAGTCGTAT
Found at i:57486121 original size:42 final size:42
Alignment explanation
Indices: 57486074--57486228 Score: 184
Period size: 42 Copynumber: 3.7 Consensus size: 42
57486064 ATAAGTTTAT
*
57486074 GTGTAAGACCATATCTAGGATATGGCATCGTTATGAGATTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGTTATGAGATTTC
* * *
57486116 GTGTAAGACCATGTCTGGGACATGGCATCGTTATGAGTTTTC
1 GTGTAAGACCATATCTGGGATATGGCATCGTTATGAGATTTC
* * * * **
57486158 GTGTAAGACCAAAGCTGGGCTATTGGCATCGATATGAGATCCC
1 GTGTAAGACCATATCTGGGATA-TGGCATCGTTATGAGATTTC
* * *
57486201 ATATAAGACCATATCTGTGATATGGCAT
1 GTGTAAGACCATATCTGGGATATGGCAT
57486229 TGGTATGATT
Statistics
Matches: 93, Mismatches: 19, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
42 61 0.66
43 32 0.34
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (42 bp):
GTGTAAGACCATATCTGGGATATGGCATCGTTATGAGATTTC
Found at i:57486247 original size:85 final size:84
Alignment explanation
Indices: 57486067--57486247 Score: 195
Period size: 85 Copynumber: 2.1 Consensus size: 84
57486057 TAGGGTTATA
* * * ** * * *
57486067 AGTTTATGTGTAAGACCATATCTAGGATATGGCATCGTTATGAGATTTCGTGTAAGACCATGTCT
1 AGTTTATGTGTAAGACCAAAGCTAGGATATGGCATCGATATGAGATCCCATATAAGACCATATCT
*
57486132 GGGACATGGCATCGTTATG
66 GGGACATGGCATCGGTATG
* *
57486151 AGTTT-TCGTGTAAGACCAAAGCTGGGCTATTGGCATCGATATGAGATCCCATATAAGACCATAT
1 AGTTTAT-GTGTAAGACCAAAGCTAGGATA-TGGCATCGATATGAGATCCCATATAAGACCATAT
* * *
57486215 CTGTGATATGGCATTGGTATG
64 CTGGGACATGGCATCGGTATG
57486236 A-TTCTATGTGTA
1 AGTT-TATGTGTA
57486248 TGTGATTCCT
Statistics
Matches: 79, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
83 1 0.01
84 25 0.32
85 52 0.66
86 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (84 bp):
AGTTTATGTGTAAGACCAAAGCTAGGATATGGCATCGATATGAGATCCCATATAAGACCATATCT
GGGACATGGCATCGGTATG
Found at i:57490568 original size:68 final size:67
Alignment explanation
Indices: 57490483--57490653 Score: 170
Period size: 68 Copynumber: 2.5 Consensus size: 67
57490473 GGTGCTGAGT
*
57490483 GCACATCATGT-GTACAAGAGAGCTACGAGATACTATG-TAGTAGCTAGGTAACATGTGTGAT-A
1 GCACACCATGTAG-ACAAGAGAGCTACGAGATA-TA-GAT-GTAGCTAGGTAACATGTGTGATCA
* *
57490545 CGGGAT
62 AGGGAA
* * *
57490551 GTATC-CCATGTAGACAAGAGAGCTACGGGAGAGATAGATGTAGCTAGGTCACATGTGTGATCCC
1 GCA-CACCATGTAGACAAGAGAGCTAC--GAGATATAGATGTAGCTAGGTAACATGTGTGAT--C
*
57490615 AAGTGAA
61 AAGGGAA
57490622 GCACACCATGTAGACAAGAGAGCTACGAGATA
1 GCACACCATGTAGACAAGAGAGCTACGAGATA
57490654 AATTGGCTAG
Statistics
Matches: 85, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
68 42 0.49
69 10 0.12
70 6 0.07
71 27 0.32
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.21
Consensus pattern (67 bp):
GCACACCATGTAGACAAGAGAGCTACGAGATATAGATGTAGCTAGGTAACATGTGTGATCAAGGG
AA
Found at i:57498105 original size:17 final size:17
Alignment explanation
Indices: 57498073--57498106 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
57498063 TGAGTGGCAG
57498073 ACACATAAACCGAAAAC
1 ACACATAAACCGAAAAC
57498090 ACACGATAAACC-AAAAC
1 ACAC-ATAAACCGAAAAC
57498107 CATGCCATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.59, C:0.29, G:0.06, T:0.06
Consensus pattern (17 bp):
ACACATAAACCGAAAAC
Found at i:57500780 original size:25 final size:26
Alignment explanation
Indices: 57500733--57500791 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
57500723 CACTTATATC
57500733 TTTA-TTTATCTTCTTTAAGTACT-T
1 TTTATTTTATCTTCTTTAAGTACTAT
*
57500757 TTTATTTTATTTTCCTTTAA-TACTAT
1 TTTATTTTATCTT-CTTTAAGTACTAT
57500783 TTTAATTTT
1 TTT-ATTTT
57500792 CGGTTCTATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 4 0.13
25 11 0.37
26 10 0.33
27 5 0.17
ACGTcount: A:0.22, C:0.10, G:0.02, T:0.66
Consensus pattern (26 bp):
TTTATTTTATCTTCTTTAAGTACTAT
Found at i:57510092 original size:47 final size:47
Alignment explanation
Indices: 57510014--57510266 Score: 425
Period size: 47 Copynumber: 5.4 Consensus size: 47
57510004 CCCTTCGGGA
* * * * *
57510014 CTTATCACATTTATACACTTTTACATCCATCACATTGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
57510061 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
57510108 CTTATCACATATATACACTTTCACATTCATCACATTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
57510155 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
57510202 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
57510249 CTTATCACATATACACAC
1 CTTATCACATATATACAC
57510267 CTTATACATC
Statistics
Matches: 195, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 195 1.00
ACGTcount: A:0.28, C:0.29, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:57510117 original size:22 final size:22
Alignment explanation
Indices: 57510089--57510211 Score: 61
Period size: 22 Copynumber: 5.3 Consensus size: 22
57510079 TTTCACATTC
57510089 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
57510111 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
*
57510135 CATCACATTGGCCACTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
** * * *
57510158 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
57510182 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
57510205 ATCACAT
1 ATCACAT
57510212 ATATACACTT
Statistics
Matches: 69, Mismatches: 22, Indels: 20
0.62 0.20 0.18
Matches are distributed among these distances:
22 28 0.41
23 10 0.14
24 10 0.14
25 21 0.30
ACGTcount: A:0.27, C:0.31, G:0.10, T:0.33
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Done.