Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 4987688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 20
Found at i:1101633 original size:21 final size:21
Alignment explanation
Indices: 1101609--1101648 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1101599 AGAAATATTA
* *
1101609 AAAAATATTAATGTTTTAAGT
1 AAAAATAATAATATTTTAAGT
1101630 AAAAATAATAATATTTTAA
1 AAAAATAATAATATTTTAA
1101649 ATAATATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AAAAATAATAATATTTTAAGT
Found at i:1104418 original size:3 final size:3
Alignment explanation
Indices: 1104398--1104458 Score: 72
Period size: 3 Copynumber: 20.0 Consensus size: 3
1104388 TTTGGGCCTG
*
1104398 TAA T-A TAA TAA -AA TTAA TAA TAAA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1104443 TAAA TAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA
1104459 AAAACCAAAT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
2 4 0.08
3 39 0.76
4 8 0.16
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1104426 original size:19 final size:19
Alignment explanation
Indices: 1104402--1104459 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
1104392 GGCCTGTAAT
1104402 ATAATAAAATTAATAATAA
1 ATAATAAAATTAATAATAA
*
1104421 ATAATAATATTAATAAT-A
1 ATAATAAAATTAATAATAA
*
1104439 ATAATAAATAATAATAATAA
1 ATAATAAA-ATTAATAATAA
1104459 A
1 A
1104460 AAACCAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 8 0.24
19 24 0.71
20 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATAAAATTAATAATAA
Found at i:1104874 original size:123 final size:123
Alignment explanation
Indices: 1104673--1105133 Score: 743
Period size: 123 Copynumber: 3.8 Consensus size: 123
1104663 ATGTAATCTA
* ** * * * *
1104673 GCAAAAAGTTGAACAAATTCTCCTCCTTATGAA---CTTCTTCTTCTTCAGATGAGTTCTTCTCA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTA
* * *
1104735 TTATGAAC-TCCTTCTGGAAATA-CTGATGATGATATATCTCCTGCTGTGATAGAGTTAT
66 TTATGAACTTTC-TCTGGAAA-AGTTGATGATGATATATCTCCTGCTGTGATAAAGTTAT
1104793 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTA
* *
1104858 TTATGAACTTTCTCTGGAAAAGTTAATGATGATATATCTCCTACTGTGATAAAGTTAT
66 TTATGAACTTTCTCTGGAAAAGTTGATGATGATATATCTCCTGCTGTGATAAAGTTAT
*
1104916 GAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTA
1104981 TTATGAACTTTCTCTGGAAAAGTTGATGATGATATATCTCCTGCTGTGATAAAGTTAT
66 TTATGAACTTTCTCTGGAAAAGTTGATGATGATATATCTCCTGCTGTGATAAAGTTAT
*
1105039 GCAAAAGGTTGAACAAGCTCTTATCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTA
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTA
1105104 TTATGAACTTTCTCTGGAAAAGTTGATGAT
66 TTATGAACTTTCTCTGGAAAAGTTGATGAT
1105134 CCATCGAATG
Statistics
Matches: 319, Mismatches: 17, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
120 28 0.09
122 1 0.00
123 288 0.90
124 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (123 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTA
TTATGAACTTTCTCTGGAAAAGTTGATGATGATATATCTCCTGCTGTGATAAAGTTAT
Found at i:1105158 original size:123 final size:117
Alignment explanation
Indices: 1104666--1105578 Score: 726
Period size: 123 Copynumber: 7.8 Consensus size: 117
1104656 TTCTGTGATG
* ** * * *
1104666 TAATCTAGCAAAAAGTTGAACAAATTCTCCTCCTTATGAA---CTTCTTCTTCTTCAGATGAGTT
1 TAAT-TAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTT
* * ** *** * *
1104728 CTTCTCATTATGAAC-TCCTTCTGGAAATACTGATGATGATATATCTCCTGCTGTGA-
65 CTTCTCATTATGAACTTTC-TCTGGAAA-A--GTTGATGATCCATCGAATGATG-AAT
1104784 TAGAGTTATGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAG
1 TA-A-TTA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAG
* ** * *
1104849 TTCTTCTTATTATGAACTTTCTCTGGAAAAGTTAATGATGATATATCTCCTACTG-TG-AT
63 TTCTTCTCATTATGAACTTTCTCTGGAAAAG-T--TGATGATCCA--T-CGAATGATGAAT
* *
1104908 AAAGTTATGAAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGT
1 TAA-TTA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGT
* ** *** * *
1104973 TCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATGATGATATATCTCCTGCTGTGAT
64 TCTTCTCATTATGAACTTTCTCTGGAAAAG-T--TGATGATCCATCGAATGATG-AAT
* *
1105031 AAAGTTATGCAAAAGGTTGAACAAGCTCTTATCATTATGAACTTCTTCTTCTTCTTCAGATAAGT
1 TAA-TTA-GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGT
*
1105096 TCTTCTTATTATGAACTTTCTCTGGAAAAGTTGATGATCCATCGAATGATG---
64 TCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGATCCATCGAATGATGAAT
* **
1105147 -AATT--CAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAG
1 TAATTAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT-A--AG
* * * * *
1105206 TTCTTCTCATTATGAACTCTAC-CAGG-CAA--TGTTGATCCATCAAATGATGAATT
63 TTCTTCTCATTATGAACT-TTCTCTGGAAAAGTTGATGATCCATCGAATGATGAA-T
*
1105259 TAA--A-CAAAAGGTTGAACAATCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTT
1 TAATTAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTT
*
1105321 CTTCTCATTATGAACTTTCTCTTG-AAA--TGATGATCCATCGAATGATGAAT
65 CTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGATCCATCGAATGATGAAT
* * * *
1105371 TCAA--A-CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGT
1 T-AATTAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGT
* ** * * * * *
1105433 TCTTCTCATTATGAACTCTAACTGG--CA-CTGCTGATCCACCGAGTGATGAAT
64 TCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGATCCATCGAATGATGAAT
* * * * * *
1105484 T--TAAGCAAAAAGTTGAACAGGTTATTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTC
1 TAATTAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTC
* * *
1105547 TTCTCATTATAAACTCT-TCTGGAAATGTTGAT
66 TTCTCATTATGAACTTTCTCTGGAAAAGTTGAT
1105579 CCATTGAATG
Statistics
Matches: 692, Mismatches: 63, Indels: 84
0.82 0.08 0.10
Matches are distributed among these distances:
108 34 0.05
109 2 0.00
110 2 0.00
111 54 0.08
112 70 0.10
113 181 0.26
114 6 0.01
115 8 0.01
116 11 0.02
118 2 0.00
119 3 0.00
120 49 0.07
121 3 0.00
122 2 0.00
123 254 0.37
124 3 0.00
125 3 0.00
126 5 0.01
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (117 bp):
TAATTAGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTC
TTCTCATTATGAACTTTCTCTGGAAAAGTTGATGATCCATCGAATGATGAAT
Found at i:1105369 original size:113 final size:111
Alignment explanation
Indices: 1105040--1105599 Score: 652
Period size: 113 Copynumber: 5.0 Consensus size: 111
1105030 TAAAGTTATG
* * * *
1105040 CAAAAGGTTGAACAAGCTCTTATCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTAT
1 CAAAAAGTTGAACAA-TTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
1105105 TATGAACTTTCTCTGGAAAAGTTGATGATCCATCGAATGATGAA-TT---
65 TATGAACTTTCTCTGG-AAA--TGATGATCCATCGAATGATGAATTTAAA
1105151 CAAAAAGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCTTCTTCAGATGACGAGTTCTTCT
1 CAAAAAGTTGAAC-AATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGAT-A--AGTTCTTCT
* * * * *
1105213 CATTATGAACTCTAC-CAGGCAATGTTGATCCATCAAATGATGAATTTAAA
62 CATTATGAACT-TTCTCTGGAAATGATGATCCATCGAATGATGAATTTAAA
*
1105263 CAAAAGGTTGAACAATCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAAGTTGAACAAT-TCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCA
* *
1105328 TTATGAACTTTCTCTTGAAATGATGATCCATCGAATGATGAATTCAAA
64 TTATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATTTAAA
* *
1105376 CAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAAGTTGAACAA-TTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCA
* ** * * * * * *
1105441 TTATGAACTCTAACTGGCACTGCTGATCCACCGAGTGATGAATTTAAG
64 TTATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATTTAAA
* * *
1105489 CAAAAAGTTGAACAGGTTATTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCAT
1 CAAAAAGTTGAACA-ATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
* * * * *
1105554 TATAAACTCT-TCTGGAAATGTTGATCCATTGAATGATGGATTTAAA
65 TATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATTTAAA
1105600 TCTTTGCTAA
Statistics
Matches: 388, Mismatches: 44, Indels: 34
0.83 0.09 0.07
Matches are distributed among these distances:
108 36 0.09
109 4 0.01
110 2 0.01
111 78 0.20
112 66 0.17
113 183 0.47
114 2 0.01
115 6 0.02
116 11 0.03
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (111 bp):
CAAAAAGTTGAACAATTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCATT
ATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATTTAAA
Found at i:1105470 original size:226 final size:218
Alignment explanation
Indices: 1105040--1105591 Score: 750
Period size: 226 Copynumber: 2.5 Consensus size: 218
1105030 TAAAGTTATG
* * *
1105040 CAAAAGGTTGAACAAGCTCTTATCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTTAT
1 CAAAAGGTTGAACAATCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
1105105 TATGAACTTTCTCTGGAAAAGTTGATGATCCATCGAATGATGAATTCAAAAAGTTGAACAAATTC
66 TATGAACTTTCTCTGG-AAA--TGATGATCCATCGAATGATGAATTCAAAAAGTTGAACAAATTC
* *
1105170 TTCTCATTATGAATTTCTTCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCAGGCAA
128 TTCTCATTATGAATTTATTCTTCTTCAGAT-A-GAGTTCTTCTCATTATGAACTCTAACAGGCAA
* *
1105235 TGTTGATCCATCAAATGATGAATTTAAA
191 TGCTGATCCACCAAATGATGAATTTAAA
1105263 CAAAAGGTTGAACAATCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAAGTTCTTCTCA
1 CAAAAGGTTGAACAATCTCTTCTCATTATGAACTTCTTCTT-CTTCTTCAGATAAGTTCTTCTCA
* *
1105328 TTATGAACTTTCTCTTGAAATGATGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAAGT
65 TTATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATT----CAAAAAGTTGAACAAAT
*
1105393 TCTTCTCATTATGAACTTCTTATTCCTTCTTCAGAT-GAGTTCTTCTCATTATGAACTCTAACTG
126 TCTTCTCATTATGAA--T-TTATT-CTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAACAG
* * * *
1105457 GCACTGCTGATCCACCGAGTGATGAATTTAAG
187 GCAATGCTGATCCACCAAATGATGAATTTAAA
* * * *
1105489 CAAAAAGTTGAACAGGT-TATTCTCATTATGAACTTCTTCTTCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACA-ATCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCA
* * * *
1105553 TTATAAACTCT-TCTGGAAATGTTGATCCATTGAATGATG
65 TTATGAACTTTCTCTGGAAATGATGATCCATCGAATGATG
1105592 GATTTAAATC
Statistics
Matches: 296, Mismatches: 23, Indels: 19
0.88 0.07 0.06
Matches are distributed among these distances:
221 24 0.08
223 42 0.14
224 63 0.21
225 62 0.21
226 88 0.30
227 2 0.01
228 4 0.01
229 11 0.04
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (218 bp):
CAAAAGGTTGAACAATCTCTTCTCATTATGAACTTCTTCTTCTTCTTCAGATAAGTTCTTCTCAT
TATGAACTTTCTCTGGAAATGATGATCCATCGAATGATGAATTCAAAAAGTTGAACAAATTCTTC
TCATTATGAATTTATTCTTCTTCAGATAGAGTTCTTCTCATTATGAACTCTAACAGGCAATGCTG
ATCCACCAAATGATGAATTTAAA
Found at i:1106839 original size:19 final size:17
Alignment explanation
Indices: 1106811--1106859 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
1106801 AAAATAAAAG
*
1106811 AATAAGTTGAATTTTCGAA
1 AATAAATTGAATTTTC--A
*
1106830 AATAAATTGAA-TCTCA
1 AATAAATTGAATTTTCA
1106846 AATAAATTGAATTT
1 AATAAATTGAATTT
1106860 AGAGAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 1 0.04
18 3 0.12
19 10 0.38
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (17 bp):
AATAAATTGAATTTTCA
Found at i:1110723 original size:10 final size:10
Alignment explanation
Indices: 1110705--1110739 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
1110695 ATTTATGAAA
*
1110705 TAAATAAATG
1 TAAAAAAATG
1110715 TAAAAAAATG
1 TAAAAAAATG
1110725 T-AAAAAATG
1 TAAAAAAATG
1110734 TAAAAA
1 TAAAAA
1110740 TGATTGCCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (10 bp):
TAAAAAAATG
Found at i:1110741 original size:8 final size:9
Alignment explanation
Indices: 1110705--1110739 Score: 52
Period size: 9 Copynumber: 3.7 Consensus size: 9
1110695 ATTTATGAAA
1110705 TAAATAAATG
1 TAAA-AAATG
1110715 TAAAAAAATG
1 T-AAAAAATG
1110725 TAAAAAATG
1 TAAAAAATG
1110734 TAAAAA
1 TAAAAA
1110740 TGATTGCCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 14 0.58
10 7 0.29
11 3 0.12
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.23
Consensus pattern (9 bp):
TAAAAAATG
Found at i:1119884 original size:3 final size:3
Alignment explanation
Indices: 1119864--1119921 Score: 66
Period size: 3 Copynumber: 19.0 Consensus size: 3
1119854 TTTGGGCCTG
*
1119864 TAA T-A TAA TAA -AA TTAA TAA TAAA TAA TAA TAT TAA TAA TAA TAAA
1 TAA TAA TAA TAA TAA -TAA TAA T-AA TAA TAA TAA TAA TAA TAA T-AA
1119910 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1119922 AAAACCAAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
2 4 0.08
3 36 0.75
4 8 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1119892 original size:19 final size:19
Alignment explanation
Indices: 1119868--1119922 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
1119858 GGCCTGTAAT
1119868 ATAATAAAATTAATAATAA
1 ATAATAAAATTAATAATAA
*
1119887 ATAATAATATTAATAAT-A
1 ATAATAAAATTAATAATAA
*
1119905 ATAA-ATAA-TAATAATAA
1 ATAATAAAATTAATAATAA
1119922 A
1 A
1119923 AAACCAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 7 0.22
17 4 0.12
18 5 0.16
19 16 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAATAAAATTAATAATAA
Found at i:1129266 original size:15 final size:15
Alignment explanation
Indices: 1129246--1129284 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
1129236 CTACATGGAG
1129246 CGATGAAGAAGGTTC
1 CGATGAAGAAGGTTC
1129261 CGATGAAGAAGGTTC
1 CGATGAAGAAGGTTC
1129276 CGATGAAGA
1 CGATGAAGA
1129285 GGAACAAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.33, T:0.18
Consensus pattern (15 bp):
CGATGAAGAAGGTTC
Found at i:1133300 original size:20 final size:19
Alignment explanation
Indices: 1133275--1133360 Score: 75
Period size: 19 Copynumber: 4.3 Consensus size: 19
1133265 TTTTGGTGGA
*
1133275 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCC-T
*
1133295 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC--T
*
1133316 GAAGGGGAACCGATTCCCCCT
1 G-A-GGGAACCGATACCCCCT
*
1133337 -AGGGGAATCGATACCCCCT
1 GA-GGGAACCGATACCCCCT
1133356 GAGGG
1 GAGGG
1133361 TTCTGGTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
19 20 0.35
20 17 0.30
21 3 0.05
22 1 0.02
23 16 0.28
ACGTcount: A:0.24, C:0.30, G:0.29, T:0.16
Consensus pattern (19 bp):
GAGGGAACCGATACCCCCT
Found at i:1133342 original size:19 final size:20
Alignment explanation
Indices: 1133277--1133360 Score: 82
Period size: 20 Copynumber: 4.1 Consensus size: 20
1133267 TTGGTGGAGA
* *
1133277 GGGAATCGATACCCCCATGA-
1 GGGAACCGATTCCCCC-TGAG
1133297 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--TG-AG
1133320 GGGAACCGATTCCCCCT-AG
1 GGGAACCGATTCCCCCTGAG
* *
1133339 GGGAATCGATACCCCCTGAG
1 GGGAACCGATTCCCCCTGAG
1133359 GG
1 GG
1133361 TTCTGGTTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
19 17 0.31
20 18 0.33
21 3 0.05
22 1 0.02
23 16 0.29
ACGTcount: A:0.24, C:0.31, G:0.29, T:0.17
Consensus pattern (20 bp):
GGGAACCGATTCCCCCTGAG
Found at i:1138016 original size:21 final size:20
Alignment explanation
Indices: 1137988--1138026 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1137978 CATTGTAGGA
*
1137988 ATTTATGGCCTCGACAAAAT
1 ATTTATGGCCTCAACAAAAT
1138008 ATTTCATGGCCTCAACAAA
1 ATTT-ATGGCCTCAACAAA
1138027 GGCCTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAT
Found at i:1165978 original size:32 final size:32
Alignment explanation
Indices: 1165939--1166105 Score: 145
Period size: 32 Copynumber: 5.2 Consensus size: 32
1165929 CATAACAGAT
*
1165939 TCAGTATTGCATTCATATAATGAACAGTAGAA
1 TCAGTATTGCATTCAGATAATGAACAGTAGAA
* * *
1165971 TCGGTATTGCATTCAGATAATGCATAGTAGAA
1 TCAGTATTGCATTCAGATAATGAACAGTAGAA
* ** ** *
1166003 TCAGTATTGCAATCAGATTTTTCATAGTAGAA
1 TCAGTATTGCATTCAGATAATGAACAGTAGAA
* ** * * * *
1166035 TCAATATTATAGTCAAATAATGCACAATAGAA
1 TCAGTATTGCATTCAGATAATGAACAGTAGAA
** * *
1166067 TCAGTATTGCATTCAGATAATCTATAGTATAA
1 TCAGTATTGCATTCAGATAATGAACAGTAGAA
1166099 TCAGTAT
1 TCAGTAT
1166106 GCCATTTATA
Statistics
Matches: 106, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 106 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (32 bp):
TCAGTATTGCATTCAGATAATGAACAGTAGAA
Found at i:1166094 original size:64 final size:64
Alignment explanation
Indices: 1165939--1166101 Score: 166
Period size: 64 Copynumber: 2.5 Consensus size: 64
1165929 CATAACAGAT
* ** * ** * * * * *
1165939 TCAGTATTGCATTCATATAATGAACAGTAGAATCGGTATTGCATTCAGATAATGCATAGTAGAA
1 TCAGTATTGCATTCAGATAATCTATAGTAGAATCAATATTACAGTCAAATAATGCACAATAGAA
* * * *
1166003 TCAGTATTGCAATCAGAT-TTTTCATAGTAGAATCAATATTATAGTCAAATAATGCACAATAGAA
1 TCAGTATTGCATTCAGATAATCT-ATAGTAGAATCAATATTACAGTCAAATAATGCACAATAGAA
*
1166067 TCAGTATTGCATTCAGATAATCTATAGTATAATCA
1 TCAGTATTGCATTCAGATAATCTATAGTAGAATCA
1166102 GTATGCCATT
Statistics
Matches: 79, Mismatches: 18, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
63 1 0.01
64 76 0.96
65 2 0.03
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (64 bp):
TCAGTATTGCATTCAGATAATCTATAGTAGAATCAATATTACAGTCAAATAATGCACAATAGAA
Found at i:1166153 original size:96 final size:96
Alignment explanation
Indices: 1165923--1166141 Score: 217
Period size: 96 Copynumber: 2.3 Consensus size: 96
1165913 CGGTTAGTGT
* * * * * * * * * *
1165923 ATAAGTCATAACAGATTCAGTATTGCATTCATATAATGAACAGTAGAATCGGTATTGCATTCAGA
1 ATAATTCATAGCAGAATCAATATTACAGTCAAATAATGCACAATAGAATCAGTATTGCATTCAGA
1165988 TAATGCATAGTAGAATCAGTATTGCAATCAG
66 TAATGCATAGTAGAATCAGTATTGCAATCAG
** * *
1166019 ATTTTTCATAGTAGAATCAATATTATAGTCAAATAATGCACAATAGAATCAGTATTGCATTCAGA
1 ATAATTCATAGCAGAATCAATATTACAGTCAAATAATGCACAATAGAATCAGTATTGCATTCAGA
* * * *
1166084 TAAT-CTATAGTATAATCAGTA-TGCCATTTAT
66 TAATGC-ATAGTAGAATCAGTATTG-CAATCAG
* * *
1166115 ATAATTCATAGCATAGTCATTATTACA
1 ATAATTCATAGCAGAATCAATATTACA
1166142 TTTAGATAAT
Statistics
Matches: 96, Mismatches: 25, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
95 3 0.03
96 93 0.97
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (96 bp):
ATAATTCATAGCAGAATCAATATTACAGTCAAATAATGCACAATAGAATCAGTATTGCATTCAGA
TAATGCATAGTAGAATCAGTATTGCAATCAG
Found at i:1169839 original size:2 final size:2
Alignment explanation
Indices: 1169832--1169861 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1169822 AAAAGGTTGA
1169832 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1169862 GATTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1169879 original size:22 final size:22
Alignment explanation
Indices: 1169829--1169899 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
1169819 TGTAAAAGGT
*
1169829 TGAATATATAT-ATATATATATA
1 TGAATATATATGATATTTAT-TA
*
1169851 T-ATATATATATGATTTTTATTA
1 TGA-ATATATATGATATTTATTA
* *
1169873 TGAATATATATGATGTTTGTTA
1 TGAATATATATGATATTTATTA
1169895 TGAAT
1 TGAAT
1169900 GTTACTTCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
21 1 0.02
22 34 0.81
23 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
TGAATATATATGATATTTATTA
Found at i:1178268 original size:32 final size:33
Alignment explanation
Indices: 1178209--1178273 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
1178199 CCTTTATAAC
* *
1178209 TCCCTAGTTTTTGATAGGCTAAACTAGAACCAA
1 TCCCTAGCTTTTGAAAGGCTAAACTAGAACCAA
* *
1178242 TCCCTAGCTTTT-AAAGGCTCAGCTAGAACCAA
1 TCCCTAGCTTTTGAAAGGCTAAACTAGAACCAA
1178274 AACCCCTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (33 bp):
TCCCTAGCTTTTGAAAGGCTAAACTAGAACCAA
Found at i:1178753 original size:20 final size:20
Alignment explanation
Indices: 1178728--1178768 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1178718 TGAGCCTTCA
* *
1178728 TGATAGCATCGGTACTTCCT
1 TGATAGCATCAGTACTACCT
*
1178748 TGATAGTATCAGTACTACCT
1 TGATAGCATCAGTACTACCT
1178768 T
1 T
1178769 TGCCTATGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (20 bp):
TGATAGCATCAGTACTACCT
Found at i:1180417 original size:24 final size:24
Alignment explanation
Indices: 1180390--1180445 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1180380 GGTTGACTAC
* *
1180390 TTCATCATCATCTTTGAAGTCATA
1 TTCATCACCATCATTGAAGTCATA
*
1180414 TTCATCACCATCATTGAAGTCATC
1 TTCATCACCATCATTGAAGTCATA
1180438 TTCATCAC
1 TTCATCAC
1180446 TCCAAGATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.27, G:0.07, T:0.38
Consensus pattern (24 bp):
TTCATCACCATCATTGAAGTCATA
Found at i:1182680 original size:112 final size:110
Alignment explanation
Indices: 1182474--1182896 Score: 567
Period size: 112 Copynumber: 3.8 Consensus size: 110
1182464 GGTATCGATA
* * * *
1182474 CAGACTTATTCCGCTGTCACTCAGGGAATATCAAATCTTAGAAGAGATAGATATGTTCCACTTCT
1 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATATTGGAAGAGAGAGATATGTTCCACTTCT
1182539 TTAAAAGGGAATATTAGATCTGGAGGAGTTGATCCATTGAATCGGGG
66 TT-AAAGGGAATATTAGATCTGGA-GAGTTGATCCATTGAATCGGGG
* * * * *
1182586 CCGACTTGTTCTGCTGTCACTCAGGGAATATCAAATCTTGGAAGAGAGGGATCTGTTCCACTTCT
1 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATATTGGAAGAGAGAGATATGTTCCACTTCT
1182651 TTATAAGGGAATATTAGATCTAGGAGAGTTGATCCATTGAATCGGGG
66 TTA-AAGGGAATATTAGATCT-GGAGAGTTGATCCATTGAATCGGGG
** *
1182698 CAGACTTGTTCCGCTGTCACTCAAAGAATATCAAATATTGAAAGAGAGAGATATGTTCCACTTCT
1 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATATTGGAAGAGAGAGATATGTTCCACTTCT
* * *
1182763 TCTAAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAGG
66 T-TAAAGGGAATATTAGATCT-GGAGAGTTGATCCATTGAATCGGGG
* * * * **
1182810 CAAACGTGTTCCGCTGTCACTCAGGGAATATCAAATATTGGAAGAGAGGGATTTGTTCTTCTTCT
1 CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATATTGGAAGAGAGAGATATGTTCCACTTCT
* * *
1182875 TCTGAAGAGAATATTATATCTG
66 T-TAAAGGGAATATTAGATCTG
1182897 CAAATTAAAC
Statistics
Matches: 276, Mismatches: 32, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
111 2 0.01
112 269 0.97
113 5 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (110 bp):
CAGACTTGTTCCGCTGTCACTCAGGGAATATCAAATATTGGAAGAGAGAGATATGTTCCACTTCT
TTAAAGGGAATATTAGATCTGGAGAGTTGATCCATTGAATCGGGG
Found at i:1182889 original size:224 final size:224
Alignment explanation
Indices: 1182474--1182895 Score: 625
Period size: 224 Copynumber: 1.9 Consensus size: 224
1182464 GGTATCGATA
** * *
1182474 CAGACTTATTCCGCTGTCACTCAGGGAATATCAAATCTTAGAAGAGATAGATATGTTCCACTTCT
1 CAGACTTATTCCGCTGTCACTCAAAGAATATCAAATATTAGAAGAGAGAGATATGTTCCACTTCT
* * ** * *
1182539 TTAAAAGGGAATATTAGATCTGGAGGAGTTGATCCATTGAATCGGGGCCGACTTGTTCTGCTGTC
66 TTAAAAGGGAATATCAGATCTGGAGGAGTTGATCCATTGAATCGAGGCAAACGTGTTCCGCTGTC
* * *
1182604 ACTCAGGGAATATCAAATCTTGGAAGAGAGGGATCTGTTCCACTTCTTTATAAGGGAATATTAGA
131 ACTCAGGGAATATCAAATATTGGAAGAGAGGGATCTGTTCCACTTCTTTAGAAGAGAATATTAGA
1182669 TCTAGGAGAGTTGATCCATTGAATCGGGG
196 TCTAGGAGAGTTGATCCATTGAATCGGGG
*
1182698 CAGACTTGTTCCGCTGTCACTCAAAGAATATCAAATATT-GAAAGAGAGAGATATGTTCCACTTC
1 CAGACTTATTCCGCTGTCACTCAAAGAATATCAAATATTAG-AAGAGAGAGATATGTTCCACTTC
*
1182762 TTCT-AAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAGGCAAACGTGTTCCGCTG
65 TT-TAAAAGGGAATATCAGATCTGGAGGAGTTGATCCATTGAATCGAGGCAAACGTGTTCCGCTG
* **
1182826 TCACTCAGGGAATATCAAATATTGGAAGAGAGGGATTTGTTCTTCTTCTTCT-GAAGAGAATATT
129 TCACTCAGGGAATATCAAATATTGGAAGAGAGGGATCTGTTCCACTTCTT-TAGAAGAGAATATT
*
1182890 ATATCT
193 AGATCT
1182896 GCAAATTAAA
Statistics
Matches: 176, Mismatches: 19, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
223 1 0.01
224 173 0.98
225 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (224 bp):
CAGACTTATTCCGCTGTCACTCAAAGAATATCAAATATTAGAAGAGAGAGATATGTTCCACTTCT
TTAAAAGGGAATATCAGATCTGGAGGAGTTGATCCATTGAATCGAGGCAAACGTGTTCCGCTGTC
ACTCAGGGAATATCAAATATTGGAAGAGAGGGATCTGTTCCACTTCTTTAGAAGAGAATATTAGA
TCTAGGAGAGTTGATCCATTGAATCGGGG
Found at i:1186297 original size:40 final size:40
Alignment explanation
Indices: 1186237--1186343 Score: 205
Period size: 40 Copynumber: 2.7 Consensus size: 40
1186227 TGCAGGTTTA
*
1186237 TAATACACTTCGGTGCATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1186277 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1186317 TAATACACTTCGGTGTATATGGTGGGC
1 TAATACACTTCGGTGTATATGGTGGGC
1186344 TATTGGCTAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 66 1.00
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1186485 original size:47 final size:45
Alignment explanation
Indices: 1186391--1186516 Score: 155
Period size: 47 Copynumber: 2.8 Consensus size: 45
1186381 GTAACCATGC
* * *
1186391 AAATAAGCTTATGAGCTTACGGAAT-AATGGCAAGTATATAGAAA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGAAA
* * **
1186435 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATATAGAAA
*
1186482 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1186517 AGATTTTATA
Statistics
Matches: 71, Mismatches: 8, Indels: 5
0.85 0.10 0.06
Matches are distributed among these distances:
44 22 0.31
45 11 0.15
46 1 0.01
47 37 0.52
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATAGAAA
Found at i:1189860 original size:40 final size:40
Alignment explanation
Indices: 1189800--1189961 Score: 288
Period size: 40 Copynumber: 4.0 Consensus size: 40
1189790 TGCATGTTTA
*
1189800 TAATACACTTCGGTGCATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
*
1189840 TAATACACTTCGGTATATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
1189880 TAATACACTTCGGTGTATATGGTGGGCGCAACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1189920 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1189960 TA
1 TA
1189962 GCACTATGGT
Statistics
Matches: 115, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 115 1.00
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1191557 original size:12 final size:13
Alignment explanation
Indices: 1191542--1191572 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1191532 GTTTCCTTTC
1191542 TTCTTTCTT-TTT
1 TTCTTTCTTATTT
1191554 TTCTTTCTTATTT
1 TTCTTTCTTATTT
1191567 TTCTTT
1 TTCTTT
1191573 TTTCTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (13 bp):
TTCTTTCTTATTT
Found at i:1191568 original size:16 final size:15
Alignment explanation
Indices: 1191538--1191584 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
1191528 ATTTGTTTCC
* *
1191538 TTTCTTCTTTCTTTT
1 TTTCTTTTTTCTATT
*
1191553 TTTC-TTTCT-TATT
1 TTTCTTTTTTCTATT
1191566 TTTCTTTTTTCTATT
1 TTTCTTTTTTCTATT
1191581 TTTC
1 TTTC
1191585 CTTTAATTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
13 7 0.27
14 7 0.27
15 12 0.46
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTCTATT
Found at i:1191595 original size:28 final size:28
Alignment explanation
Indices: 1191538--1191600 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
1191528 ATTTGTTTCC
* * **
1191538 TTTCTTCTTTCTTTTTTTCTTTCTTATT
1 TTTCTTTTTTCTTTTTTCCTTTAATATT
1191566 TTTCTTTTTTCTATTTTTCCTTTAAT-TT
1 TTTCTTTTTTCT-TTTTTCCTTTAATATT
1191594 TTTCTTT
1 TTTCTTT
1191601 AATTTTTTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (28 bp):
TTTCTTTTTTCTTTTTTCCTTTAATATT
Found at i:1191608 original size:12 final size:12
Alignment explanation
Indices: 1191578--1191608 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1191568 TCTTTTTTCT
*
1191578 ATTTTTCCTTTA
1 ATTTTTTCTTTA
1191590 ATTTTTTCTTTA
1 ATTTTTTCTTTA
1191602 ATTTTTT
1 ATTTTTT
1191609 GTGTGTTTTT
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:0.16, C:0.10, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTTTCTTTA
Found at i:1195282 original size:129 final size:129
Alignment explanation
Indices: 1194935--1195269 Score: 393
Period size: 129 Copynumber: 2.6 Consensus size: 129
1194925 TTTTAAGAGT
* *
1194935 GAAAACGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTTGTGCATTAAAACATTCA
1 GAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACC-TTTGTGCATTAAAACAATCA
* * * * *
1195000 TTTATTACTCCAATTGAAATAAAGAGATGTTACTATTTCATCTTAAAATTCAATATCAATTCAAG
65 TTTATTACTCCAATTGAAATAAAGAGA-GTAAATATTCCATCTAAAAAATCAATATCAATTCAAG
*
1195065 T
129 A
* * * *
1195066 GAAAATAATAACATCTAATGATTTCCAATCGAGAATAAATGACCTTTCGTGCATTAAAACAATTA
1 GAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTT-GTGCATTAAAACAATCA
* * * * * *
1195131 TTTGTTACCCCAATTGAAATAAAGAGA-TAAATATTCCGTCTAAAAAATCGATATTAATTCGAGA
65 TTTATTACTCCAATTGAAATAAAGAGAGTAAATATTCCATCTAAAAAATCAATATCAATTCAAGA
* * * * * * * *
1195195 GAAAATGACAATATCAAATTATTTCTAATCGAGAATAAATGACCTCTTATGCCTGAAAGCAGTCA
1 GAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCT-TTGTGCATTAAAACAATCA
1195260 TTTATTACTC
65 TTTATTACTC
1195270 TGATCAAAAT
Statistics
Matches: 170, Mismatches: 32, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
129 85 0.50
130 5 0.03
131 80 0.47
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.33
Consensus pattern (129 bp):
GAAAATGATAATATCTAATTATTTCCAATCGAGAATAAATGACCTTTGTGCATTAAAACAATCAT
TTATTACTCCAATTGAAATAAAGAGAGTAAATATTCCATCTAAAAAATCAATATCAATTCAAGA
Found at i:1197183 original size:3 final size:3
Alignment explanation
Indices: 1197175--1197213 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
1197165 AAAACTTAAT
1197175 TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
1197214 AAAAAAGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1197199 original size:14 final size:14
Alignment explanation
Indices: 1197175--1197210 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
1197165 AAAACTTAAT
1197175 TAATAATAATAATAA
1 TAAT-ATAATAATAA
1197190 TAATATAATAATAA
1 TAATATAATAATAA
1197204 TAATATA
1 TAATATA
1197211 TAAAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:1207555 original size:11 final size:11
Alignment explanation
Indices: 1207541--1207596 Score: 51
Period size: 11 Copynumber: 4.8 Consensus size: 11
1207531 CTCTTTTGAA
1207541 TTTCTTTTTCT
1 TTTCTTTTTCT
1207552 TTTCTTTTTTTCT
1 TTTC--TTTTTCT
*
1207565 GATTCTTCTTT-T
1 -TTTCTT-TTTCT
*
1207577 TGTCTTTTTCT
1 TTTCTTTTTCT
1207588 TTTCTTTTT
1 TTTCTTTTT
1207597 GCACTCCAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
10 3 0.08
11 17 0.47
12 3 0.08
13 10 0.28
14 3 0.08
ACGTcount: A:0.02, C:0.16, G:0.04, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:1208335 original size:20 final size:20
Alignment explanation
Indices: 1208310--1208361 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1208300 GAAACCCCTT
1208310 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTGA
*
1208330 TGAAAATACATGATTTTTTA
1 TGAAAATACATGATTTTTGA
1208350 TGAAAATACATG
1 TGAAAATACATG
1208362 CTCTTTGCCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTGA
Found at i:1210455 original size:22 final size:22
Alignment explanation
Indices: 1210421--1210482 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
1210411 TCCAGCACTT
*
1210421 TGTAACTCATGCAATAAA-TCTA
1 TGTAACTCTTGCAATAAAGT-TA
* *
1210443 TGTGACTCTTGCAATAAAGTTT
1 TGTAACTCTTGCAATAAAGTTA
*
1210465 TGTAACTCTTGCATTAAA
1 TGTAACTCTTGCAATAAA
1210483 CCTGTAACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
22 33 0.97
23 1 0.03
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.37
Consensus pattern (22 bp):
TGTAACTCTTGCAATAAAGTTA
Found at i:1210499 original size:25 final size:25
Alignment explanation
Indices: 1210468--1210517 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1210458 AAAGTTTTGT
1210468 AACTCTTGCATTAAACCTGTAACAG
1 AACTCTTGCATTAAACCTGTAACAG
1210493 AACTCTTGCATTAAACCTGTAACAG
1 AACTCTTGCATTAAACCTGTAACAG
1210518 CTCAATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (25 bp):
AACTCTTGCATTAAACCTGTAACAG
Found at i:1213391 original size:25 final size:25
Alignment explanation
Indices: 1213362--1213436 Score: 125
Period size: 25 Copynumber: 3.0 Consensus size: 25
1213352 CCAACAACCC
1213362 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1213387 ATCAGATTAGGGTTTCAAACCCTAAA
1 ATCAGATTAGGGTTTCAAACCCT-AA
*
1213413 ACCA-ATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1213437 TCCCCTACTC
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
24 2 0.04
25 41 0.85
26 5 0.10
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1215783 original size:15 final size:14
Alignment explanation
Indices: 1215756--1215800 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
1215746 AACGTAGATC
1215756 AAATTTTTGTCTTATA
1 AAATTTTT-TCTTA-A
1215772 AAATTTTTTCTTAA
1 AAATTTTTTCTTAA
*
1215786 AAATTGTTT-TTAA
1 AAATTTTTTCTTAA
1215799 AA
1 AA
1215801 GACGTTTTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 6 0.21
14 9 0.32
15 5 0.18
16 8 0.29
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (14 bp):
AAATTTTTTCTTAA
Found at i:1227764 original size:130 final size:129
Alignment explanation
Indices: 1227492--1227767 Score: 305
Period size: 130 Copynumber: 2.1 Consensus size: 129
1227482 TGACCGAACT
*
1227492 TCCTCATCACGTAGGAGCGTGTCAACATTAGGATAACCAGTCGTCCTCATCACGTAGGAACCGAG
1 TCCTCATCACGTAGGAGCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGAG
* * * * *
1227557 TTATCACCCTTCCTAAGGTGGCCAGAGTTTTCATCATATGAACCGTGTCATCCCCAGACCAGATC
66 CTATCACCCTT-CTAAGATGGCCAGAGTTTTCATCATAAGAACCGTGTCAACCCCAAACCAGATC
* *
1227622 TCTTCATCACGTATGAGCCGTGTCAACCA-TA-GATAACCAGCCGTCCTCATCACGTAGGAACCG
1 TCCTCATCACGTAGGAG-CGTGTCAA-CATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCG
* * **
1227685 TGCTATCA-CCTT-T-AGATGGCCAGA-TCTCTTCATCACGTAAGAGCCGTGTCAACCTGATAAC
64 AGCTATCACCCTTCTAAGATGGCCAGAGT-T-TTCATCA--TAAGAACCGTGTCAACCCCA-AAC
1227746 CAG-TC
124 CAGATC
*
1227751 GTCCTCATTACGTAGGA
1 -TCCTCATCACGTAGGA
1227768 ACCGAGTTAT
Statistics
Matches: 123, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
125 1 0.01
126 11 0.09
127 8 0.07
129 21 0.17
130 70 0.57
131 10 0.08
132 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.20, T:0.25
Consensus pattern (129 bp):
TCCTCATCACGTAGGAGCGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTAGGAACCGAG
CTATCACCCTTCTAAGATGGCCAGAGTTTTCATCATAAGAACCGTGTCAACCCCAAACCAGATC
Found at i:1227779 original size:87 final size:90
Alignment explanation
Indices: 1227613--1227824 Score: 295
Period size: 89 Copynumber: 2.4 Consensus size: 90
1227603 GTCATCCCCA
*
1227613 GACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
* **
1227678 GGAACCGTGCTATCA-CCTTTAGAT
66 GGAACCGAGCTATCACCCTAAAGAT
* * *
1227702 GGCCAGATCTCTTCATCACGTAAGAGCCGTGTCAACC-T-GATAACCAGTCGTCCTCATTACGTA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
*
1227765 GGAACCGAGTTATCATCCCTAAAGAT
66 GGAACCGAGCTATCA-CCCTAAAGAT
* * *
1227791 GACCAGATCTCCTCATCACGTAGGAGCCATGTCA
1 GACCAGATCTCTTCATCACGTAAGAGCCGTGTCA
1227825 CCCTTAGACG
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
87 36 0.33
88 1 0.01
89 72 0.66
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (90 bp):
GACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGCTATCACCCTAAAGAT
Found at i:1228030 original size:3 final size:3
Alignment explanation
Indices: 1228019--1228076 Score: 50
Period size: 3 Copynumber: 20.0 Consensus size: 3
1228009 TTTTTTTCCG
* ** *
1228019 TTA TT- TTA TTA TTA TTA GTA TTA TCG TTA -TC TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1228064 TTA TTTA TTA TTA
1 TTA -TTA TTA TTA
1228077 CAATTTTTGC
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
2 5 0.12
3 35 0.81
4 3 0.07
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1228220 original size:25 final size:25
Alignment explanation
Indices: 1228158--1228280 Score: 207
Period size: 25 Copynumber: 5.0 Consensus size: 25
1228148 CCAACAACCC
1228158 ATCAGATTAGGGTTTCAAACCCT-A
1 ATCAGATTAGGGTTTCAAACCCTAA
1228182 ATCA-ATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1228206 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
1228231 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
1228256 ACCCA-ATTAGGGTTTCAAACCCTAA
1 A-TCAGATTAGGGTTTCAAACCCTAA
1228281 TCCCCTACTC
Statistics
Matches: 95, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
23 18 0.19
24 9 0.09
25 66 0.69
26 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:1246072 original size:23 final size:23
Alignment explanation
Indices: 1246042--1246091 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
1246032 CTGCGCGTCA
1246042 GTTGGGTTCATATCAGGTGATCT
1 GTTGGGTTCATATCAGGTGATCT
1246065 GTTGGGTTCATATCAGGTGATCT
1 GTTGGGTTCATATCAGGTGATCT
1246088 GTTG
1 GTTG
1246092 CTTGTTGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (23 bp):
GTTGGGTTCATATCAGGTGATCT
Found at i:1247440 original size:30 final size:29
Alignment explanation
Indices: 1247389--1247446 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
1247379 TTACATCGGG
*
1247389 GACCATATTGCAAATGAACTAAATGTTGGA
1 GACCATATTGCAAATCAACTAAA-GTTGGA
1247419 GACCATATTGCAAA-CATACTAAAGTTGG
1 GACCATATTGCAAATCA-ACTAAAGTTGG
1247447 GGACTGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (29 bp):
GACCATATTGCAAATCAACTAAAGTTGGA
Found at i:1256634 original size:34 final size:33
Alignment explanation
Indices: 1256573--1256685 Score: 106
Period size: 33 Copynumber: 3.5 Consensus size: 33
1256563 TTTTAGTTTC
* * *
1256573 ATTCATATCATATAACATGTACTTTTCACAATT
1 ATTCAAATCATATAATATTTACTTTTCACAATT
* *
1256606 ATCCAAATCATATAATAATTTACTTTTCA-TATT
1 ATTCAAATCATATAAT-ATTTACTTTTCACAATT
* * * *
1256639 CATTTAAATAATGTAATTTTTACTTTTCACAA--
1 -ATTCAAATCATATAATATTTACTTTTCACAATT
1256671 ATTCAAATCATATAA
1 ATTCAAATCATATAA
1256686 CCTATGCTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 8
0.74 0.16 0.09
Matches are distributed among these distances:
31 12 0.19
33 27 0.43
34 24 0.38
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (33 bp):
ATTCAAATCATATAATATTTACTTTTCACAATT
Found at i:1265138 original size:34 final size:33
Alignment explanation
Indices: 1265060--1265177 Score: 91
Period size: 33 Copynumber: 3.6 Consensus size: 33
1265050 ACTTTTTAGT
**
1265060 ATTATTCATGTCATATAACATGCACTTTTCACA
1 ATTATTCAAATCATATAACATGCACTTTTCACA
* *
1265093 ATTGTTCAAATCATATAATCATGTACTTTTCAC-
1 ATTATTCAAATCATATAA-CATGCACTTTTCACA
* * ** ***
1265126 ATTCATTTAAATCA-CTAATTTTTTCTTTTCACA
1 ATT-ATTCAAATCATATAACATGCACTTTTCACA
1265159 A--ATTCAAATCATATAACAT
1 ATTATTCAAATCATATAACAT
1265178 ATGCTTTTCA
Statistics
Matches: 66, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
30 9 0.14
31 4 0.06
32 10 0.15
33 22 0.33
34 21 0.32
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (33 bp):
ATTATTCAAATCATATAACATGCACTTTTCACA
Found at i:1267164 original size:31 final size:31
Alignment explanation
Indices: 1267114--1267181 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 31
1267104 ATATATTTAT
1267114 TTTAAA-TAAAAAGTTAAATTTATG-TATTAA
1 TTTAAATTAAAAAGTTAAATTTA-GATATTAA
1267144 TTTAAATTAATAAA-TTAAATTTAGATATTAA
1 TTTAAATTAA-AAAGTTAAATTTAGATATTAA
1267175 TTTAAAT
1 TTTAAAT
1267182 CTTAACCTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
30 7 0.20
31 25 0.71
32 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (31 bp):
TTTAAATTAAAAAGTTAAATTTAGATATTAA
Found at i:1267179 original size:18 final size:18
Alignment explanation
Indices: 1267127--1267181 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
1267117 AAATAAAAAG
1267127 TTAAATTTATG-TATTAAT
1 TTAAATTTA-GATATTAAT
1267145 TTAAA-TTA-ATA--AA-
1 TTAAATTTAGATATTAAT
1267158 TTAAATTTAGATATTAAT
1 TTAAATTTAGATATTAAT
1267176 TTAAAT
1 TTAAAT
1267182 CTTAACCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 12
0.72 0.00 0.28
Matches are distributed among these distances:
13 5 0.16
14 5 0.16
15 3 0.10
16 2 0.06
17 5 0.16
18 11 0.35
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (18 bp):
TTAAATTTAGATATTAAT
Found at i:1267499 original size:22 final size:21
Alignment explanation
Indices: 1267453--1267499 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
1267443 AATTAGTATA
*
1267453 ATTAATATATCATTTTTAATT
1 ATTAATATATAATTTTTAATT
1267474 -TTAATATA-AATTATTTAAATT
1 ATTAATATATAATT-TTT-AATT
1267495 ATTAA
1 ATTAA
1267500 AAAATGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 4 0.18
22 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTAATATATAATTTTTAATT
Found at i:1269152 original size:138 final size:136
Alignment explanation
Indices: 1268993--1269300 Score: 465
Period size: 136 Copynumber: 2.2 Consensus size: 136
1268983 AGGACCAAAG
1268993 ATCAAGGCTCTAATATTAATCCTAATCAATTTTAGCCATTTATTGAATCAAATAGTTAAAATGGA
1 ATCAAGGCTCTAATATTAATCCTAATCAATTTTAGCCATTTATTGAATCAAATAGTT-AAATGGA
** * *
1269058 ATCTGGGGCATAAAAGTGAGGACTAAATTAAAAATTCTCCTAAATTAAAGGACCAAAGATGATAT
65 ATCTCAGGCATAAAAG-GAGGACTAAATTAAAAAATCTCCT-AATTAAAGGACCAAAGATGAAAT
1269123 TAATAT-AA
128 TAATATAAA
* *
1269131 ATCAAGGCTCTAATATTAATCCTAATCAAATTTATCCATTTATTGAATCAAATAGTTAAATGGAA
1 ATCAAGGCTCTAATATTAATCCTAATCAATTTTAGCCATTTATTGAATCAAATAGTTAAATGGAA
* * *
1269196 TCTCAGGCATATAAGGAGGACTAAATTAAAAAATCTCCTAATTAAAGGACTAACGATGAAATTAA
66 TCTCAGGCATAAAAGGAGGACTAAATTAAAAAATCTCCTAATTAAAGGACCAAAGATGAAATTAA
*
1269261 TCTAAA
131 TATAAA
* * *
1269267 ATGAAGGCTCTAATACTAATCCTAACCAATTTTA
1 ATCAAGGCTCTAATATTAATCCTAATCAATTTTA
1269301 ACAAATTATT
Statistics
Matches: 155, Mismatches: 14, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
135 25 0.16
136 55 0.35
137 20 0.13
138 55 0.35
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (136 bp):
ATCAAGGCTCTAATATTAATCCTAATCAATTTTAGCCATTTATTGAATCAAATAGTTAAATGGAA
TCTCAGGCATAAAAGGAGGACTAAATTAAAAAATCTCCTAATTAAAGGACCAAAGATGAAATTAA
TATAAA
Found at i:1269661 original size:14 final size:15
Alignment explanation
Indices: 1269644--1269684 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
1269634 TTTAAAGGAC
1269644 TGAAATTAAAATG-T
1 TGAAATTAAAATGTT
*
1269658 TGAAATTAAAAGGTT
1 TGAAATTAAAATGTT
*
1269673 TGAAATAAAAAT
1 TGAAATTAAAAT
1269685 TGGTTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.32
Consensus pattern (15 bp):
TGAAATTAAAATGTT
Found at i:1269683 original size:15 final size:14
Alignment explanation
Indices: 1269630--1269682 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
1269620 TGAAATACTA
* *
1269630 GAAATTTAAAGGACT
1 GAAATTAAAAGG-TT
*
1269645 GAAATTAAAATGTT
1 GAAATTAAAAGGTT
1269659 GAAATTAAAAGGTTT
1 GAAATTAAAAGG-TT
1269674 GAAA-TAAAA
1 GAAATTAAAA
1269683 ATTGGTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
14 17 0.52
15 16 0.48
ACGTcount: A:0.53, C:0.02, G:0.17, T:0.28
Consensus pattern (14 bp):
GAAATTAAAAGGTT
Found at i:1271173 original size:17 final size:17
Alignment explanation
Indices: 1271121--1271175 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
1271111 ATAAATCGTT
1271121 CCTTTTCGAGAATAAGTG
1 CCTTTTC-AGAATAAGTG
* * * *
1271139 TC-TTTC-CAAGACGTG
1 CCTTTTCAGAATAAGTG
1271154 CCTTTTCAGAATAAGTG
1 CCTTTTCAGAATAAGTG
1271171 CCTTT
1 CCTTT
1271176 CCTGAGCGTT
Statistics
Matches: 27, Mismatches: 8, Indels: 5
0.68 0.20 0.12
Matches are distributed among these distances:
15 7 0.26
16 4 0.15
17 15 0.56
18 1 0.04
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (17 bp):
CCTTTTCAGAATAAGTG
Found at i:1271592 original size:18 final size:20
Alignment explanation
Indices: 1271550--1271599 Score: 77
Period size: 18 Copynumber: 2.6 Consensus size: 20
1271540 CATCCAAAAG
*
1271550 CATGTACTTTCATTAAAACT
1 CATGTATTTTCATTAAAACT
1271570 CATGTATTTTCATT-AAA-T
1 CATGTATTTTCATTAAAACT
1271588 CATGTATTTTCA
1 CATGTATTTTCA
1271600 AAAGATTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 13 0.45
19 3 0.10
20 13 0.45
ACGTcount: A:0.32, C:0.16, G:0.06, T:0.46
Consensus pattern (20 bp):
CATGTATTTTCATTAAAACT
Found at i:1273096 original size:45 final size:45
Alignment explanation
Indices: 1272761--1273086 Score: 409
Period size: 45 Copynumber: 7.2 Consensus size: 45
1272751 TATCATTTAT
* ** * *
1272761 TTTCATTTATAGCATCATTTCATGCTTATAATGCACCATTATGTCT
1 TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTTATG-CA
* *
1272807 TTTCATTTATGGCATCCTTTCATGCCGATAATGCACCGTTATTCA
1 TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTTATGCA
** * *
1272852 TTTCATTTATGGCATTTTTTCATGCCAATAATGCACCATTATGCA
1 TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTTATGCA
* * *
1272897 TTTTATTTATGGCATCCTTTCATGCCGATAATGCATCGTTATGCA
1 TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTTATGCA
* * ** *
1272942 TTTCGTTTATGGCCTCATTTCATGCCGATAACACACCGTTATGTA
1 TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTTATGCA
** * * *
1272987 TTTCATTTATAACATCCTTTCATGTCGATAATGCACTGTTATGCA
1 TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTTATGCA
* *
1273032 TTTCATTTATGGCATCATTTCATGTCGATAATGCACCATTATGCA
1 TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTTATGCA
1273077 TTTCATTTAT
1 TTTCATTTAT
1273087 TCATTCATTT
Statistics
Matches: 239, Mismatches: 41, Indels: 1
0.85 0.15 0.00
Matches are distributed among these distances:
45 202 0.85
46 37 0.15
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (45 bp):
TTTCATTTATGGCATCATTTCATGCCGATAATGCACCGTTATGCA
Found at i:1275090 original size:27 final size:27
Alignment explanation
Indices: 1275059--1275123 Score: 69
Period size: 27 Copynumber: 2.4 Consensus size: 27
1275049 ACCTTTTATA
*
1275059 CTATTTATTATTTTTGTCATT-TTCTTT
1 CTATTTATTAATTTT-TCATTATTCTTT
* *
1275086 CTATTTCTTAATTTTTCATTATTTTTT
1 CTATTTATTAATTTTTCATTATTCTTT
* *
1275113 CTCTTAATTAA
1 CTATTTATTAA
1275124 AATTAATTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
26 5 0.16
27 26 0.84
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (27 bp):
CTATTTATTAATTTTTCATTATTCTTT
Found at i:1278727 original size:139 final size:138
Alignment explanation
Indices: 1278249--1278750 Score: 447
Period size: 139 Copynumber: 3.6 Consensus size: 138
1278239 TAAAGAACTT
* * * ** *
1278249 TTTTGACAACTTATTGAATCAAATAATAAAAATGGAACCTCATGAATAAAAATAAGGACCAAATT
1 TTTT-ACAAATTATTGAATCAAATAATTAAAATGGAACCTCAGGAATAAAAGCAAGAACCAAATT
* * * * *
1278314 AAAAATTCACTTAAATTAAACT-ACT-AAGGTGAAATTAAACCT-AAATGTAGTCTCTAGTATTA
65 AAAAATTCTCTTAAATTAAA-TAACTAAAGATGAAA-TAAACTTAAAATGAAGTCTCTAATATTA
* * *
1278376 ATCTTATCTAA
128 ATCCTAACCAA
* * ** * * *
1278387 TTGTTAACAAATTATTGAATCGAATAATTAAAATGGAACATTGGGCACAAAAGCGAGAACCAAAT
1 TT-TT-ACAAATTATTGAATCAAATAATTAAAATGGAACCTCAGGAATAAAAGCAAGAACCAAAT
* * * *
1278452 TAAAAATTCTCTTAAATTAAA-AGACTAAAGATGAAATTAA-TCTAAAATAAATTTTCTAATATT
64 TAAAAATTCTCTTAAATTAAATA-ACTAAAGATGAAATAAACT-TAAAATGAAGTCTCTAATATT
1278515 AATCCTAACCAA
127 AATCCTAACCAA
* * ** * **
1278527 TTTTAGCCATTTATTGAATCAAATAATTAAAATGGAACCTTGGGAATGAAAGTGAGAACCAAATT
1 TTTTA-CAAATTATTGAATCAAATAATTAAAATGGAACCTCAGGAATAAAAGCAAGAACCAAATT
** * * *
1278592 AAAAAAGCTCCTAAACTAAATAACTAAAGATGAAATCAACTTAAAATGAAGTCTCTAATATTAAT
65 AAAAATTCTCTTAAATTAAATAACTAAAGATGAAATAAACTTAAAATGAAGTCTCTAATATTAAT
1278657 CCTAACCAA
130 CCTAACCAA
* * * * * * * * *
1278666 TTTTGACTAATCATTGGATCAAATAACTAATATGGAACCTCAAGCATAAAAGCAAGGACCAAATC
1 TTTT-ACAAATTATTGAATCAAATAATTAAAATGGAACCTCAGGAATAAAAGCAAGAACCAAATT
* * *
1278731 AAGAATTCACCTAAATTAAA
65 AAAAATTCTCTTAAATTAAA
1278751 AAGTTTAGGG
Statistics
Matches: 292, Mismatches: 62, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
138 3 0.01
139 253 0.87
140 36 0.12
ACGTcount: A:0.47, C:0.14, G:0.11, T:0.28
Consensus pattern (138 bp):
TTTTACAAATTATTGAATCAAATAATTAAAATGGAACCTCAGGAATAAAAGCAAGAACCAAATTA
AAAATTCTCTTAAATTAAATAACTAAAGATGAAATAAACTTAAAATGAAGTCTCTAATATTAATC
CTAACCAA
Found at i:1279731 original size:94 final size:95
Alignment explanation
Indices: 1279617--1279798 Score: 224
Period size: 94 Copynumber: 1.9 Consensus size: 95
1279607 AGCGATGTAG
* *
1279617 TATCGATACCATGGTAAGGGTATAAATACCAAGAAACATCGAACCTAAT-TATGGTATCGGTAC-
1 TATCGAGACCATGGTAAGGGTATAAATACCAAGAAACATCGAACCTAATAT-TGGTATCGATACT
*
1279680 CGAAGGGGGTATCGATACCTTAGTGTACTAA
65 CGAAGGGGGTATCGATACCATAGTGTACTAA
* ** * ** * * * *
1279711 TATCGAGACCATGGTGAGGGTATCGATACCAGGCTATATCGAAGCTAATATTGGTATTGATACTG
1 TATCGAGACCATGGTAAGGGTATAAATACCAAGAAACATCGAACCTAATATTGGTATCGATACTC
1279776 GAAGGGGGTATCGATACCATAGT
66 GAAGGGGGTATCGATACCATAGT
1279799 AGGGTAGTAT
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
94 50 0.68
95 23 0.32
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (95 bp):
TATCGAGACCATGGTAAGGGTATAAATACCAAGAAACATCGAACCTAATATTGGTATCGATACTC
GAAGGGGGTATCGATACCATAGTGTACTAA
Found at i:1279811 original size:22 final size:22
Alignment explanation
Indices: 1279783--1279836 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
1279773 CTGGAAGGGG
*
1279783 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAATAGGGTA
1279805 GTATCGATACCATAATAGGGTA
1 GTATCGATACCATAATAGGGTA
1279827 GTATCGATAC
1 GTATCGATAC
1279837 TAAAGGGCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (22 bp):
GTATCGATACCATAATAGGGTA
Found at i:1280677 original size:46 final size:46
Alignment explanation
Indices: 1280625--1280744 Score: 172
Period size: 46 Copynumber: 2.6 Consensus size: 46
1280615 TGGAACACAT
1280625 AGTGCATCGATGCATAAAATGCATTCGATGTTT-CA-AACAAGTCAGG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAA-AA-TCAGG
* **
1280671 AGTGCATCGACGCATAAAATGCATTCGATGTTTCCATAAAATCCTG
1 AGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAATCAGG
*
1280717 AGTGCATCGATGCATAAAATTCATTCGA
1 AGTGCATCGATGCATAAAATGCATTCGA
1280745 AATGGGGTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 61 0.91
47 4 0.06
48 2 0.03
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (46 bp):
AGTGCATCGATGCATAAAATGCATTCGATGTTTCCATAAAATCAGG
Found at i:1283461 original size:23 final size:23
Alignment explanation
Indices: 1283388--1283468 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 23
1283378 CACTACTGAT
* *
1283388 TGCATCGGTGCACATTCA-AGGA
1 TGCATCGATGCACTTTCATAGGA
* *
1283410 GTGCATTGGTGCA-TCTTCAT--GA
1 -TGCATCGATGCACT-TTCATAGGA
*
1283432 TGTATCGATGCACTTTCATAGGA
1 TGCATCGATGCACTTTCATAGGA
1283455 TGCATCGATGCACT
1 TGCATCGATGCACT
1283469 GGATAGTGTA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
21 14 0.30
22 3 0.06
23 30 0.64
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (23 bp):
TGCATCGATGCACTTTCATAGGA
Found at i:1285731 original size:18 final size:18
Alignment explanation
Indices: 1285689--1285731 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1285679 AAAAACCGGG
*
1285689 TGATTTTAATAAAATATT
1 TGATTTTAATAAAATATC
*
1285707 TTATTTTAATAAAATA-C
1 TGATTTTAATAAAATATC
1285724 TGAGTTTT
1 TGA-TTTT
1285732 GGGGTCTGCG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
TGATTTTAATAAAATATC
Found at i:1289096 original size:113 final size:112
Alignment explanation
Indices: 1288898--1289169 Score: 427
Period size: 113 Copynumber: 2.4 Consensus size: 112
1288888 TTCAGGGAAT
* *
1288898 ATTGAATCAGGGTAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAAAGAGAT
1 ATTGAATCA-GGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAAAGAGAC
* * *
1288963 ATGTTCCACTTACTCTGAAGGGAATATCATATTTTGGGGAGTTAATCC
65 ATGTTCCACTTACTCTGAAGGGAATATCATATCTGGGGGAATTAATCC
* * *
1289011 ATTGAATCTAGGAAGACTTGTTCCACCTACTCTAAATGGAATATCAAATCTTGGAAAAAAGAGAC
1 ATTGAATC-AGGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAAAGAGAC
* *
1289076 ATGTTCCGCTTACTCTGAAGGGAATATCATATCTGGGGGAATTGATCC
65 ATGTTCCACTTACTCTGAAGGGAATATCATATCTGGGGGAATTAATCC
1289124 ATTGAATCAGGATAGACTTGTTCCACTTACTCTGAAGGGAATATCA
1 ATTGAATCAGGA-AGACTTGTTCCACTTACTCTGAAGGGAATATCA
1289170 GATATGGGGG
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
112 4 0.03
113 139 0.97
114 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Consensus pattern (112 bp):
ATTGAATCAGGAAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAAAAGAGACA
TGTTCCACTTACTCTGAAGGGAATATCATATCTGGGGGAATTAATCC
Found at i:1289159 original size:65 final size:65
Alignment explanation
Indices: 1289072--1289239 Score: 282
Period size: 65 Copynumber: 2.6 Consensus size: 65
1289062 TGGAAAAAAG
* * *
1289072 AGACATGTTCCGCTTACTCTGAAGGGAATATCATATCTGGGGGAATTGATCCATTGAATCAGGAT
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTGGGGGAATTGATCCATTGAATCAGGAT
* * *
1289137 AGACTTGTTCCACTTACTCTGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAATCAGGGT
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTGGGGGAATTGATCCATTGAATCAGGAT
1289202 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCT
1 AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCT
1289240 TGGATAAGAG
Statistics
Matches: 96, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 96 1.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (65 bp):
AGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTGGGGGAATTGATCCATTGAATCAGGAT
Found at i:1289263 original size:178 final size:178
Alignment explanation
Indices: 1288964--1289347 Score: 592
Period size: 178 Copynumber: 2.2 Consensus size: 178
1288954 AAAAGAGATA
* * * *
1288964 TGTTCCACTTACTCTGAAGGGAATATCATATTTTGGGGAGTTAATCCATTGAATCTAGGAAGACT
1 TGTTCCACTTACTCTGAAGGGAATATCAGATATGGGGGAATTAATCCATTGAATCTAGGAAGACT
*
1289029 TGTTCCACCTACTCTAAATGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCGCTTACTCTGA
66 TGTTCCACCTACTCTAAAGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCGCTTACTCTGA
* *
1289094 AGGGAATATCATATCTGGGGGAATTGATCCATTGAATC-AGGATAGACT
131 AGGGAATATCAGATCTGGGGGAATTGATCCATTGAATCGAGG-TAAACT
* *
1289142 TGTTCCACTTACTCTGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAATC-AGGGTAGAC
1 TGTTCCACTTACTCTGAAGGGAATATCAGATATGGGGGAATTAATCCATTGAATCTA-GGAAGAC
* * * * *
1289206 TTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAGAGACCTGTTCCGCTTACTCTG
65 TTGTTCCACCTACTCTAAAGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCGCTTACTCTG
* *
1289271 AAGGGAATATCAGATCTGGGGGAGTTGATTCATTGAATCGAGGTAAACT
130 AAGGGAATATCAGATCTGGGGGAATTGATCCATTGAATCGAGGTAAACT
1289320 TGTTCCACTTACTCTGAAGGGAATATCA
1 TGTTCCACTTACTCTGAAGGGAATATCA
1289348 AATCTTGAAA
Statistics
Matches: 188, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
177 1 0.01
178 184 0.98
179 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (178 bp):
TGTTCCACTTACTCTGAAGGGAATATCAGATATGGGGGAATTAATCCATTGAATCTAGGAAGACT
TGTTCCACCTACTCTAAAGGGAATATCAAATCTTGGAAAAAAGAGACATGTTCCGCTTACTCTGA
AGGGAATATCAGATCTGGGGGAATTGATCCATTGAATCGAGGTAAACT
Found at i:1289416 original size:111 final size:112
Alignment explanation
Indices: 1289137--1289505 Score: 600
Period size: 111 Copynumber: 3.3 Consensus size: 112
1289127 GAATCAGGAT
* * * *
1289137 AGACTTGTTCCACTTACTCTGAAGGGAATATCAGATATGGGGGAATTGATCCATTGAATC-AGGG
1 AGACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGA-GG
*
1289201 TAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGATAAGAG
65 TAAACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGA-AAGAG
*
1289250 AGACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATTCATTGAATCGAGGT
1 AGACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAGGT
1289315 AAACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTT-GAAAGAG
66 AAACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAGAG
* * *
1289361 AGACCTGTTTCGCTTATTCTGAAGGGAATATCAGATCTGGAGGAGTTGATCCATTGAATCGAGG-
1 AGACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAGGT
1289425 AAGACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAGAG
66 AA-ACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAGAG
*
1289473 AGACATGTTCCGCTTACTCTGAAGGGAATATCA
1 AGACCTGTTCCGCTTACTCTGAAGGGAATATCA
1289506 TATTCTAAAT
Statistics
Matches: 240, Mismatches: 13, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
110 2 0.01
111 102 0.43
112 39 0.16
113 96 0.40
114 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (112 bp):
AGACCTGTTCCGCTTACTCTGAAGGGAATATCAGATCTGGGGGAGTTGATCCATTGAATCGAGGT
AAACTTGTTCCACTTACTCTGAAGGGAATATCAAATCTTGGAAAGAG
Found at i:1303397 original size:15 final size:15
Alignment explanation
Indices: 1303379--1303455 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
1303369 TTGGTCATTT
*
1303379 TTTATATTTTTATCA
1 TTTATATTTTTATTA
*
1303394 TTTATATGTTTAAATTA
1 TTTATAT-TTT-TATTA
* *
1303411 -GTATTTTATTTATTTA
1 TTTATATT-TTTA-TTA
* *
1303427 TTCATATATTTATTA
1 TTTATATTTTTATTA
1303442 TTTATATTTTTATT
1 TTTATATTTTTATT
1303456 CACTAATATT
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
15 24 0.52
16 16 0.35
17 6 0.13
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (15 bp):
TTTATATTTTTATTA
Found at i:1303449 original size:29 final size:28
Alignment explanation
Indices: 1303412--1303468 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
1303402 TTTAAATTAG
1303412 TATTTTATTTATTTATTCA-T-ATATTTAT
1 TATTTTA-TT-TTTATTCACTAATATTTAT
1303440 TATTTATATTTTTATTCACTAATATTTAT
1 TATTT-TATTTTTATTCACTAATATTTAT
1303469 ATGAAATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 8 0.31
28 8 0.31
29 10 0.38
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (28 bp):
TATTTTATTTTTATTCACTAATATTTAT
Found at i:1303453 original size:27 final size:29
Alignment explanation
Indices: 1303415--1303468 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
1303405 AAATTAGTAT
1303415 TTTATTTATTTATTCA-T-ATATTTATTA
1 TTTATTTATTTATTCACTAATATTTATTA
1303442 TTTATATT-TTTATTCACTAATATTTAT
1 TTTAT-TTATTTATTCACTAATATTTAT
1303469 ATGAAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 3 0.12
29 8 0.33
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTATTTATTTATTCACTAATATTTATTA
Found at i:1304295 original size:18 final size:18
Alignment explanation
Indices: 1304272--1304312 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1304262 TTCTTTCAAA
1304272 TTTTTTAT-TACTTATTAT
1 TTTTTTATATA-TTATTAT
1304290 TTTTTTATATATTATTAT
1 TTTTTTATATATTATTAT
1304308 TTTTT
1 TTTTT
1304313 ATTTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTATATATTATTAT
Found at i:1304310 original size:15 final size:15
Alignment explanation
Indices: 1304284--1304352 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
1304274 TTTTATTACT
*
1304284 TATTATTTTTTTATA
1 TATTATTATTTTATA
1304299 TATTATTATTTT-T-
1 TATTATTATTTTATA
*
1304312 TATT-TTA-TTTATT
1 TATTATTATTTTATA
* *
1304325 TATTA-TATTTAAGA
1 TATTATTATTTTATA
1304339 -ATTAATTATTTTAT
1 TATT-ATTATTTTAT
1304353 TTGTTTGTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
11 3 0.07
12 4 0.10
13 13 0.31
14 5 0.12
15 17 0.40
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.68
Consensus pattern (15 bp):
TATTATTATTTTATA
Found at i:1304314 original size:25 final size:26
Alignment explanation
Indices: 1304276--1304335 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 26
1304266 TTCAAATTTT
*
1304276 TTATTACTTATTATTTT-TTTATATA
1 TTATTATTTATTATTTTATTTATATA
* *
1304301 TTATTATTTTTTATTTTATTTATTTA
1 TTATTATTTATTATTTTATTTATATA
1304327 TTA-TATTTA
1 TTATTATTTA
1304336 AGAATTAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.72
Consensus pattern (26 bp):
TTATTATTTATTATTTTATTTATATA
Found at i:1304320 original size:18 final size:18
Alignment explanation
Indices: 1304271--1304320 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1304261 TTTCTTTCAA
1304271 ATTTTTTA--TTACTTATT
1 ATTTTTTATTTTA-TTATT
*
1304288 ATTTTTT-TATATATTATT
1 ATTTTTTAT-TTTATTATT
1304306 ATTTTTTATTTTATT
1 ATTTTTTATTTTATT
1304321 TATTTATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 7 0.26
18 17 0.63
19 3 0.11
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
ATTTTTTATTTTATTATT
Found at i:1305774 original size:15 final size:14
Alignment explanation
Indices: 1305749--1305790 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1305739 TTTTCATGCA
1305749 TACAT-TTGCATTT
1 TACATCTTGCATTT
1305762 TACATCCTTGCATTT
1 TACAT-CTTGCATTT
* *
1305777 TTCATTTTGCATTT
1 TACATCTTGCATTT
1305791 ATACTGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 8 0.32
15 12 0.48
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (14 bp):
TACATCTTGCATTT
Found at i:1313046 original size:22 final size:22
Alignment explanation
Indices: 1313015--1313069 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1313005 ATCTACACTC
**
1313015 TTCAAAGATGGTAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
1313037 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
1313059 TTCAAAGATGA
1 TTCAAAGATGA
1313070 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:1313808 original size:112 final size:112
Alignment explanation
Indices: 1313470--1314013 Score: 691
Period size: 112 Copynumber: 4.9 Consensus size: 112
1313460 AGCAAAGTTC
* * * * *
1313470 AAATCCATCATTCAATGGATCAACA-TTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
1313534 AAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAA-TCTTTTGCTC
66 AA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACT-TTTTGCTT
* * *
1313582 AAATCCATCATTCGATGGATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
1313647 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AA-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* * * * *
1313695 AAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
1313760 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
66 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
** * * * *
1313807 AAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * * *
1313872 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCT
66 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
* * * ** * * *
1313919 GAATTCATCACTT-GATGAATTA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAA
1 AAATTCATCA-TTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAA
*
1313982 GAGGAAGAAGAAGTTCATAATGAGAAGAACTT
65 GAAGAAGAAGAAGTTCATAATGAGAAGAACTT
1314014 ATCTGAAGAG
Statistics
Matches: 382, Mismatches: 47, Indels: 7
0.88 0.11 0.02
Matches are distributed among these distances:
111 63 0.16
112 181 0.47
113 137 0.36
114 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (112 bp):
AAATTCATCATTCGATGGATCAGCATTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTT
Found at i:1313866 original size:225 final size:223
Alignment explanation
Indices: 1313470--1314013 Score: 730
Period size: 225 Copynumber: 2.4 Consensus size: 223
1313460 AGCAAAGTTC
* ** * * *
1313470 AAATCCATCATTCAATGGATCAACATTCCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AAATTCATCATTTGATGGATCATCATTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * **
1313535 AGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAATCTTTTGCTCAAATCCATCATTCGATGG
66 A-GAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTCAAATCCATCACCCGATGG
* * *
1313600 ATCAGCATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
130 ATCAGCAGTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAATTCAT
* * *
1313665 AATGAGAAGAACTTGTTCAACTTTTTGCTT
194 AATGAGAAGAACTTGTTCAACCTTTTCCCT
* *
1313695 AAATTCATCATTTGATGGATCATCATTACCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAG
1 AAATTCATCATTTGATGGATCATCATT-CCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
1313760 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTTGCTTAAATTCATCACCCGGTG
65 AAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATC-TTTTGCTCAAATCCATCACCCGATG
** *
1313824 GATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCAT
129 GATCAGCAGTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCAT
*
1313889 AATGAGAAGAATTTGTTCAACCTTTTCCCT
194 AATGAGAAGAACTTGTTCAACCTTTTCCCT
* * * * ** * * *
1313919 GAATTCATCACTTGATGAATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGA
1 AAATTCATCATTTGATGGATCATCATTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGA
*
1313984 GGAAGAAGAAGTTCATAATGAGAAGAACTT
66 AGAAGAAGAAGTTCATAATGAGAAGAACTT
1314014 ATCTGAAGAG
Statistics
Matches: 281, Mismatches: 36, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
223 62 0.22
224 64 0.23
225 119 0.42
226 36 0.13
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (223 bp):
AAATTCATCATTTGATGGATCATCATTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTCAAATCCATCACCCGATGGA
TCAGCAGTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAA
TGAGAAGAACTTGTTCAACCTTTTCCCT
Found at i:1313990 original size:19 final size:19
Alignment explanation
Indices: 1313966--1314029 Score: 53
Period size: 19 Copynumber: 3.3 Consensus size: 19
1313956 TTCATAATGA
1313966 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
**
1313985 GAAGAA-GAAGTTCAT-AATGA-
1 GAAGAACTTA--TC-TGAA-GAG
1314005 GAAGAACTTATCTGAAGAG
1 GAAGAACTTATCTGAAGAG
1314024 GAAGAA
1 GAAGAA
1314030 GAATTTCATA
Statistics
Matches: 34, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 4 0.12
19 16 0.47
20 10 0.29
21 4 0.12
ACGTcount: A:0.47, C:0.08, G:0.27, T:0.19
Consensus pattern (19 bp):
GAAGAACTTATCTGAAGAG
Found at i:1313992 original size:22 final size:22
Alignment explanation
Indices: 1313965--1314032 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
1313955 GTTCATAATG
1313965 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
* *
1313987 AGAAGAA-GT-TC--ATA-ATG-
1 AGAAGAACTTATCTGA-AGAGGA
1314004 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
1314026 AGAAGAA
1 AGAAGAA
1314033 TTTCATAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
17 7 0.20
18 4 0.11
19 3 0.09
20 3 0.09
21 4 0.11
22 14 0.40
ACGTcount: A:0.49, C:0.07, G:0.26, T:0.18
Consensus pattern (22 bp):
AGAAGAACTTATCTGAAGAGGA
Found at i:1314007 original size:39 final size:39
Alignment explanation
Indices: 1313953--1314052 Score: 191
Period size: 39 Copynumber: 2.6 Consensus size: 39
1313943 TTTCCAGAGA
1313953 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1313992 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
*
1314031 AATTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
1314053 GTTTAACCTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
Found at i:1314021 original size:150 final size:151
Alignment explanation
Indices: 1313843--1314161 Score: 525
Period size: 150 Copynumber: 2.1 Consensus size: 151
1313833 TGCCAGTTAG
*
1313843 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
**
1313908 ACCTTTTCC-CTGAATTCATCACTTGATGAATT-ATTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 ACCTTTTCCTC-GAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGA
1313971 ACTTATCTGAAGAGGAAGAAGA
130 ACTTATCTGAAGAGGAAGAAGA
* * *
1313993 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
* * *
1314058 ACCTTTTGCTCGAATTCATTACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
1314123 CTTATCTGAAGAGGAAGAAGA
131 CTTATCTGAAGAGGAAGAAGA
*
1314144 AATTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
1314162 TTTGTTTAAC
Statistics
Matches: 157, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
150 88 0.56
151 69 0.44
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.28
Consensus pattern (151 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTCA
ACCTTTTCCTCGAATTCATCACTTGATGAATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
CTTATCTGAAGAGGAAGAAGA
Found at i:1314031 original size:262 final size:263
Alignment explanation
Indices: 1313731--1314535 Score: 1335
Period size: 262 Copynumber: 3.1 Consensus size: 263
1313721 TACCAGTTAG
* * *
1313731 AGTTCATAATGAGAAGAACTCATTTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCA
1 AGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
* ** * ** * * * * * ** *
1313796 ACTTTTTGCTTAAATTCATCACCCGGTGGATCAGCAGTGCCAGTTAGAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCGAATTCATTACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
* * *
1313861 CTCATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTCCCTGAATTCA
131 CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
* *
1313926 TCACTTGATGAATT-ATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGA
196 TCACTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGA
1313990 AGA
261 AGA
* *
1313993 AGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1314058 ACCTTTTGCTCGAATTCATTACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCGAATTCATTACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
1314123 CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
131 CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
1314188 TCACTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGA
196 TCACTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGA
1314253 AGA
261 AGA
1314256 AGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
1 AGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
*
1314321 ACCTTTT-CTCGAATTCATTACTTGATGGATTAACATTTACAGAGAAAGTTCATAATGAGAAGAA
66 ACCTTTTGCTCGAATTCATTACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
1314385 CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
131 CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
* * *
1314450 TCACTTGATGGATTAACTTTTCCAAAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAG
196 TCACTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAG
1314515 AAGA
260 AAGA
1314519 AGTTCATAATGAGAAGA
1 AGTTCATAATGAGAAGA
1314536 GCTTGTTCAA
Statistics
Matches: 511, Mismatches: 30, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
262 362 0.71
263 149 0.29
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (263 bp):
AGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTA
ACCTTTTGCTCGAATTCATTACTTGATGGATTAACATTTCCAGAGAAAGTTCATAATGAGAAGAA
CTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCCTGAATTCA
TCACTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGA
AGA
Found at i:1314119 original size:112 final size:112
Alignment explanation
Indices: 1313992--1314276 Score: 509
Period size: 112 Copynumber: 2.5 Consensus size: 112
1313982 GAGGAAGAAG
*
1313992 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAATTTCATAATGAGAAGAACTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTT
*
1314057 AACCTTTTG-CTCGAATTCATTACTTGATGGATTAACATTTCCAGAGA
66 AACCTTTTGCCT-GAATTCATCACTTGATGGATTAACATTTCCAGAGA
*
1314104 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTT
*
1314169 AACCTTTTGCCTGAATTCATCACTTGATGGATTAACTTTTCCAGAGA
66 AACCTTTTGCCTGAATTCATCACTTGATGGATTAACATTTCCAGAGA
*
1314216 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTT
1314277 ATTTGAAGAG
Statistics
Matches: 166, Mismatches: 6, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
112 164 0.99
113 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTT
AACCTTTTGCCTGAATTCATCACTTGATGGATTAACATTTCCAGAGA
Found at i:1314255 original size:22 final size:22
Alignment explanation
Indices: 1314228--1314295 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
1314218 GTTCATAATG
1314228 AGAAGAACTTATCTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
* *
1314250 AGAAGAA-GT-TC--ATA-ATG-
1 AGAAGAACTTATCTGA-AGAGGA
*
1314267 AGAAGAACTTATTTGAAGAGGA
1 AGAAGAACTTATCTGAAGAGGA
1314289 AGAAGAA
1 AGAAGAA
1314296 GTTCATAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 14
0.64 0.09 0.26
Matches are distributed among these distances:
17 7 0.21
18 4 0.12
19 2 0.06
20 3 0.09
21 4 0.12
22 14 0.41
ACGTcount: A:0.49, C:0.06, G:0.26, T:0.19
Consensus pattern (22 bp):
AGAAGAACTTATCTGAAGAGGA
Found at i:1314270 original size:39 final size:39
Alignment explanation
Indices: 1314216--1314315 Score: 191
Period size: 39 Copynumber: 2.6 Consensus size: 39
1314206 TTTCCAGAGA
1314216 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
*
1314255 AAGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1314294 AAGTTCATAATGAGAAGAACTT
1 AAGTTCATAATGAGAAGAACTT
1314316 GTTTAACCTT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.23
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
Found at i:1314381 original size:111 final size:112
Alignment explanation
Indices: 1314255--1314550 Score: 461
Period size: 111 Copynumber: 2.6 Consensus size: 112
1314245 GAGGAAGAAG
*
1314255 AAGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AAGTTCATAATGAGAAGAACTTATATGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
* *
1314320 AACCTTTT--CTCGAATTCATTACTTGATGGATTAACATTTACAGAGA
66 AACCTTTTGCCT-GAATTCATCACTTGATGGATTAACATTTACAAAGA
* * *
1314366 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AAGTTCATAATGAGAAGAACTTATATGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
* *
1314431 AACCTTTTGCCTGAATTCATCACTTGATGGATTAACTTTTCCAAAGA
66 AACCTTTTGCCTGAATTCATCACTTGATGGATTAACATTTACAAAGA
* *
1314478 AAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTTATATGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1314543 CAACCTTT
65 TAACCTTT
1314551 GTTTGATGCT
Statistics
Matches: 169, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
111 70 0.41
112 59 0.35
113 40 0.24
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (112 bp):
AAGTTCATAATGAGAAGAACTTATATGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
AACCTTTTGCCTGAATTCATCACTTGATGGATTAACATTTACAAAGA
Found at i:1314406 original size:150 final size:151
Alignment explanation
Indices: 1314104--1314423 Score: 554
Period size: 150 Copynumber: 2.1 Consensus size: 151
1314094 TTTCCAGAGA
*
1314104 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTT
* *
1314169 AACCTTTTGCCTGAATTCATCACTTGATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGA
66 AACCTTTTGCCTGAATTCATCACTTGATGGATTAACATTTACAGAGAAAGTTCATAATGAGAAGA
1314234 ACTTATCTGAAGAGGAAGAAG
131 ACTTATCTGAAGAGGAAGAAG
* *
1314255 AAGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTT
*
1314320 AACCTTTT--CTCGAATTCATTACTTGATGGATTAACATTTACAGAGAAAGTTCATAATGAGAAG
66 AACCTTTTGCCT-GAATTCATCACTTGATGGATTAACATTTACAGAGAAAGTTCATAATGAGAAG
1314383 AACTTATCTGAAGAGGAAGAAG
130 AACTTATCTGAAGAGGAAGAAG
*
1314405 AAATTCATAATGAGAAGAA
1 AAGTTCATAATGAGAAGAA
1314424 TTTGTTTAAC
Statistics
Matches: 161, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
149 2 0.01
150 89 0.55
151 70 0.43
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.28
Consensus pattern (151 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTT
AACCTTTTGCCTGAATTCATCACTTGATGGATTAACATTTACAGAGAAAGTTCATAATGAGAAGA
ACTTATCTGAAGAGGAAGAAG
Found at i:1314565 original size:112 final size:111
Alignment explanation
Indices: 1314255--1314556 Score: 444
Period size: 112 Copynumber: 2.7 Consensus size: 111
1314245 GAGGAAGAAG
*
1314255 AAGTTCATAATGAGAAGAACTTATTTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
1 AAGTTCATAATGAGAAGAACTTATATGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
* * *
1314320 AACCTTT-TCTCGAATTCATTACTTGATGGATTAACATTTACAGAGA
66 AACCTTTGT-TTGAATTCATCACTTGATGGATTAACATTTACAAAGA
* * *
1314366 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTT
1 AAGTTCATAATGAGAAGAACTTATATGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
** * *
1314431 AACCTTTTGCCTGAATTCATCACTTGATGGATTAACTTTTCCAAAGA
66 AACC-TTTGTTTGAATTCATCACTTGATGGATTAACATTTACAAAGA
* *
1314478 AAGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTTATATGAAG-AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1314543 CAACCTTTGTTTGA
65 TAACCTTTGTTTGA
1314557 TGCTATCACA
Statistics
Matches: 170, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
111 66 0.39
112 69 0.41
113 35 0.21
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (111 bp):
AAGTTCATAATGAGAAGAACTTATATGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTT
AACCTTTGTTTGAATTCATCACTTGATGGATTAACATTTACAAAGA
Found at i:1315748 original size:15 final size:15
Alignment explanation
Indices: 1315730--1315806 Score: 57
Period size: 15 Copynumber: 4.9 Consensus size: 15
1315720 TTGGTCATTT
*
1315730 TTTATATTTTTATCA
1 TTTATATTTTTATTA
*
1315745 TTTATATGTTTAAATTA
1 TTTATAT-TTT-TATTA
* *
1315762 -GTATTTTATTTATTTA
1 TTTATATT-TTTA-TTA
* *
1315778 TTCATATATTTATTA
1 TTTATATTTTTATTA
1315793 TTTATATTTTTATT
1 TTTATATTTTTATT
1315807 CACTAATATT
Statistics
Matches: 46, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
15 24 0.52
16 16 0.35
17 6 0.13
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (15 bp):
TTTATATTTTTATTA
Found at i:1315800 original size:29 final size:28
Alignment explanation
Indices: 1315763--1315819 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
1315753 TTTAAATTAG
1315763 TATTTTATTTATTTATTCA-T-ATATTTAT
1 TATTTTA-TT-TTTATTCACTAATATTTAT
1315791 TATTTATATTTTTATTCACTAATATTTAT
1 TATTT-TATTTTTATTCACTAATATTTAT
1315820 ATGAAATGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 8 0.31
28 8 0.31
29 10 0.38
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (28 bp):
TATTTTATTTTTATTCACTAATATTTAT
Found at i:1315804 original size:27 final size:29
Alignment explanation
Indices: 1315766--1315819 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
1315756 AAATTAGTAT
1315766 TTTATTTATTTATTCA-T-ATATTTATTA
1 TTTATTTATTTATTCACTAATATTTATTA
1315793 TTTATATT-TTTATTCACTAATATTTAT
1 TTTAT-TTATTTATTCACTAATATTTAT
1315820 ATGAAATGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 13 0.54
28 3 0.12
29 8 0.33
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.65
Consensus pattern (29 bp):
TTTATTTATTTATTCACTAATATTTATTA
Found at i:1321803 original size:22 final size:22
Alignment explanation
Indices: 1321739--1321804 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
1321729 GGGAGCATGT
1321739 GTGCATCGATGCAT-AGT-TAA
1 GTGCATCGATGCATCAGTGTAA
*
1321759 GGTGCATCGATGCATCAACTGTAA
1 -GTGCATCGATGCATC-AGTGTAA
1321783 -TGCATCGATGCATCGAGTGTAA
1 GTGCATCGATGCATC-AGTGTAA
1321805 AATTAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
21 14 0.36
22 20 0.51
23 2 0.05
24 3 0.08
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCATCAGTGTAA
Found at i:1322645 original size:45 final size:45
Alignment explanation
Indices: 1322581--1322833 Score: 271
Period size: 45 Copynumber: 5.6 Consensus size: 45
1322571 GTAAAAGAAT
* *** * *
1322581 AATGCATAAGGGTGCATTATTGGCATG-AAAGGATGCCAGAGTTGA
1 AATGCATATGGGTGCATTATCAACA-GAAAAGTATGCTAGAGTTGA
*
1322626 AATGCATATGGGTGAATTATCAACAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
1322671 AATGCATAT-GGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
* ** * * *
1322715 AATGTATATGGGTATATTATCAAAAGAAAATTATACTATG-GTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTA-GAGTTGA
* * * * * *
1322760 GATGAATATGAGTACATTATCAACATAAAAGTATACTATG-GTTGA
1 AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTA-GAGTTGA
*
1322805 AATTCATATGGGTGCATTATCAACAGAAA
1 AATGCATATGGGTGCATTATCAACAGAAA
1322834 GGTTGTTATA
Statistics
Matches: 178, Mismatches: 27, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
44 43 0.24
45 134 0.75
46 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
Found at i:1322743 original size:89 final size:89
Alignment explanation
Indices: 1322608--1322833 Score: 262
Period size: 89 Copynumber: 2.5 Consensus size: 89
1322598 TATTGGCATG
* * * *
1322608 AAAGGATGCCAGAGTTGAAATGCATATGGGTGAATTATCAACAGAAAAGTATGCTA-GAGTTGAA
1 AAAGTATGCTAGAGTTGAAATGTATATGGGT-AATTATCAACAGAAAAGTATACTATG-GTTGAA
* *
1322672 ATGCATATG-GTGCATTATCAACAGA
64 ATGAATATGAGTACATTATCAACAGA
* * *
1322697 AAAGTATGCTAGAGTTGAAATGTATATGGGTATATTATCAAAAGAAAATTATACTATGGTTGAGA
1 AAAGTATGCTAGAGTTGAAATGTATATGGGTA-ATTATCAACAGAAAAGTATACTATGGTTGAAA
*
1322762 TGAATATGAGTACATTATCAACATA
65 TGAATATGAGTACATTATCAACAGA
* *
1322787 AAAGTATACTATG-GTTGAAAT-TCATATGGGTGCATTATCAACAGAAA
1 AAAGTATGCTA-GAGTTGAAATGT-ATATGGGT-AATTATCAACAGAAA
1322834 GGTTGTTATA
Statistics
Matches: 118, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
88 1 0.01
89 62 0.53
90 54 0.46
91 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (89 bp):
AAAGTATGCTAGAGTTGAAATGTATATGGGTAATTATCAACAGAAAAGTATACTATGGTTGAAAT
GAATATGAGTACATTATCAACAGA
Found at i:1322869 original size:90 final size:87
Alignment explanation
Indices: 1322618--1322878 Score: 212
Period size: 90 Copynumber: 2.9 Consensus size: 87
1322608 AAAGGATGCC
* * * *
1322618 AGAGTTGAAATGCATATGGGTGAATTATCAACAGAAAAGTATGCTAGAGTTGAAA-TGCATATGG
1 AGAGTTGAAATTCATATGGGTGAATTATCAACAG-AAAGT-TGATATAGTT-AAAGTGCATATGA
* * *
1322682 TGCATTATCAACAGAAAAGTATGCT
63 TGTATTATCAACATAAAAGTATACT
* * * *
1322707 AGAGTTGAAATGT-ATATGGGT-ATATTATCAAAAGAAAATT-ATACTATGGTT-GAGATGAATA
1 AGAGTTGAAAT-TCATATGGGTGA-ATTATCAACAGAAAGTTGATA-TA--GTTAAAG-TGCATA
1322768 TGA-GTACATTATCAACATAAAAGTATACT
60 TGATGT--ATTATCAACATAAAAGTATACT
* *
1322797 ATG-GTTGAAATTCATATGGGTGCATTATCAACAGAAAGGTTGTTATAGCTTAAAGTGCATAATG
1 A-GAGTTGAAATTCATATGGGTGAATTATCAACAGAAA-GTTGATATAG-TTAAAGTGCAT-ATG
*
1322861 ATGTATTATAAACATAAA
62 ATGTATTATCAACATAAA
1322879 TGGAGGTTAC
Statistics
Matches: 136, Mismatches: 18, Indels: 35
0.72 0.10 0.19
Matches are distributed among these distances:
86 2 0.01
87 3 0.02
88 6 0.04
89 41 0.30
90 69 0.51
91 11 0.08
92 4 0.03
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (87 bp):
AGAGTTGAAATTCATATGGGTGAATTATCAACAGAAAGTTGATATAGTTAAAGTGCATATGATGT
ATTATCAACATAAAAGTATACT
Found at i:1329135 original size:22 final size:23
Alignment explanation
Indices: 1329107--1329151 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
1329097 CTAGAAGGGG
1329107 GTATCGATACCATAGTA-GGGTA
1 GTATCGATACCATAGTATGGGTA
1329129 GTATCGATACCATAGTATGGGTA
1 GTATCGATACCATAGTATGGGTA
1329152 TTGATACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.29
Consensus pattern (23 bp):
GTATCGATACCATAGTATGGGTA
Found at i:1329696 original size:79 final size:79
Alignment explanation
Indices: 1329562--1329712 Score: 266
Period size: 79 Copynumber: 1.9 Consensus size: 79
1329552 AAAACGAATG
* *
1329562 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGTATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGCTGAAATGGATATGG
1329627 GTACATTGTCAGCA
66 GTACATTGTCAGCA
*
1329641 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGTTGAAATGGATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGCTGAAATGGATATGG
*
1329706 GTGCATT
66 GTACATT
1329713 ATCAACAGAA
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 68 1.00
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAGAGCTGAAATGGATATGG
GTACATTGTCAGCA
Found at i:1329736 original size:45 final size:45
Alignment explanation
Indices: 1329650--1329928 Score: 285
Period size: 45 Copynumber: 6.2 Consensus size: 45
1329640 ATAAAAGAAT
* *** * *
1329650 AATGCATATGGGTGCATTATTGGCATG-AAAGGATGCCAGAGTTGA
1 AATGCATATGGGTACATTATCAACA-GAAAAGTATGCTAGAGTTGA
* *
1329695 AATGGATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGA
*
1329740 AATGCATATGGGTACATTATCAACAGAAAAGTATGTTAGAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGA
* * * *
1329785 AATGTATATGGGTACATTATCAACAAAAAAAATATACTATG-GTTGA
1 AATGCATATGGGTACATTATCAAC-AGAAAAGTATGCTA-GAGTTGA
* * * * * * *
1329831 GATGTATATGAGTACATTATCAACATAAAAATATACTATAGTTGA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGA
* * * *
1329876 AATGCATATGGGTGCATTATCAACAGAAAA-TATGTTATAGTTTA
1 AATGCATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGA
1329920 AAGTGCATA
1 AA-TGCATA
1329929 ATGATGTATT
Statistics
Matches: 203, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
44 14 0.07
45 151 0.74
46 37 0.18
47 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.21, T:0.30
Consensus pattern (45 bp):
AATGCATATGGGTACATTATCAACAGAAAAGTATGCTAGAGTTGA
Found at i:1329876 original size:91 final size:91
Alignment explanation
Indices: 1329687--1329905 Score: 280
Period size: 91 Copynumber: 2.4 Consensus size: 91
1329677 AAAGGATGCC
* * * * *
1329687 AGAGTTGAAATGGATATGGGTGCATTATCAAC-AGAAAAGTATGCTAGAGTTGAAATGCATATGG
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAAAAAAAATATACTAGAGTTGAAATGCATATGA
* **
1329751 GTACATTATCAACAGAAAAGTATGTT
66 GTACATTATCAACAGAAAAATATACT
* * * *
1329777 AGAGTTGAAATGTATATGGGTACATTATCAACAAAAAAAATATACTATG-GTTGAGATGTATATG
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAAAAAAAATATACTA-GAGTTGAAATGCATATG
*
1329841 AGTACATTATCAACATAAAAATATACT
65 AGTACATTATCAACAGAAAAATATACT
* *
1329868 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAA
1 AGAGTTGAAATGCATATGGGTGCATTATCAACAAAAAA
1329906 TATGTTATAG
Statistics
Matches: 111, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
90 30 0.27
91 80 0.72
92 1 0.01
ACGTcount: A:0.42, C:0.09, G:0.20, T:0.29
Consensus pattern (91 bp):
AGAGTTGAAATGCATATGGGTGCATTATCAACAAAAAAAATATACTAGAGTTGAAATGCATATGA
GTACATTATCAACAGAAAAATATACT
Found at i:1329940 original size:136 final size:135
Alignment explanation
Indices: 1329690--1329945 Score: 336
Period size: 136 Copynumber: 1.9 Consensus size: 135
1329680 GGATGCCAGA
* * * *
1329690 GTTGAAATGGATATGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATGCATATGGGTAC
1 GTTGAAATGGATATGAGTACATTATCAACAGAAAAATATACTAGAGTTGAAATGCATATGGGTAC
* *
1329755 ATTATCAACAGAAAAGTATGTTAGAGTTGAAATGTATATGGGTACATTATCAACAAAAAAAATAT
66 ATTATCAACAGAAAAGTATGTTAGAGTTGAAATGCATATGGGTA-ATTATAAACAAAAAAAATAT
1329820 ACTATG
130 ACTATG
* * * * *
1329826 GTTGAGATGTATATGAGTACATTATCAACATAAAAATATACTATAGTTGAAATGCATATGGGTGC
1 GTTGAAATGGATATGAGTACATTATCAACAGAAAAATATACTAGAGTTGAAATGCATATGGGTAC
* * *
1329891 ATTATCAACAGAAAA-TATGTTATAGTTTAAAGTGCATAATGATGT-ATTATAAACA
66 ATTATCAACAGAAAAGTATGTTAGAGTTGAAA-TGCAT-ATG-GGTAATTATAAACA
1329946 TAAATGGAGG
Statistics
Matches: 103, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
135 14 0.14
136 84 0.82
137 3 0.03
138 2 0.02
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (135 bp):
GTTGAAATGGATATGAGTACATTATCAACAGAAAAATATACTAGAGTTGAAATGCATATGGGTAC
ATTATCAACAGAAAAGTATGTTAGAGTTGAAATGCATATGGGTAATTATAAACAAAAAAAATATA
CTATG
Found at i:1330629 original size:15 final size:16
Alignment explanation
Indices: 1330592--1330636 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
1330582 AATGAAATTC
*
1330592 TGGAAATTTAAAGGAT
1 TGGAAATTAAAAGGAT
* *
1330608 TGAAAATTAAAATGA-
1 TGGAAATTAAAAGGAT
1330623 TGGAAATTAAAAGG
1 TGGAAATTAAAAGG
1330637 GAAAAAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.22, T:0.27
Consensus pattern (16 bp):
TGGAAATTAAAAGGAT
Found at i:1342136 original size:21 final size:21
Alignment explanation
Indices: 1342106--1342147 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1342096 TCTATATTGA
*
1342106 GGGTTCGGTATCAAGACCAAG
1 GGGTTCGGTATCAAAACCAAG
*
1342127 GGGTTTGGTATCAAAACCAAG
1 GGGTTCGGTATCAAAACCAAG
1342148 ATTTCATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (21 bp):
GGGTTCGGTATCAAAACCAAG
Found at i:1342310 original size:20 final size:20
Alignment explanation
Indices: 1342287--1342335 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1342277 TTGAGGAGAG
*
1342287 AGTATCGATGCTATAAGGTC
1 AGTATCGATGCTATAAGGCC
* *
1342307 AGTATCGATGTTGTAAGGCC
1 AGTATCGATGCTATAAGGCC
1342327 AGTATCGAT
1 AGTATCGAT
1342336 ACCAAGGTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.31
Consensus pattern (20 bp):
AGTATCGATGCTATAAGGCC
Found at i:1343969 original size:21 final size:21
Alignment explanation
Indices: 1343943--1343991 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1343933 GAAGATGTTC
1343943 AATTTTTTTGTTAATTGTTGT
1 AATTTTTTTGTTAATTGTTGT
1343964 AATTTTTTTGTTAATTGTTGT
1 AATTTTTTTGTTAATTGTTGT
1343985 AATTTTT
1 AATTTTT
1343992 AAGACATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.67
Consensus pattern (21 bp):
AATTTTTTTGTTAATTGTTGT
Found at i:1344669 original size:2 final size:2
Alignment explanation
Indices: 1344664--1344701 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1344654 TTTTTGGGGG
1344664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1344702 TAGTACTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1346778 original size:20 final size:21
Alignment explanation
Indices: 1346753--1346845 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
1346743 TTTTCCCAAT
*
1346753 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1346773 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
1346794 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1346814 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1346835 TCGCAATGCGA
1 TCGCAATGCGA
1346846 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1346798 original size:41 final size:41
Alignment explanation
Indices: 1346753--1346845 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
1346743 TTTTCCCAAT
1346753 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1346794 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1346835 TCGCAATGCGA
1 TCGCAATGCGA
1346846 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:1346858 original size:41 final size:41
Alignment explanation
Indices: 1346772--1346906 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
1346762 GAATAAGTAA
** *
1346772 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
1346813 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * *
1346854 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
1346895 TTCGCAACGCGA
1 ATCGCAACGCGA
1346907 TACTGACTTT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
40 5 0.06
41 74 0.91
42 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:1346859 original size:20 final size:20
Alignment explanation
Indices: 1346834--1346927 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
1346824 AATTGGGAAA
*
1346834 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
1346854 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
*
1346875 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTTACT
* *
1346895 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTTACT
*
1346915 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1346928 TTACATAATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.71
21 12 0.19
22 3 0.05
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:1347143 original size:22 final size:22
Alignment explanation
Indices: 1347115--1347158 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1347105 CACTCTCTCA
1347115 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1347137 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1347159 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1348697 original size:18 final size:18
Alignment explanation
Indices: 1348676--1348720 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1348666 TCCACTTCGG
* *
1348676 GAGCCATCACCTCGCCCA
1 GAGCCATCACCCCACCCA
*
1348694 GAGCTATCACCCCACCCA
1 GAGCCATCACCCCACCCA
1348712 GAGCCATCA
1 GAGCCATCA
1348721 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.47, G:0.16, T:0.11
Consensus pattern (18 bp):
GAGCCATCACCCCACCCA
Found at i:1349246 original size:19 final size:20
Alignment explanation
Indices: 1349203--1349258 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1349193 TTGCAACACA
1349203 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1349223 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
1349242 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1349259 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1349266 original size:14 final size:14
Alignment explanation
Indices: 1349247--1349304 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1349237 ATGCGAAATG
1349247 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
1349261 AAAATCGCAACGCAAA
1 AAAATCGCAACG--AC
1349277 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1349293 AAAATCGCAACG
1 AAAATCGCAACG
1349305 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.50, C:0.26, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1349289 original size:32 final size:33
Alignment explanation
Indices: 1349231--1349321 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
1349221 GGAAATGGCT
*
1349231 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
1349264 ATCGCAACGCAAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
1349296 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
1349322 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:1349315 original size:19 final size:19
Alignment explanation
Indices: 1349211--1349326 Score: 74
Period size: 19 Copynumber: 6.6 Consensus size: 19
1349201 CAAAATGACT
***
1349211 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGAAA
*
1349231 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1349250 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
*
1349264 ATCGCAACGCAAAATG-AA
1 ATCGCAACGCGAAATGAAA
*
1349282 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAATGAAA
1349296 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1349315 ATCGCAATGCGA
1 ATCGCAACGCGA
1349327 TTTGTATTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 23
0.69 0.10 0.21
Matches are distributed among these distances:
14 20 0.27
15 1 0.01
16 4 0.05
17 2 0.03
18 11 0.15
19 27 0.36
20 9 0.12
ACGTcount: A:0.44, C:0.23, G:0.21, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1349357 original size:14 final size:14
Alignment explanation
Indices: 1349338--1349395 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
1349328 TTGTATTTCG
1349338 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
1349352 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
1349368 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
1349384 CGTTGCGATTTT
1 CGTTGCGATTTT
1349396 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Done.