Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008164.1 Hibiscus syriacus cultivar Beakdansim tig00110744_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: 2577652
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1123593 original size:24 final size:23
Alignment explanation
Indices: 1123561--1123612 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
1123551 AGTATTCAAA
*
1123561 ATTTGATCTTGGTCAATACCCGG
1 ATTTTATCTTGGTCAATACCCGG
*
1123584 ACTTTTATCTTGGTCAATACTCGG
1 A-TTTTATCTTGGTCAATACCCGG
1123608 ATTTT
1 ATTTT
1123613 GATGATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (23 bp):
ATTTTATCTTGGTCAATACCCGG
Found at i:1123834 original size:14 final size:14
Alignment explanation
Indices: 1123805--1123841 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1123795 AGAAAAAGAA
1123805 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
1123820 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
1123834 GAAGAAAA
1 GAAGAAAA
1123842 TACCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:1126214 original size:140 final size:140
Alignment explanation
Indices: 1125962--1126243 Score: 501
Period size: 140 Copynumber: 2.0 Consensus size: 140
1125952 GCAAACGTTT
* * *
1125962 TATTATGTGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATTTATTAGTAACTTGATT
1 TATTATATGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
*
1126027 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTGTTACACATTCATTTGAATATCGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
*
1126092 CGAATTTGAC
131 CGAATTTCAC
1126102 TATTATATGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
1 TATTATATGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
* *
1126167 TTGAACATTGCTATGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATTGCAACG
66 TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
1126232 CGAATTTCAC
131 CGAATTTCAC
1126242 TA
1 TA
1126244 ACGCAACGTG
Statistics
Matches: 135, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 135 1.00
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (140 bp):
TATTATATGTATTTTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGT
TTGAACATTGCTATGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACG
CGAATTTCAC
Found at i:1126268 original size:20 final size:20
Alignment explanation
Indices: 1126215--1126269 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 20
1126205 TTACACATTC
*
1126215 ATTTGAATATTGCAACGCGA
1 ATTTGAATATCGCAACGCGA
* * * *
1126235 ATTTCACTAACGCAACGTGA
1 ATTTGAATATCGCAACGCGA
*
1126255 ATTTGATTATCGCAA
1 ATTTGAATATCGCAA
1126270 TGAGAAAATC
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
ATTTGAATATCGCAACGCGA
Found at i:1126335 original size:20 final size:20
Alignment explanation
Indices: 1126310--1126401 Score: 121
Period size: 20 Copynumber: 4.6 Consensus size: 20
1126300 GCAACGCGAA
* *
1126310 TTGACTTTCGCGTTGCGATT
1 TTGACTTTCGCATTGCAATT
*
1126330 TTGACTTTCGCGTTGCAATT
1 TTGACTTTCGCATTGCAATT
*
1126350 TTGGCTTTCGCATTGCAATT
1 TTGACTTTCGCATTGCAATT
* *
1126370 TTGGCTTTCGCATTGCGATT
1 TTGACTTTCGCATTGCAATT
*
1126390 TTGACTATCGCA
1 TTGACTTTCGCA
1126402 ACGTGAATTT
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.14, C:0.21, G:0.22, T:0.43
Consensus pattern (20 bp):
TTGACTTTCGCATTGCAATT
Found at i:1126412 original size:20 final size:20
Alignment explanation
Indices: 1126384--1126563 Score: 128
Period size: 20 Copynumber: 9.1 Consensus size: 20
1126374 CTTTCGCATT
*
1126384 GCGATTTTGACTATCGCAAC
1 GCGAATTTGACTATCGCAAC
* *
1126404 GTGAATTTGATTATCGCAAC
1 GCGAATTTGACTATCGCAAC
* * *
1126424 GGGGATTTGACTATCGCAAA
1 GCGAATTTGACTATCGCAAC
* * * *
1126444 GTGTATTAGACCATCGCAAC
1 GCGAATTTGACTATCGCAAC
* * **
1126464 GCGAA-TTGACTTTCACATT
1 GCGAATTTGACTATCGCAAC
* * * * **
1126483 GCGATTTTGGCTTTCACATT
1 GCGAATTTGACTATCGCAAC
*
1126503 GCGATTTTGACTATCGCAAC
1 GCGAATTTGACTATCGCAAC
* *
1126523 GTGAATTTGATTATCGCAAC
1 GCGAATTTGACTATCGCAAC
* *
1126543 GGGAATTTGACTATCGTAAC
1 GCGAATTTGACTATCGCAAC
1126563 G
1 G
1126564 AGAAAATCCC
Statistics
Matches: 126, Mismatches: 33, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
19 12 0.10
20 114 0.90
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (20 bp):
GCGAATTTGACTATCGCAAC
Found at i:1126719 original size:14 final size:14
Alignment explanation
Indices: 1126700--1126738 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1126690 CATCAATTAA
1126700 ACAAATCAATTTTT
1 ACAAATCAATTTTT
**
1126714 ACAAATCAGCTTTT
1 ACAAATCAATTTTT
1126728 ACAAATCAATT
1 ACAAATCAATT
1126739 AAACAAGCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.36
Consensus pattern (14 bp):
ACAAATCAATTTTT
Found at i:1128111 original size:41 final size:41
Alignment explanation
Indices: 1128054--1128178 Score: 128
Period size: 41 Copynumber: 3.0 Consensus size: 41
1128044 TGTGTGAATC
* * *
1128054 GGGCTCTAGAATGGTGGGAGGGACCTCTTCAACGATGACAG
1 GGGCTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAG
** *
1128095 GGGCTCTTGAACGGTGGGAGGGGACC-CTTGAGGGATGATAG
1 GGGCTCTTGAACGGTGGGA-GGGACCTCTTGAACGATGACAG
* * *
1128136 GGGCCTCTTAAACGATAGGAGAGG-CCTCTTGAACGATGACAG
1 GGG-CTCTTGAACGGTGGGAG-GGACCTCTTGAACGATGACAG
1128178 G
1 G
1128179 TGAGTCCGAC
Statistics
Matches: 68, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
41 34 0.50
42 34 0.50
ACGTcount: A:0.24, C:0.18, G:0.38, T:0.19
Consensus pattern (41 bp):
GGGCTCTTGAACGGTGGGAGGGACCTCTTGAACGATGACAG
Found at i:1128174 original size:42 final size:42
Alignment explanation
Indices: 1128070--1128178 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
1128060 TAGAATGGTG
* * * *
1128070 GGAG-GGACCTCTTCAACGATGACAGGGGCTCTTGAACGGTG
1 GGAGAGGACCTCTTGAACGATGACAGGGGCTCTTAAACGATA
* ** *
1128111 GGAGGGGACC-CTTGAGGGATGATAGGGGCCTCTTAAACGATA
1 GGAGAGGACCTCTTGAACGATGACAGGGG-CTCTTAAACGATA
1128153 GGAGAGG-CCTCTTGAACGATGACAGG
1 GGAGAGGACCTCTTGAACGATGACAGG
1128179 TGAGTCCGAC
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
41 20 0.37
42 34 0.63
ACGTcount: A:0.25, C:0.19, G:0.38, T:0.18
Consensus pattern (42 bp):
GGAGAGGACCTCTTGAACGATGACAGGGGCTCTTAAACGATA
Found at i:1128651 original size:20 final size:20
Alignment explanation
Indices: 1128628--1128695 Score: 109
Period size: 20 Copynumber: 3.4 Consensus size: 20
1128618 GAAACTTAAA
1128628 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
*
1128648 ATCGCAATACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* *
1128668 ATCGCAACACGGAACTGACT
1 ATCGCAACACGAAAATGACT
1128688 ATCGCAAC
1 ATCGCAAC
1128696 GGGATAATCG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.41, C:0.26, G:0.16, T:0.16
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:1128822 original size:20 final size:20
Alignment explanation
Indices: 1128809--1128879 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
1128799 TAGTCAAATT
1128809 CACGTTGCGATAGTCATTTC
1 CACGTTGCGATAGTCATTTC
*
1128829 CGCGTTGCGATAGTCATTTC
1 CACGTTGCGATAGTCATTTC
* *
1128849 CGCGTTGCGATAGTCATTTT
1 CACGTTGCGATAGTCATTTC
1128869 CACGTTGCGAT
1 CACGTTGCGAT
1128880 TTTATGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.35
Consensus pattern (20 bp):
CACGTTGCGATAGTCATTTC
Found at i:1130735 original size:20 final size:20
Alignment explanation
Indices: 1130712--1130752 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1130702 TCTGAAACTT
1130712 AAAATTGCAACACGAAAATG
1 AAAATTGCAACACGAAAATG
1130732 AAAATTGCAACACGAAAATG
1 AAAATTGCAACACGAAAATG
1130752 A
1 A
1130753 CTATCGCAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATTGCAACACGAAAATG
Found at i:1130812 original size:19 final size:19
Alignment explanation
Indices: 1130712--1130831 Score: 81
Period size: 20 Copynumber: 6.4 Consensus size: 19
1130702 TCTGAAACTT
*
1130712 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
*
1130732 AAAATTGCAACACGAAAATG
1 AAAATCGCAACACG-AAATG
** * * *
1130752 ACTATCGCAACGCGAATTT
1 AAAATCGCAACACGAAATG
*
1130771 AACTATCGC-A-ACG--A-G
1 AA-AATCGCAACACGAAATG
*
1130786 ATAATCGCAACACGAAATG
1 AAAATCGCAACACGAAATG
1130805 AAAATCGCAACACGAAACT-
1 AAAATCGCAACACGAAA-TG
1130824 AAAATCGC
1 AAAATCGC
1130832 GTTGCGATTT
Statistics
Matches: 80, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
14 5 0.06
15 2 0.03
16 3 0.04
18 3 0.04
19 30 0.38
20 37 0.46
ACGTcount: A:0.47, C:0.22, G:0.15, T:0.16
Consensus pattern (19 bp):
AAAATCGCAACACGAAATG
Found at i:1131225 original size:20 final size:21
Alignment explanation
Indices: 1131200--1131263 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
1131190 CTCTGAGAGA
1131200 TGGAGAT-AGACGGATTTCGC
1 TGGAGATGAGACGGATTTCGC
*
1131220 TGGAGATGGGGACGGATTTCG-
1 TGGAGAT-GAGACGGATTTCGC
* *
1131241 TCGGAGATGGGGACGGATGTCGC
1 T-GGAGAT-GAGACGGATTTCGC
1131264 CGTAGAGAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
20 7 0.18
21 1 0.03
22 30 0.79
ACGTcount: A:0.20, C:0.14, G:0.44, T:0.22
Consensus pattern (21 bp):
TGGAGATGAGACGGATTTCGC
Found at i:1131236 original size:22 final size:23
Alignment explanation
Indices: 1131208--1131263 Score: 89
Period size: 22 Copynumber: 2.5 Consensus size: 23
1131198 GATGGAGATA
1131208 GACGGATTTCGCT-GGAGATGGG
1 GACGGATTTCGCTCGGAGATGGG
1131230 GACGGATTTCG-TCGGAGATGGG
1 GACGGATTTCGCTCGGAGATGGG
*
1131252 GACGGATGTCGC
1 GACGGATTTCGC
1131264 CGTAGAGAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.21
Consensus pattern (23 bp):
GACGGATTTCGCTCGGAGATGGG
Found at i:1131576 original size:20 final size:19
Alignment explanation
Indices: 1131553--1131598 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1131543 GGAAACTGAT
*
1131553 TTGCGATAATGGAGATCGCA
1 TTGCGAT-ATAGAGATCGCA
* *
1131573 TTGCGATTTAGAGATTGCA
1 TTGCGATATAGAGATCGCA
1131592 TTGCGAT
1 TTGCGAT
1131599 TTTATTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (19 bp):
TTGCGATATAGAGATCGCA
Found at i:1131592 original size:19 final size:19
Alignment explanation
Indices: 1131564--1131600 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
1131554 TGCGATAATG
1131564 GAGATCGCATTGCGATTTA
1 GAGATCGCATTGCGATTTA
*
1131583 GAGATTGCATTGCGATTT
1 GAGATCGCATTGCGATTT
1131601 TATTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.14, G:0.27, T:0.35
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:1132022 original size:3 final size:3
Alignment explanation
Indices: 1132014--1132085 Score: 126
Period size: 3 Copynumber: 24.0 Consensus size: 3
1132004 ATGTTATTTA
* *
1132014 TAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TAT TAT AAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1132062 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
1132086 ATAATTACAA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1144730 original size:17 final size:16
Alignment explanation
Indices: 1144710--1144753 Score: 61
Period size: 17 Copynumber: 2.7 Consensus size: 16
1144700 TATTATGCTT
1144710 AAAGAGAAAAAGAAAA
1 AAAGAGAAAAAGAAAA
*
1144726 GAAAGAAAAAAAGAAAA
1 -AAAGAGAAAAAGAAAA
*
1144743 AAAAAGAAAAA
1 AAAGAGAAAAA
1144754 AGGGGGTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAGAAAAAGAAAA
Found at i:1144738 original size:8 final size:8
Alignment explanation
Indices: 1144710--1144755 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
1144700 TATTATGCTT
*
1144710 AAAGAGAA
1 AAAGAAAA
1144718 AAAGAAAA
1 AAAGAAAA
1144726 GAAAGAAAA
1 -AAAGAAAA
1144735 AAAGAAAA
1 AAAGAAAA
*
1144743 AAAAAGAAA
1 AAAGA-AAA
1144752 AAAG
1 AAAG
1144756 GGGGTCAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
8 19 0.58
9 14 0.42
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:1144743 original size:18 final size:17
Alignment explanation
Indices: 1144710--1144754 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
1144700 TATTATGCTT
* *
1144710 AAAGAGAAAAAGAAAAG
1 AAAGAAAAAAAGAAAAA
1144727 AAAGAAAAAAAGAAAAAA
1 AAAGAAAAAAAG-AAAAA
1144745 AAAGAAAAAA
1 AAAGAAAAAA
1144755 GGGGGTCAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAAGAAAAA
Found at i:1145815 original size:89 final size:89
Alignment explanation
Indices: 1145603--1145925 Score: 567
Period size: 89 Copynumber: 3.6 Consensus size: 89
1145593 CAAGTAGAAC
*
1145603 AAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCCTA
1 AAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAA----A
1145668 AAAACCAATCATTGAATTTGGAAGATGA
62 AAAACCAATCATTGAATTTGGAAGATGA
1145696 AAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAAAAAA
1 AAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAAAAAA
*
1145761 CCAATCATTAAATTTGGAAGATGA
66 CCAATCATTGAATTTGGAAGATGA
1145785 AAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAAAAAA
1 AAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAAAAAA
1145850 CCAATCATTGAATTTGGAAGATGA
66 CCAATCATTGAATTTGGAAGATGA
* *
1145874 AAGTGCTCATAACATCTT-TGGAAGTGTTCTTTGAGTTAGCTGATCTGGTTTG
1 AAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1145926 GTAAGAACCA
Statistics
Matches: 225, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
88 33 0.15
89 133 0.59
93 59 0.26
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (89 bp):
AAGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAAAAAAA
CCAATCATTGAATTTGGAAGATGA
Found at i:1146862 original size:116 final size:116
Alignment explanation
Indices: 1146653--1147453 Score: 1251
Period size: 116 Copynumber: 7.0 Consensus size: 116
1146643 GCAAAGATTC
* *
1146653 AAATCCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAAAAGAACTCATCATCTG
1 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
*
1146718 AAGAGGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
1146769 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
*
1146834 AAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
1146885 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1146950 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
1147001 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
1147066 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
*
1147117 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATTATCTG
1 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
* * * *
1147182 AAGAAGGAATAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGCTC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * * * * * * *
1147233 AAATCCACCACTTGATGAATTAGCTTTGCCAGATAGAGTTCATAATGAAAAGAA--C-TCATCTG
1 AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
* * *
1147295 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
* * * *
1147346 AAA-TCTATCATTTGATGGATCAAC-TTTCCAGAG-AAAGTTCATAATGAGAAGAA--C-TCATC
1 AAATTC-ATCAATTGATGGATTAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCATC
* * * ** *
1147405 TGAAGAAAGAAGAAAAAGTTCATAATAAGAAGAGCTTATTCAACCTTTT
64 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTT
1147454 AAATGACTCT
Statistics
Matches: 644, Mismatches: 39, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
112 73 0.11
113 70 0.11
114 1 0.00
116 500 0.78
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (116 bp):
AAATTCATCAATTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCATCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
Found at i:1147692 original size:3 final size:3
Alignment explanation
Indices: 1147684--1147734 Score: 75
Period size: 3 Copynumber: 17.0 Consensus size: 3
1147674 ATGTTATTTA
* * *
1147684 TAT TAT TAT TAT TAT TAT AAT TAG TAT TAT TAT TAT TAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1147732 TAT
1 TAT
1147735 ATAATTACAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:1154733 original size:64 final size:63
Alignment explanation
Indices: 1154621--1154746 Score: 146
Period size: 64 Copynumber: 2.0 Consensus size: 63
1154611 CGGGTGATCA
**
1154621 TTTTGAAACTTTTAATAGTCGAGAGACTTAACAAAGCAACATTATATAGTTGAAGGAACATTTT
1 TTTTGAAACTTTTAATAGTCGAGAGACTTAACAAAGCAACACCATATAGTTG-AGGAACATTTT
* * * ** * *
1154685 TTTTTAAATTTTTAATAGTCGAG-GAACTTAATAAAGCAGTACCCTATAGTTGAGGACCATTT
1 TTTTGAAACTTTTAATAGTCGAGAG-ACTTAACAAAGCAACACCATATAGTTGAGGAACATTT
1154747 GTCTACTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
63 10 0.19
64 42 0.81
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.36
Consensus pattern (63 bp):
TTTTGAAACTTTTAATAGTCGAGAGACTTAACAAAGCAACACCATATAGTTGAGGAACATTTT
Found at i:1159499 original size:21 final size:21
Alignment explanation
Indices: 1159453--1159507 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
1159443 AATTATCTAC
*
1159453 AAAATAAAATA-TAAATATAA
1 AAAAGAAAATATTAAATATAA
* *
1159473 ATAAAGAAAATATTAAATTTTA
1 A-AAAGAAAATATTAAATATAA
*
1159495 AAAAGAAATTATT
1 AAAAGAAAATATT
1159508 TATGAACAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 1 0.03
21 20 0.69
22 8 0.28
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAGAAAATATTAAATATAA
Found at i:1162766 original size:19 final size:20
Alignment explanation
Indices: 1162742--1162790 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1162732 CTATTTTTAA
*
1162742 TATCGATACTC-AGGGTGAG
1 TATCGATACTCAAGGGTCAG
*
1162761 TATCGATACCCAAGGGTCAG
1 TATCGATACTCAAGGGTCAG
*
1162781 TATCAATACT
1 TATCGATACT
1162791 ACTAGCATAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 10 0.40
20 15 0.60
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (20 bp):
TATCGATACTCAAGGGTCAG
Found at i:1165857 original size:15 final size:15
Alignment explanation
Indices: 1165839--1165868 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1165829 ATGTGGATGC
*
1165839 AGAAGATGATGAGGA
1 AGAAGAAGATGAGGA
1165854 AGAAGAAGATGAGGA
1 AGAAGAAGATGAGGA
1165869 TTTCAACAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.40, T:0.10
Consensus pattern (15 bp):
AGAAGAAGATGAGGA
Found at i:1170770 original size:22 final size:22
Alignment explanation
Indices: 1170745--1170795 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1170735 TAATTCCTTT
1170745 TATTTTAGCCATTATTAAATAC
1 TATTTTAGCCATTATTAAATAC
* *
1170767 TATTTTAGTCATTATTTAATAC
1 TATTTTAGCCATTATTAAATAC
*
1170789 AATTTTA
1 TATTTTA
1170796 TTCTATTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (22 bp):
TATTTTAGCCATTATTAAATAC
Found at i:1171057 original size:19 final size:22
Alignment explanation
Indices: 1171016--1171061 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1171006 TTATATATAT
*
1171016 ATATATATTTAATGTTTTATTA
1 ATATTTATTTAATGTTTTATTA
1171038 ATATTTATTT-AT-TTTT-TTA
1 ATATTTATTTAATGTTTTATTA
1171057 ATATT
1 ATATT
1171062 AAGAAATGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 8 0.35
20 4 0.17
21 2 0.09
22 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
ATATTTATTTAATGTTTTATTA
Found at i:1171103 original size:122 final size:120
Alignment explanation
Indices: 1170916--1171138 Score: 333
Period size: 123 Copynumber: 1.8 Consensus size: 120
1170906 AATAATTGCG
* * *
1170916 TAATATTTATTTATTTTTAATCTTAAAAAAGGGCAGTCTTAAAGCAACTGGATGTCCATTTTCTG
1 TAATATTTATTTATTTTTAATATTAAAAAAGGGCAGTCTTAAAGCAACTAGAAGTCCATTTTCTG
*
1170981 ATATTTTTAA-TAAATAAATATTTTATTATATATATATATATATTTAATGTTTTAT
66 ATATTTCTAAGTAAATAAATATTTTATT-TATATATATATATATTTAATGTTTTAT
* * *
1171036 TAATATTTATTTATTTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGT-CATTTT
1 TAATATTTATTTA--TTTTTAATATTAA-AAAAGGGCAGTCTTAAAGCAACTAGAAGTCCATTTT
1171100 CTGATATTTCTAAGTAAATAAATATTTTATTTATATATA
63 CTGATATTTCTAAGTAAATAAATATTTTATTTATATATA
1171139 AAAAATATAT
Statistics
Matches: 92, Mismatches: 7, Indels: 6
0.88 0.07 0.06
Matches are distributed among these distances:
120 13 0.14
122 38 0.41
123 41 0.45
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (120 bp):
TAATATTTATTTATTTTTAATATTAAAAAAGGGCAGTCTTAAAGCAACTAGAAGTCCATTTTCTG
ATATTTCTAAGTAAATAAATATTTTATTTATATATATATATATTTAATGTTTTAT
Found at i:1171163 original size:123 final size:120
Alignment explanation
Indices: 1170916--1171164 Score: 288
Period size: 123 Copynumber: 2.0 Consensus size: 120
1170906 AATAATTGCG
* * *
1170916 TAATATTTATTTATTTTTAATCTTAAAAAAGGGCAGTCTTAAAGCAACTGGATGTCCATTTTCTG
1 TAATATTTATTTATTTTTAATATTAAAAAAGGGCAGTCTTAAAGCAACTAGAAGTCCATTTTCTG
* * * * **** *
1170981 ATATTTTTAATAAATAAATATTTTATTATATATATATATATATTTAATGTTTTAT
66 ATATTTCTAATAAATAAATATTTTATTATATATAAAAATATATATAATGAAACAC
* * *
1171036 TAATATTTATTTATTTTTTTAATATTAAGAAATGGGCTGTCTTAAAGCACCTAGAAGT-CATTTT
1 TAATATTTATTTA--TTTTTAATATTAA-AAAAGGGCAGTCTTAAAGCAACTAGAAGTCCATTTT
1171100 CTGATATTTCTAAGTAAATAAATATTTTATTTATATATAAAAA-ATATATATAT-AAACAC
63 CTGATATTTCTAA-TAAATAAATATTTTA-TTATATATAAAAATATATATA-ATGAAACAC
1171159 TAATAT
1 TAATAT
1171165 ATTTTCTTAA
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
120 13 0.12
122 30 0.28
123 52 0.48
124 13 0.12
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.46
Consensus pattern (120 bp):
TAATATTTATTTATTTTTAATATTAAAAAAGGGCAGTCTTAAAGCAACTAGAAGTCCATTTTCTG
ATATTTCTAATAAATAAATATTTTATTATATATAAAAATATATATAATGAAACAC
Found at i:1171714 original size:21 final size:20
Alignment explanation
Indices: 1171690--1171748 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
1171680 ATTTTCATAA
1171690 TATTTATATGTATATTATTTT
1 TATTTATAT-TATATTATTTT
*
1171711 TATTAATATT-T-TTA-TTT
1 TATTTATATTATATTATTTT
*
1171728 TATTTAAATTTCATATTATTT
1 TATTTATA-TT-ATATTATTT
1171749 GTTTGTCAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
17 9 0.30
18 5 0.17
19 1 0.03
20 2 0.07
21 11 0.37
22 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTTATATTATATTATTTT
Found at i:1176157 original size:15 final size:15
Alignment explanation
Indices: 1176137--1176169 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1176127 CTCATTCAAA
*
1176137 AAAAAGGGAAAAAGG
1 AAAAAGGAAAAAAGG
1176152 AAAAAGGAAAAAAGG
1 AAAAAGGAAAAAAGG
1176167 AAA
1 AAA
1176170 GAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (15 bp):
AAAAAGGAAAAAAGG
Found at i:1176167 original size:8 final size:8
Alignment explanation
Indices: 1176136--1176169 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
1176126 ACTCATTCAA
1176136 AAAAAAGG
1 AAAAAAGG
*
1176144 GAAAAAGG
1 AAAAAAGG
1176152 -AAAAAGG
1 AAAAAAGG
1176159 AAAAAAGG
1 AAAAAAGG
1176167 AAA
1 AAA
1176170 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.29
8 17 0.71
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:1180877 original size:22 final size:22
Alignment explanation
Indices: 1180852--1180925 Score: 103
Period size: 22 Copynumber: 3.4 Consensus size: 22
1180842 TACACTTTCT
*
1180852 AAAGATGATATATTTTCTCTCC
1 AAAGATGATAGATTTTCTCTCC
*
1180874 AAAGATGATAGATTTCCTCTCC
1 AAAGATGATAGATTTTCTCTCC
* * *
1180896 AAAGATGATAGATTCTCTTTTC
1 AAAGATGATAGATTTTCTCTCC
1180918 AAAGATGA
1 AAAGATGA
1180926 AAGTTTTATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (22 bp):
AAAGATGATAGATTTTCTCTCC
Found at i:1181462 original size:113 final size:113
Alignment explanation
Indices: 1181311--1181835 Score: 752
Period size: 113 Copynumber: 4.7 Consensus size: 113
1181301 CATTTCCAGA
* *
1181311 AGAGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
1181376 TCAACTTTTTGCTTAAATTTATCATTCGATGGATCAGTATTGCCAGGT
66 TCAACCTTTTGCTTTAATTCATCACTCGATGGATCAGTATTGCCAGGT
*
1181424 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * * *
1181489 TCAACCTTTTGCTTGAATTCATCACTCGGTGGATCAGCAGTGCCAGGT
66 TCAACCTTTTGCTTTAATTCATCACTCGATGGATCAGTATTGCCAGGT
* * *
1181537 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTTT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
* * *
1181602 TTAACCTTTTGCTTTAATTCATCACTCGATGGATTA-TCATTGCCAGTT
66 TCAACCTTTTGCTTTAATTCATCACTCGATGGATCAGT-ATTGCCAGGT
* * *
1181650 AGAGTTCATAATGAGAAGAACTTAACTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
** * *
1181715 TCAACAATTTGCTTTAATTCATCACTCGATGGATTAGCT-TTTCCAGAG-
66 TCAACCTTTTGCTTTAATTCATCACTCGATGGATCAG-TATTGCCAG-GT
* * *
1181763 AAAATTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAGCTTGT
1 AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
1181827 TCAACCTTT
66 TCAACCTTT
1181836 GTATGACTCT
Statistics
Matches: 372, Mismatches: 36, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
112 35 0.09
113 336 0.90
115 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
AGAGTTCATAATGAGAAGAACTTATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGT
TCAACCTTTTGCTTTAATTCATCACTCGATGGATCAGTATTGCCAGGT
Found at i:1182316 original size:3 final size:3
Alignment explanation
Indices: 1182308--1182355 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
1182298 TTTGTTTTAT
* *
1182308 TTA TTA TTA TTA TT- TTA TT- TTA ATA TTA TTA TTA -TA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1182353 TTA
1 TTA
1182356 AATAATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1182334 original size:19 final size:19
Alignment explanation
Indices: 1182302--1182355 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1182292 ATTTCATTTG
*
1182302 TTTTA-TTTATTATTATTA
1 TTTTATTTTAATATTATTA
1182320 TTTTATTTTAATATTATTA
1 TTTTATTTTAATATTATTA
* *
1182339 TTATATTATAATTATTA
1 TTTTATTTTAA-TATTA
1182356 AATAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTTTATTTTAATATTATTA
Found at i:1184058 original size:22 final size:22
Alignment explanation
Indices: 1184033--1184081 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1184023 TAATTCCTTT
1184033 TATTTTAGCCATTATTAAATAC
1 TATTTTAGCCATTATTAAATAC
* *
1184055 TATTTTAGTCATTATTTAATAC
1 TATTTTAGCCATTATTAAATAC
*
1184077 AATTT
1 TATTT
1184082 ATTCTATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (22 bp):
TATTTTAGCCATTATTAAATAC
Found at i:1184349 original size:120 final size:119
Alignment explanation
Indices: 1184200--1184416 Score: 330
Period size: 121 Copynumber: 1.8 Consensus size: 119
1184190 AATAATTGCG
* * *
1184200 TAATATTTATTTATTTTTAATCTTAAGAAA-GGGCAGTCTTAAAGCAACTGGATGTCTATTTTCT
1 TAATATTTATTTATTTTTAATATTAAGAAATGGGCAGTCTTAAAGCAACTAGAAGTC-ATTTTCT
*
1184264 GATATTTTTAA-TAAATAAATATTTTATTATATATATATATATATTAATGTTTTAT
65 GATATTTCTAAGTAAATAAATATTTTATT-TATATATATATATATTAATGTTTTAT
* * *
1184319 TAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGTACCTAGAAGTCATTTTCT
1 TAATATTTATTTA-TTTTTAATATTAAGAAATGGGCAGTCTTAAAGCAACTAGAAGTCATTTTCT
1184384 GATATTTCTAAGTAAATAAATATTTTATTTATA
65 GATATTTCTAAGTAAATAAATATTTTATTTATA
1184417 AAAATAAAAA
Statistics
Matches: 88, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
119 13 0.15
120 37 0.42
121 38 0.43
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (119 bp):
TAATATTTATTTATTTTTAATATTAAGAAATGGGCAGTCTTAAAGCAACTAGAAGTCATTTTCTG
ATATTTCTAAGTAAATAAATATTTTATTTATATATATATATATTAATGTTTTAT
Found at i:1184444 original size:121 final size:118
Alignment explanation
Indices: 1184200--1184447 Score: 286
Period size: 121 Copynumber: 2.1 Consensus size: 118
1184190 AATAATTGCG
* * *
1184200 TAATATTTATTTATTTTTAATCTTAAGAAAGGGCAGTCTTAAAGCAACTGGATGTCTATTTTCTG
1 TAATATTTATTTATTTTTAATATTAAGAAAGGGCAGTCTTAAAGCAACTAGAAGTCTATTTTCTG
* * * * * ** *
1184265 ATATTTTTAATAAATAAATATTTTATTATATATATATATATATTAATGTTTTAT
66 ATATTTCTAATAAATAAATATTTTATTATAAAAATAAAAATATTAATG-TACAC
* * *
1184319 TAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAGTACCTAGAAGTC-ATTTTC
1 TAATATTTATTTA-TTTTTAATATTAAGAAA-GGGCAGTCTTAAAGCAACTAGAAGTCTATTTTC
1184383 TGATATTTCTAAGTAAATAAATATTTTATTTATAAAAATAAAAATA-TATATAG-ACAC
64 TGATATTTCTAA-TAAATAAATATTTTA-TTATAAAAATAAAAATATTA-AT-GTACAC
1184440 TAATATTT
1 TAATATTT
1184448 TTTCTTAAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
119 13 0.12
120 33 0.30
121 47 0.43
122 15 0.14
123 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.09, T:0.46
Consensus pattern (118 bp):
TAATATTTATTTATTTTTAATATTAAGAAAGGGCAGTCTTAAAGCAACTAGAAGTCTATTTTCTG
ATATTTCTAATAAATAAATATTTTATTATAAAAATAAAAATATTAATGTACAC
Found at i:1193381 original size:9 final size:9
Alignment explanation
Indices: 1193367--1193439 Score: 66
Period size: 8 Copynumber: 8.4 Consensus size: 9
1193357 TTACTTTAAG
1193367 AAAAAATGAAA
1 AAAAAATG--A
1193378 AAAAAAT-A
1 AAAAAATGA
*
1193386 AAAAAATAA
1 AAAAAATGA
1193395 AAAAAATG-
1 AAAAAATGA
1193403 AAAAAATG-
1 AAAAAATGA
*
1193411 AAAAAA-GG
1 AAAAAATGA
1193419 AAAAAA-GA
1 AAAAAATGA
*
1193427 AAAAAAAGA
1 AAAAAATGA
1193436 AAAA
1 AAAA
1193440 GGAAAAAGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
7 1 0.02
8 35 0.61
9 14 0.25
11 7 0.12
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.07
Consensus pattern (9 bp):
AAAAAATGA
Found at i:1193396 original size:17 final size:17
Alignment explanation
Indices: 1193376--1193439 Score: 69
Period size: 17 Copynumber: 3.8 Consensus size: 17
1193366 GAAAAAATGA
*
1193376 AAAAAAAATAAAAAAAT
1 AAAAAAAAGAAAAAAAT
1193393 AAAAAAAATG-AAAAAAT
1 AAAAAAAA-GAAAAAAAT
* * *
1193410 -GAAAAAAGGAAAAAAG
1 AAAAAAAAGAAAAAAAT
1193426 AAAAAAAAGAAAAA
1 AAAAAAAAGAAAAA
1193440 GGAAAAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 1 0.03
16 12 0.31
17 26 0.67
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.06
Consensus pattern (17 bp):
AAAAAAAAGAAAAAAAT
Found at i:1193432 original size:8 final size:8
Alignment explanation
Indices: 1193377--1193453 Score: 59
Period size: 8 Copynumber: 9.4 Consensus size: 8
1193367 AAAAAATGAA
*
1193377 AAAAAAAT
1 AAAAAAAG
*
1193385 AAAAAAATA
1 AAAAAAA-G
1193394 AAAAAAATG
1 AAAAAAA-G
*
1193403 AAAAAATG
1 AAAAAAAG
1193411 -AAAAAAG
1 AAAAAAAG
*
1193418 GAAAAAAG
1 AAAAAAAG
1193426 AAAAAAA-
1 AAAAAAAG
*
1193433 AGAAAAAGG
1 A-AAAAAAG
1193442 AAAAAGAAG
1 AAAAA-AAG
1193451 AAA
1 AAA
1193454 GGAGGAAGAT
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
7 7 0.12
8 30 0.53
9 20 0.35
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (8 bp):
AAAAAAAG
Found at i:1193438 original size:23 final size:24
Alignment explanation
Indices: 1193364--1193446 Score: 72
Period size: 23 Copynumber: 3.7 Consensus size: 24
1193354 ATTTTACTTT
*
1193364 AAGAAAAAATGAAAAAA--AAATAA
1 AAGAAAAAAGGAAAAAATGAAA-AA
*
1193387 AA-AAATAA--AAAAAATGAAAAA
1 AAGAAAAAAGGAAAAAATGAAAAA
*
1193408 ATGAAAAAAGGAAAAAA-GAAAAA
1 AAGAAAAAAGGAAAAAATGAAAAA
1193431 AA-AGAAAAAGGAAAAA
1 AAGA-AAAAAGGAAAAA
1193447 GAAGAAAGGA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
20 6 0.12
21 3 0.06
22 14 0.28
23 21 0.42
24 6 0.12
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (24 bp):
AAGAAAAAAGGAAAAAATGAAAAA
Found at i:1193444 original size:16 final size:16
Alignment explanation
Indices: 1193364--1193453 Score: 83
Period size: 16 Copynumber: 5.4 Consensus size: 16
1193354 ATTTTACTTT
1193364 AAGAAAAAATGAAAAAAA
1 AAGAAAAAA-G-AAAAAA
* *
1193382 AATAAAAAAATAAAAAA
1 AA-GAAAAAAGAAAAAA
1193399 AATGAAAAAATG-AAAAA
1 AA-GAAAAAA-GAAAAAA
*
1193416 AGGAAAAAAGAAAAAA
1 AAGAAAAAAGAAAAAA
* *
1193432 AAGAAAAAGGAAAAAG
1 AAGAAAAAAGAAAAAA
1193448 AAGAAA
1 AAGAAA
1193454 GGAGGAAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
15 1 0.02
16 31 0.51
17 21 0.34
18 2 0.03
19 6 0.10
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:1193462 original size:14 final size:13
Alignment explanation
Indices: 1193412--1193456 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
1193402 GAAAAAATGA
1193412 AAAAAGGAAAAA-
1 AAAAAGGAAAAAG
*
1193424 AGAAA--AAAAAG
1 AAAAAGGAAAAAG
1193435 AAAAAGGAAAAAG
1 AAAAAGGAAAAAG
1193448 AAGAAAGGA
1 AA-AAAGGA
1193457 GGAAGATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
10 5 0.19
11 4 0.15
12 4 0.15
13 8 0.30
14 6 0.22
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAAAAG
Found at i:1194852 original size:54 final size:54
Alignment explanation
Indices: 1194784--1195762 Score: 1180
Period size: 54 Copynumber: 18.2 Consensus size: 54
1194774 AAGCAAATGT
* * * * *
1194784 AGATTGTTCGAGTTCCTACTCCATAAAGAAAGAGAGAGTGAACCCGTAGGCAAA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* **
1194838 ATATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTA-ATAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCG-TAGGCAGA
* * *
1194892 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGAGAGCGAACCCCTTGGCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* * **
1194946 AGATTGTTCGAGTTCCTATTCCCTAAAGAAAGATAGAGCGAACCCGTAGGCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* * * * * *
1195000 ATATCGTTCAAGTTCCTACTCCCTAAAGAAAGAGAGAGTGAACCAGTTGGCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* * * * **
1195054 ATATTGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAAC-AAACCGTTA-ATAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCG-TAGGCAGA
** * * * *
1195107 AGATCGTTCGAGTTATTACT-GCTAAAGAAAGAGAGACCGAACCCGTTGGCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* * *
1195160 AGATTGTTCGAGTTCCTATTCCCTAAAGAAAGAGGGAGCGAACCCATAGGCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* *
1195214 ATATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* * * * * *
1195268 AGATTGTTAGAGTTCCTTCTCCTTAAAGAAAGAGGGAGCGAACTCGTTGGCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* ** *
1195322 AGATCGTCCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTA-AAAAA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCG-TAGGCAGA
* * * *
1195376 AGATCGTTCGATTTCCTACTCCATAAAGAAAGAGGGAGCGAACCCGTTGGTAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
** * * * * *
1195430 AGATCGTTCGAGTTTATACTCCCTAAAGAAAGAGTGAGCGAAACTGTTGACAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* * ** ** * *
1195484 AGATCATCCGAGTTCCTACTCTGTAAAGAAAGAGGGAGAAAACCCATTA-ACAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCC-GTAGGCAGA
* *
1195538 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGTAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* *
1195592 AGATCATTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTTGGCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
* * *
1195646 AGATCGTTCGAGTTCATACTCCCTAAAGAAAGAGGGAGTGAACCCATTA-GCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCC-GTAGGCAGA
*
1195700 AGATCGTTCGAGTTCCTACTCCCTAAACAAAGAGGGAGCGAACCCGTAGGCAGA
1 AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
*
1195754 AGATTGTTC
1 AGATCGTTC
1195763 AAATTCTATT
Statistics
Matches: 784, Mismatches: 129, Indels: 24
0.84 0.14 0.03
Matches are distributed among these distances:
52 16 0.02
53 52 0.07
54 711 0.91
55 5 0.01
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (54 bp):
AGATCGTTCGAGTTCCTACTCCCTAAAGAAAGAGGGAGCGAACCCGTAGGCAGA
Found at i:1196648 original size:15 final size:15
Alignment explanation
Indices: 1196624--1196657 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1196614 CAATTAGTAT
*
1196624 TCAAGTTTATCCCGG
1 TCAAGGTTATCCCGG
*
1196639 TCAAGGTTATCTCGG
1 TCAAGGTTATCCCGG
1196654 TCAA
1 TCAA
1196658 TTTGCATCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (15 bp):
TCAAGGTTATCCCGG
Found at i:1207126 original size:3 final size:3
Alignment explanation
Indices: 1207118--1207144 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1207108 TACATGACTA
1207118 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1207145 TAAATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1208515 original size:3 final size:3
Alignment explanation
Indices: 1208507--1208567 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
1208497 CTATAATGTA
* *
1208507 AAT AAT AAT TAT AA- AAT AAT AAT AGT AAT AAAT AA- AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
1208551 AAC AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
1208568 AAACAAATGG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1209073 original size:20 final size:20
Alignment explanation
Indices: 1209050--1209113 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
1209040 GGTTGAAAAA
1209050 GTTCTTCTCATTATGAACTT
1 GTTCTTCTCATTATGAACTT
*
1209070 GTTCTTTCTC-TTCA-G-A-TAA
1 GTTC-TTCTCATT-ATGAACT-T
1209089 GTTCTTCTCATTATGAACTT
1 GTTCTTCTCATTATGAACTT
*
1209109 CTTCT
1 GTTCT
1209114 GGAAAAGTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 14
0.67 0.06 0.27
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 12 0.35
21 7 0.21
ACGTcount: A:0.19, C:0.22, G:0.09, T:0.50
Consensus pattern (20 bp):
GTTCTTCTCATTATGAACTT
Found at i:1209174 original size:122 final size:122
Alignment explanation
Indices: 1208947--1209613 Score: 884
Period size: 122 Copynumber: 5.5 Consensus size: 122
1208937 GTTGAACATA
* ** *
1208947 TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGGAAATGTTGATGTTGAT
1 TTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGAT
* *
1209010 CTATCTCCGTCTGTGATAGAGTCATGCAAAGGTTGAAAAAGTTCTTCTCATTATGAAC
65 CTATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * *
1209068 TTGTTCTTTCTCTTCAGATAAGTTCTTCTCATTATGAAC-TTCTTCTGGAAAAGTTGATGCTGAT
1 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGTTGATGTTGAT
** *
1209132 CTATCTCCTTCTACGATAGAATCGA-GCAAAGGTTGAACAAGTTCTTCTCATTATGAAC
65 CTATCTCCTTCTGTGATAGAGTC-ATGCAAAGGTTGAACAAGTTCTTCTCATTATGAAC
1209190 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATC
1 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATC
* *
1209255 TATTTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAAC
66 TATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* ** * **
1209312 TTCTTCTTCCTCTTCAGATTAGTTCTTCTTGTTACGAACTTTCTCTGGAAAAGTTGA--TCCATC
1 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATC
* * ** *** * * *
1209375 GA-AT-GATGAATGAT-GAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
66 TATCTCCTTCTGTGATAG-AGTCATGC-AAAGGTTGAACAAGTTCTTCTCATTATGAAC
*
1209431 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAAAGTTGATGTTG
1 TTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACT-TT-CTCTGGAAAAGTTGATGTTG
*
1209496 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAAC
63 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAAC
* * *
1209556 TTATTCTTCCTCTTTAGATAAGTTCTTCTCATTACGAACTTTCTCTGGAAAAGTTGAT
1 TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGAT
1209614 CCATCAAATG
Statistics
Matches: 473, Mismatches: 57, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
117 1 0.00
118 11 0.02
119 40 0.08
120 32 0.07
121 36 0.08
122 264 0.56
123 6 0.01
124 32 0.07
125 39 0.08
126 11 0.02
127 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (122 bp):
TTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGATC
TATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGTTCTTCTCATTATGAAC
Found at i:1209302 original size:244 final size:238
Alignment explanation
Indices: 1208947--1209708 Score: 1092
Period size: 244 Copynumber: 3.2 Consensus size: 238
1208937 GTTGAACATA
** *
1208947 TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACACT-TCTGGAAATGTTGATGTTGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGAT
* * * *
1209010 CTATCTCCGTCTGTGATAGAGTCATGCAAAGGTTGAAAAAGTTCTTCTCATTATGAACTTGTTCT
66 CTATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCT
* *
1209075 TTCTCTTCAGATAAGTTCTTCTCATTATGAAC-TTCTTCTGGAAAAGTTGATGCTGATCTATCTC
131 TCCTCTTCAGATAAGTTCTTCTCATTACGAACTTTC-TCTGGAAAAGTTGAT-C--ATC-A--T-
** * * *
1209139 CTTCTACGATAGAA-TCGAGC-AAAGGTTGAACAAGTTCTTCTCATTATGAAC
188 C-TAAATGAT-GAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
*
1209190 TTCTTCTTCC-TCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGAT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGAT
* *
1209254 CTATTTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCT
66 CTATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCT
* ** * *
1209319 TCCTCTTCAGATTAGTTCTTCTTGTTACGAACTTTCTCTGGAAAAGTTGATCCATCGAATGATGA
131 TCCTCTTCAGATAAGTTCTTCTCATTACGAACTTTCTCTGGAAAAGTTGAT-CATC--AT-CTAA
1209384 ATGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
192 ATGATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
1209431 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCCTCTGGAAAAGTTGATGTTG
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TT-CTCTGGAAAAGTTGATGTTG
1209496 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTATT
64 ATCTATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTATT
*
1209561 CTTCCTCTTTAGATAAGTTCTTCTCATTACGAACTTTCTCTGGAAAAGTTGATC--CATC-AAAT
129 CTTCCTCTTCAGATAAGTTCTTCTCATTACGAACTTTCTCTGGAAAAGTTGATCATCATCTAAAT
1209623 GATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
194 GATGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
* *
1209668 TTTTTCTTCCTTTTTCAGATGAGTTCTTCTCATTATGAACT
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT
1209709 CTACCTGGAA
Statistics
Matches: 476, Mismatches: 34, Indels: 24
0.89 0.06 0.04
Matches are distributed among these distances:
237 87 0.18
239 5 0.01
240 10 0.02
241 42 0.09
242 32 0.07
243 39 0.08
244 258 0.54
245 3 0.01
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (238 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGTTGATGTTGAT
CTATCTCCTTCTGTGATAGAGTCATGCAAAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCT
TCCTCTTCAGATAAGTTCTTCTCATTACGAACTTTCTCTGGAAAAGTTGATCATCATCTAAATGA
TGAATTCAAGCAAAAGGTTAAACAAGTTCTTCTCATTATGAAC
Found at i:1209815 original size:114 final size:112
Alignment explanation
Indices: 1209525--1209843 Score: 401
Period size: 113 Copynumber: 2.8 Consensus size: 112
1209515 AGAGTCATGC
* * *
1209525 AAAGGTTGAACAAGCTCTTCTCATTATGAACTTATTCTTCCTCTTT-AGATAAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAA-TTTTTCTTCCTTTTTCAGATGAGTTCTTCTCATT
* * * *
1209589 ACGAACTTTCTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAGCA
65 ATGAACTTACTCTGGAAAAGTTAATCCATCAAATGATGAATTCAAACA
* *
1209637 AAAGGTTAAACAAGTTCTTCTCATTATGAACTTTTTCTTCCTTTTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGCTCTTCTCATTATGAA-TTTTTCTTCCTTTTTCAGATGAGTTCTTCTCATT
* * * *
1209702 ATGAACTCTAC-CTGGAAATGTTAATCTATCGAGTGATGAATTCAAACA
65 ATGAACT-TACTCTGGAAAAGTTAATCCATCAAATGATGAATTCAAACA
* * *
1209750 AAAGGTTTGAACAAACTCTTCTCATTATGAATTTCTTCTTCTTTTTTCCGATGAGTTCTTCTCAT
1 AAAGG-TTGAACAAGCTCTTCTCATTATGAATTT-TTCTTCCTTTTTCAGATGAGTTCTTCTCAT
* * *
1209815 TATGAACTT-CTTTGGAAATGTTGATCCAT
64 TATGAACTTACTCTGGAAAAGTTAATCCAT
1209844 TGAGTAATGG
Statistics
Matches: 181, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
112 43 0.24
113 78 0.43
114 60 0.33
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.39
Consensus pattern (112 bp):
AAAGGTTGAACAAGCTCTTCTCATTATGAATTTTTCTTCCTTTTTCAGATGAGTTCTTCTCATTA
TGAACTTACTCTGGAAAAGTTAATCCATCAAATGATGAATTCAAACA
Found at i:1210721 original size:17 final size:17
Alignment explanation
Indices: 1210692--1210739 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
1210682 TTTTATCATT
*
1210692 TTTTTC-TCTTTTTTTC
1 TTTTTCATCATTTTTTC
1210708 -TTTTCATTCATTTTTTC
1 TTTTTCA-TCATTTTTTC
1210725 TTTTTCATCATTTTT
1 TTTTTCATCATTTTT
1210740 CTTCTTCAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 5 0.18
17 17 0.61
18 6 0.21
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCATCATTTTTTC
Found at i:1211467 original size:17 final size:17
Alignment explanation
Indices: 1211419--1211467 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1211409 TTTTTTCTCT
1211419 TTTTTTCTTTTCATTTCA
1 TTTTTTCTTTTCA-TTCA
*
1211437 TTTTTTATTTTTCA-TCA
1 TTTTTT-CTTTTCATTCA
1211454 TTTTTTCTTCTTCA
1 TTTTTTCTT-TTCA
1211468 AGCATAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 2 0.07
17 13 0.48
18 6 0.22
19 6 0.22
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTCTTTTCATTCA
Found at i:1218582 original size:30 final size:30
Alignment explanation
Indices: 1218548--1218611 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
1218538 AAATATAAAG
1218548 AAAAT-AATGCAATG-AATAATGAATGTATGC
1 AAAATGAATG-AATGCAA-AATGAATGTATGC
*
1218578 AAAATGAATGTATGCAAAATGAATGTATGC
1 AAAATGAATGAATGCAAAATGAATGTATGC
1218608 AAAA
1 AAAA
1218612 GGTATTGACC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 25 0.81
31 6 0.19
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.25
Consensus pattern (30 bp):
AAAATGAATGAATGCAAAATGAATGTATGC
Found at i:1218585 original size:15 final size:15
Alignment explanation
Indices: 1218565--1218611 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
1218555 TGCAATGAAT
1218565 AATGAATGTATGCAA
1 AATGAATGTATGCAA
1218580 AATGAATGTATGCAA
1 AATGAATGTATGCAA
1218595 AATGAATGTATGCAA
1 AATGAATGTATGCAA
1218610 AA
1 AA
1218612 GGTATTGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.26
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1222668 original size:3 final size:3
Alignment explanation
Indices: 1222660--1222692 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1222650 TACATGACTA
1222660 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1222693 TAAATATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1223647 original size:13 final size:15
Alignment explanation
Indices: 1223637--1223669 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1223627 TTGTTCTGTT
1223637 CTCTCTGTCTGGTTG
1 CTCTCTGTCTGGTTG
1223652 CTCTC--TCTGGTTG
1 CTCTCTGTCTGGTTG
1223665 CTCTC
1 CTCTC
1223670 CTTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
15 5 0.28
ACGTcount: A:0.00, C:0.33, G:0.21, T:0.45
Consensus pattern (15 bp):
CTCTCTGTCTGGTTG
Found at i:1224147 original size:3 final size:3
Alignment explanation
Indices: 1224141--1224214 Score: 82
Period size: 3 Copynumber: 25.0 Consensus size: 3
1224131 ATTTTTTTAT
* *
1224141 TAA TAA TAA TAA TAA TAA TTA TAA -AA TAA TAA TAGA -AA TAA -AT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
*
1224184 TAAA TAA TAA TAA CAA TAA TAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1224215 AAACAAATGG
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
2 4 0.07
3 53 0.88
4 3 0.05
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1225439 original size:43 final size:43
Alignment explanation
Indices: 1225323--1225513 Score: 188
Period size: 43 Copynumber: 4.4 Consensus size: 43
1225313 GAAAAATGCT
* * *
1225323 GCAATAGGTATTGATATTTAGCGGCGTTTTTCAT-ACAAACGCC
1 GCAATAGGTGTTGAGATTTAGCGGCGTTTTTC-TCACAAACACC
* * ** * *
1225366 GCAATACGTGTTAATTTTTAACGGCGTTTTTCCCACAAACACC
1 GCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACACC
* * *
1225409 GCAATAGGTGTTGAGATTTAGCGGCATTTTTATCACAAA-ATTC
1 GCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACA-CC
* * * ** *
1225452 GCAATATGTCTTGTGATTTAGCGGCGTTTTTCTTGCAAACGCC
1 GCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACACC
1225495 GCAATAGGTGTTGAGATTT
1 GCAATAGGTGTTGAGATTT
1225514 CGCAAAGTTT
Statistics
Matches: 117, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
42 1 0.01
43 116 0.99
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (43 bp):
GCAATAGGTGTTGAGATTTAGCGGCGTTTTTCTCACAAACACC
Found at i:1234457 original size:45 final size:44
Alignment explanation
Indices: 1234326--1234555 Score: 245
Period size: 45 Copynumber: 5.2 Consensus size: 44
1234316 TAATCAAAGA
* * ** *
1234326 CTTTTAATTATTGGGTTGAAAAAAACAAAATTAAAGGATTAGTTC
1 CTTTTGATTATT-GGTTGCAAAAATTAAAATCAAAGGATTAGTTC
* * *
1234371 CTTTTGATTATTGAGTTGCCAAAATTAAAAATAAAAGGATTAGTTT
1 CTTTTGATTATTG-GTTGCAAAAATT-AAAATCAAAGGATTAGTTC
* *
1234417 CTTTTGATTGATTGGTTGCAAAAATTAAAATCAAATGATTATTTC
1 CTTTTGATT-ATTGGTTGCAAAAATTAAAATCAAAGGATTAGTTC
* *
1234462 TTTTTGATTATTGGATTGCGAAAATTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGG-TTGCAAAAATTAAAATCAAAGGATTAGTTC
* *
1234507 CTTTTGATTATTGGGTTG---AAA--AAAATTAAAGGATTAATTC
1 CTTTTGATTATT-GGTTGCAAAAATTAAAATCAAAGGATTAGTTC
1234547 CTTTTGATT
1 CTTTTGATT
1234556 TCTATTTGTT
Statistics
Matches: 161, Mismatches: 19, Indels: 15
0.83 0.10 0.08
Matches are distributed among these distances:
40 26 0.16
42 3 0.02
44 6 0.04
45 83 0.52
46 39 0.24
47 4 0.02
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.40
Consensus pattern (44 bp):
CTTTTGATTATTGGTTGCAAAAATTAAAATCAAAGGATTAGTTC
Found at i:1234486 original size:91 final size:90
Alignment explanation
Indices: 1234326--1234536 Score: 273
Period size: 91 Copynumber: 2.3 Consensus size: 90
1234316 TAATCAAAGA
* ** *
1234326 CTTTTAATTATTGGGTTGAAAAAAACAAAATTAAAGGATTAGTTCCTTTTGATTATTGAGTTGCC
1 CTTTTGATTATTGGGTTGAAAAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAGTTGCC
*
1234391 AAAATTAAAAATAAAAGGATTAGTTT
66 AAAATT-AAAATAAAAGGATTAGTTC
* * * *
1234417 CTTTTGATTGATT-GGTTGCAAAAATTAAAATCAAATGATTATTTCTTTTTGATTATTG-GATTG
1 CTTTTGATT-ATTGGGTTGAAAAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAG-TTG
* *
1234480 CGAAAATTAAAATCAAAGGATTAGTTC
64 CCAAAATTAAAATAAAAGGATTAGTTC
1234507 CTTTTGATTATTGGGTTGAAAAAAATTAAA
1 CTTTTGATTATTGGGTTG-AAAAAATTAAA
1234537 GGATTAATTC
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
89 3 0.03
90 32 0.31
91 66 0.63
92 3 0.03
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.39
Consensus pattern (90 bp):
CTTTTGATTATTGGGTTGAAAAAATTAAAATCAAAGGATTAGTTCCTTTTGATTATTGAGTTGCC
AAAATTAAAATAAAAGGATTAGTTC
Found at i:1234784 original size:58 final size:58
Alignment explanation
Indices: 1234638--1234798 Score: 148
Period size: 58 Copynumber: 2.7 Consensus size: 58
1234628 TAACATAATA
*** * *
1234638 TAAAGAAAATAAATCACTGAATTTATTTCATCGTTAGAATCTTGCGTTGATTCTAACTTTG
1 TAAAGAAAATAAATTGTTGAATGTATTTC--C-TTAGAATCTTGCGATGATTCTAACTTTG
* *
1234699 TAAGGAAAATAAATTGTTGAATGTATTTCCTTGAGAATCTTG-GATGATTCT-ATTTTG
1 TAAAGAAAATAAATTGTTGAATGTATTTCCTT-AGAATCTTGCGATGATTCTAACTTTG
* * *
1234756 TAAAAGTAAATAAATTGGTT-AATTTATTTTCTTAGGAATCTTG
1 T-AAAGAAAATAAATT-GTTGAATGTATTTCCTTA-GAATCTTG
1234799 AAGGATCCTG
Statistics
Matches: 85, Mismatches: 11, Indels: 11
0.79 0.10 0.10
Matches are distributed among these distances:
57 7 0.08
58 41 0.48
59 13 0.15
61 24 0.28
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (58 bp):
TAAAGAAAATAAATTGTTGAATGTATTTCCTTAGAATCTTGCGATGATTCTAACTTTG
Found at i:1237905 original size:20 final size:20
Alignment explanation
Indices: 1237880--1237925 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1237870 TTGTTAGTAC
1237880 CGATACTGAACCTTTGGTAT
1 CGATACTGAACCTTTGGTAT
1237900 CGATACTGAACCTTTGGTAT
1 CGATACTGAACCTTTGGTAT
1237920 CGATAC
1 CGATAC
1237926 CAACTGATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.33
Consensus pattern (20 bp):
CGATACTGAACCTTTGGTAT
Found at i:1238917 original size:3 final size:3
Alignment explanation
Indices: 1238897--1238959 Score: 51
Period size: 3 Copynumber: 21.3 Consensus size: 3
1238887 CTTGTTGATT
* * *
1238897 TTA TTA ATA TTAA TTA TTA TTA TT- TAA TTA TTA TTG TT- TCTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
1238942 TTA TTA TCA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA T
1238960 ATTTATATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
2 4 0.08
3 40 0.83
4 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1243837 original size:8 final size:7
Alignment explanation
Indices: 1243824--1243873 Score: 55
Period size: 7 Copynumber: 6.7 Consensus size: 7
1243814 CTGAAGAAAG
1243824 GAAAAAA
1 GAAAAAA
1243831 TGAAAAAAA
1 -G-AAAAAA
1243840 GAGAAAAA
1 GA-AAAAA
*
1243848 GAAAGAA
1 GAAAAAA
*
1243855 GACAAAA
1 GAAAAAA
1243862 GAAAAAA
1 GAAAAAA
1243869 GAAAA
1 GAAAA
1243874 TAAAATAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
7 21 0.58
8 9 0.25
9 6 0.17
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (7 bp):
GAAAAAA
Found at i:1245690 original size:3 final size:3
Alignment explanation
Indices: 1245670--1245735 Score: 66
Period size: 3 Copynumber: 22.3 Consensus size: 3
1245660 CTTGTTGATT
* * *
1245670 TTA TTA ATA TTAA TTA TTA TTA TT- TAA TTA TTA TTG TT- TCTA TTA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1245715 TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA T
1245736 ATTTATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
2 4 0.08
3 45 0.85
4 4 0.08
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1245744 original size:16 final size:17
Alignment explanation
Indices: 1245725--1245762 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
1245715 TTATTATTAT
1245725 TATTAT-TTTATATTTA
1 TATTATCTTTATATTTA
*
1245741 TATTATCTTTATTTTTA
1 TATTATCTTTATATTTA
1245758 T-TTAT
1 TATTAT
1245763 ACAGACCCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATCTTTATATTTA
Found at i:1246944 original size:109 final size:109
Alignment explanation
Indices: 1246728--1246966 Score: 276
Period size: 109 Copynumber: 2.2 Consensus size: 109
1246718 TAAGTTAGTC
* *
1246728 GTGTTTTTACATGTTGGTCACCTACGAGGTCCAAAGTTGCTATTTATCTGTTTTCATGCATGCTA
1 GTGTTTTTGCATGTTGGTCACCTA-GAGGACCAAAGTTGCTATTTATCTGTTTTCATGCATGCTA
1246793 TATATTTTTTGAGATATTTATTGTTTAATCCCCAATAGTTTA-GA
65 TATATTTTTTGAGATATTTATTGTTTAATCCCCAATAGTTTAGGA
* *
1246837 GTGTTTTTGCATGTTGGTCACCT-GTAGGAACCAAAGTTGTTATTTA-CTAGTTTTCATGCATGT
1 GTGTTTTTGCATGTTGGTCACCTAG-AGG-ACCAAAGTTGCTATTTATCT-GTTTTCATGCATGC
* * ** *
1246900 TATGTATTTTTTTG-GAATATTTGTTGTTTAGA-CCCCCTTA-TTTAGGC
63 TATATA-TTTTTTGAG-ATATTTATTGTTTA-ATCCCCAATAGTTTAGGA
1246947 GTGTTTTTGCAT-TTCGGTCA
1 GTGTTTTTGCATGTT-GGTCA
1246967 TGTGTAGTGA
Statistics
Matches: 113, Mismatches: 9, Indels: 15
0.82 0.07 0.11
Matches are distributed among these distances:
107 1 0.01
108 5 0.04
109 62 0.55
110 44 0.39
111 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.46
Consensus pattern (109 bp):
GTGTTTTTGCATGTTGGTCACCTAGAGGACCAAAGTTGCTATTTATCTGTTTTCATGCATGCTAT
ATATTTTTTGAGATATTTATTGTTTAATCCCCAATAGTTTAGGA
Found at i:1246973 original size:110 final size:109
Alignment explanation
Indices: 1246728--1246929 Score: 277
Period size: 109 Copynumber: 1.8 Consensus size: 109
1246718 TAAGTTAGTC
* *
1246728 GTGTTTTTACATGTTGGTCACCTACG-AGG-TCCAAAGTTGCTATTTATCTGTTTTCATGCATGC
1 GTGTTTTTGCATGTTGGTCACCT--GTAGGAACCAAAGTTGCTATTTATCTGTTTTCATGCATGC
1246791 TATATATTTTTTGAGATATTTATTGTTTAATCCCCAATAGTTTAGA
64 TATATATTTTTTGAGATATTTATTGTTTAATCCCCAATAGTTTAGA
* *
1246837 GTGTTTTTGCATGTTGGTCACCTGTAGGAACCAAAGTTGTTATTTA-CTAGTTTTCATGCATGTT
1 GTGTTTTTGCATGTTGGTCACCTGTAGGAACCAAAGTTGCTATTTATCT-GTTTTCATGCATGCT
* *
1246901 ATGTATTTTTTTG-GAATATTTGTTGTTTA
65 ATATA-TTTTTTGAG-ATATTTATTGTTTA
1246930 GACCCCCTTA
Statistics
Matches: 82, Mismatches: 6, Indels: 9
0.85 0.06 0.09
Matches are distributed among these distances:
107 1 0.01
108 5 0.06
109 56 0.68
110 20 0.24
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (109 bp):
GTGTTTTTGCATGTTGGTCACCTGTAGGAACCAAAGTTGCTATTTATCTGTTTTCATGCATGCTA
TATATTTTTTGAGATATTTATTGTTTAATCCCCAATAGTTTAGA
Found at i:1248054 original size:131 final size:130
Alignment explanation
Indices: 1247804--1248067 Score: 429
Period size: 131 Copynumber: 2.0 Consensus size: 130
1247794 ATAAATAGCA
*
1247804 CTCGAATTAATATTGAATTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAAT
1 CTCGAATCAATATTGAATTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAAT
* * *
1247869 GACTACTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATTATTAGATATTATCGTTTTCT
66 GACTACTTTAAGGCATGAGAGGTCATTTATTCTCGATTGAAAATAATTAAATATTATCGTTTTCT
*
1247934 CTCGAATCAATATTGAATTTTAGGACGAAATAGTAATATTTCTTCATTTCGATTGGAGTAATAAA
1 CTCGAATCAATATTGAA-TTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAA
* * * * *
1247999 TGATTGCTTTAAGGCATGAGAGGTCATTTATTCTTGTTTGAAAATAATTAAATATTATTGTTTTC
65 TGACTACTTTAAGGCATGAGAGGTCATTTATTCTCGATTGAAAATAATTAAATATTATCGTTTTC
1248064 T
130 T
1248065 CTC
1 CTC
1248068 TTAATATTCA
Statistics
Matches: 123, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
130 16 0.13
131 107 0.87
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (130 bp):
CTCGAATCAATATTGAATTTAGGACGAAATAGTAATATCTCTTCATTTCGATTGGAGTAATAAAT
GACTACTTTAAGGCATGAGAGGTCATTTATTCTCGATTGAAAATAATTAAATATTATCGTTTTCT
Found at i:1250607 original size:2 final size:2
Alignment explanation
Indices: 1250600--1250655 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1250590 TGGATGATTG
1250600 AT AT 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 AT AT
1250642 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1250656 GATTTTCAGT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1251957 original size:45 final size:44
Alignment explanation
Indices: 1251815--1252023 Score: 224
Period size: 45 Copynumber: 4.6 Consensus size: 44
1251805 TAATCCAAGA
* ** *
1251815 CTTTTAATTATTGGGTTG-AAAAAACAAAATTAAAGGATTAGTTC
1 CTTTTGATTATT-GGTTGCAAAAATTAAAATCAAAGGATTAGTTC
* *
1251859 CTTTTGATTATTGAGTTGCCAAAATTAAAAGTAAAAGGATTAGTTC
1 CTTTTGATTATTG-GTTGCAAAAATTAAAA-TCAAAGGATTAGTTC
** *
1251905 CTTTTGATTACTTGGTTGCAAAAATTAAAATCAAATTATTATTTC
1 CTTTTGATTA-TTGGTTGCAAAAATTAAAATCAAAGGATTAGTTC
* **
1251950 TTTTTGATTATTGGATTGTGAAAATTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGG-TTGCAAAAATTAAAATCAAAGGATTAGTTC
*
1251995 CTTCTGATTATTGGGTTG-ATAAAATTAAA
1 CTTTTGATTATT-GGTTGCA-AAAATTAAA
1252024 GGATTAATTC
Statistics
Matches: 139, Mismatches: 19, Indels: 13
0.81 0.11 0.08
Matches are distributed among these distances:
43 1 0.01
44 19 0.14
45 75 0.54
46 41 0.29
47 3 0.02
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (44 bp):
CTTTTGATTATTGGTTGCAAAAATTAAAATCAAAGGATTAGTTC
Found at i:1255070 original size:6 final size:6
Alignment explanation
Indices: 1255059--1255109 Score: 75
Period size: 6 Copynumber: 8.2 Consensus size: 6
1255049 ATTATTATAA
*
1255059 TTTTAT TTTTAT TTTTAT TTTTAT TTTTTT TTATTAT TTTTAT TTTCTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TT-TTAT TTTTAT TTT-TAT
1255109 T
1 T
1255110 ATATATATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
6 32 0.78
7 9 0.22
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:1255095 original size:25 final size:25
Alignment explanation
Indices: 1255060--1255109 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
1255050 TTATTATAAT
1255060 TTTATTTTTATTTTTATTTT-TATT
1 TTTATTTTTATTTTTATTTTCTATT
*
1255084 TTTTTTTATTATTTTTATTTTCTATT
1 TTTATTT-TTATTTTTATTTTCTATT
1255110 ATATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.26
25 13 0.57
26 4 0.17
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (25 bp):
TTTATTTTTATTTTTATTTTCTATT
Found at i:1255110 original size:16 final size:15
Alignment explanation
Indices: 1255061--1255111 Score: 66
Period size: 16 Copynumber: 3.3 Consensus size: 15
1255051 TATTATAATT
1255061 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
* *
1255076 TTTTTATTTTTTTTTA
1 TTATT-TTTATTTTTA
1255092 TTATTTTTATTTTCTA
1 TTATTTTTATTTT-TA
1255108 TTAT
1 TTAT
1255112 ATATATATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.18, C:0.02, G:0.00, T:0.80
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:1255111 original size:19 final size:18
Alignment explanation
Indices: 1255048--1255111 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 18
1255038 AACTATTAAA
1255048 TATTATTATAATTTTATTTT
1 TATTATTAT--TTTTATTTT
*
1255068 TATTTTTATTTTTATTTTT
1 TATTATTATTTTTA-TTTT
*
1255087 TTTTATTATTTTTATTTT
1 TATTATTATTTTTATTTT
1255105 CTATTAT
1 -TATTAT
1255112 ATATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 9 0.24
19 21 0.55
20 8 0.21
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.77
Consensus pattern (18 bp):
TATTATTATTTTTATTTT
Found at i:1255116 original size:2 final size:2
Alignment explanation
Indices: 1255109--1255133 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1255099 TATTTTCTAT
1255109 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1255134 TTACTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1262929 original size:16 final size:17
Alignment explanation
Indices: 1262903--1262935 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1262893 TTATGGGTGT
1262903 TTGACAAAGTGACAAGA
1 TTGACAAAGTGACAAGA
*
1262920 TTGA-AAAGTGATAAGA
1 TTGACAAAGTGACAAGA
1262936 CAAGGACCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.21
Consensus pattern (17 bp):
TTGACAAAGTGACAAGA
Found at i:1265923 original size:38 final size:38
Alignment explanation
Indices: 1265830--1267291 Score: 1418
Period size: 38 Copynumber: 36.9 Consensus size: 38
1265820 AATCTTTCAA
* * *
1265830 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTTAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
*
1265869 CAATGTTATTCTTGACTTCCTCGTGAAGAGAAGTCGATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* *
1265910 TGTTATTCTTGACTTCCTCATGAAGATAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
1265948 TGTTATTCTTGACTCCCTCGTGAAAAGGAGTCAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* *
1265987 CAATGTTACTCTTGACTTCCTCATGAAGAGAAGTCAATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * *
1266028 TATTATTCTCGACTCCCTCGTGAAGAGGAGTCAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* *
1266067 CAATGTTATTCTTGGA-TTCCTCTTAAAGAGAAGTCAATCTT
1 ---TGTTATTCTT-GACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
1266108 TTTTATTCTTGATTTCCTCGTGAAGAGAAGTTAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
*
1266146 TGTTATTCTTGAC-TCTCTCGTGAAGAGGAGTCAATCTTT
1 TGTTATTCTTGACTTC-CTCGTGAAGAGAAGTCAATC-TT
*
1266185 CAATTTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* *
1266226 TGTTATTCTTAACTTCCTCGTAAAG-GAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * *
1266263 TGTTATTATTGACTCCCTCGTTAAGA-AGATTCAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGA-AGTCAATC-TT
* *
1266302 CAATGTTATTCTTGTCTTCCTCGTGAAGAGAAAT-ATATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA-ATCTT
* *
1266343 TGTTATTCTTGACTTCCTCATGAAGAAAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* *
1266381 TTTTATTCTTGACTTCATCGTGAAGATG-AGTCAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATC-TT
1266420 CAATGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * *
1266461 TTTTATTATGGACTTCCTCATGAAGATG-AGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATCTT
* *
1266499 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* *
1266538 CAATGTTATTCTTGACTCCCT-GTGAAGAGGAGTCAATCTTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* *
1266579 CAATGTTATTCTTGATTTCCTCATGAAGAGAAGTCAATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* *
1266620 TGTTATTCTTGACTTCCTCATGAAGAGAAGTTAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
1266658 TGTTATTCTTGAC-ACCGTAGTGAAGAGGAGTCAATCTTT
1 TGTTATTCTTGACTTCC-TCGTGAAGAGAAGTCAATC-TT
* ** *
1266697 CAATGTTATTCTTGACTTTCTAATGAAGAGAAGTCGATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
1266738 TTTTATTCTTGACTTCCTCATGAAAAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* *
1266776 TGTTATTCTTGACTCCCTCATGAAGA-AGAGTCAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGA-AGTCAATC-TT
* * *
1266815 CAATGTTATTTTTGACTTCCTTGTGAAGAGAAGTCGATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
1266856 T-TGTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
1 TGT-TATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
1266894 TGTTATTCTTGACTCCCTCGTGAAGAGAAATCATTCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
*
1266933 CAATGTTATTCTTGACTTCCTCGTGAAGAGAAGTCGATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
*
1266974 TGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* *
1267012 TGTTATCCTTGACTCCCTCGTGAAGATG-AGTCAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATC-TT
* *
1267051 CAATGTTATTCTTGACTTTCTCATGAAGAGAAGTCAATCTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
1267092 TGTTATTTTTGACTCCCTCGTGAAGAGGAGTCAATCTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
1267130 TCATTGTCTTCCTTGACTTCCTCGTGAAAAGAAGTCAATCTT
1 T--GT-TATT-CTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * *
1267172 TGTTATTCTTGACTTTCTCATGAAGAGGAGTTAATCTTT
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* * * * *
1267211 CAATTTTATTCTTTACTCCCTTGTGAAGAGGAGTCAATCTTT
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* * *
1267253 CAATGTTATTCTTCACTTTCTCGTGAAGAGAAGCCAATC
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC
1267292 ATTCAATATT
Statistics
Matches: 1199, Mismatches: 151, Indels: 140
0.80 0.10 0.09
Matches are distributed among these distances:
37 43 0.04
38 626 0.52
39 29 0.02
40 2 0.00
41 67 0.06
42 425 0.35
43 7 0.01
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (38 bp):
TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
Found at i:1265946 original size:80 final size:77
Alignment explanation
Indices: 1265830--1267291 Score: 1431
Period size: 80 Copynumber: 18.5 Consensus size: 77
1265820 AATCTTTCAA
* * *
1265830 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTTAATCTTTCAATGTTATTCTTGACTTCCTCGTGA
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTT---TGTTATTCTTGACTTCCTCGTGA
*
1265895 AGAGAAGTCGATCTT
63 AGAGAAGTCAATCTT
* * * *
1265910 TGTTATTCTTGACTTCCTCATGAAGATAAGTCAATC-TTTGTTATTCTTGACTCCCTCGTGAAAA
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTCCTCGTGAAGA
*
1265974 GGAGTCAATCTTT
66 GAAGTCAATC-TT
* * * * *
1265987 CAATGTTACTCTTGACTTCCTCATGAAGAGAAGTCAATC-TTTATTATTCTCGACTCCCTCGTGA
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTCCTCGTGA
*
1266051 AGAGGAGTCAATCTTT
63 AGAGAAGTCAATC-TT
* * *
1266067 CAATGTTATTCTTGGA-TTCCTCTTAAAGAGAAGTCAATCTTTT-TTATTCTTGATTTCCTCGTG
1 ---TGTTATTCTT-GACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTCCTCGTG
*
1266130 AAGAGAAGTTAATCTT
62 AAGAGAAGTCAATCTT
* *
1266146 TGTTATTCTTGAC-TCTCTCGTGAAGAGGAGTCAATCTTTCAATTTTATTCTTGACTTCCTCGTG
1 TGTTATTCTTGACTTC-CTCGTGAAGAGAAGTCAATCTTT---TGTTATTCTTGACTTCCTCGTG
1266210 AAGAGAAGTCAATCTT
62 AAGAGAAGTCAATCTT
* * * * *
1266226 TGTTATTCTTAACTTCCTCGTAAAG-GAAGTCAATC-TTTGTTATTATTGACTCCCTCGTTAAGA
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTCCTCGTGAAGA
*
1266289 -AGATTCAATCTTT
66 GA-AGTCAATC-TT
* * *
1266302 CAATGTTATTCTTGTCTTCCTCGTGAAGAGAAAT-ATATC-TTTGTTATTCTTGACTTCCTCATG
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCA-ATCTTTTGTTATTCTTGACTTCCTCGTG
*
1266365 AAGAAAAGTCAATCTT
62 AAGAGAAGTCAATCTT
* *
1266381 TTTTATTCTTGACTTCATCGTGAAGATG-AGTCAATCTTTCAATGTTATTCTTGACTTCCTCGTG
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATCTTT---TGTTATTCTTGACTTCCTCGTG
1266445 AAGAGAAGTCAATCTT
62 AAGAGAAGTCAATCTT
* * * * *
1266461 TTTTATTATGGACTTCCTCATGAAGATG-AGTCAATC-TTTGTTATTCTTGACTCCCTCGTGAAG
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATCTTTTGTTATTCTTGACTTCCTCGTGAAG
*
1266524 AGGAGTCAATCTTT
65 AGAAGTCAATC-TT
* * * *
1266538 CAATGTTATTCTTGACTCCCT-GTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGATTTCCTCA
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTT---TGTTATTCTTGACTTCCTCG
1266602 TGAAGAGAAGTCAATCTT
60 TGAAGAGAAGTCAATCTT
* * * *
1266620 TGTTATTCTTGACTTCCTCATGAAGAGAAGTTAATC-TTTGTTATTCTTGAC-ACCGTAGTGAAG
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTCC-TCGTGAAG
*
1266683 AGGAGTCAATCTTT
65 AGAAGTCAATC-TT
* ** * *
1266697 CAATGTTATTCTTGACTTTCTAATGAAGAGAAGTCGATCTTTT-TTATTCTTGACTTCCTCATGA
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTCCTCGTGA
*
1266761 AAAGAAGTCAATCTT
63 AGAGAAGTCAATCTT
* * * *
1266776 TGTTATTCTTGACTCCCTCATGAAGA-AGAGTCAATCTTTCAATGTTATTTTTGACTTCCTTGTG
1 TGTTATTCTTGACTTCCTCGTGAAGAGA-AGTCAATCTTT---TGTTATTCTTGACTTCCTCGTG
*
1266840 AAGAGAAGTCGATCTT
62 AAGAGAAGTCAATCTT
*
1266856 T-TGTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TTTGTTATTCTTGACTCCCTCGTGAAG
1 TGT-TATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTCCTCGTGAAG
* *
1266919 AGAAATCATTCTTT
65 AGAAGTCAATC-TT
* *
1266933 CAATGTTATTCTTGACTTCCTCGTGAAGAGAAGTCGATC-TTTGTTATTCTTGACTTCCTCATGA
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTCCTCGTGA
1266997 AGAGAAGTCAATCTT
63 AGAGAAGTCAATCTT
* * * *
1267012 TGTTATCCTTGACTCCCTCGTGAAGATG-AGTCAATCTTTCAATGTTATTCTTGACTTTCTCATG
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATCTTT---TGTTATTCTTGACTTCCTCGTG
1267076 AAGAGAAGTCAATCTT
62 AAGAGAAGTCAATCTT
* * * *
1267092 TGTTATTTTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCATTGTCT-TCCTTGACTTCCTCGTG
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT--TTGT-TATTCTTGACTTCCTCGTG
*
1267156 AAAAGAAGTCAATCTT
62 AAGAGAAGTCAATCTT
* * * * * * * *
1267172 TGTTATTCTTGACTTTCTCATGAAGAGGAGTTAATCTTTCAATTTTATTCTTTACTCCCTTGTGA
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTT---TGTTATTCTTGACTTCCTCGTGA
*
1267237 AGAGGAGTCAATCTTT
63 AGAGAAGTCAATC-TT
* * *
1267253 CAATGTTATTCTTCACTTTCTCGTGAAGAGAAGCCAATC
1 ---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC
1267292 ATTCAATATT
Statistics
Matches: 1176, Mismatches: 132, Indels: 144
0.81 0.09 0.10
Matches are distributed among these distances:
74 1 0.00
75 36 0.03
76 248 0.21
77 16 0.01
78 3 0.00
79 86 0.07
80 700 0.60
81 20 0.02
82 2 0.00
83 33 0.03
84 31 0.03
ACGTcount: A:0.25, C:0.18, G:0.17, T:0.40
Consensus pattern (77 bp):
TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTTGTTATTCTTGACTTCCTCGTGAAGA
GAAGTCAATCTT
Found at i:1265971 original size:118 final size:118
Alignment explanation
Indices: 1265830--1267339 Score: 1584
Period size: 118 Copynumber: 12.7 Consensus size: 118
1265820 AATCTTTCAA
* *
1265830 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTTAATCTTTCAATGTTATTCTTGACTTCCTCGTGA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCATGA
* * *
1265895 AGAGAAGTCGATCTTTGTTATTCTTGACTTCCTCATGAAGATAAGTCAATCTT
66 AGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* *
1265948 TGTTATTCTTGACTCCCTCGTGAAAAGGAGTCAATCTTTCAATGTTACTCTTGACTTCCTCATGA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCATGA
* * * *
1266013 AGAGAAGTCAATCTTTATTATTCTCGACTCCCTCGTGAAGAGGAGTCAATCTTT
66 AGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* * * * *
1266067 CAATGTTATTCTTGGA-TTCCTCTTAAAGAGAAGTCAATCTTT---T-TTATTCTTGATTTCCTC
1 ---TGTTATTCTT-GACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTC
* * *
1266127 GTGAAGAGAAGTTAATCTTTGTTATTCTTGAC-TCTCTCGTGAAGAGGAGTCAATCTTT
62 ATGAAGAGAAGTCAATCTTTGTTATTCTTGACTTC-CTCGTGAAGAGAAGTCAATC-TT
* * * * *
1266185 CAATTTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT---TGTTATTCTTAACTTCCTCG
1 ---TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCA
* * * * *
1266246 TAAAG-GAAGTCAATCTTTGTTATTATTGACTCCCTCGTTAAGA-AGATTCAATCTTT
63 TGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGA-AGTCAATC-TT
* * * *
1266302 CAATGTTATTCTTGTCTTCCTCGTGAAGAGAAAT-ATATC-TT---TGTTATTCTTGACTTCCTC
1 ---TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCA-ATCTTTCAATGTTATTCTTGACTTCCTC
* * *
1266362 ATGAAGAAAAGTCAATCTTTTTTATTCTTGACTTCATCGTGAAGATG-AGTCAATCTTT
62 ATGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATC-TT
* * * *
1266420 CAATGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTT---T-TTATTATGGACTTCCTCA
1 ---TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCA
* *
1266481 TGAAGATG-AGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTT
63 TGAAGA-GAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
*
1266538 CAATGTTATTCTTGACTCCCT-GTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGATTTCCTCA
1 ---TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCA
* *
1266602 TGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTTAATCTT
63 TGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * * *
1266658 TGTTATTCTTGACACCGTAGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTTCTAATGA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCATGA
* * * *
1266723 AGAGAAGTCGATCTTTTTTATTCTTGACTTCCTCATGAAAAGAAGTCAATCTT
66 AGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * **
1266776 TGTTATTCTTGACTCCCTCATGAAGAAGAGTCAATCTTTCAATGTTATTTTTGACTTCCTTGTGA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCATGA
*
1266841 AGAGAAGTCGATCTTT-TGTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
66 AGAGAAGTCAATCTTTGT-TATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * *
1266894 TGTTATTCTTGACTCCCTCGTGAAGAGAAATCATTCTTTCAATGTTATTCTTGACTTCCTCGTGA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCATGA
* *
1266959 AGAGAAGTCGATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTT
66 AGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * *
1267012 TGTTATCCTTGACTCCCTCGTGAAGATGAGTCAATCTTTCAATGTTATTCTTGACTTTCTCATGA
1 TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCATGA
* * *
1267077 AGAGAAGTCAATCTTTGTTATTTTTGACTCCCTCGTGAAGAGGAGTCAATCTT
66 AGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
* * * * * *
1267130 TCATTGTCTTCCTTGACTTCCTCGTGAAAAGAAGTCAATC-TT---TGTTATTCTTGACTTTCTC
1 T--GT-TATT-CTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTC
* * * * * * *
1267191 ATGAAGAGGAGTTAATCTTTCAATTTTATTCTTTACTCCCTTGTGAAGAGGAGTCAATCTTT
62 ATGAAGAGAAGTCAATC-TT---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT
* ** * * * * *
1267253 CAATGTTATTCTTCACTTTCTCGTGAAGAGAAGCCAATCATTCAATATTGTCATTCTTGACTTTC
1 ---TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTC-A-A-TGTTATTCTTGACTTCC
* *
1267318 TCACGAAGAGAAGTCGATCTTT
60 TCATGAAGAGAAGTCAATCTTT
1267340 TGGTATTGTC
Statistics
Matches: 1218, Mismatches: 129, Indels: 83
0.85 0.09 0.06
Matches are distributed among these distances:
116 1 0.00
117 143 0.12
118 834 0.68
119 10 0.01
120 5 0.00
121 67 0.06
122 113 0.09
123 9 0.01
124 1 0.00
125 1 0.00
126 1 0.00
128 2 0.00
129 31 0.03
ACGTcount: A:0.25, C:0.18, G:0.16, T:0.40
Consensus pattern (118 bp):
TGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTCAATGTTATTCTTGACTTCCTCATGA
AGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTT
Found at i:1267326 original size:45 final size:45
Alignment explanation
Indices: 1267260--1267369 Score: 121
Period size: 45 Copynumber: 2.4 Consensus size: 45
1267250 TTTCAATGTT
* **
1267260 ATTCTTCACTTTCTCGTGAAGAGAAGCCAATCATTCAATATTGTC
1 ATTCTTGACTTTCTCACGAAGAGAAGCCAATCATTCAATATTGTC
* * * ***
1267305 ATTCTTGACTTTCTCACGAAGAGAAGTCGATCTTTTGGTATTGTC
1 ATTCTTGACTTTCTCACGAAGAGAAGCCAATCATTCAATATTGTC
* *
1267350 CTTTTTGACTTTCTCACGAA
1 ATTCTTGACTTTCTCACGAA
1267370 TAAGAGTCAA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (45 bp):
ATTCTTGACTTTCTCACGAAGAGAAGCCAATCATTCAATATTGTC
Found at i:1268207 original size:134 final size:134
Alignment explanation
Indices: 1267929--1268218 Score: 352
Period size: 134 Copynumber: 2.2 Consensus size: 134
1267919 CAAATAAAGT
**
1267929 TCAATTCAATCTTCTCTAAAGAACAGTGGAATGAATCAACGTCCGTAGATCTAATTTTCCCTCAA
1 TCAATTCAATCTTCTCTAAAGAACAGTGGAATGAATCAACGTCCCCAGATCTAATTTTCCCTCAA
* *
1267994 GAAGAAGCGGAACGTATCATTCTCTTTAAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC
66 GAAGAAGCGGAACGTATCATTCTCTTTAAACATTTGATATTCCCTGAGTAACAGAGGAACAAGTC
**
1268059 TTTC
131 TACC
* * * * * *
1268063 TCGATCCAATCTT-TGCTTAAGAACATTGGAATGAATCAATGTCCCCAGATCTGATTTTCCCTCA
1 TCAATTCAATCTTCT-CTAAAGAACAGTGGAATGAATCAACGTCCCCAGATCTAATTTTCCCTCA
* * * * * * **
1268127 AGAAGAAGCGGAACAG-ATCCTTCTCTTTCAACATTTGATCTTGCCTTAGTGATTGAGGAACAAG
65 AGAAGAAGCGGAAC-GTATCATTCTCTTTAAACATTTGATATTCCCTGAGTAACAGAGGAACAAG
1268191 TCTACC
129 TCTACC
*
1268197 TCAATTCAATCTTC-CTGAAGAA
1 TCAATTCAATCTTCTCTAAAGAA
1268219 ACAACGGAGT
Statistics
Matches: 130, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
133 8 0.06
134 121 0.93
135 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (134 bp):
TCAATTCAATCTTCTCTAAAGAACAGTGGAATGAATCAACGTCCCCAGATCTAATTTTCCCTCAA
GAAGAAGCGGAACGTATCATTCTCTTTAAACATTTGATATTCCCTGAGTAACAGAGGAACAAGTC
TACC
Found at i:1268461 original size:26 final size:28
Alignment explanation
Indices: 1268431--1268492 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
1268421 AACTATTAAA
1268431 TATTATTATAATT-TTATTTTTATTCTC
1 TATTATTATAATTATTATTTTTATTCTC
**
1268458 -ATTA-TATTTTTATTATTTTTATTCTC
1 TATTATTATAATTATTATTTTTATTCTC
*
1268484 TATTTTTAT
1 TATTATTAT
1268493 TTATATATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
25 5 0.17
26 18 0.62
27 3 0.10
28 3 0.10
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (28 bp):
TATTATTATAATTATTATTTTTATTCTC
Found at i:1268479 original size:17 final size:17
Alignment explanation
Indices: 1268433--1268473 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1268423 CTATTAAATA
* *
1268433 TTATTATAATTTTATTT
1 TTATTATCATTATATTT
*
1268450 TTATTCTCATTATATTT
1 TTATTATCATTATATTT
1268467 TTATTAT
1 TTATTAT
1268474 TTTTATTCTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATTATCATTATATTT
Found at i:1271323 original size:20 final size:20
Alignment explanation
Indices: 1271271--1271323 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1271261 CCTTCTGGGA
*
1271271 GTATCGATACTCCTGCCTTG
1 GTATCGATACTCTTGCCTTG
1271291 GTATCGATACTCTTGCCTTG
1 GTATCGATACTCTTGCCTTG
1271311 GTATCGATACTCT
1 GTATCGATACTCT
1271324 ATATGAGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (20 bp):
GTATCGATACTCTTGCCTTG
Found at i:1274029 original size:104 final size:104
Alignment explanation
Indices: 1273901--1274106 Score: 304
Period size: 104 Copynumber: 2.0 Consensus size: 104
1273891 GTGCTATAAT
* *
1273901 TCGTTGACTGATTTTAGTGATTAAATAAAGTCATGTTCACTTTTAAGATTTTGGGTTCGAGTAGC
1 TCGTTGAATAATTTTAGTGATTAAATAAAGTCATGTTCACTTTTAAGATTTTGGGTTCGAGTAGC
* * *
1273966 TACGTCTATAGTGTGTGTGTGCGTCGCTAATGGTTAAGA
66 TACGTCTACAGTGTGTGTGCGCGTCGCCAATGGTTAAGA
* * * *
1274005 TCGTTGAATAATTTTAGTGATTAAATAGAGTCGTGTTCTCTTTTAAGATTTTGGGTTCGAGTAGT
1 TCGTTGAATAATTTTAGTGATTAAATAAAGTCATGTTCACTTTTAAGATTTTGGGTTCGAGTAGC
* * *
1274070 TACGTCTGCATTGTGTGTGCGTGTCGCCAATGGTTAA
66 TACGTCTACAGTGTGTGTGCGCGTCGCCAATGGTTAA
1274107 AAAATATTAC
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
104 90 1.00
ACGTcount: A:0.23, C:0.12, G:0.25, T:0.40
Consensus pattern (104 bp):
TCGTTGAATAATTTTAGTGATTAAATAAAGTCATGTTCACTTTTAAGATTTTGGGTTCGAGTAGC
TACGTCTACAGTGTGTGTGCGCGTCGCCAATGGTTAAGA
Found at i:1284405 original size:22 final size:23
Alignment explanation
Indices: 1284379--1284433 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
1284369 ATAGGGCAGA
*
1284379 GGGAATCGATACCCAC-TTGAAG
1 GGGAACCGATACCCACTTTGAAG
* *
1284401 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATACCCACTTTGAAG
1284424 GGGAACCGAT
1 GGGAACCGAT
1284434 TCCCCCTAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
22 13 0.45
23 16 0.55
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.18
Consensus pattern (23 bp):
GGGAACCGATACCCACTTTGAAG
Found at i:1284425 original size:23 final size:23
Alignment explanation
Indices: 1284395--1284440 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1284385 CGATACCCAC
1284395 TTGAAGGGGAACCGATTCCCCCT
1 TTGAAGGGGAACCGATTCCCCCT
1284418 TTGAAGGGGAACCGATTCCCCCT
1 TTGAAGGGGAACCGATTCCCCCT
1284441 AGGGAAATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCCT
Found at i:1288982 original size:20 final size:22
Alignment explanation
Indices: 1288957--1289014 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
1288947 TTCCCCTTGA
1288957 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
1288977 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
1289000 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1289015 CTACCTATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:1289125 original size:64 final size:63
Alignment explanation
Indices: 1289002--1289163 Score: 175
Period size: 64 Copynumber: 2.5 Consensus size: 63
1288992 TCTTTAACAT
* * *
1289002 GTGCATCGATGCACTACCTATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAGGG
1 GTGCATCGATGCACTACCTATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGA
* * * *
1289065 GATGCATCGATGCACT-CCTTATGCATCGATGCACCAATTGCATTCGATG-TTTCTTCTTTAAAG
1 G-TGCATCGATGCACTACC-TATGCATCGATACACAAATTACATTCGATGTTTTCAT-TTTAAAG
1289128 A
63 A
* **
1289129 GTGCATTGATGCACATTAAATATGCATCGATACAC
1 GTGCATCGATGCAC--TACCTATGCATCGATACAC
1289164 CTTGCCCATA
Statistics
Matches: 82, Mismatches: 11, Indels: 10
0.80 0.11 0.10
Matches are distributed among these distances:
63 20 0.24
64 47 0.57
65 15 0.18
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (63 bp):
GTGCATCGATGCACTACCTATGCATCGATACACAAATTACATTCGATGTTTTCATTTTAAAGA
Found at i:1293174 original size:20 final size:20
Alignment explanation
Indices: 1293145--1293242 Score: 151
Period size: 20 Copynumber: 4.7 Consensus size: 20
1293135 TTCCCCTTGA
1293145 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
1293165 AGTACATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1293185 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1293205 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1293228 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1293243 CTACCAATGC
Statistics
Matches: 72, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 55 0.76
22 1 0.01
23 3 0.04
24 13 0.18
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1295580 original size:64 final size:63
Alignment explanation
Indices: 1295498--1295703 Score: 211
Period size: 65 Copynumber: 3.2 Consensus size: 63
1295488 CTAAGAGTGT
* * *
1295498 ATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGTGC
1 ATCGATGCATCAAATGCATTTGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TGGTGC
** * *
1295562 ATCGATGCATCAAATGCATTTGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTAAGTG
1 ATCGATGCATCAAATGCATTTGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-GGTG
1295626 C
63 C
* ** *
1295627 ATCGATGCATAAAATGCATTTGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGATTGGT
1 ATCGATGCATCAAATGCATTTGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--TGGT
1295690 GC
62 GC
*
1295692 ATCGGTGCATCA
1 ATCGATGCATCA
1295704 CTCTGAAAAA
Statistics
Matches: 117, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 42 0.36
65 66 0.56
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
ATCGATGCATCAAATGCATTTGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTGGTGC
Found at i:1297842 original size:13 final size:13
Alignment explanation
Indices: 1297814--1297852 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1297804 TGGGCAATGT
*
1297814 TTTGAAAA-ACTA
1 TTTGAAAATAATA
1297826 TTTGAAAATAATA
1 TTTGAAAATAATA
*
1297839 TTTGTAAATAATA
1 TTTGAAAATAATA
1297852 T
1 T
1297853 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:1298372 original size:23 final size:22
Alignment explanation
Indices: 1298343--1298424 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
1298333 GCATGACCCC
1298343 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* *
1298365 CGTGCATCGATGCATCA-AC-ATG
1 -GTGCATCGATGCA-CATTCAAGG
* *
1298387 ATGAATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
1298410 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
1298425 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
20 2 0.04
21 12 0.26
22 2 0.04
23 16 0.35
24 14 0.30
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.22
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:1298413 original size:24 final size:24
Alignment explanation
Indices: 1298344--1298424 Score: 84
Period size: 24 Copynumber: 3.5 Consensus size: 24
1298334 CATGACCCCG
1298344 TGCATCGATGCACATTC-AAGGCG-
1 TGCATCGATGCACATTCAAAGG-GA
*
1298367 TGCATCGATG--CA-TCAACA-TGA
1 TGCATCGATGCACATTCAA-AGGGA
*
1298388 TGAATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTCAAAGGGA
1298412 TGCATCGATGCAC
1 TGCATCGATGCAC
1298425 TGTTAAGTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
20 3 0.06
21 12 0.26
22 1 0.02
23 13 0.28
24 18 0.38
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.22
Consensus pattern (24 bp):
TGCATCGATGCACATTCAAAGGGA
Found at i:1302967 original size:10 final size:10
Alignment explanation
Indices: 1302952--1302982 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1302942 GATTTAAGAC
1302952 CATTGAAAAT
1 CATTGAAAAT
1302962 CATTGAAAAT
1 CATTGAAAAT
*
1302972 CGTTGAAAAT
1 CATTGAAAAT
1302982 C
1 C
1302983 TATTCGTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (10 bp):
CATTGAAAAT
Found at i:1309284 original size:63 final size:62
Alignment explanation
Indices: 1309211--1309332 Score: 147
Period size: 63 Copynumber: 2.0 Consensus size: 62
1309201 AGATATTTTT
* * *
1309211 TATCTTTTTAACTTTGAATATTAAAGAT-AATTATATACTTTTGTATATTTCAAATTAAAATAA
1 TATCTATTTAACTTTGAATAGTAAA-ATGAATTATAT-CTTTTGAATATTTCAAATTAAAATAA
* * * * *
1309274 TATCTATTTAAGTTTGAATGGTAAAATGAGTTTTATCTTTTGAATATTTTAAATTAAAA
1 TATCTATTTAACTTTGAATAGTAAAATGAATTATATCTTTTGAATATTTCAAATTAAAA
1309333 GATATTGTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
62 23 0.46
63 27 0.54
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (62 bp):
TATCTATTTAACTTTGAATAGTAAAATGAATTATATCTTTTGAATATTTCAAATTAAAATAA
Found at i:1315408 original size:19 final size:19
Alignment explanation
Indices: 1315384--1315424 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
1315374 TTATTTTTTT
1315384 TATTTTTA-ATTAAAAATAA
1 TATTTTTATATTAAAAA-AA
1315403 TATTTTTATTATTAAAAAAA
1 TATTTTTA-TATTAAAAAAA
1315423 TA
1 TA
1315425 AAAAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 4 0.20
21 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATTTTTATATTAAAAAAA
Found at i:1315408 original size:25 final size:23
Alignment explanation
Indices: 1315380--1315425 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
1315370 TTTTTTATTT
*
1315380 TTTTTATTTTTAATTAAAAATAATA
1 TTTTTATTATTAA--AAAAATAATA
1315405 TTTTTATTATTAAAAAAATAA
1 TTTTTATTATTAAAAAAATAA
1315426 AAAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
25 12 0.60
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTTATTATTAAAAAAATAATA
Found at i:1321428 original size:20 final size:20
Alignment explanation
Indices: 1321403--1321452 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1321393 CATAACCTTG
*
1321403 GTATCGATACTGGTC-TTACA
1 GTATCGATACT-CTCTTTACA
*
1321423 GTATCGATACTCTCTTTTCA
1 GTATCGATACTCTCTTTACA
1321443 GTATCGATAC
1 GTATCGATAC
1321453 CCTACCGAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (20 bp):
GTATCGATACTCTCTTTACA
Found at i:1323802 original size:77 final size:75
Alignment explanation
Indices: 1323715--1323878 Score: 198
Period size: 69 Copynumber: 2.2 Consensus size: 75
1323705 AGGATATAGT
* *
1323715 TGTACCTAATTAGCATGGTATATTGGTATGGTTCCATCAACTTGTAGTG-TAGGATATGGATTAT
1 TGTACCTAATTAGCATGG-AT-TGGGTATGGTTCCATCAACTTGTAGTGTTACGATATGGATTAT
1323779 ACAGAGATATAAC
64 AC-GAGATATAAC
*
1323792 TGTACTTAATT---A---ATTGGGTATGGTTCCATCAACTTGTAGTGTTACGATATGGATTATAC
1 TGTACCTAATTAGCATGGATTGGGTATGGTTCCATCAACTTGTAGTGTTACGATATGGATTATAC
*
1323851 GGGATATAAC
66 GAGATATAAC
* *
1323861 TATACCTAATGAGCATGG
1 TGTACCTAATTAGCATGG
1323879 CATGGTACGA
Statistics
Matches: 73, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
69 43 0.59
70 18 0.25
72 1 0.01
74 1 0.01
77 10 0.14
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.35
Consensus pattern (75 bp):
TGTACCTAATTAGCATGGATTGGGTATGGTTCCATCAACTTGTAGTGTTACGATATGGATTATAC
GAGATATAAC
Found at i:1323817 original size:69 final size:69
Alignment explanation
Indices: 1323739--1323870 Score: 212
Period size: 69 Copynumber: 1.9 Consensus size: 69
1323729 ATGGTATATT
* * *
1323739 GGTATGGTTCCATCAACTTGTAGTG-TAGGATATGGATTATACAGAGATATAACTGTACTTAATT
1 GGTATGGTTCCATCAACTTGTAGTGTTACGATATGGATTATAC-GAGATATAACTATACCTAATT
1323803 AATTG
65 AATTG
*
1323808 GGTATGGTTCCATCAACTTGTAGTGTTACGATATGGATTATACGGGATATAACTATACCTAAT
1 GGTATGGTTCCATCAACTTGTAGTGTTACGATATGGATTATACGAGATATAACTATACCTAAT
1323871 GAGCATGGCA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
69 42 0.72
70 16 0.28
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (69 bp):
GGTATGGTTCCATCAACTTGTAGTGTTACGATATGGATTATACGAGATATAACTATACCTAATTA
ATTG
Found at i:1324580 original size:17 final size:17
Alignment explanation
Indices: 1324558--1324625 Score: 57
Period size: 17 Copynumber: 3.9 Consensus size: 17
1324548 CTTCTTTTTA
1324558 AATATAATATTTAAAAT
1 AATATAATATTTAAAAT
*
1324575 AATAT-ATGTTTTAAATTAT
1 AATATAAT-ATTTAAA--AT
** * *
1324594 TTTTTATTATTTAAAAT
1 AATATAATATTTAAAAT
1324611 AATATAATATTTAAA
1 AATATAATATTTAAA
1324626 GAGTATCAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
16 2 0.05
17 24 0.65
19 10 0.27
20 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (17 bp):
AATATAATATTTAAAAT
Found at i:1325237 original size:20 final size:20
Alignment explanation
Indices: 1325214--1325252 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1325204 CGATTAGATA
*
1325214 TTGACAAAATCAGTTGAAAT
1 TTGACAAAACCAGTTGAAAT
* *
1325234 TTGAGAAAACCGGTTGAAA
1 TTGACAAAACCAGTTGAAA
1325253 GAAAATCGGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.26
Consensus pattern (20 bp):
TTGACAAAACCAGTTGAAAT
Found at i:1325299 original size:11 final size:11
Alignment explanation
Indices: 1325283--1325309 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1325273 CGACATTGTT
1325283 GAAATTTAAAA
1 GAAATTTAAAA
1325294 GAAATTTAAAA
1 GAAATTTAAAA
1325305 GAAAT
1 GAAAT
1325310 GAAAAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (11 bp):
GAAATTTAAAA
Found at i:1326368 original size:230 final size:229
Alignment explanation
Indices: 1325962--1326423 Score: 714
Period size: 230 Copynumber: 2.0 Consensus size: 229
1325952 TGTTGTCGAG
* *
1325962 ACCCTAGTTTTTTAGTATTACAATAATCAGAAATAGGGGTTAGGTTTATGGGGTTTGGGGTTTTC
1 ACCCTAGTTTTTTAGTATTACAATAATCAAAAATAGGGATTAGGTTTATGGGGTTTGGGGTTTTC
* *
1326027 AAAGTAAAGAAGCATTTGAGACCGATTACAATTAGAAAGTGATATTCTAGTTAGAAAATAAATAT
66 AAAGTAAAGAAGCATTTGAGACCGATTACAATTAGAAAGTGATATTCTAGGTAAAAAATAAATAT
* * * *
1326092 CGATACTTTTTTATAATATTATAGGTAGAAAATGATATTGTAGGTTGTGTAAAGGTAAC-AATAC
131 CGACACTTTTATATAATATTATAGGTAGAAAATGATATTATAGGTTGTATAAAGGT-ACTAATAC
*
1326156 TTGTACTAGAGAGTATT-CTCATTCCTTTGAAGGAA
195 TTGTACTAGAGAGTATTCCT-ATTCCTTTAAAGGAA
*
1326191 ACCCTAGTTTTTTTAGTATTACAATATTCAAAAATAGGGATTAGGTTTAT-GGGTTTGGGGTTTT
1 ACCCTAG-TTTTTTAGTATTACAATAATCAAAAATAGGGATTAGGTTTATGGGGTTTGGGGTTTT
* * * * *
1326255 CGAAGTCAAGAAGGATTTGAGACTGATTACAATTAGAAAGTGATATTTTAGGTACAAAAATAAAT
65 CAAAGTAAAGAAGCATTTGAGACCGATTACAATTAGAAAGTGATATTCTAGGTA-AAAAATAAAT
*
1326320 ATCGACACTTTTATATAATATTATAGGTAGAAAATGATATTATAGGTTGTATAAAGGTACTGATA
129 ATCGACACTTTTATATAATATTATAGGTAGAAAATGATATTATAGGTTGTATAAAGGTACTAATA
*
1326385 CTTGTAGTAGAGAGTATTCCTATTCCTTTAAAGGAA
194 CTTGTACTAGAGAGTATTCCTATTCCTTTAAAGGAA
1326421 ACC
1 ACC
1326424 ATTTTATTAT
Statistics
Matches: 212, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
229 71 0.33
230 139 0.66
231 2 0.01
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (229 bp):
ACCCTAGTTTTTTAGTATTACAATAATCAAAAATAGGGATTAGGTTTATGGGGTTTGGGGTTTTC
AAAGTAAAGAAGCATTTGAGACCGATTACAATTAGAAAGTGATATTCTAGGTAAAAAATAAATAT
CGACACTTTTATATAATATTATAGGTAGAAAATGATATTATAGGTTGTATAAAGGTACTAATACT
TGTACTAGAGAGTATTCCTATTCCTTTAAAGGAA
Found at i:1340691 original size:32 final size:32
Alignment explanation
Indices: 1340632--1340693 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
1340622 TCTTACCTTT
1340632 ACTAACTAATTTATTTTATTTTATTTGTGTAC
1 ACTAACTAATTTATTTTATTTTATTTGTGTAC
* * * *
1340664 ACTAACTTATTTCTTTTCTTTTGTTTGTGT
1 ACTAACTAATTTATTTTATTTTATTTGTGT
1340694 CATTTTTCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (32 bp):
ACTAACTAATTTATTTTATTTTATTTGTGTAC
Found at i:1341687 original size:21 final size:21
Alignment explanation
Indices: 1341663--1341708 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
1341653 AATATGTTGA
1341663 TAATACCGATAACAAATTAAG
1 TAATACCGATAACAAATTAAG
*
1341684 TAATACTGATAACAAATTAAG
1 TAATACCGATAACAAATTAAG
1341705 TAAT
1 TAAT
1341709 TAACCTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.28
Consensus pattern (21 bp):
TAATACCGATAACAAATTAAG
Found at i:1341889 original size:247 final size:247
Alignment explanation
Indices: 1341437--1341934 Score: 786
Period size: 247 Copynumber: 2.0 Consensus size: 247
1341427 AATATGTTGA
* *
1341437 TAATATTGATAAAAATTTAAGTAACTAACCTATTTTGTTATCGTTGGATTTCTAAGGCCCCATCA
1 TAATACTGATAAAAATTTAAGTAACTAACCTATTTTGTTATCGTTAGATTTCTAAGGCCCCATCA
* * * *
1341502 GCTTTAAGAAGGCTTTACCTATTACGTTACATAAGCGCTACCTAATATGTTATTATGGTTGGTAA
66 GCTTTAAAAAGGCTCTACCTATTACGTTACATAAGCACTACCTAATATGTTATTATGGTTGATAA
* * *
1341567 CAAATCAAGTAATTAATCGGTTATGTTATCGTCAGATTTCTAAGGCTCCATCAGCTTAAACTTTG
131 CAAATCAAGTAATTAACCGATTATGTTATCGTCAGATTTCTAAGGCTCCATCAACTTAAACTTTG
1341632 GTAACATTTTAGGCGTTACCTAATATGTTGATAATACCGATAACAAATTAAG
196 GTAACATTTTAGGCGTTACCTAATATGTTGATAATACCGATAACAAATTAAG
* * * *
1341684 TAATACTGATAACAAA-TTAAGTAATTAACCTATTTTGTTATC-TTCATATTTTTATGGCCCCAT
1 TAATACTGATAA-AAATTTAAGTAACTAACCTATTTTGTTATCGTT-AGATTTCTAAGGCCCCAT
* * *
1341747 CAGCTTTAAAAAGG-TGCTACCTATTACGTTATATAAGCACTACCTAATATGTTGTTTTGGTTGA
64 CAGCTTTAAAAAGGCT-CTACCTATTACGTTACATAAGCACTACCTAATATGTTATTATGGTTGA
*
1341811 TAACAAATCAAGTAATTAACCGATTATGTTATCGTCGGATTTCTAAGGCTCCATCAACTTAAACT
128 TAACAAATCAAGTAATTAACCGATTATGTTATCGTCAGATTTCTAAGGCTCCATCAACTTAAACT
*
1341876 TTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACTGATAACAAATTAAG
193 TTGGTAACATTTTAGGCGTTACCTAATATGTTGATAATACCGATAACAAATTAAG
1341931 TAAT
1 TAAT
1341935 TAACCTATTT
Statistics
Matches: 230, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
246 3 0.01
247 224 0.97
248 3 0.01
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (247 bp):
TAATACTGATAAAAATTTAAGTAACTAACCTATTTTGTTATCGTTAGATTTCTAAGGCCCCATCA
GCTTTAAAAAGGCTCTACCTATTACGTTACATAAGCACTACCTAATATGTTATTATGGTTGATAA
CAAATCAAGTAATTAACCGATTATGTTATCGTCAGATTTCTAAGGCTCCATCAACTTAAACTTTG
GTAACATTTTAGGCGTTACCTAATATGTTGATAATACCGATAACAAATTAAG
Found at i:1342939 original size:26 final size:26
Alignment explanation
Indices: 1342904--1342962 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 26
1342894 TCAGTATTGC
1342904 GGTGGAAGTACACAATCA-TGAATTGGG
1 GGTGG-AGTACACAAT-ATTGAATTGGG
*
1342931 GGTGGAGTACACAATATTGAATTGGT
1 GGTGGAGTACACAATATTGAATTGGG
1342957 GGTGGA
1 GGTGGA
1342963 ATTATCACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 1 0.03
26 24 0.80
27 5 0.17
ACGTcount: A:0.31, C:0.08, G:0.36, T:0.25
Consensus pattern (26 bp):
GGTGGAGTACACAATATTGAATTGGG
Found at i:1343145 original size:30 final size:30
Alignment explanation
Indices: 1343109--1343171 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
1343099 AAAATAATGA
*
1343109 GTATGCACTAGAGTCACCTTATTGTATAAG
1 GTATGCACTAGAATCACCTTATTGTATAAG
1343139 GTATGCACTAGAATCACCTTATTGTATAAG
1 GTATGCACTAGAATCACCTTATTGTATAAG
1343169 GTA
1 GTA
1343172 GCTTCAAATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (30 bp):
GTATGCACTAGAATCACCTTATTGTATAAG
Found at i:1344576 original size:3 final size:3
Alignment explanation
Indices: 1344568--1344647 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
1344558 TCCCGACATT
1344568 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1344616 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1344648 TACATACCCA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1351784 original size:2 final size:2
Alignment explanation
Indices: 1351777--1351830 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
1351767 TAAAGTCGAT
1351777 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1351819 TA TA TA TA TA TA
1 TA TA TA TA TA TA
1351831 ATAAAATTGA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1352971 original size:17 final size:18
Alignment explanation
Indices: 1352932--1352980 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
1352922 TGTTTCTGAG
1352932 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTGAA
*
1352950 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
*
1352967 GGAATTGAAATCTG
1 GGAATTGGAATCTG
1352981 AAACTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.33, C:0.08, G:0.31, T:0.29
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Done.