Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold164
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: 2248410
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 25 characters in sequence are not A, C, G, or T
File 9 of 15
Found at i:1253911 original size:51 final size:53
Alignment explanation
Indices: 1253807--1253929 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 53
1253797 GATCAACGGG
* * *
1253807 GTTGGAGTATCCCCGATTGTGAAGAAATGGGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATGAGTG-TTTTTGAAAATAAAATCGGA
*
1253861 GTTGGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATGAGTGTTTTTGAAAATAAAATCGGA
*
1253912 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
1253930 GTGGAGAATT
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
51 35 0.56
52 2 0.03
53 7 0.11
54 19 0.30
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATGAGTGTTTTTGAAAATAAAATCGGA
Found at i:1256314 original size:13 final size:13
Alignment explanation
Indices: 1256296--1256321 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1256286 ACAAAGATCC
1256296 ATGTATCGATACA
1 ATGTATCGATACA
1256309 ATGTATCGATACA
1 ATGTATCGATACA
1256322 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1256317 original size:33 final size:33
Alignment explanation
Indices: 1256275--1256341 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1256265 AAAATTTCCA
***
1256275 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1256308 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1256341 A
1 A
1256342 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1256385 original size:19 final size:18
Alignment explanation
Indices: 1256361--1256428 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1256351 CAGTAGCTAA
1256361 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1256380 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1256395 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1256412 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1256429 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1256401 original size:13 final size:13
Alignment explanation
Indices: 1256383--1256407 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1256373 ACAATACTTA
1256383 TGTATCGATACAT
1 TGTATCGATACAT
1256396 TGTATCGATACA
1 TGTATCGATACA
1256408 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1256405 original size:32 final size:32
Alignment explanation
Indices: 1256364--1256426 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1256354 TAGCTAATTA
*
1256364 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1256396 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1256427 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1257320 original size:55 final size:54
Alignment explanation
Indices: 1257225--1257979 Score: 952
Period size: 55 Copynumber: 13.4 Consensus size: 54
1257215 ATAAAGTGTA
* * * * * *
1257225 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
1257280 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* **
1257335 TCCTGCTCTTTAAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GTG
* *
1257396 TCCTGCTCTTTGAGGATTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
*
1257451 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* * * **
1257506 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GTG
* *
1257567 TCCTACTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
1257622 TCCTGCTCTTTGAGGACTGGAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* **
1257676 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTT-AAAAG-----GTG
*
1257737 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
* *
1257792 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGTTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
*
1257847 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
*
1257902 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
*
1257957 TCCTGCTCTTTGGGGACTGAAAA
1 TCCTGCTCTTTGAGGACTGAAAA
1257980 GCGGAAGGAG
Statistics
Matches: 623, Mismatches: 50, Indels: 55
0.86 0.07 0.08
Matches are distributed among these distances:
54 62 0.10
55 395 0.63
56 18 0.03
60 16 0.03
61 126 0.20
62 6 0.01
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
Found at i:1257445 original size:171 final size:171
Alignment explanation
Indices: 1257224--1257979 Score: 1180
Period size: 171 Copynumber: 4.5 Consensus size: 171
1257214 AATAAAGTGT
* * * *
1257224 ATCCTTCTCATTGAGGAGT-AAAAAGTGCCACCAA-CTCGTGTGGGCTTTAAAAGGCGTCCTGCT
1 ATCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACCT-GTGTGGGCTTTAAAAGGTGTCCTGCT
* *
1257287 CTTTGAGGACT-GAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTAAGG
64 CTTTGAGGACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGG
*
1257350 ACTGGAAA-ATGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGC
127 ACT-GAAAGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
*
1257395 ATCCTGCTCTTTGAGGATTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
*
1257460 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTG
66 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
* *
1257525 AAAGGTGCCACCAACCTGTGTGGGCTTTGAAAAGAAAAAGC
131 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
*
1257566 ATCCTACTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1257631 TTGAGGACTGG-AAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
66 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
*
1257695 AAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
131 AAAGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
1257736 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
*
1257801 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGTTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
66 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-
*
1257866 GAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GT
130 GAAAGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
* * * *
1257901 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
*
1257966 TTGGGGACT-GAAAA
66 TTGAGGACTGGAAAA
1257980 GCGGAAGGAG
Statistics
Matches: 555, Mismatches: 23, Indels: 21
0.93 0.04 0.04
Matches are distributed among these distances:
164 5 0.01
165 70 0.13
170 175 0.32
171 288 0.52
172 17 0.03
ACGTcount: A:0.25, C:0.20, G:0.27, T:0.28
Consensus pattern (171 bp):
ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
AAAGATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
Found at i:1257869 original size:27 final size:27
Alignment explanation
Indices: 1257839--1257924 Score: 68
Period size: 27 Copynumber: 3.1 Consensus size: 27
1257829 TGTGGGTTTT
1257839 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
* ** * * * *
1257866 GAAA-ATG-CCACCAACTTGTGTGGGCTTT
1 GAAAGGTGTCCTGC-TCTT-TGAGGAC-TG
1257894 GAAAGGTGTCCTGCTCTTTGAGGACTG
1 GAAAGGTGTCCTGCTCTTTGAGGACTG
1257921 GAAA
1 GAAA
1257925 ATGCCACCAA
Statistics
Matches: 40, Mismatches: 14, Indels: 10
0.62 0.22 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.12
27 14 0.35
28 10 0.25
29 5 0.12
30 3 0.08
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.28
Consensus pattern (27 bp):
GAAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:1258976 original size:16 final size:15
Alignment explanation
Indices: 1258972--1259005 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
1258962 CTTTGTTTTG
1258972 TTTTTTGTTTTGTTTT
1 TTTTTTGTTTTG-TTT
1258988 TTTTTTGTTTT-TTT
1 TTTTTTGTTTTGTTT
1259002 TTTT
1 TTTT
1259006 GAAAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 7 0.39
16 11 0.61
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (15 bp):
TTTTTTGTTTTGTTT
Found at i:1258980 original size:12 final size:12
Alignment explanation
Indices: 1258963--1259006 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
1258953 TCTCTTTTTC
1258963 TTTGTTTTGTTT
1 TTTGTTTTGTTT
1258975 TTTGTTTTGTTT
1 TTTGTTTTGTTT
1258987 TTT-TTTTGTTT
1 TTTGTTTTGTTT
*
1258998 TTTTTTTTG
1 TTTGTTTTG
1259007 AAAAAGAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.35
12 20 0.65
ACGTcount: A:0.00, C:0.00, G:0.14, T:0.86
Consensus pattern (12 bp):
TTTGTTTTGTTT
Found at i:1258993 original size:11 final size:11
Alignment explanation
Indices: 1258967--1259004 Score: 67
Period size: 11 Copynumber: 3.4 Consensus size: 11
1258957 TTTTTCTTTG
1258967 TTTTGTTTTTT
1 TTTTGTTTTTT
1258978 GTTTTGTTTTTT
1 -TTTTGTTTTTT
1258990 TTTTGTTTTTT
1 TTTTGTTTTTT
1259001 TTTT
1 TTTT
1259005 TGAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:1271466 original size:79 final size:79
Alignment explanation
Indices: 1271376--1271561 Score: 266
Period size: 79 Copynumber: 2.4 Consensus size: 79
1271366 TGTTCCCTTG
* * *
1271376 AAAATAACGGGGCTGGAGTATCCCCGGTTATGAGAAATCGATGA-TTAGAAAAAAAAATCGGGAT
1 AAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAGAAAAAAAAATCGGGAT
1271440 TGGAGTATCCCCTCA
65 TGGAGTATCCCCTCA
* * * * * *
1271455 AAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGAAATAAAGTCGGGGTT
1 AAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGAAAAAAAAATCGGGATT
1271520 GGAGTATCCCCTCA
66 GGAGTATCCCCTCA
*
1271534 GAAATAACGGGGTTGGAGTATCCCCGAT
1 AAAATAACGGGGTTGGAGTATCCCCGAT
1271562 GATCAACGGG
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 1 0.01
79 94 0.99
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (79 bp):
AAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGAAAAAAAAATCGGGATT
GGAGTATCCCCTCA
Found at i:1271470 original size:28 final size:29
Alignment explanation
Indices: 1271425--1271479 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
1271415 GATGATTAGA
1271425 AAAAAAAATCGGGATTGGAGTATCCCCTC
1 AAAAAAAATCGGGATTGGAGTATCCCCTC
* *
1271454 AAAAATAA-CGGGGTTGGAGTATCCCC
1 AAAAAAAATCGGGATTGGAGTATCCCC
1271480 AATTATGAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (29 bp):
AAAAAAAATCGGGATTGGAGTATCCCCTC
Found at i:1271577 original size:27 final size:26
Alignment explanation
Indices: 1271513--1271588 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 26
1271503 GAAATAAAGT
1271513 CGGGGTTGGAGTATCCCCTCAGA-AATAA
1 CGGGGTTGGAGTAT-CCC-C-GATAATAA
*
1271541 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
1271568 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1271589 TGTGAAGAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
25 2 0.04
26 3 0.07
27 26 0.58
28 14 0.31
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:1271680 original size:51 final size:53
Alignment explanation
Indices: 1271572--1271694 Score: 153
Period size: 51 Copynumber: 2.3 Consensus size: 53
1271562 GATCAACGGG
* * *
1271572 GTTGGAGTATCCCCGATTGTGAAGAAATGGGTGTTTTTTGGAAATAAAATCGAA
1 GTTGGAGTATCCCCGATTATGAAGAAATGAGTG-TTTTTGAAAATAAAATCGAA
* *
1271626 GTTGGAGTATCCCCGATTAT--AGAAAATTAGTG-TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATGAGTGTTTTTGAAAATAAAATCGAA
*
1271677 GTTGGAATATCCCCGATT
1 GTTGGAGTATCCCCGATT
1271695 GTGGAGAATT
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
51 34 0.55
52 2 0.03
53 7 0.11
54 19 0.31
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATGAAGAAATGAGTGTTTTTGAAAATAAAATCGAA
Found at i:1274079 original size:13 final size:13
Alignment explanation
Indices: 1274061--1274086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1274051 ACAAAGATCC
1274061 ATGTATCGATACA
1 ATGTATCGATACA
1274074 ATGTATCGATACA
1 ATGTATCGATACA
1274087 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1274082 original size:33 final size:33
Alignment explanation
Indices: 1274040--1274106 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1274030 AAAATTTCCA
***
1274040 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1274073 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1274106 A
1 A
1274107 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1274166 original size:13 final size:13
Alignment explanation
Indices: 1274148--1274172 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1274138 ACAATATTTA
1274148 TGTATCGATACAT
1 TGTATCGATACAT
1274161 TGTATCGATACA
1 TGTATCGATACA
1274173 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1274170 original size:32 final size:32
Alignment explanation
Indices: 1274129--1274191 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1274119 TAGCTAATTA
* * *
1274129 TGTATCGATACAATATTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATAGATACAT
1274161 TGTATCGATACAAAACTTATGTATAGATACA
1 TGTATCGATACAAAACTTATGTATAGATACA
1274192 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATAGATACAT
Found at i:1281902 original size:79 final size:77
Alignment explanation
Indices: 1281805--1282095 Score: 293
Period size: 79 Copynumber: 3.7 Consensus size: 77
1281795 GGATGTGGAA
*
1281805 TATCCCCGATTATGGAAAATCGGTGTTCTGAAAATAAAATCGAGGTTGGAGTATCCCCTCAGAAA
1 TATCCCCGATTAT-GAAAATCGGTGTT-TGAAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAA
*
1281870 TAACAGGGTTAGAG
64 TAACGGGGTTAGAG
* * *
1281884 TATCCCTGATTATAGAAAATTGGTGTTGTGAAAATAAAATCGGGGTTAGAGTATCCCCTC-GAAA
1 TATCCCCGATTAT-GAAAATCGGTGTT-TGAAAATAAAATCGGGGTTGGAGTATCCCCTCAG-AA
*
1281948 ATAACGGGGTTGGAG
63 ATAACGGGGTTAGAG
* ** ** *
1281963 TATCCCCGATTGTGAAAAATCAATGCTTT-AGAAATAAGGTCGGGGTTGGAGTAT-CCC-GATGA
1 TATCCCCGATTATG-AAAATCGGTG-TTTGA-AAATAAAATCGGGGTTGGAGTATCCCCTCA-GA
1282025 TAATAACGGGGTTAGAG
62 -AATAACGGGGTTAGAG
* * * * *
1282042 TATCCTCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTAT
1 TATCCCCGATTATGA-AAATCGGTG-TTTGAAAATAAAATCGGGGTTGGAGTAT
1282096 TCCCGATTGT
Statistics
Matches: 176, Mismatches: 27, Indels: 18
0.80 0.12 0.08
Matches are distributed among these distances:
78 8 0.05
79 166 0.94
80 2 0.01
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.28
Consensus pattern (77 bp):
TATCCCCGATTATGAAAATCGGTGTTTGAAAATAAAATCGGGGTTGGAGTATCCCCTCAGAAATA
ACGGGGTTAGAG
Found at i:1282146 original size:52 final size:51
Alignment explanation
Indices: 1282031--1282151 Score: 163
Period size: 52 Copynumber: 2.4 Consensus size: 51
1282021 ATGATAATAA
* * * *
1282031 CGGGGTTAGAGTA-TCCTCGATTGTGAGAAATTGGTGTTTTGGAAATAAAAT
1 CGGGGTTAGAGTATTCC-CGATTGTGAAAAATCGGTATTTTAGAAATAAAAT
* *
1282082 CGGAGTTGGAGTATTCCCGATTGTGAAAAAATCGGTATTTTAGAAATAAAAT
1 CGGGGTTAGAGTATTCCCGATTGTG-AAAAATCGGTATTTTAGAAATAAAAT
1282134 CGGGGTTAGAGTATTCCC
1 CGGGGTTAGAGTATTCCC
1282152 TCGAAAATAA
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
51 19 0.32
52 41 0.68
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (51 bp):
CGGGGTTAGAGTATTCCCGATTGTGAAAAATCGGTATTTTAGAAATAAAAT
Found at i:1282218 original size:108 final size:108
Alignment explanation
Indices: 1282097--1282366 Score: 312
Period size: 108 Copynumber: 2.5 Consensus size: 108
1282087 TTGGAGTATT
* *
1282097 CCCGATTGTGAAAAAATCGGTATTTTAGAAATAAAATCGGGGTTAGAGTATTCCCTCGAAAATAA
1 CCCGATTATGAAAAAATCGGTATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAA
* *
1282162 C-GGGATTGGAGTATCCCCGATGACACAACAGGGTCAGAGTACC
66 CAAGG-TTGGAGTATCCCCGATGAAACAACAGGGTCAGAGTACC
* ** * *
1282205 CCCGATTTTGAAAAAATCAATATTTTAGACAT-AAATCCGGGGTTAGAGTATCCCCTCGGAAATA
1 CCCGATTATGAAAAAATCGGTATTTTAGAAATAAAAT-CGGGGTTAGAGTATCCCCTCGAAAATA
* ** ** *
1282269 ACAAGGTTGGAGTATCCCCGATGAAATAATGGGGTTGGAGTATC
65 ACAAGGTTGGAGTATCCCCGATGAAACAACAGGGTCAGAGTACC
* * * * * *
1282313 CCCAATTATG-AAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 CCCGATTATGAAAAAATCGGTATTTTAGAAATAAAATCGGGGTTAGAGTATCCCC
1282367 GATTAAGAAA
Statistics
Matches: 135, Mismatches: 24, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
107 35 0.26
108 98 0.73
109 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.23, T:0.26
Consensus pattern (108 bp):
CCCGATTATGAAAAAATCGGTATTTTAGAAATAAAATCGGGGTTAGAGTATCCCCTCGAAAATAA
CAAGGTTGGAGTATCCCCGATGAAACAACAGGGTCAGAGTACC
Found at i:1282281 original size:28 final size:28
Alignment explanation
Indices: 1282245--1282315 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
1282235 ATAAATCCGG
* **
1282245 GGTTAGAGTATCCCCTCGGAAATAACAA
1 GGTTGGAGTATCCCCGAGGAAATAACAA
* ***
1282273 GGTTGGAGTATCCCCGATGAAATAATGG
1 GGTTGGAGTATCCCCGAGGAAATAACAA
1282301 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1282316 AATTATGAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.24
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGAGGAAATAACAA
Found at i:1282362 original size:51 final size:50
Alignment explanation
Indices: 1282300--1282416 Score: 162
Period size: 51 Copynumber: 2.3 Consensus size: 50
1282290 TGAAATAATG
* * *
1282300 GGGTTGGAGTATCCCCAATTATGAAAAATTGGTGTTTTGGAAATAAAATC
1 GGGTTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAACC
* **
1282350 GGAGTTGGAGTATCCCCGATTAAGAAAAATTGATGTTTTGGAAATGGAACC
1 GG-GTTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAACC
1282401 GGGATTGGAGTATCCC
1 GGG-TTGGAGTATCCC
1282417 TGAGATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 3 0.05
51 56 0.95
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (50 bp):
GGGTTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAACC
Found at i:1284738 original size:21 final size:21
Alignment explanation
Indices: 1284712--1284767 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 21
1284702 AAAATGCTTG
*
1284712 AATGTATCGATACATATG-AGC
1 AATGTATCGATACATATGCA-A
1284733 AATGTATCGATACA-ATGCAA
1 AATGTATCGATACATATGCAA
*
1284753 AATATATCGATACAT
1 AATGTATCGATACAT
1284768 CTGGGTAAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATATGCAA
Found at i:1284829 original size:13 final size:13
Alignment explanation
Indices: 1284782--1284811 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1284772 GTAAACTCAG
1284782 AATGTATCGATAC
1 AATGTATCGATAC
*
1284795 AATGTATTGATAC
1 AATGTATCGATAC
1284808 AATG
1 AATG
1284812 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:1285226 original size:22 final size:21
Alignment explanation
Indices: 1285194--1285243 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
1285184 TATTTAACTT
*
1285194 TAAAAATATTTAAATATCAAA
1 TAAAAATATTTAAAAATCAAA
**
1285215 TAAAAATAATTTAAAAATTTAA
1 TAAAAAT-ATTTAAAAATCAAA
1285237 TAAAAAT
1 TAAAAAT
1285244 TAAAAAACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 7 0.28
22 18 0.72
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAAAATATTTAAAAATCAAA
Found at i:1285622 original size:13 final size:13
Alignment explanation
Indices: 1285604--1285643 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1285594 GGATCAAGAC
*
1285604 TTTAAATATAAAA
1 TTTAAAAATAAAA
1285617 TTTAAAAATAAAA
1 TTTAAAAATAAAA
*
1285630 TTAAAAAACTAAAA
1 TTTAAAAA-TAAAA
1285644 AATATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (13 bp):
TTTAAAAATAAAA
Found at i:1292124 original size:22 final size:21
Alignment explanation
Indices: 1292093--1292133 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1292083 ATTTTTTATT
1292093 TAAATTTAAT-TATAAAATATA
1 TAAATTTAATAT-TAAAATATA
1292114 TAAATATTAATATTAAAATA
1 TAAAT-TTAATATTAAAATA
1292134 ATTTTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 12 0.67
23 1 0.06
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTTAATATTAAAATATA
Found at i:1292588 original size:14 final size:13
Alignment explanation
Indices: 1292554--1292592 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1292544 TTTTAAAATA
1292554 TTTTTTATTTAAT
1 TTTTTTATTTAAT
**
1292567 TTCATTATTTATAT
1 TTTTTTATTTA-AT
1292581 TTTTTTATTTAA
1 TTTTTTATTTAA
1292593 AGATAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTATTTAAT
Found at i:1292627 original size:25 final size:23
Alignment explanation
Indices: 1292573--1292627 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
1292563 TAATTTCATT
*
1292573 ATTT-ATATTTTTTTATTTAAAG
1 ATTTAATATTTTTTTATTAAAAG
**
1292595 ATAAAATATTTTTTTAATTAAAAG
1 ATTTAATATTTTTTT-ATTAAAAG
1292619 AATTTAATA
1 -ATTTAATA
1292628 AATTATATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
22 2 0.08
23 10 0.40
24 7 0.28
25 6 0.24
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATTTAATATTTTTTTATTAAAAG
Found at i:1293490 original size:20 final size:20
Alignment explanation
Indices: 1293479--1293526 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
1293469 AATTTTTATT
1293479 ATTTTATTTGAATTTATTAA
1 ATTTTATTTGAATTTATTAA
* *
1293499 ATTTTATTTGTAA-ATATTTA
1 ATTTTATTTG-AATTTATTAA
1293519 ATTTTATT
1 ATTTTATT
1293527 GTATTAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTTTATTTGAATTTATTAA
Found at i:1293629 original size:14 final size:12
Alignment explanation
Indices: 1293601--1293631 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1293591 TCATTCATTT
1293601 ATAATATATCTA
1 ATAATATATCTA
1293613 ATAATATATCTA
1 ATAATATATCTA
1293625 A-AATATA
1 ATAATATA
1293632 GTTTCTAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 6 0.32
12 13 0.68
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (12 bp):
ATAATATATCTA
Found at i:1302929 original size:21 final size:20
Alignment explanation
Indices: 1302909--1302947 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1302899 TTTGAGTGAT
1302909 TTTAAT-TTGAAAACATATGA
1 TTTAATCTTGAAAA-ATATGA
1302929 TTTAATGCTTGAAAAATAT
1 TTTAAT-CTTGAAAAATAT
1302948 TTATACTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 4 0.24
22 7 0.41
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTAATCTTGAAAAATATGA
Found at i:1305663 original size:3 final size:3
Alignment explanation
Indices: 1305648--1305678 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1305638 AACCATCAAA
*
1305648 GAT GAT GAA GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1305679 TTGACTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:1311211 original size:34 final size:35
Alignment explanation
Indices: 1311148--1311214 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1311138 CTAAGTGATT
1311148 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1311184 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1311215 TTTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1312904 original size:84 final size:84
Alignment explanation
Indices: 1312726--1312891 Score: 196
Period size: 84 Copynumber: 2.0 Consensus size: 84
1312716 TCTAAACTCA
* * * *
1312726 AAAAAGAAAATAAATCAATAAGTGTAGAAAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAG
1 AAAATGAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAG
* *
1312791 AAGAGTATGAAAGAGTTAC
66 AAGAGAAAGAAAGAGTTAC
* *
1312810 AAAATGAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATT--
1 AAAATGAAAATAAATCAATAAGTGTAGAAAATCATATTC--TTAAAAAGAAAATAAATGAATTAG
1312871 AGAAGAGAAAAGAAATGAGTT
64 AGAAGAG-AAAGAAA-GAGTT
1312892 GCAAGTCGAA
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
82 11 0.16
83 6 0.09
84 53 0.76
ACGTcount: A:0.55, C:0.04, G:0.16, T:0.25
Consensus pattern (84 bp):
AAAATGAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAG
AAGAGAAAGAAAGAGTTAC
Found at i:1314424 original size:13 final size:13
Alignment explanation
Indices: 1314406--1314430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1314396 TTTTCCAGAT
1314406 TGTATCGATACAA
1 TGTATCGATACAA
1314419 TGTATCGATACA
1 TGTATCGATACA
1314431 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1316349 original size:13 final size:13
Alignment explanation
Indices: 1316331--1316356 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1316321 TACACAAAGT
1316331 ATGTATCGATACA
1 ATGTATCGATACA
1316344 ATGTATCGATACA
1 ATGTATCGATACA
1316357 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1316354 original size:32 final size:33
Alignment explanation
Indices: 1316313--1316376 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1316303 TAGCCAAACT
**
1316313 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
1316345 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1316377 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1316877 original size:34 final size:35
Alignment explanation
Indices: 1316814--1316880 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
1316804 CTAAGTGATT
1316814 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
1316850 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
1316881 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:1319731 original size:13 final size:13
Alignment explanation
Indices: 1319713--1319737 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1319703 CATGGCATAT
1319713 TGTATCGATACAA
1 TGTATCGATACAA
1319726 TGTATCGATACA
1 TGTATCGATACA
1319738 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1328512 original size:63 final size:63
Alignment explanation
Indices: 1328409--1328528 Score: 204
Period size: 63 Copynumber: 1.9 Consensus size: 63
1328399 ATCACTATTT
* ***
1328409 ATGTATCGATACATCACTGTTCATCACTATACATTGAGCCCAATGGCTATAATTTCACGGTTC
1 ATGTATCGATACATCACTGTTCATCACTATACATTAAGCCCAACAACTATAATTTCACGGTTC
1328472 ATGTATCGATACATCACTGTTCATCACTATACATTAAGCCCAACAACTATAATTTCA
1 ATGTATCGATACATCACTGTTCATCACTATACATTAAGCCCAACAACTATAATTTCA
1328529 AATATATGTA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 53 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.33
Consensus pattern (63 bp):
ATGTATCGATACATCACTGTTCATCACTATACATTAAGCCCAACAACTATAATTTCACGGTTC
Found at i:1328967 original size:33 final size:33
Alignment explanation
Indices: 1328925--1329043 Score: 127
Period size: 33 Copynumber: 3.6 Consensus size: 33
1328915 CTAAGTGATT
*
1328925 GAAAGGTTCTATCTTAGCCTTGAAAGAGAGGGA
1 GAAAGGTTCTATCTTAGCCTTGAAAGATAGGGA
*
1328958 GAAAGGTTCTATCTTAGCCAGTGAAAAGATAGGGA
1 GAAAGGTTCTATCTTAGCC-TTG-AAAGATAGGGA
* *
1328993 G---GTTTCTATCTTAGCCTTGAAAGATAGTGGT
1 GAAAGGTTCTATCTTAGCCTTGAAAGATAG-GGA
* * *
1329024 GTAAGGTTATACCTTAGCCT
1 GAAAGGTTCTATCTTAGCCT
1329044 CAAAGGTAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
30 8 0.11
31 5 0.07
32 14 0.19
33 19 0.26
34 15 0.21
35 11 0.15
ACGTcount: A:0.30, C:0.13, G:0.27, T:0.29
Consensus pattern (33 bp):
GAAAGGTTCTATCTTAGCCTTGAAAGATAGGGA
Found at i:1330031 original size:20 final size:20
Alignment explanation
Indices: 1330002--1330043 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1329992 TGTTCATAAA
1330002 TTTGGCTTTATCAACTTAGC
1 TTTGGCTTTATCAACTTAGC
*
1330022 TTTGGTTTTATCAACTTAGC
1 TTTGGCTTTATCAACTTAGC
1330042 TT
1 TT
1330044 ATAACAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (20 bp):
TTTGGCTTTATCAACTTAGC
Found at i:1331037 original size:22 final size:22
Alignment explanation
Indices: 1331009--1331057 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1330999 TTTATAACTA
1331009 TTCATGTATCGATACATCACTG
1 TTCATGTATCGATACATCACTG
*
1331031 TTCATGTATCGATACATCATTG
1 TTCATGTATCGATACATCACTG
1331053 TTCAT
1 TTCAT
1331058 CATTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (22 bp):
TTCATGTATCGATACATCACTG
Found at i:1331121 original size:95 final size:95
Alignment explanation
Indices: 1330993--1331185 Score: 287
Period size: 95 Copynumber: 2.0 Consensus size: 95
1330983 TCACTATTCA
* *
1330993 TCACTGTTTATAACTATTCATGTATCGATACATCACTGTTCATGTATCGATACATCATTGTTCAT
1 TCACTGTTTATAACTACTAATGTATCGATACATCACTGTTCATGTATCGATACATCATTGTTCAT
* * *
1331058 CATTATATATTGAGCTCAACAATTATAATT
66 CACTATACATTGAGCCCAACAATTATAATT
* * *
1331088 TCACTGTTTATCACTGCTAATGTATCGATACATCAGTGTTCATGTATCGATACATCATTGTTCAT
1 TCACTGTTTATAACTACTAATGTATCGATACATCACTGTTCATGTATCGATACATCATTGTTCAT
* **
1331153 CACTATACATTGCGCCCAACGGTTATAATT
66 CACTATACATTGAGCCCAACAATTATAATT
1331183 TCA
1 TCA
1331186 AATGCATGTA
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 87 1.00
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (95 bp):
TCACTGTTTATAACTACTAATGTATCGATACATCACTGTTCATGTATCGATACATCATTGTTCAT
CACTATACATTGAGCCCAACAATTATAATT
Found at i:1331122 original size:22 final size:22
Alignment explanation
Indices: 1331097--1331144 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
1331087 TTCACTGTTT
1331097 ATCACTGCTAATGTATCGATAC
1 ATCACTGCTAATGTATCGATAC
* * *
1331119 ATCAGTGTTCATGTATCGATAC
1 ATCACTGCTAATGTATCGATAC
1331141 ATCA
1 ATCA
1331145 TTGTTCATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (22 bp):
ATCACTGCTAATGTATCGATAC
Found at i:1331149 original size:22 final size:22
Alignment explanation
Indices: 1331107--1331152 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
1331097 ATCACTGCTA
1331107 ATGTATCGATACATCAGTGTTC
1 ATGTATCGATACATCAGTGTTC
*
1331129 ATGTATCGATACATCATTGTTC
1 ATGTATCGATACATCAGTGTTC
1331151 AT
1 AT
1331153 CACTATACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (22 bp):
ATGTATCGATACATCAGTGTTC
Found at i:1331221 original size:20 final size:19
Alignment explanation
Indices: 1331187--1331224 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1331177 ATAATTTCAA
*
1331187 ATGCATGTATTGATACATT
1 ATGCATGTATCGATACATT
1331206 ATGCATTGTATCGATACAT
1 ATGCA-TGTATCGATACAT
1331225 AGGAGTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (19 bp):
ATGCATGTATCGATACATT
Found at i:1331638 original size:33 final size:30
Alignment explanation
Indices: 1331595--1331683 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 30
1331585 AGTGATTGAG
*
1331595 GGGTTCTATCTTAGCCTTGAAAGAGAGGGA
1 GGGTTCTATCTTAGCCTTGAAAGAGAAGGA
* *
1331625 GAAAGGTTCTATCTTAGCCCATGAAACGATAAGGA
1 G---GGTTCTATCTTAG-CCTTGAAA-GAGAAGGA
*
1331660 GGTTTCTATCTTAGCCTTGAAAGA
1 GGGTTCTATCTTAGCCTTGAAAGA
1331684 TAGTGTTGTA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
30 3 0.06
31 7 0.14
32 12 0.24
33 13 0.27
34 7 0.14
35 7 0.14
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (30 bp):
GGGTTCTATCTTAGCCTTGAAAGAGAAGGA
Found at i:1337826 original size:58 final size:59
Alignment explanation
Indices: 1337684--1338260 Score: 222
Period size: 58 Copynumber: 10.1 Consensus size: 59
1337674 ATTTTTACCT
* * * * * *
1337684 AATGACCCTAAAATGCATGAAA-ATGCATAAATG-GCCTAAAATTATGAAAAATTACTAA
1 AATGACTCTAAAATGCATGAAATTTGCATAAAAGTCCCT-AAATCATGGAAAATTACTAA
** * * *
1337742 GCTGTCCCTAATATGCATGAAA-TTGCATAAAAAGTCCC-AAATCATGGAAAATTACTAA
1 AATGACTCTAAAATGCATGAAATTTGCAT-AAAAGTCCCTAAATCATGGAAAATTACTAA
** * * *
1337800 AATGACTCTAAAATGCAT-AAATTTGCATAATGGTCCCTAAGTCATAGAAAATGACTAA
1 AATGACTCTAAAATGCATGAAATTTGCATAAAAGTCCCTAAATCATGGAAAATTACTAA
* * * * *
1337858 AATGA-TCCTAAAATGTATGAAATTAT--ATAATAA-TACCTAAATCATAGAACATGACTAA
1 AATGACT-CTAAAATGCATGAAATT-TGCATAA-AAGTCCCTAAATCATGGAAAATTACTAA
* * * * * * *
1337916 AATGGC-CTTAAAGTGCATGAAA-TTACATAATAGTCTCTAAACCATGGAAAATGAC-AA
1 AATGACTC-TAAAATGCATGAAATTTGCATAAAAGTCCCTAAATCATGGAAAATTACTAA
** * * **** ** *
1337973 TGTAAC-CTTAAAATGCAT-AAATTTACATGGTGGTCCCTAAATCATAAAAAATGACTAA
1 AATGACTC-TAAAATGCATGAAATTTGCATAAAAGTCCCTAAATCATGGAAAATTACTAA
* * * * ** ** *
1338031 AATG-GTCCTAAAATGCATGAAA-TTACATGATAGTCCCTAAAAAAAAGAAGA-TACCTAA
1 AATGACT-CTAAAATGCATGAAATTTGCATAAAAGTCCCTAAATCATGGAAAATTA-CTAA
* * * ** *
1338089 AATAGGC-CTAAAATGCAAGAAA-TTGCATAAATGAT-CCTAAATCATGTCAAATTACTAG
1 AAT-GACTCTAAAATGCATGAAATTTGCATAAAAG-TCCCTAAATCATGGAAAATTACTAA
* * * * *
1338147 AAT-AATCCTCAAATGCATG--A----CATAAAGGTCCCTAAATCATGAAAAATGACTAA
1 AATGACT-CTAAAATGCATGAAATTTGCATAAAAGTCCCTAAATCATGGAAAATTACTAA
* * * ** ** * *
1338200 TATGACAT-AAAAAGGCATGAAA-TAACATAAAAGTCCCTACGTCATTGAAAATGACTAA
1 AATGAC-TCTAAAATGCATGAAATTTGCATAAAAGTCCCTAAATCATGGAAAATTACTAA
1338258 AAT
1 AAT
1338261 AACATACGAA
Statistics
Matches: 394, Mismatches: 92, Indels: 66
0.71 0.17 0.12
Matches are distributed among these distances:
52 1 0.00
53 36 0.09
54 1 0.00
55 2 0.01
56 5 0.01
57 56 0.14
58 273 0.69
59 17 0.04
60 3 0.01
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (59 bp):
AATGACTCTAAAATGCATGAAATTTGCATAAAAGTCCCTAAATCATGGAAAATTACTAA
Found at i:1342583 original size:101 final size:102
Alignment explanation
Indices: 1342405--1342626 Score: 365
Period size: 101 Copynumber: 2.2 Consensus size: 102
1342395 ACATTGCTAG
* *
1342405 AATGTATCGATACAAGGTCCCAACGGTCAAAAATTTTGAATTTTAACAATTTGTATTGATACAAA
1 AATGTATCGATACAAAGTCCCAACGGTCAAAAATTTTGAATTTTAACAATTTGTATCGATACAAA
* * *
1342470 TAGTAACTGTATCGATACATAAGTGTTGTAGCGATAC
66 CAGTAACTGTATCGATACATAACTGTTGTAGCAATAC
*
1342507 ATTGTATCGATACAAAG-CCCAACGGTCAAAAATTTTGAATTTTAACAATTTGTATCGATACAAA
1 AATGTATCGATACAAAGTCCCAACGGTCAAAAATTTTGAATTTTAACAATTTGTATCGATACAAA
*
1342571 CAGTAACTGTATCGATACATAACTGTTGTATCAATAC
66 CAGTAACTGTATCGATACATAACTGTTGTAGCAATAC
1342608 AATGTATCGATACATAAGT
1 AATGTATCGATACA-AAGT
1342627 TTTGTATCGA
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 92 0.84
102 18 0.16
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (102 bp):
AATGTATCGATACAAAGTCCCAACGGTCAAAAATTTTGAATTTTAACAATTTGTATCGATACAAA
CAGTAACTGTATCGATACATAACTGTTGTAGCAATAC
Found at i:1342602 original size:19 final size:18
Alignment explanation
Indices: 1342556--1342641 Score: 56
Period size: 19 Copynumber: 4.8 Consensus size: 18
1342546 TTTTAACAAT
*
1342556 TTGTATCGATACAAACAG
1 TTGTATCGATACAAACTG
1342574 TAACTGTATCGATACATAACTG
1 T---TGTATCGATACA-AACTG
*
1342596 TTGTATCAATAC-AA---
1 TTGTATCGATACAAACTG
* *
1342610 -TGTATCGATACATAAGTT
1 TTGTATCGATACA-AACTG
1342628 TTGTATCGATACAA
1 TTGTATCGATACAA
1342642 TGTATCGTTA
Statistics
Matches: 55, Mismatches: 3, Indels: 20
0.71 0.04 0.26
Matches are distributed among these distances:
13 10 0.18
15 2 0.04
17 2 0.04
18 2 0.04
19 22 0.40
21 12 0.22
22 5 0.09
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (18 bp):
TTGTATCGATACAAACTG
Found at i:1342619 original size:32 final size:32
Alignment explanation
Indices: 1342578--1342648 Score: 115
Period size: 32 Copynumber: 2.2 Consensus size: 32
1342568 AAACAGTAAC
1342578 TGTATCGATACATAACTGTTGTATCAATACAA
1 TGTATCGATACATAACTGTTGTATCAATACAA
* * *
1342610 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAACTGTTGTATCAATACAA
1342642 TGTATCG
1 TGTATCG
1342649 TTACGAAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAACTGTTGTATCAATACAA
Found at i:1347769 original size:21 final size:23
Alignment explanation
Indices: 1347743--1347785 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1347733 GAATTTTATT
*
1347743 TAAAATC-TA-TATTATAGTTGA
1 TAAAATCGTACTATAATAGTTGA
1347764 TAAAATCGTACTATAATAGTTG
1 TAAAATCGTACTATAATAGTTG
1347786 GTAATAGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 2 0.11
23 10 0.53
ACGTcount: A:0.42, C:0.07, G:0.12, T:0.40
Consensus pattern (23 bp):
TAAAATCGTACTATAATAGTTGA
Found at i:1348243 original size:58 final size:58
Alignment explanation
Indices: 1348164--1348645 Score: 355
Period size: 58 Copynumber: 8.4 Consensus size: 58
1348154 AGAATAGTGT
* * *
1348164 TAAAATGCATTG-AATTGCATAATAATCCCTTGAA-CATAAAAAATGACTAAAATGATCC
1 TAAAATGCA-TGAAATTGCATAATAAT-CCTTAAATCATGAAAAATTACTAAAATGATCC
* * * *
1348222 TAAAATGCATGAAATTACATAA-AAGTCCTCAAAACATGAAAAATTACTAAAATGACCC
1 TAAAATGCATGAAATTGCATAATAA-TCCTTAAATCATGAAAAATTACTAAAATGATCC
* * * * ** *
1348280 TAAAATGCATTAAAATGCATAAATAAT-TTTAAAACATG-GTAATTACTAAAAT-AACC
1 TAAAATGCATGAAATTGCAT-AATAATCCTTAAATCATGAAAAATTACTAAAATGATCC
** * ** *
1348336 TTAAAAT-CATGAAATTGCATAAATGGT-CTTAAAACATGGCAAATTACTAAAATGATTC
1 -TAAAATGCATGAAATTGCAT-AATAATCCTTAAATCATGAAAAATTACTAAAATGATCC
* * *
1348394 -AAAAGGCATGAAATTACATAATAATTCC-TAAATCATGGAAAATTACTAAAATGA-CC
1 TAAAATGCATGAAATTGCATAATAA-TCCTTAAATCATGAAAAATTACTAAAATGATCC
** * * * * ** * * *
1348450 CCAAATGCACGAAGTTGCATAGTAACCCCCAAATCATGAAAAATAACTAAAATAATGC
1 TAAAATGCATGAAATTGCATAATAATCCTTAAATCATGAAAAATTACTAAAATGATCC
* * * * *
1348508 TAAAATGGATGAAATTACTTAATAA-CCTCTAAATCAT-AAAAGATGACTAAAAT-AGTTC
1 TAAAATGCATGAAATTGCATAATAATCCT-TAAATCATGAAAA-ATTACTAAAATGA-TCC
* ** * *
1348566 TAAAATGTATGAAATTATATAATAACCCTTAAATCATGAAAAATTACTTAAATGA-CC
1 TAAAATGCATGAAATTGCATAATAATCCTTAAATCATGAAAAATTACTAAAATGATCC
*
1348623 TTAAAATGCATAAAATTGCATAA
1 -TAAAATGCATGAAATTGCATAA
1348646 ATAGTTCTAA
Statistics
Matches: 339, Mismatches: 64, Indels: 42
0.76 0.14 0.09
Matches are distributed among these distances:
56 39 0.12
57 124 0.37
58 163 0.48
59 11 0.03
60 2 0.01
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (58 bp):
TAAAATGCATGAAATTGCATAATAATCCTTAAATCATGAAAAATTACTAAAATGATCC
Found at i:1348284 original size:29 final size:29
Alignment explanation
Indices: 1348196--1348447 Score: 88
Period size: 29 Copynumber: 8.8 Consensus size: 29
1348186 TAATCCCTTG
* *
1348196 AACATAAAAAATGACTAAAATGATCCTAA
1 AACATGAAAAATTACTAAAATGATCCTAA
1348225 AATGCATG--AAATTACATAAAA-G-TCCTCAA
1 AA--CATGAAAAATTAC-TAAAATGATCCT-AA
*
1348254 AACATGAAAAATTACTAAAATGACCCTAA
1 AACATGAAAAATTACTAAAATGATCCTAA
* * * **
1348283 AATGCAT-TAAAA-TGC-ATAAATAATTTTAA
1 AA--CATGAAAAATTACTA-AAATGATCCTAA
** *
1348312 AACATG-GTAATTACTAAAAT-AACCTTAA
1 AACATGAAAAATTACTAAAATGATCC-TAA
* * *
1348340 AATCATG--AAATTGC-ATAAATGGTCTTAA
1 AA-CATGAAAAATTACTA-AAATGATCCTAA
** *
1348368 AACATGGCAAATTACTAAAATGATTC-AA
1 AACATGAAAAATTACTAAAATGATCCTAA
1348396 AAGGCATG--AAATTACATAATAAT--TCCTAA
1 AA--CATGAAAAATTAC-TAA-AATGATCCTAA
* *
1348425 ATCATGGAAAATTACTAAAATGA
1 AACATGAAAAATTACTAAAATGA
1348448 CCCCAAATGC
Statistics
Matches: 167, Mismatches: 26, Indels: 60
0.66 0.10 0.24
Matches are distributed among these distances:
27 22 0.13
28 51 0.31
29 68 0.41
30 20 0.12
31 6 0.04
ACGTcount: A:0.51, C:0.13, G:0.10, T:0.27
Consensus pattern (29 bp):
AACATGAAAAATTACTAAAATGATCCTAA
Found at i:1348359 original size:28 final size:28
Alignment explanation
Indices: 1348271--1348359 Score: 65
Period size: 28 Copynumber: 3.1 Consensus size: 28
1348261 AAAATTACTA
* * * *
1348271 AAATGACCCTAAAATGCATTAAAATGCAT
1 AAATAACCTTAAAAT-CATGAAATTGCAT
** * *
1348300 AAATAATTTTAAAA-CATGGTAATTAC-T
1 AAATAACCTTAAAATCAT-GAAATTGCAT
1348327 AAAATAACCTTAAAATCATGAAATTGCAT
1 -AAATAACCTTAAAATCATGAAATTGCAT
1348356 AAAT
1 AAAT
1348360 GGTCTTAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 9
0.68 0.18 0.14
Matches are distributed among these distances:
27 4 0.09
28 26 0.59
29 14 0.32
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.29
Consensus pattern (28 bp):
AAATAACCTTAAAATCATGAAATTGCAT
Found at i:1348386 original size:28 final size:27
Alignment explanation
Indices: 1348299--1348386 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 27
1348289 TTAAAATGCA
** *
1348299 TAAATAATTTTAAAACATGGTAATTAC
1 TAAATAACCTTAAAACATGGAAATTAC
*
1348326 TAAAATAACCTTAAAATCAT-GAAATTGC
1 T-AAATAACCTTAAAA-CATGGAAATTAC
***
1348354 ATAAATGGTCTTAAAACATGGCAAATTAC
1 -TAAATAACCTTAAAACATGG-AAATTAC
1348383 TAAA
1 TAAA
1348387 ATGATTCAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
27 4 0.08
28 34 0.71
29 10 0.21
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (27 bp):
TAAATAACCTTAAAACATGGAAATTAC
Found at i:1348438 original size:114 final size:116
Alignment explanation
Indices: 1348203--1348685 Score: 303
Period size: 114 Copynumber: 4.2 Consensus size: 116
1348193 TTGAACATAA
* *
1348203 AAAATGACTAAAATGATCCTAAAATGCATGAAATTACATAAAAGTCCTCAAAACATGAAAAATTA
1 AAAATTACTAAAATGAACCTAAAATGCATGAAATTACATAAAAGTCCTCAAAACATGAAAAATTA
* * * *
1348268 CTAAAATGACCCTAAAATGCATTAAAATGCATAAATAATTTTAAAACATGG
66 CTAAAATGACCCTAAAAGGCATGAAAATACATAAATAATTCTAAAACATGG
* * * * **
1348319 -TAATTACTAAAAT-AACCTTAAAAT-CATGAAATTGCATAAATGGT-CTTAAAACATGGCAAAT
1 AAAATTACTAAAATGAACC-TAAAATGCATGAAATTACATAAA-AGTCCTCAAAACATGAAAAAT
** * *
1348380 TACTAAAATGATTC-AAAAGGCATGAAATTACAT-AATAATTCCTAAATCATGG
64 TACTAAAATGACCCTAAAAGGCATGAAAATACATAAATAATT-CTAAAACATGG
** * * * * * * * *
1348432 AAAATTACTAAAATG-ACCCCAAATGCACGAAGTTGCATAGTAA-CCCCCAAATCATGAAAAATA
1 AAAATTACTAAAATGAACCTAAAATGCATGAAATTACATA-AAAGTCCTCAAAACATGAAAAATT
* ** * * * * *
1348495 ACTAAAATAATGCTAAAATGG-ATGAAATTAC-TTAATAACCTCTAAATCAT-A
65 ACTAAAATGACCCTAAAA-GGCATGAAAATACATAAATAA-TTCTAAAACATGG
* ** * * * * *
1348546 AAAGATGACTAAAAT-AGTTCTAAAATGTATGAAATTATATAATAA-CCCTTAAATCATGAAAAA
1 AAA-ATTACTAAAATGA-ACCTAAAATGCATGAAATTACATAA-AAGTCCTCAAAACATGAAAAA
* * * * * * *
1348609 TTACTTAAATGACCTTAAAATGCAT-AAAATTGCATAAATAGTTCTAAAATATAG
63 TTACTAAAATGACCCTAAAAGGCATGAAAA-TACATAAATAATTCTAAAACATGG
* * *
1348663 CAAATTAC-AAGATGAACTTAAAA
1 AAAATTACTAAAATGAACCTAAAA
1348686 CACATAAGAA
Statistics
Matches: 278, Mismatches: 68, Indels: 43
0.71 0.17 0.11
Matches are distributed among these distances:
112 7 0.03
113 28 0.10
114 98 0.35
115 71 0.26
116 67 0.24
117 7 0.03
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (116 bp):
AAAATTACTAAAATGAACCTAAAATGCATGAAATTACATAAAAGTCCTCAAAACATGAAAAATTA
CTAAAATGACCCTAAAAGGCATGAAAATACATAAATAATTCTAAAACATGG
Found at i:1352202 original size:11 final size:11
Alignment explanation
Indices: 1352185--1352217 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1352175 TGGTAAATTA
1352185 AATAATTATTT
1 AATAATTATTT
*
1352196 GATAATTATTT
1 AATAATTATTT
1352207 AATAA-TATTT
1 AATAATTATTT
1352217 A
1 A
1352218 CATGAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 6 0.30
11 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (11 bp):
AATAATTATTT
Found at i:1352954 original size:20 final size:20
Alignment explanation
Indices: 1352931--1352987 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1352921 AAGTACCCAG
* *
1352931 ATGTATAGATACATTTTTCA
1 ATGTATCGATACATTCTTCA
1352951 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
1352971 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
1352988 GTCTTTTTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1354662 original size:9 final size:9
Alignment explanation
Indices: 1354648--1354674 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1354638 ACTAGATGAT
1354648 TTTTCCAAA
1 TTTTCCAAA
1354657 TTTTCCAAA
1 TTTTCCAAA
1354666 TTTTCCAAA
1 TTTTCCAAA
1354675 CATTTTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.00, T:0.44
Consensus pattern (9 bp):
TTTTCCAAA
Found at i:1358826 original size:21 final size:19
Alignment explanation
Indices: 1358800--1358855 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
1358790 TTCAACAATT
1358800 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAA-AGT-AA
* **
1358821 TGTATCGATACATAAGTGT
1 TGTATCGATACAAAAGTAA
1358840 TGTATCGATACAAAAG
1 TGTATCGATACAAAAG
1358856 CTACCCTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.48
20 3 0.10
21 13 0.42
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAAGTAA
Found at i:1363018 original size:13 final size:13
Alignment explanation
Indices: 1363000--1363024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1362990 CATTTTGGGA
1363000 TGTATCGATACAG
1 TGTATCGATACAG
1363013 TGTATCGATACA
1 TGTATCGATACA
1363025 TATTGTGTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1363022 original size:33 final size:32
Alignment explanation
Indices: 1362980--1363043 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
1362970 TACAAGCCAA
*
1362980 TGTATCGATACATTTTGGGATGTATCGATACAG
1 TGTATCGATACATATTGGG-TGTATCGATACAG
*
1363013 TGTATCGATACATATTGTGTGTATCGATACA
1 TGTATCGATACATATTGGGTGTATCGATACA
1363044 AATTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATATTGGGTGTATCGATACAG
Found at i:1363173 original size:20 final size:20
Alignment explanation
Indices: 1363150--1363190 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1363140 CTGTGCAATT
1363150 TGTATCGATACATTTAAAGG
1 TGTATCGATACATTTAAAGG
* *
1363170 TGTATCGATACTTTTCAAGG
1 TGTATCGATACATTTAAAGG
1363190 T
1 T
1363191 TTTTTCCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTAAAGG
Found at i:1363722 original size:22 final size:22
Alignment explanation
Indices: 1363695--1363739 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
1363685 TTTTCTTTTC
1363695 TCTCCCCCTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
1363717 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
1363739 T
1 T
1363740 AACAATTTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.36, C:0.29, G:0.00, T:0.36
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:1365178 original size:21 final size:21
Alignment explanation
Indices: 1365147--1365191 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
1365137 GCTACTACTG
**
1365147 TGGGGGCTGCCCGGTTGCGACC
1 TGGGGGCTG-CCGGTCACGACC
1365169 TGGGGG-TGCCGGTCACGACC
1 TGGGGGCTGCCGGTCACGACC
1365189 TGG
1 TGG
1365192 TGAGTGCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.07, C:0.29, G:0.47, T:0.18
Consensus pattern (21 bp):
TGGGGGCTGCCGGTCACGACC
Found at i:1365489 original size:20 final size:21
Alignment explanation
Indices: 1365460--1365500 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1365450 TGTTTTTGTT
1365460 GATGATTTTG-A-TGAAAAAC
1 GATGATTTTGAAGTGAAAAAC
1365479 GATGTATTTTGAAGTGAAAAAC
1 GATG-ATTTTGAAGTGAAAAAC
1365501 AAGAAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (21 bp):
GATGATTTTGAAGTGAAAAAC
Found at i:1365687 original size:47 final size:50
Alignment explanation
Indices: 1365632--1365728 Score: 130
Period size: 47 Copynumber: 2.0 Consensus size: 50
1365622 ATAAACCCCT
*
1365632 TGTATCGATACA-GAGAATGCTGTATCGATAC-TTCT-GAA-TTTTCCAGA
1 TGTATCGATACATGAGAA-CCTGTATCGATACATTCTGGAATTTTTCCAGA
**
1365679 TGTATCGATACATTTGAACCTGTATCGATACATTCTGGAATTTTTCCAGA
1 TGTATCGATACATGAGAACCTGTATCGATACATTCTGGAATTTTTCCAGA
1365729 ATTTGACCCT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
47 24 0.56
48 7 0.16
49 3 0.07
50 9 0.21
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (50 bp):
TGTATCGATACATGAGAACCTGTATCGATACATTCTGGAATTTTTCCAGA
Found at i:1369842 original size:32 final size:32
Alignment explanation
Indices: 1369801--1369884 Score: 123
Period size: 32 Copynumber: 2.6 Consensus size: 32
1369791 GTTCGTAGCA
* *
1369801 ATACATTGTATCGATACAAAACTTATGTATCG
1 ATACATTGTATCGATACAAAACTAATGCATCG
*
1369833 ATACATTGTATCGATACAACACTAATGCATCG
1 ATACATTGTATCGATACAAAACTAATGCATCG
* *
1369865 ATATATTGTATCGTTACAAA
1 ATACATTGTATCGATACAAA
1369885 TTGTTGAAAT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.33
Consensus pattern (32 bp):
ATACATTGTATCGATACAAAACTAATGCATCG
Found at i:1369844 original size:13 final size:13
Alignment explanation
Indices: 1369826--1369850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1369816 ACAAAACTTA
1369826 TGTATCGATACAT
1 TGTATCGATACAT
1369839 TGTATCGATACA
1 TGTATCGATACA
1369851 ACACTAATGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1370816 original size:49 final size:49
Alignment explanation
Indices: 1370699--1371665 Score: 874
Period size: 49 Copynumber: 19.8 Consensus size: 49
1370689 TGAAGAAAAA
* ** * * * * *
1370699 TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA--AA-GATGAAGG
* * *
1370751 TGCCAATACGCTGATTCAAGGCCAACGATATTGGACTTAAGGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * *
1370800 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGG-TTTGAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AAAGAT---GAAGG
* *
1370852 CGCCAATATGCCGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
1370901 TGCCAATGTGCTGATTAAAGGCCAGCAACATTGGACTTAAAGATGACGAACG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGG
** * * *
1370953 TGCCAATATGCTGATTCAAGGCCAGCGATACCGAACTTTAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
1371002 TGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
1371054 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* ** * * *
1371097 TGCCAATGTGCTGATTCAAGGCCAATGACATTGGTCTTTAAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-TTAAAGATGAAGG
*
1371146 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGG
*** * *
1371198 TGCCAATATGCTGATTCAAGGCCAGCGATACCAGACTCAAAGATGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
1371247 TGCTAATGTGCTGATTCAAGGCTAGCGACATTGGGCTT----AT----G
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * * *
1371288 T--CAATGTGTTGATTCAAGGCCAACGACATTAGTCTTAAAGATGAA-G
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* **
1371334 TGCCAATATGCTGATTCAAGGCCAACGATACCGGACTTAAAGATG-AGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * **
1371382 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGG
1 -TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
*
1371432 CGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * *
1371475 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG--AAGG
* *
1371526 -GCACTAATATACTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
1 TGC-C-AATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
* * * * *
1371576 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAATGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAA-GG
*
1371625 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTTAAA
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1371666 AGAAGATGTC
Statistics
Matches: 745, Mismatches: 125, Indels: 93
0.77 0.13 0.10
Matches are distributed among these distances:
39 29 0.04
41 1 0.00
43 76 0.10
44 2 0.00
45 3 0.00
46 2 0.00
47 2 0.00
48 49 0.07
49 332 0.45
50 9 0.01
51 6 0.01
52 232 0.31
53 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (49 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
Found at i:1370831 original size:101 final size:97
Alignment explanation
Indices: 1370699--1371664 Score: 979
Period size: 101 Copynumber: 9.9 Consensus size: 97
1370689 TGAAGAAAAA
** * ** * *
1370699 TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGGCTTAGGAATGTTAAAGATGCCAATACGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTA--AA-GACAAAGGTGCCAATATGCTG
*
1370764 ATTCAAGGCCAACGATATTGGACTTAAGGATGAAGG
63 ATTCAAGGCCAGCGATATTGGACTTAA-GATGAAGG
* * * * *
1370800 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGG-TTTGAAAGATGACGAAGGCGCCAATATGCC
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT--AA-A-GACAAAGGTGCCAATATGCT
1370864 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGG
62 GATTCAAGGCCAGCGATATTGGACTT-AAGATGAAGG
* * * *
1370901 TGCCAATGTGCTGATTAAAGGCCAGCAACATTGGACTTAAAGATGACGAACGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-GACAAAGGTGCCAATATGCTG
** * *
1370966 ATTCAAGGCCAGCGATACCGAACTTTAAGATGAAGA
63 ATTCAAGGCCAGCGATATTGGAC-TTAAGATGAAGG
*
1371002 TGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-GACAAAGGTGCCAATATGCTG
1371067 ATTCAAGGCCAGCGATATTGGACTT---A--AAGG
63 ATTCAAGGCCAGCGATATTGGACTTAAGATGAAGG
** *
1371097 TGCCAATGTGCTGATTCAAGGCCAATGACATTGGTCTTTAAAGAC-AAGGTGCCAATATGCTGAT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC-TTAAAGACAAAGGTGCCAATATGCTGAT
*
1371161 TCAAGGCCAGCAATATTGGACTTAAAGATGACAAAGG
65 TCAAGGCCAGCGATATTGGACTT-AAGATG---AAGG
* * *** * ** * * *
1371198 TGCCAATATGCTGATTCAAGGCCAGCGATACCAGACTCAAAGATGAAGATGCTAATGTGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGACAAAGGTGCCAATATGCTGATT
* * *
1371263 CAAGGCTAGCGACATTGGGCTT---AT----G
66 CAAGGCCAGCGATATTGGACTTAAGATGAAGG
* * * * **
1371288 T--CAATGTGTTGATTCAAGGCCAACGACATTAGTCTTAAAGATGAA-GTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGACAAAGGTGCCAATATGCTGATT
* **
1371350 CAAGGCCAACGATACCGGACTTAAAGATG-AGG
66 CAAGGCCAGCGATATTGGACTT-AAGATGAAGG
* * *
1371382 ATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGCGCCAATATGCTGAT
1 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGACAAAGGTGCCAATATGCTGAT
1371447 TCAAGGCCAGCGATATTGGACTT---A--AAGG
65 TCAAGGCCAGCGATATTGGACTTAAGATGAAGG
** * *
1371475 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGCACTAATATACTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTT-AA-A-GACAAAGGTGCCAATATGCTG
*
1371540 ATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGA
63 ATTCAAGGCCAGCGATATTGGACTT-AAGATGAAGG
* * *
1371576 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAATGGTGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGACAAAGGTGCCAATATGCTGATT
*
1371641 CAAGGCCAGCGATATTGGGCTTAA
66 CAAGGCCAGCGATATTGGACTTAA
1371665 AAGAAGATGT
Statistics
Matches: 735, Mismatches: 92, Indels: 80
0.81 0.10 0.09
Matches are distributed among these distances:
87 30 0.04
88 36 0.05
90 2 0.00
91 2 0.00
92 78 0.11
93 8 0.01
94 4 0.01
95 82 0.11
96 3 0.00
97 44 0.06
98 75 0.10
99 2 0.00
100 13 0.02
101 349 0.47
102 7 0.01
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (97 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGACAAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTTAAGATGAAGG
Found at i:1370872 original size:52 final size:52
Alignment explanation
Indices: 1370699--1371285 Score: 515
Period size: 52 Copynumber: 11.8 Consensus size: 52
1370689 TGAAGAAAAA
* ** * * *** *
1370699 TGCCAATGTGCTGAGGCAAGGCCAGCGACATTGGGCTT-AGGAATGTTAAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAG-ATGACGAAGG
* * * *
1370751 TGCCAATACGCTGATTCAAGGCCAACGATATTGGACTT-AAG--GATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
* * *
1370800 TGCCAATGTGTTGATTCAAGGCCAGCGACATTGG-TTTGAAAGATGACGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGATGACGAAGG
* * *
1370852 CGCCAATATGCCGATTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
* * * *
1370901 TGCCAATGTGCTGATTAAAGGCCAGCAACATTGGACTTAAAGATGACGAACG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
* ** * * *
1370953 TGCCAATATGCTGATTCAAGGCCAGCGATACCGAACTTTAAGAT---GAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
* * *
1371002 TGCCAATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
*
1371054 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-A--AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
* ** * *
1371097 TGCCAATGTGCTGATTCAAGGCCAATGACATTGGTCTTTAA-A-GAC-AAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
* * *
1371146 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGACAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
* *** * *
1371198 TGCCAATATGCTGATTCAAGGCCAGCGATACCAGACTCAAAGAT---GAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
* * * *
1371247 TGCTAATGTGCTGATTCAAGGCTAGCGACATTGGGCTTA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTA
1371286 TGTCAATGTG
Statistics
Matches: 433, Mismatches: 81, Indels: 45
0.77 0.14 0.08
Matches are distributed among these distances:
43 35 0.08
44 1 0.00
45 1 0.00
46 1 0.00
48 3 0.01
49 188 0.43
50 4 0.01
51 4 0.01
52 194 0.45
53 2 0.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (52 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGG
Found at i:1371151 original size:144 final size:144
Alignment explanation
Indices: 1370646--1371665 Score: 799
Period size: 144 Copynumber: 7.0 Consensus size: 144
1370636 CGAAGATGCT
* * * * * * **
1370646 AAGA-ATGACAATGTGCTGATTCATGGCCAACGACATTTAGACTTGAAGAAAAATGCCAATGTGC
1 AAGAGATGCCAATGTGCTGATTCAAGGCCAGCGACA-TTGGTCTTAAAGAAAGGTGCCAATGTGC
** * * ** * *
1370710 TGAGGCAAGGCCAGCGACATTGGGCTT-AGGAATGTTAAAGATGCCAATACGCTGATTCAAGGCC
65 TGATTCAAGGCCAGCGACATTGGACTTAAAG-ATGACAAAGGTGCCAATATGCTGATTCAAGGCC
*
1370774 AACGATATTGGACTTA
129 AGCGATATTGGACTTA
* * *
1370790 AGGATGAAGGTGCCAATGTGTTGATTCAAGGCCAGCGACATTGGT-TTGAAAGATGACGAAGGCG
1 A--A-G-AGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTT--AA-A-GA--AAGGTG
* * * *
1370854 CCAATATGCCGATTCAAGGCCAGCGATATTGGACTTAAAGATG---AAGGTGCCAATGTGCTGAT
56 CCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGAT
* * *
1370916 TAAAGGCCAGCAACATTGGACTTAA
121 TCAAGGCCAGCGATATTGGACTT-A
* * ** ** * *
1370941 AGATGACGAACGTGCCAATATGCTGATTCAAGGCCAGCGATACCGAACTTTAAGATGAAGATGCC
1 A-A-GA-G-A--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA--AAGGTGCC
*
1371006 AATGTGCTGATTCAAGGCCAGTGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTC
58 AATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTC
1371071 AAGGCCAGCGATATTGGACTTA
123 AAGGCCAGCGATATTGGACTTA
** *
1371093 AAG-G-TGCCAATGTGCTGATTCAAGGCCAATGACATTGGTCTTTAAAGACAAGGTGCCAATATG
1 AAGAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC-TTAAAGA-AAGGTGCCAATGTG
* *
1371156 CTGATTCAAGGCCAGCAATATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCC
64 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCC
*** *
1371221 AGCGATACCAGACTCAA
129 AGCGATATTGGACT-TA
* * * *
1371238 AGATGAAGATGCTAATGTGCTGATTCAAGGCTAGCGACATTGGGCTT------A--TGTCAATGT
1 A-A-G-AGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAGGTGCCAATGT
* * * *
1371295 GTTGATTCAAGGCCAACGACATTAGTCTTAAAGATG---AA-GTGCCAATATGCTGATTCAAGGC
63 GCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGC
* **
1371356 CAACGATACCGGACTTAA
128 CAGCGATATTGGACTT-A
*
1371374 AGATGAGGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAAGGCGCCAAT
1 A-A-GA-GATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAG--AAAGGTGCCAAT
* * *
1371439 ATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---AAAGGTGCCAATGTGCTGATTCAAG
61 GTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAAG
*
1371495 GCCAGCGACATTGGACTTA
126 GCCAGCGATATTGGACTTA
* * * * * *
1371514 AAGATGACAAAGGCACTAATATACTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGATGC
1 AAGA-G----ATGC-C-AATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA--AAGGTGC
* * *
1371579 CAATGTGTTGATTCAAGGCCAGCGACATTGGTCTT-AA-A-GACAATGGTGCCAATATGCTGATT
57 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATT
*
1371641 CAAGGCCAGCGATATTGGGCTTA
122 CAAGGCCAGCGATATTGGACTTA
1371664 AA
1 AA
1371666 AGAAGATGTC
Statistics
Matches: 707, Mismatches: 112, Indels: 108
0.76 0.12 0.12
Matches are distributed among these distances:
135 1 0.00
136 79 0.11
137 2 0.00
138 3 0.00
139 1 0.00
140 42 0.06
141 34 0.05
142 5 0.01
143 1 0.00
144 183 0.26
145 10 0.01
146 30 0.04
147 4 0.01
148 5 0.01
149 31 0.04
150 161 0.23
151 6 0.01
152 3 0.00
153 102 0.14
154 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (144 bp):
AAGAGATGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAAAGGTGCCAATGTGCT
GATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCCAG
CGATATTGGACTTA
Found at i:1371832 original size:68 final size:67
Alignment explanation
Indices: 1371758--1372062 Score: 320
Period size: 68 Copynumber: 4.5 Consensus size: 67
1371748 TTATGGACTT
*
1371758 AAAAAGGTGCCACGGAG-TGTGGACTTAAAAGGGAAAAAGAGA-GCCACAGAGTTGTGGGCTTTA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAA-GGAAAAAGAGATGCCAC-GAGTTGTGGAC-TTA
*
1371821 AAAAG
63 AAAGG
* * * *
1371826 AAAAAGGTGTCACGGAGTTGTGGACTT-ACAGGAAAAAAAGATGCCACTGAGTTGTGGACTT-AC
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGATGCCAC-GAGTTGTGGACTTAAA
1371889 AGG
65 AGG
* **
1371892 AAAAAGGGATGCCACTGAGTTGTGGACTTTGAAGG--AAAGAGATGCCACGGAGTTGTGGACTTT
1 AAAAA-GG-TGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGATGCCAC-GAGTTGTGGAC-TT
*
1371955 AAAATG
62 AAAAGG
* * *
1371961 AAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAGG-AAAA-AGATGCCACGAAGTTGTGGACTTAA
1 AAAAAG-GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGATGCCACG-AGTTGTGGACTTAA
1372024 AAGG
64 AAGG
* *
1372028 AACAAGGTGCCACGGAGCTGTGGACTTTAAAAGGA
1 AAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGA
1372063 TGCCACGGAG
Statistics
Matches: 201, Mismatches: 24, Indels: 24
0.81 0.10 0.10
Matches are distributed among these distances:
66 24 0.12
67 57 0.28
68 96 0.48
69 24 0.12
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (67 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGATGCCACGAGTTGTGGACTTAAAA
GG
Found at i:1371864 original size:34 final size:34
Alignment explanation
Indices: 1371758--1372062 Score: 275
Period size: 34 Copynumber: 9.0 Consensus size: 34
1371748 TTATGGACTT
*
1371758 AAAAAGGTGCCACGGAG-TGTGGACTTAAAAGGG
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * *
1371791 AAAAAGAGAGCCACAGAGTTGTGGGCTTTAAAAAG-
1 AAAAAG-GTGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
1371826 AAAAAGGTGTCACGGAGTTGTGGACTT-ACAGGAA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGG-A
* * *
1371860 AAAAAGATGCCACTGAGTTGTGGACTT-ACAGGA
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * **
1371893 AAAAGGGATGCCACTGAGTTGTGGACTTTGAAGG-
1 AAAAAGG-TGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1371927 AAAGAGATGCCACGGAGTTGTGGACTTTAAAATG-
1 AAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGA
* * *
1371961 AAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAGG-
1 AAAAAG-GTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1371995 AAAAAGATGCCACGAAGTTGTGGACTTAAAAGG-
1 AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1372028 AACAAGGTGCCACGGAGCTGTGGACTTTAAAAGGA
1 AAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGA
1372063 TGCCACGGAG
Statistics
Matches: 222, Mismatches: 39, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
32 3 0.01
33 74 0.33
34 107 0.48
35 31 0.14
36 7 0.03
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (34 bp):
AAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:1371897 original size:101 final size:100
Alignment explanation
Indices: 1371758--1372062 Score: 323
Period size: 101 Copynumber: 3.0 Consensus size: 100
1371748 TTATGGACTT
* * *
1371758 AAAAAGGTGCCACGGAG-TGTGGACTTAAAAGGGAAAAAGAGAGCCACAGAGTTGTGGGCTTTAA
1 AAAAAAGTGCCACAGAGTTGTGGACTT-AAA-GGAAAAAGAGAGCCAC-GAGTTGTGGACTTTAA
* * *
1371822 AAAGAAAAAGGTGTCACGGAGTTGTGGACTT-ACAGGA
63 AAGGAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * *
1371859 AAAAAAGATGCCACTGAGTTGTGGACTTACAGGAAAAAGGGATGCCACTGAGTTGTGGACTTT-G
1 AAAAAAG-TGCCACAGAGTTGTGGACTTAAAGGAAAAAGAGA-GCCAC-GAGTTGTGGACTTTAA
* * *
1371923 AAGGAAAGAGATGCCACGGAGTTGTGGACTTTAAAATGA
63 AAGGAAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGA
* * *
1371962 AAAAGAGTGCCACAGAGTTGTGGGCTTTAAAGGAAAAAGA-TGCCACGAAGTTGTGGAC-TTAAA
1 AAAAAAGTGCCACAGAGTTGTGGAC-TTAAAGGAAAAAGAGAGCCACG-AGTTGTGGACTTTAAA
* *
1372025 AGGAACAAGGTGCCACGGAGCTGTGGACTTTAAAAGGA
64 AGGAAAAAGGTGCCACGGAGTTGTGGAC-TTAAAAGGA
1372063 TGCCACGGAG
Statistics
Matches: 171, Mismatches: 25, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
100 3 0.02
101 90 0.53
102 47 0.27
103 31 0.18
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (100 bp):
AAAAAAGTGCCACAGAGTTGTGGACTTAAAGGAAAAAGAGAGCCACGAGTTGTGGACTTTAAAAG
GAAAAAGGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:1372070 original size:28 final size:27
Alignment explanation
Indices: 1372031--1372088 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
1372021 TAAAAGGAAC
1372031 AAGGTGCCACGGAGCTGTGGACTTTAA
1 AAGGTGCCACGGAGCTGTGGACTTTAA
* * *
1372058 AAGGATGCCACGGAGTTGTGGGCTTTGA
1 AAGG-TGCCACGGAGCTGTGGACTTTAA
1372086 AAG
1 AAG
1372089 AAAAGGCACG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.26, C:0.16, G:0.36, T:0.22
Consensus pattern (27 bp):
AAGGTGCCACGGAGCTGTGGACTTTAA
Found at i:1372203 original size:30 final size:30
Alignment explanation
Indices: 1372111--1372251 Score: 160
Period size: 30 Copynumber: 4.6 Consensus size: 30
1372101 TTGGCTTAAT
*
1372111 CACTGAGCCGTGGACTTT--GAAAAGAGATTGC
1 CACTGAGTCGTGGACTTTGGGAAAA-A-A-TGC
*
1372142 CACTGAGTTGTGGACTTTGGAGAAAAAAATGC
1 CACTGAGTCGTGGACTTTGG-G-AAAAAATGC
* *
1372174 CACTAAGTCGTGGACTTTGGGACAAAATGC
1 CACTGAGTCGTGGACTTTGGGAAAAAATGC
* * *
1372204 CCCTGAGTCGTGGGCTTTGGGATAAAATGC
1 CACTGAGTCGTGGACTTTGGGAAAAAATGC
1372234 CACTGAGTCGTGGACTTT
1 CACTGAGTCGTGGACTTT
1372252 AAGAAGGTAT
Statistics
Matches: 95, Mismatches: 11, Indels: 9
0.83 0.10 0.08
Matches are distributed among these distances:
30 50 0.53
31 17 0.18
32 21 0.22
33 1 0.01
34 2 0.02
35 4 0.04
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.26
Consensus pattern (30 bp):
CACTGAGTCGTGGACTTTGGGAAAAAATGC
Found at i:1373860 original size:24 final size:26
Alignment explanation
Indices: 1373827--1373875 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
1373817 CAAGTTTCAA
* *
1373827 ATTTCCTTT-CAAGATTTT-TTTATT
1 ATTTCATTTCCAAAATTTTATTTATT
1373851 ATTTCATTTCCAAAATTTTATTTAT
1 ATTTCATTTCCAAAATTTTATTTAT
1373876 GATTATTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.27, C:0.12, G:0.02, T:0.59
Consensus pattern (26 bp):
ATTTCATTTCCAAAATTTTATTTATT
Found at i:1375333 original size:42 final size:42
Alignment explanation
Indices: 1375269--1375354 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
1375259 CCATGTTACC
*
1375269 TATTTAGGGTAAAATTGTCATTTCTTGGTTATTTAAGGTCAT
1 TATTCAGGGTAAAATTGTCATTTCTTGGTTATTTAAGGTCAT
*
1375311 TATTCAGGGTAAAATTGTCATTTCTTGGTTATTTAATGTCAT
1 TATTCAGGGTAAAATTGTCATTTCTTGGTTATTTAAGGTCAT
1375353 TA
1 TA
1375355 GAATGTTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (42 bp):
TATTCAGGGTAAAATTGTCATTTCTTGGTTATTTAAGGTCAT
Found at i:1375350 original size:21 final size:21
Alignment explanation
Indices: 1375284--1375353 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
1375274 AGGGTAAAAT
1375284 TGTCATTTCTTGGTTATTTAA
1 TGTCATTTCTTGGTTATTTAA
* * * *
1375305 GGTCATTAT-TCAGGGTA--AAA
1 TGTCATT-TCT-TGGTTATTTAA
1375325 TTGTCATTTCTTGGTTATTTAA
1 -TGTCATTTCTTGGTTATTTAA
1375347 TGTCATT
1 TGTCATT
1375354 AGAATGTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
20 7 0.20
21 21 0.60
22 7 0.20
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.50
Consensus pattern (21 bp):
TGTCATTTCTTGGTTATTTAA
Found at i:1376901 original size:52 final size:52
Alignment explanation
Indices: 1376776--1376964 Score: 195
Period size: 52 Copynumber: 3.7 Consensus size: 52
1376766 TTTGAAAAGA
* * * * * * **
1376776 AAATGTATCGATAAATT-TTTATTGTATCAATATATT-TTGG-GTTTGGTCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCTAGGTTTTTGAACC
* *
1376825 AAATGTATCGATACATTTTTCATTGTATCGATACATTCTAGGTTTTTGACCC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCTAGGTTTTTGAACC
* * * * * *
1376877 GACTGTATCAATATATTATTCATTGTATCGATAAATTCTGGGTTTTTGAACC
1 AAATGTATCGATACATTATTCATTGTATCGATACATTCTAGGTTTTTGAACC
* *
1376929 AAATGTATCGATACATTCTTCAATGTATCGATACAT
1 AAATGTATCGATACATTATTCATTGTATCGATACAT
1376965 CCAGTTACAT
Statistics
Matches: 114, Mismatches: 23, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
49 16 0.14
50 16 0.14
51 3 0.03
52 79 0.69
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (52 bp):
AAATGTATCGATACATTATTCATTGTATCGATACATTCTAGGTTTTTGAACC
Found at i:1379323 original size:69 final size:70
Alignment explanation
Indices: 1379176--1379334 Score: 223
Period size: 69 Copynumber: 2.3 Consensus size: 70
1379166 ATTCTTCCAA
* *
1379176 GGCGATACTCCAACCCCATTTTTAAACTTGTCACAATCTAAATTTTATTTTTGCTCAAATTATCA
1 GGCGATACTCCAACCCTATTTTTAAACTTGTCACAATCTAAATTTTATTTTTGATCAAATTATCA
1379241 TCATC
66 TCATC
* * * ** *
1379246 GGCGATACTCTAACCCTATTTTTATACTTTTCATGATCTAAA-TTTATTTTTGATCAAATTATTA
1 GGCGATACTCCAACCCTATTTTTAAACTTGTCACAATCTAAATTTTATTTTTGATCAAATTATCA
1379310 TCATC
66 TCATC
1379315 GAG-GATACTCCAACCCTATT
1 G-GCGATACTCCAACCCTATT
1379335 CCTTTGAGGG
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
69 42 0.53
70 37 0.47
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (70 bp):
GGCGATACTCCAACCCTATTTTTAAACTTGTCACAATCTAAATTTTATTTTTGATCAAATTATCA
TCATC
Found at i:1381263 original size:19 final size:20
Alignment explanation
Indices: 1381239--1381277 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1381229 CATAATTTGA
1381239 ATAATTATGAT-TTTTATTT
1 ATAATTATGATATTTTATTT
* *
1381258 ATAATTTTGGTATTTTATTT
1 ATAATTATGATATTTTATTT
1381278 TTTACTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.28, C:0.00, G:0.08, T:0.64
Consensus pattern (20 bp):
ATAATTATGATATTTTATTT
Found at i:1382882 original size:78 final size:78
Alignment explanation
Indices: 1382795--1382953 Score: 282
Period size: 78 Copynumber: 2.0 Consensus size: 78
1382785 ATTTAAGAAT
*
1382795 GAAGATAGAAGCAAAAGTAAAGGAAGTGAAAAGAATGGAAGAAAAGTATAATTTAATGAAGAATG
1 GAAGATAGAAGCAAAAGTAAAGGAAGTGAAAAGAATGGAAGAAAAGTATAATTTAATGAAGAATA
1382860 ATTGGATTGAGCA
66 ATTGGATTGAGCA
* *
1382873 GAAGATAGAAGCAAAAGTAAAGGATGTGAATAGAATGGAAGAAAAGTATAATTTAATGAAGAATA
1 GAAGATAGAAGCAAAAGTAAAGGAAGTGAAAAGAATGGAAGAAAAGTATAATTTAATGAAGAATA
*
1382938 ATTGGATTGGGCA
66 ATTGGATTGAGCA
1382951 GAA
1 GAA
1382954 CAAGAAACTA
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.50, C:0.03, G:0.27, T:0.20
Consensus pattern (78 bp):
GAAGATAGAAGCAAAAGTAAAGGAAGTGAAAAGAATGGAAGAAAAGTATAATTTAATGAAGAATA
ATTGGATTGAGCA
Found at i:1383709 original size:4 final size:4
Alignment explanation
Indices: 1383700--1383765 Score: 59
Period size: 4 Copynumber: 17.0 Consensus size: 4
1383690 TCATACCATG
* * *
1383700 CATA CATA CATTA TATA CATA CATA C-T- CATG CATA CATA CATTA TATA
1 CATA CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CA-TA CATA
1383748 CATA CATA C-T- CATA CATA
1 CATA CATA CATA CATA CATA
1383766 ACTATTAATT
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
2 2 0.04
3 4 0.08
4 39 0.76
5 6 0.12
ACGTcount: A:0.44, C:0.23, G:0.02, T:0.32
Consensus pattern (4 bp):
CATA
Found at i:1383717 original size:13 final size:13
Alignment explanation
Indices: 1383701--1383754 Score: 63
Period size: 13 Copynumber: 3.8 Consensus size: 13
1383691 CATACCATGC
1383701 ATACATACATTAT
1 ATACATACATTAT
1383714 ATACATACATACTCAT
1 ATACATACAT--T-AT
1383730 GCATACATACATTAT
1 --ATACATACATTAT
1383745 ATACATACAT
1 ATACATACAT
1383755 ACTCATACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
13 20 0.56
15 3 0.08
16 3 0.08
18 10 0.28
ACGTcount: A:0.44, C:0.20, G:0.02, T:0.33
Consensus pattern (13 bp):
ATACATACATTAT
Found at i:1383731 original size:31 final size:31
Alignment explanation
Indices: 1383691--1383765 Score: 134
Period size: 31 Copynumber: 2.5 Consensus size: 31
1383681 TTCATGTATT
1383691 CATAC-CATGCATACATACATTATATACATA
1 CATACTCATGCATACATACATTATATACATA
1383721 CATACTCATGCATACATACATTATATACATA
1 CATACTCATGCATACATACATTATATACATA
*
1383752 CATACTCATACATA
1 CATACTCATGCATA
1383766 ACTATTAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 5 0.12
31 38 0.88
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.31
Consensus pattern (31 bp):
CATACTCATGCATACATACATTATATACATA
Found at i:1389218 original size:42 final size:42
Alignment explanation
Indices: 1389159--1389245 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
1389149 GAGTTTCCAA
*
1389159 CAACTGAAGAAACACAAGAAAAACAAGAATCAACAAGTAATC
1 CAACTGAAGAAAAACAAGAAAAACAAGAATCAACAAGTAATC
1389201 CAACTGAAGAAAAACAAGAAAAACAAGAATCAACAAGTAATC
1 CAACTGAAGAAAAACAAGAAAAACAAGAATCAACAAGTAATC
1389243 CAA
1 CAA
1389246 GCATTCAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.61, C:0.18, G:0.11, T:0.09
Consensus pattern (42 bp):
CAACTGAAGAAAAACAAGAAAAACAAGAATCAACAAGTAATC
Found at i:1390227 original size:125 final size:125
Alignment explanation
Indices: 1390005--1390255 Score: 412
Period size: 125 Copynumber: 2.0 Consensus size: 125
1389995 GAAGTGTGAA
*
1390005 AAATCATCGTAAATGGACCACGAGTTCCAACAAGGAAGGTTGATGACATCCTCATTCCAAAGGAG
1 AAATCATCGTAAATGGACCACGAGTTCCAAAAAGGAAGGTTGATGACATCCTCATTCCAAAGGAG
* * * * *
1390070 GAAGAAGGGTGGGATGAATAAGACACAAAAATGGCATAACTTAATACCAAAGCAATGCAT
66 GAAGAAGAGTGGGATGAACAAGACACAAAAATGGCACAACTCAACACCAAAGCAATGCAT
* * *
1390130 AAATCATCGTAAATGGACCACGAGTTCCAAAAAGGAAGGTTGATGACGTGCTTATTCCAAAGGAG
1 AAATCATCGTAAATGGACCACGAGTTCCAAAAAGGAAGGTTGATGACATCCTCATTCCAAAGGAG
*
1390195 GAAGAAGAGTGGGATGAACAAGACACAAAAATGGCACAACTCAACGCCAAAGCAATGCAT
66 GAAGAAGAGTGGGATGAACAAGACACAAAAATGGCACAACTCAACACCAAAGCAATGCAT
1390255 A
1 A
1390256 CATTGTTTTG
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 116 1.00
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.17
Consensus pattern (125 bp):
AAATCATCGTAAATGGACCACGAGTTCCAAAAAGGAAGGTTGATGACATCCTCATTCCAAAGGAG
GAAGAAGAGTGGGATGAACAAGACACAAAAATGGCACAACTCAACACCAAAGCAATGCAT
Found at i:1395812 original size:14 final size:14
Alignment explanation
Indices: 1395793--1395838 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
1395783 ATCATCATCG
1395793 AACCTTCAAAATCA
1 AACCTTCAAAATCA
*
1395807 AACCTTC---ATCG
1 AACCTTCAAAATCA
1395818 AACCTTCAAAATCA
1 AACCTTCAAAATCA
1395832 AACCTTC
1 AACCTTC
1395839 TTCAAAGTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
11 10 0.37
14 17 0.63
ACGTcount: A:0.41, C:0.33, G:0.02, T:0.24
Consensus pattern (14 bp):
AACCTTCAAAATCA
Found at i:1395815 original size:25 final size:25
Alignment explanation
Indices: 1395787--1395838 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1395777 AAGTGCATCA
1395787 TCATCGAACCTTCAAAATCAAACCT
1 TCATCGAACCTTCAAAATCAAACCT
1395812 TCATCGAACCTTCAAAATCAAACCT
1 TCATCGAACCTTCAAAATCAAACCT
1395837 TC
1 TC
1395839 TTCAAAGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.33, G:0.04, T:0.25
Consensus pattern (25 bp):
TCATCGAACCTTCAAAATCAAACCT
Found at i:1396437 original size:20 final size:21
Alignment explanation
Indices: 1396412--1396466 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1396402 TTGCACATAC
**
1396412 AATGTATCGATACATGACCA-
1 AATGTATCGATACATGAAAAG
*
1396432 AATGTATCGATACTTGAAAAG
1 AATGTATCGATACATGAAAAG
1396453 AATGTATCGATACA
1 AATGTATCGATACA
1396467 GGTCATTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAG
Found at i:1396517 original size:13 final size:13
Alignment explanation
Indices: 1396499--1396523 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1396489 TAGCCAAATT
1396499 TGTATCGATACAC
1 TGTATCGATACAC
1396512 TGTATCGATACA
1 TGTATCGATACA
1396524 TCCCAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1405172 original size:13 final size:13
Alignment explanation
Indices: 1405156--1405215 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
1405146 AATGATGGAA
1405156 AAAAAAACAAAAC
1 AAAAAAACAAAAC
1405169 AAAAAAA-ACAAAC
1 AAAAAAACA-AAAC
1405182 AAAAAAAACAACAAC
1 -AAAAAAACAA-AAC
* *
1405197 AAAAAAGC-ACAC
1 AAAAAAACAAAAC
1405209 AAAAAAA
1 AAAAAAA
1405216 AGAGAGGCAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 9 0.22
13 12 0.30
14 15 0.38
15 4 0.10
ACGTcount: A:0.82, C:0.17, G:0.02, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAC
Found at i:1405172 original size:14 final size:14
Alignment explanation
Indices: 1405155--1405202 Score: 80
Period size: 13 Copynumber: 3.4 Consensus size: 14
1405145 AAATGATGGA
1405155 AAAAAAAACAAAAC
1 AAAAAAAACAAAAC
1405169 AAAAAAAAC-AAAC
1 AAAAAAAACAAAAC
1405182 AAAAAAAACAACAAC
1 AAAAAAAACAA-AAC
1405197 AAAAAA
1 AAAAAA
1405203 GCACACAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.41
14 10 0.31
15 9 0.28
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAACAAAAC
Found at i:1405176 original size:9 final size:9
Alignment explanation
Indices: 1405155--1405192 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1405145 AAATGATGGA
1405155 AAAAAAAAC
1 AAAAAAAAC
1405164 AAAACAAAA-
1 AAAA-AAAAC
*
1405173 AAAACAAAC
1 AAAAAAAAC
1405182 AAAAAAAAC
1 AAAAAAAAC
1405191 AA
1 AA
1405193 CAACAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 3 0.12
9 18 0.72
10 4 0.16
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1405185 original size:27 final size:27
Alignment explanation
Indices: 1405155--1405216 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
1405145 AAATGATGGA
1405155 AAAAAAAACAA-AACAAAAAAAACAAAC
1 AAAAAAAACAACAAC-AAAAAAACAAAC
* *
1405182 AAAAAAAACAACAACAAAAAAGCACAC
1 AAAAAAAACAACAACAAAAAAACAAAC
1405209 AAAAAAAA
1 AAAAAAAA
1405217 GAGAGGCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (27 bp):
AAAAAAAACAACAACAAAAAAACAAAC
Found at i:1405210 original size:15 final size:12
Alignment explanation
Indices: 1405155--1405216 Score: 70
Period size: 13 Copynumber: 4.7 Consensus size: 12
1405145 AAATGATGGA
1405155 AAAAAAAACAAAAC
1 AAAAAAAAC--AAC
1405169 AAAAAAAACAAAC
1 AAAAAAAAC-AAC
1405182 AAAAAAAACAAC
1 AAAAAAAACAAC
1405194 AACAAAAAAGCACAC
1 AA-AAAAAA-CA-AC
1405209 AAAAAAAA
1 AAAAAAAA
1405217 GAGAGGCAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.11
13 19 0.42
14 17 0.38
15 4 0.09
ACGTcount: A:0.82, C:0.16, G:0.02, T:0.00
Consensus pattern (12 bp):
AAAAAAAACAAC
Found at i:1406623 original size:31 final size:30
Alignment explanation
Indices: 1406497--1406670 Score: 199
Period size: 30 Copynumber: 5.7 Consensus size: 30
1406487 ATACCTTCTT
1406497 AAAGTCCACGACTCAGTGGCATTTTGTCCC
1 AAAGTCCACGACTCAGTGGCATTTTGTCCC
* * *
1406527 AAAGCCCACAACTTAGTGGCATTTTGTCCC
1 AAAGTCCACGACTCAGTGGCATTTTGTCCC
* *
1406557 AAAGCCCACGACTTAGTGGCATTTTGTCCC
1 AAAGTCCACGACTCAGTGGCATTTTGTCCC
* *
1406587 AAAGTCCACGAGTCAGTGGCATTTTTTCTCC
1 AAAGTCCACGACTCAGTGGCATTTTGTC-CC
** * *
1406618 AAAGTCCATAACTTAGTGGCAATCTCTT-T-TC
1 AAAGTCCACGACTCAGTGGC-AT-T-TTGTCCC
1406649 AAAGTCCACGACTCAGTGGCAT
1 AAAGTCCACGACTCAGTGGCAT
1406671 CTTTTCTTCA
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
30 82 0.66
31 36 0.29
32 2 0.02
33 2 0.02
34 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (30 bp):
AAAGTCCACGACTCAGTGGCATTTTGTCCC
Found at i:1406665 original size:62 final size:61
Alignment explanation
Indices: 1406497--1406692 Score: 218
Period size: 60 Copynumber: 3.2 Consensus size: 61
1406487 ATACCTTCTT
* * * * * * *
1406497 AAAGTCCACGACTCAGTGGCATTTTGTCCCAAAGCCCACAACTTAGTGGCATTTTGTC-CC
1 AAAGCCCACAACTTAGTGGCATTTTGTCCCAAAGTCCACGACTCAGTGGCATTTTTTCTCC
* *
1406557 AAAGCCCACGACTTAGTGGCATTTTGTCCCAAAGTCCACGAGTCAGTGGCATTTTTTCTCC
1 AAAGCCCACAACTTAGTGGCATTTTGTCCCAAAGTCCACGACTCAGTGGCATTTTTTCTCC
* * * * *
1406618 AAAGTCCATAACTTAGTGGCAATCTCTT-T-TCAAAGTCCACGACTCAGTGGCATCTTTTCTTC
1 AAAGCCCACAACTTAGTGGC-AT-T-TTGTCCCAAAGTCCACGACTCAGTGGCATTTTTTCTCC
1406680 AAAGCCCACAACT
1 AAAGCCCACAACT
1406693 CCGTGGCACC
Statistics
Matches: 116, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
60 51 0.44
61 19 0.16
62 42 0.36
63 2 0.02
64 2 0.02
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (61 bp):
AAAGCCCACAACTTAGTGGCATTTTGTCCCAAAGTCCACGACTCAGTGGCATTTTTTCTCC
Found at i:1406761 original size:33 final size:33
Alignment explanation
Indices: 1406650--1407008 Score: 286
Period size: 34 Copynumber: 10.8 Consensus size: 33
1406640 TCTCTTTTCA
* * * **
1406650 AAGTCCACGACTCAGTGGCATC-TTTT-CTTCA
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
*
1406681 AAGCCCACAACTCCGTGGCACCTTTTT-CTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* * *
1406713 CAAAGCCCACAACTCCATGGCACCTTGTTCCTTTT
1 --AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
1406748 AAGTCCACAACTCCGTGGCATCTTTTTCCTTTA
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
1406781 AAGACCACAACTCCGTGGCATTCC-TTTTCTTTTT
1 AAGTCCACAACTCCGTGGCA--CCTTTTTCCTTTT
* * **
1406815 AAAGTCCACAACTCCGTGGCATCTCTTTCCTTCA
1 -AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* * *
1406849 AAGTCCACAACTCAGTGGCATCCCTTTTTTC-TGT
1 AAGTCCACAACTCCGTGGCA--CCTTTTTCCTTTT
* * *
1406883 AAGTCCATAACTCAGTGGCATCTCTTTT-C---T
1 AAGTCCACAACTCCGTGGCACCT-TTTTCCTTTT
* * * *
1406913 AAATCCACGACTCTGTGACACCTTTTTCCTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
* *
1406946 AAAGCCCACAACTCCATGGCACTCTTTTTCCCTTTT
1 -AAGTCCACAACTCCGTGGCAC-CTTTTT-CCTTTT
*
1406982 AAGTCCACAACTTCGTGGCACCTTTTT
1 AAGTCCACAACTCCGTGGCACCTTTTT
1407009 AAGTCTATAA
Statistics
Matches: 264, Mismatches: 46, Indels: 33
0.77 0.13 0.10
Matches are distributed among these distances:
29 4 0.02
30 19 0.07
31 18 0.07
32 10 0.04
33 72 0.27
34 80 0.30
35 55 0.21
36 6 0.02
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (33 bp):
AAGTCCACAACTCCGTGGCACCTTTTTCCTTTT
Found at i:1406835 original size:68 final size:66
Alignment explanation
Indices: 1406649--1407007 Score: 333
Period size: 68 Copynumber: 5.4 Consensus size: 66
1406639 ATCTCTTTTC
* * * * * * *
1406649 AAAGTCCACGACTCAGTGGCATCTTTT-C-TTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAAGTCCACAACTCCGTGGCATCTTTTTCCTT
1406712 T
66 T
* *
1406713 CAAAGCCCACAACTCCATGGCACCTTGTTCCTTTT-AAGTCCACAACTCCGTGGCATCTTTTTCC
1 -AAAGTCCACAACTCCGTGGCACCTT-TTCCTTTTAAAGTCCACAACTCCGTGGCATCTTTTTCC
1406777 TTT
64 TTT
* * *
1406780 AAAGACCACAACTCCGTGGCATTCCTTTTCTTTTTAAAGTCCACAACTCCGTGGCATCTCTTTCC
1 AAAGTCCACAACTCCGTGGCA--CCTTTTCCTTTTAAAGTCCACAACTCCGTGGCATCTTTTTCC
*
1406845 TTC
64 TTT
* * *
1406848 AAAGTCCACAACTCAGTGGCATCCCTTTT--TTCTGT-AAGTCCATAACTCAGTGGCATCTCTTT
1 AAAGTCCACAACTCCGTGGCA--CCTTTTCCTT-T-TAAAGTCCACAACTCCGTGGCATCT-TTT
1406910 T-C--T
61 TCCTTT
* * * * *
1406913 AAA-TCCACGACTCTGTGACACCTTTTTCCTTTTAAAGCCCACAACTCCATGGCACTCTTTTTCC
1 AAAGTCCACAACTCCGTGGCACC-TTTTCCTTTTAAAGTCCACAACTCCGTGGCA-TCTTTTT-C
1406977 CTTT
63 CTTT
* *
1406981 TAAGTCCACAACTTCGTGGCACCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTT
1407008 TAAGTCTATA
Statistics
Matches: 242, Mismatches: 33, Indels: 35
0.78 0.11 0.11
Matches are distributed among these distances:
62 2 0.01
63 5 0.02
64 35 0.14
65 28 0.12
66 24 0.10
67 60 0.25
68 73 0.30
69 15 0.06
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (66 bp):
AAAGTCCACAACTCCGTGGCACCTTTTCCTTTTAAAGTCCACAACTCCGTGGCATCTTTTTCCTT
T
Found at i:1406836 original size:166 final size:165
Alignment explanation
Indices: 1406642--1407007 Score: 400
Period size: 166 Copynumber: 2.2 Consensus size: 165
1406632 AGTGGCAATC
* * * * *
1406642 TCTTTTCAAAGTCCACGACTCAGTGGCATCTTTT-CTTCAAAGCCCACAACTCCGTGGCA-CCTT
1 TCTTTTTAAAGTCCACAACTCCGTGGCATCTTTTCCTTCAAAGCCCACAACTCAGTGGCATCCCT
* * * * * *
1406705 TTTCTTTTCAAAGCCCACAACTCCA-TGGCACCTTGTTCCTTTTAAGTCCACAACTCCGTGGCAT
66 TTT-TTCTCAAAGCCCACAACT-CAGTGGCACC-TCTT--TTCTAAATCCACAACTCCGTGACAC
* *
1406769 CTTTTTCC-TTTAAAGACCACAACTCCGTGGCATTCCTTT
126 CTTTTTCCTTTTAAAGACCACAACTCCATGGCACTCCTTT
*
1406808 TCTTTTTAAAGTCCACAACTCCGTGGCATCTCTTTCCTTCAAAGTCCACAACTCAGTGGCATCCC
1 TCTTTTTAAAGTCCACAACTCCGTGGCATCT-TTTCCTTCAAAGCCCACAACTCAGTGGCATCCC
** * * * * *
1406873 TTTTTTCTGTAAGTCCATAACTCAGTGGCATCTCTTTTCTAAATCCACGACTCTGTGACACCTTT
65 TTTTTTCTCAAAGCCCACAACTCAGTGGCACCTCTTTTCTAAATCCACAACTCCGTGACACCTTT
* *
1406938 TTCCTTTTAAAGCCCACAACTCCATGGCACTCTTTT
130 TTCCTTTTAAAGACCACAACTCCATGGCACTCCTTT
* * *
1406974 TCCCTTTT-AAGTCCACAACTTCGTGGCACCTTTT
1 T-CTTTTTAAAGTCCACAACTCCGTGGCATCTTTT
1407008 TAAGTCTATA
Statistics
Matches: 168, Mismatches: 26, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
165 30 0.18
166 77 0.46
167 13 0.08
168 42 0.25
169 6 0.04
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.35
Consensus pattern (165 bp):
TCTTTTTAAAGTCCACAACTCCGTGGCATCTTTTCCTTCAAAGCCCACAACTCAGTGGCATCCCT
TTTTTCTCAAAGCCCACAACTCAGTGGCACCTCTTTTCTAAATCCACAACTCCGTGACACCTTTT
TCCTTTTAAAGACCACAACTCCATGGCACTCCTTT
Found at i:1406973 original size:35 final size:35
Alignment explanation
Indices: 1406643--1407008 Score: 301
Period size: 33 Copynumber: 11.0 Consensus size: 35
1406633 GTGGCAATCT
* *
1406643 CTTTTCAAAGTCCACGACTCAGTGGCA-TC-TTTT-
1 CTTTT-AAAGTCCACAACTCCGTGGCACTCTTTTTC
* *
1406676 C-TTCAAAGCCCACAACTCCGTGGCAC-CTTTTT-
1 CTTTTAAAGTCCACAACTCCGTGGCACTCTTTTTC
* * *
1406708 CTTTTCAAAGCCCACAACTCCATGGCAC-CTTGTTC
1 CTTTT-AAAGTCCACAACTCCGTGGCACTCTTTTTC
1406743 CTTTT-AAGTCCACAACTCCGTGGCA-TCTTTTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACTCTTTTTC
* * *
1406776 C-TTTAAAGACCACAACTCCGTGGCATTCCTTTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACTCTTTTTC
* *
1406810 TTTTTAAAGTCCACAACTCCGTGGCA-TCTCTTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACTCTTTTTC
* * * *
1406844 C-TTCAAAGTCCACAACTCAGTGGCATCCCTTTTTT
1 CTTTTAAAGTCCACAACTCCGTGGCA-CTCTTTTTC
* * *
1406879 C-TGT-AAGTCCATAACTCAGTGGCA-TCTCTTTT-
1 CTTTTAAAGTCCACAACTCCGTGGCACTCT-TTTTC
* * *
1406911 C---TAAA-TCCACGACTCTGTGACAC-CTTTTTC
1 CTTTTAAAGTCCACAACTCCGTGGCACTCTTTTTC
* *
1406941 CTTTTAAAGCCCACAACTCCATGGCACTCTTTTTCC
1 CTTTTAAAGTCCACAACTCCGTGGCACTCTTTTT-C
*
1406977 CTTTT-AAGTCCACAACTTCGTGGCAC-CTTTTT
1 CTTTTAAAGTCCACAACTCCGTGGCACTCTTTTT
1407009 AAGTCTATAA
Statistics
Matches: 274, Mismatches: 38, Indels: 41
0.78 0.11 0.12
Matches are distributed among these distances:
29 4 0.01
30 17 0.06
31 21 0.08
32 13 0.05
33 77 0.28
34 77 0.28
35 59 0.22
36 6 0.02
ACGTcount: A:0.22, C:0.32, G:0.12, T:0.35
Consensus pattern (35 bp):
CTTTTAAAGTCCACAACTCCGTGGCACTCTTTTTC
Found at i:1407027 original size:27 final size:27
Alignment explanation
Indices: 1406978--1407033 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 27
1406968 TCTTTTTCCC
* *
1406978 TTTTAAGTCCACAACTTCGTGGCACCT
1 TTTTAAGTCCACAACTCCCTGGCACCT
* * *
1407005 TTTTAAGTCTATAACTCCCTGGCATCT
1 TTTTAAGTCCACAACTCCCTGGCACCT
1407032 TT
1 TT
1407034 CTCCTTTTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.27, G:0.12, T:0.39
Consensus pattern (27 bp):
TTTTAAGTCCACAACTCCCTGGCACCT
Found at i:1407171 original size:49 final size:48
Alignment explanation
Indices: 1407101--1407866 Score: 629
Period size: 49 Copynumber: 15.9 Consensus size: 48
1407091 GACATCTTCT
* *
1407101 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATTGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTATC
* * * * *
1407150 TTTAAGACCAATGTCGCTGGCCTTAAATCAGCACATTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATC
* *
1407199 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTAGCGCCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-T-ATC
* * * *
1407251 TTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGGCA-C----C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATC
* * *
1407294 TTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TTATC
* * * * * *
1407343 TTTAAGACCAATGTTGCTGGCCTTGAATCAACACATTGGCATCCTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTTATC
** * *
1407392 TTTAAGTCCGGTATCGCTGGCCTTGAATCACCATATTAGCA-CTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATC
* * * * * *
1407440 TTTAAGACTAATGTCGTTGGCCTTGAATCAACACATT-G-A-C--A--
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATC
* * * *
1407481 --TAAG-CCTAATGTCGCGGGCCTTGAATCAGCACATTGGCATCTTCATC
1 TTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATC
* **
1407528 TTTGAGTCCGGTATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-T--T-ATC
* * *
1407580 TTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCTTGTT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATC
* * * * * *
1407628 TTTAAAGACCAATGTCGCTGGCCTTGAATCAGTACATCGG-A---T-CC
1 TTT-AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATC
* * *
1407672 TTTAAGTCCAATATCACTGGCCTTGAATCAGCAGATTGGCGCCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-T-ATC
* * * *
1407724 TTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTT-ATC
** *
1407773 TTTAAGTCCGGTATCGCTAGCCTTGAATCAGCATATTGGCACCCTCGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCT--T-ATC
*
1407825 TTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCAC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1407867 TGTTAGGATC
Statistics
Matches: 576, Mismatches: 101, Indels: 78
0.76 0.13 0.10
Matches are distributed among these distances:
38 1 0.00
39 29 0.05
40 1 0.00
41 1 0.00
42 1 0.00
43 67 0.12
44 4 0.01
45 2 0.00
46 2 0.00
47 3 0.01
48 39 0.07
49 249 0.43
50 9 0.02
51 4 0.01
52 164 0.28
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (48 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTATC
Found at i:1407352 original size:193 final size:191
Alignment explanation
Indices: 1407101--1407863 Score: 916
Period size: 193 Copynumber: 4.0 Consensus size: 191
1407091 GACATCTTCT
* *
1407101 TTTAAGCCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATTGTCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
*
1407166 CTGGCCTTAAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
66 CTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
* * * *
1407231 ATATTAGCGCCTTTGTCATCTTTAAGTCCAATGTCACTAGCCTTGAATCAGCACATTGGCACC
131 ATATTAGCACC-TTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG-ACC
* * *
1407294 TTTAAGTCCAATATCGCTGGCCTTGAATTAGCATATTGGCGCCTTTGTCTTTAAGACCAATGTTG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
* * ** *
1407359 CTGGCCTTGAATCAACACATTGGCATCCTCATCTTTAAGTCCGGTATCGCTGGCCTTGAATCACC
66 CTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
* * *
1407424 ATATTAGCA-C-T-TCATCTTTAAGACTAATGTCGTTGGCCTTGAATCAACACATT-GA-C
131 ATATTAGCACCTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGACC
* * * * * ** * * ** *
1407480 -ATAAG-CCTAATGTCGCGGGCCTTGAATCAGCACATTGGCATCTTCATCTTTGAGTCCGGTATC
1 TTTAAGTCC-AATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTC
* * *
1407543 GCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGTCCAATATTGCTGGCCTTGAAT
65 GCTGGCCTTGAATCAGCACATTGGCA---TCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAAT
* * *
1407608 CAGCATATTGGCACCTTGT--T-TTTAAAGACCAATGTCGCTGGCCTTGAATCAGTACATCGGAT
127 CAGCATATTAGCACCTTGTCATCTTT-AAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGA-
1407670 CC
190 CC
* * * *
1407672 TTTAAGTCCAATATCACTGGCCTTGAATCAGCAGATTGGCGCCTTTGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTG---TCTTTAAGACCAATG
* ** *
1407737 TTGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCGGTATCGCTAGCCTTGAATC
63 TCGCTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATC
* * * *
1407802 AGCATATTGGCACCCTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGG
128 AGCATATTAGCA-CCTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGG
1407864 CACTGTTAGG
Statistics
Matches: 479, Mismatches: 71, Indels: 37
0.82 0.12 0.06
Matches are distributed among these distances:
184 2 0.00
185 69 0.14
186 1 0.00
187 1 0.00
188 47 0.10
189 67 0.14
190 4 0.01
191 1 0.00
192 2 0.00
193 205 0.43
194 7 0.01
196 70 0.15
197 3 0.01
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (191 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCG
CTGGCCTTGAATCAGCACATTGGCATCTTCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGC
ATATTAGCACCTTGTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGACC
Found at i:1407501 original size:39 final size:39
Alignment explanation
Indices: 1407442--1407516 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
1407432 ACTTCATCTT
**
1407442 TAAGACTAATGTCGTTGGCCTTGAATCAACACATTGACA
1 TAAGACTAATGTCGCGGGCCTTGAATCAACACATTGACA
* *
1407481 TAAGCCTAATGTCGCGGGCCTTGAATCAGCACATTG
1 TAAGACTAATGTCGCGGGCCTTGAATCAACACATTG
1407517 GCATCTTCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (39 bp):
TAAGACTAATGTCGCGGGCCTTGAATCAACACATTGACA
Found at i:1407790 original size:144 final size:144
Alignment explanation
Indices: 1407539--1407803 Score: 379
Period size: 144 Copynumber: 1.8 Consensus size: 144
1407529 TTGAGTCCGG
* *
1407539 TATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCATCTTTAAGTCCAATATTGCTGGCCTT
1 TATCACTGGCCTTGAATCAGCAGATTGGCACCTTCATCATCTTTAAGTCCAATATTGCTGGCCTT
* * * * *
1407604 GAATCAGCATATTGGCACCTTGTTTTTAAAGACCAATGTCGCTGGCCTTGAATCAGTACATCGGA
66 GAATCAGCACATTGGCACCTTATCTTTAAAGACCAATATCGCTAGCCTTGAATCAGTACATCGGA
1407669 TCCTTTAAGTCCAA
131 TCCTTTAAGTCCAA
* ** *
1407683 TATCACTGGCCTTGAATCAGCAGATTGGCGCCTTTGTCATCTTTAAGTCCAATGTTGCTGGCCTT
1 TATCACTGGCCTTGAATCAGCAGATTGGCACCTTCATCATCTTTAAGTCCAATATTGCTGGCCTT
* * **
1407748 GAATCAGCACATTGGCATCTTCATCTTT-AAGTCCGGTATCGCTAGCCTTGAATCAG
66 GAATCAGCACATTGGCACCTT-ATCTTTAAAGACCAATATCGCTAGCCTTGAATCAG
1407804 CATATTGGCA
Statistics
Matches: 105, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
144 101 0.96
145 4 0.04
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (144 bp):
TATCACTGGCCTTGAATCAGCAGATTGGCACCTTCATCATCTTTAAGTCCAATATTGCTGGCCTT
GAATCAGCACATTGGCACCTTATCTTTAAAGACCAATATCGCTAGCCTTGAATCAGTACATCGGA
TCCTTTAAGTCCAA
Found at i:1407846 original size:101 final size:99
Alignment explanation
Indices: 1407492--1407865 Score: 408
Period size: 101 Copynumber: 3.8 Consensus size: 99
1407482 AAGCCTAATG
* * * * ** *
1407492 TCGCGGGCCTTGAATCAGCACATTGGCA--TCTTCATCTTTGAGTCCGGTATCGCTGGCCTTGAA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAA
*
1407555 TCAGCATATTGGCACCTTCATCATCTTTAAGTCCAATA
66 TCAGCACATTGGCA---TC-TCATCTTTAAGTCCAATA
* * *
1407593 TTGCTGGCCTTGAATCAGCATATTGGCACCTTGT--T-TTTAAAGACCAATGTCGCTGGCCTTGA
1 TCGCTGGCCTTGAATCAGCATATTGGCACCTCGTCATCTTT-AAGTCCAATGTCGCTGGCCTTGA
* *
1407655 ATCAGTACATCGG-A--TC--CTTTAAGTCCAATA
65 ATCAGCACATTGGCATCTCATCTTTAAGTCCAATA
* * * * *
1407685 TCACTGGCCTTGAATCAGCAGATTGGCGCCTTTGTCATCTTTAAGTCCAATGTTGCTGGCCTTGA
1 TCGCTGGCCTTGAATCAGCATATTGGCACC-TCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGA
**
1407750 ATCAGCACATTGGCATCTTCATCTTTAAGTCCGGTA
65 ATCAGCACATTGGCATC-TCATCTTTAAGTCCAATA
*
1407786 TCGCTAGCCTTGAATCAGCATATTGGCACCCTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGA
1 TCGCTGGCCTTGAATCAGCATATTGGCA-CCTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGA
*
1407851 ATCAGCATATTGGCA
65 ATCAGCACATTGGCA
1407866 CTGTTAGGAT
Statistics
Matches: 229, Mismatches: 30, Indels: 28
0.80 0.10 0.10
Matches are distributed among these distances:
92 40 0.17
93 4 0.02
94 2 0.01
95 33 0.14
96 4 0.02
99 2 0.01
100 4 0.02
101 136 0.59
102 2 0.01
103 2 0.01
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (99 bp):
TCGCTGGCCTTGAATCAGCATATTGGCACCTCGTCATCTTTAAGTCCAATGTCGCTGGCCTTGAA
TCAGCACATTGGCATCTCATCTTTAAGTCCAATA
Found at i:1407863 original size:52 final size:51
Alignment explanation
Indices: 1407671--1407866 Score: 252
Period size: 52 Copynumber: 3.8 Consensus size: 51
1407661 ACATCGGATC
* * * *
1407671 CTTTAAGTCCAATATCACTGGCCTTGAATCAGCAGATTGGCGCCTTTGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TCGTCAT
* * * *
1407723 CTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACATTGGCA--TCTTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCGTCAT
** *
1407772 CTTTAAGTCCGGTATCGCTAGCCTTGAATCAGCATATTGGCACCCTCGTCAT
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTCGTCAT
*
1407824 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC
1407867 TGTTAGGATC
Statistics
Matches: 123, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
49 41 0.33
51 1 0.01
52 81 0.66
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.32
Consensus pattern (51 bp):
CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCGTCAT
Found at i:1408163 original size:20 final size:20
Alignment explanation
Indices: 1408138--1408187 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1408128 ACCTTGAAAA
*
1408138 GTATCGATACACATTTAATT
1 GTATCGATACACATTGAATT
** *
1408158 GTATCGATACATGTTGCATT
1 GTATCGATACACATTGAATT
1408178 GTATCGATAC
1 GTATCGATAC
1408188 TTGAAAAAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (20 bp):
GTATCGATACACATTGAATT
Found at i:1408293 original size:20 final size:20
Alignment explanation
Indices: 1408268--1408305 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1408258 GTATGTATCA
*
1408268 ATAAAATGTATCGATACACC
1 ATAAAATATATCGATACACC
1408288 ATAAAATATATCGATACA
1 ATAAAATATATCGATACA
1408306 TTGGCTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (20 bp):
ATAAAATATATCGATACACC
Done.