Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008772.1 Hibiscus syriacus cultivar Beakdansim tig00111877_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3098974
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 16
Found at i:1238980 original size:33 final size:34
Alignment explanation
Indices: 1238923--1239016 Score: 127
Period size: 33 Copynumber: 2.8 Consensus size: 34
1238913 CATTTTCGCA
* * *
1238923 TTGCGATAGTCATTTTCGCGTTGCGATTTTGTTG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTGTCG
** *
1238957 TTGCGATTTTCA-TTTCGTATTGCGATTCTGTCG
1 TTGCGATAGTCATTTTCGCATTGCGATTCTGTCG
1238990 TTGCGATAGTCATTTTCGCATTGCGAT
1 TTGCGATAGTCATTTTCGCATTGCGAT
1239017 AATAAAATAT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
33 27 0.54
34 23 0.46
ACGTcount: A:0.14, C:0.17, G:0.23, T:0.46
Consensus pattern (34 bp):
TTGCGATAGTCATTTTCGCATTGCGATTCTGTCG
Found at i:1240922 original size:20 final size:20
Alignment explanation
Indices: 1240879--1240952 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
1240869 GAAATTTTAA
**
1240879 ATCGTAACACGAAAATGAAA
1 ATCGTAACACGAAAATGACT
1240899 ATCGTAACACGAAAATGACT
1 ATCGTAACACGAAAATGACT
* * **
1240919 ATCGCAACGCGAATTTGACT
1 ATCGTAACACGAAAATGACT
*
1240939 ATCGTAACGCGAAA
1 ATCGTAACACGAAA
1240953 TAAAAATCTC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGTAACACGAAAATGACT
Found at i:1241326 original size:22 final size:22
Alignment explanation
Indices: 1241301--1241376 Score: 89
Period size: 22 Copynumber: 3.5 Consensus size: 22
1241291 TGACCGTGAA
*
1241301 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGCCGGAGATGGGGAC
* *
1241323 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGCCGGAGATGGGGAC
* *
1241345 TGATTTCGTCAGAGATGGGGAC
1 TGATTTCGCCGGAGATGGGGAC
* *
1241367 GGATGTCGCC
1 TGATTTCGCC
1241377 TTAGAGAGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 46 1.00
ACGTcount: A:0.21, C:0.17, G:0.38, T:0.24
Consensus pattern (22 bp):
TGATTTCGCCGGAGATGGGGAC
Found at i:1241584 original size:20 final size:20
Alignment explanation
Indices: 1241561--1241654 Score: 125
Period size: 20 Copynumber: 4.7 Consensus size: 20
1241551 CGATAGTCAG
1241561 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1241581 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* * **
1241601 AATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
* *
1241622 ATTTGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
1241642 ATTCGCATTGCGA
1 ATTCGCATTGCGA
1241655 ATTAGGAAAA
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:1241642 original size:61 final size:60
Alignment explanation
Indices: 1241541--1241654 Score: 174
Period size: 61 Copynumber: 1.9 Consensus size: 60
1241531 GCGCTATGTA
*
1241541 AATCGCATTGCGATAGTCAGATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
** * *
1241601 AATCGCATTGCGATTTTCCAAATTTGCGTTGCGATTTACGTATTCGCATTGCGA
1 AATCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGTATTCGCATTGCGA
1241655 ATTAGGAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
60 15 0.31
61 33 0.69
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGT
Found at i:1241690 original size:20 final size:21
Alignment explanation
Indices: 1241651--1241695 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1241641 TATTCGCATT
*
1241651 GCGAATTAGGAAAATTGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
1241672 GCGAATTTGG-AAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1241692 GCGA
1 GCGA
1241696 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1241695 original size:61 final size:61
Alignment explanation
Indices: 1241561--1241696 Score: 148
Period size: 61 Copynumber: 2.2 Consensus size: 61
1241551 CGATAGTCAG
* * ** *
1241561 ATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGAATTACGAAATCGCAACGCGAATTTCCAA
* * * * **
1241622 ATTTGCGTTGCGATTTACGTATTCGCATTGCGAATTAGGAAAATTGCAACGCGAATTTGGAA
1 ATTCGCATTGCGATTTACGTATTCGCATTGCGAATTACG-AAATCGCAACGCGAATTTCCAA
*
1241684 A-TCGCAATGCGAT
1 ATTCGCATTGCGAT
1241697 AGTCAGAATC
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
61 44 0.73
62 16 0.27
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (61 bp):
ATTCGCATTGCGATTTACGTATTCGCATTGCGAATTACGAAATCGCAACGCGAATTTCCAA
Found at i:1243889 original size:29 final size:29
Alignment explanation
Indices: 1243856--1243913 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1243846 CCATGATCGG
*
1243856 ACAATGTATGGCCCTGATTGGAAAAGCAT
1 ACAATGTATGGACCTGATTGGAAAAGCAT
*
1243885 ACAATGTATGGACTTGATTGGAAAAGCAT
1 ACAATGTATGGACCTGATTGGAAAAGCAT
1243914 GGGACTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (29 bp):
ACAATGTATGGACCTGATTGGAAAAGCAT
Found at i:1244542 original size:24 final size:25
Alignment explanation
Indices: 1244495--1244550 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
1244485 CAACATTTTA
*
1244495 TAAAAATTTGATAAATTATAAGGTC
1 TAAAAATTTGATAAAGTATAAGGTC
* *
1244520 TAAAAATTTGA-AAAGTCTGAGGTC
1 TAAAAATTTGATAAAGTATAAGGTC
*
1244544 CAAAAAT
1 TAAAAAT
1244551 GTAGTTATAC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 16 0.59
25 11 0.41
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.30
Consensus pattern (25 bp):
TAAAAATTTGATAAAGTATAAGGTC
Found at i:1244912 original size:31 final size:31
Alignment explanation
Indices: 1244877--1244943 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
1244867 AACACATTAG
*
1244877 TCACT-AATATTATCGATTTATAACAAAATGA
1 TCACTGAA-ATTATCAATTTATAACAAAATGA
* * *
1244908 TCACTGAAGTTATCAATTTGTAACAAAATGT
1 TCACTGAAATTATCAATTTATAACAAAATGA
1244939 TCACT
1 TCACT
1244944 CAATCGTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (31 bp):
TCACTGAAATTATCAATTTATAACAAAATGA
Found at i:1253006 original size:12 final size:12
Alignment explanation
Indices: 1252989--1253013 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1252979 AATCTGTTTA
1252989 TGTATTCTTGAG
1 TGTATTCTTGAG
1253001 TGTATTCTTGAG
1 TGTATTCTTGAG
1253013 T
1 T
1253014 TAAGTGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.24, T:0.52
Consensus pattern (12 bp):
TGTATTCTTGAG
Found at i:1253922 original size:22 final size:22
Alignment explanation
Indices: 1253897--1253938 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1253887 ATTCGAGGGT
1253897 TTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
*
1253919 TTCATAGGTCCTTGGGGACA
1 TTCATAGGTCCTTCGGGACA
1253939 AATTTCACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.31
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACATA
Found at i:1260072 original size:15 final size:15
Alignment explanation
Indices: 1260049--1260080 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1260039 CTGGTAAGGT
*
1260049 AGTATCGATACCATA
1 AGTAACGATACCATA
1260064 AGTAACGATACCATA
1 AGTAACGATACCATA
1260079 AG
1 AG
1260081 AAAGGTATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.22
Consensus pattern (15 bp):
AGTAACGATACCATA
Found at i:1263863 original size:2 final size:2
Alignment explanation
Indices: 1263856--1263881 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1263846 ACAATAGTGA
1263856 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1263882 GCAAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1266768 original size:24 final size:24
Alignment explanation
Indices: 1266723--1266772 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
1266713 TGGTGGTTGG
1266723 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
1266747 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
1266771 TT
1 TT
1266773 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:1270011 original size:13 final size:14
Alignment explanation
Indices: 1269993--1270022 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1269983 TTTGTTTGTT
1269993 TTTCTTTA-TTTTA
1 TTTCTTTATTTTTA
1270006 TTTCTTTATTTTTA
1 TTTCTTTATTTTTA
1270020 TTT
1 TTT
1270023 TTAATATTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTCTTTATTTTTA
Found at i:1272129 original size:24 final size:24
Alignment explanation
Indices: 1272084--1272132 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
1272074 TGGTGGTTGG
1272084 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
1272108 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
1272132 T
1 T
1272133 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:1291831 original size:59 final size:59
Alignment explanation
Indices: 1291766--1291923 Score: 167
Period size: 59 Copynumber: 2.6 Consensus size: 59
1291756 TGCAACAATT
* * * * *
1291766 AAAACCATAAAAGA-AAAATAATCCACATG-AACCACATGGTAAAAGATAAAACTATAAAA
1 AAAACCA-AAAACATAAAACAAACCACATGCAA-CACATGCTAAAAGACAAAACTATAAAA
* *
1291825 AAAACCAAAAACATAACACAAAGCACATGCAACACATGCTAAAAGACAAAACTATAAAA
1 AAAACCAAAAACATAAAACAAACCACATGCAACACATGCTAAAAGACAAAACTATAAAA
* * * *
1291884 AAAACCCCAAAAACATAACACAAAGCACATACACCACATG
1 AAAA--CCAAAAACATAAAACAAACCACATGCAACACATG
1291924 AACCACGTGC
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
58 5 0.06
59 47 0.55
60 2 0.02
61 32 0.37
ACGTcount: A:0.59, C:0.22, G:0.07, T:0.11
Consensus pattern (59 bp):
AAAACCAAAAACATAAAACAAACCACATGCAACACATGCTAAAAGACAAAACTATAAAA
Found at i:1291922 original size:61 final size:59
Alignment explanation
Indices: 1291796--1291923 Score: 202
Period size: 61 Copynumber: 2.1 Consensus size: 59
1291786 ATCCACATGA
* * *
1291796 ACCACATGGTAAAAGATAAAACTATAAAAAAAACCAAAAACATAACACAAAGCACATGC
1 ACCACATGCTAAAAGACAAAACTATAAAAAAAACCAAAAACATAACACAAAGCACATAC
*
1291855 AACACATGCTAAAAGACAAAACTATAAAAAAAACCCCAAAAACATAACACAAAGCACATAC
1 ACCACATGCTAAAAGACAAAACTATAAAAAAAA--CCAAAAACATAACACAAAGCACATAC
1291916 ACCACATG
1 ACCACATG
1291924 AACCACGTGC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
59 30 0.48
61 32 0.52
ACGTcount: A:0.59, C:0.23, G:0.07, T:0.11
Consensus pattern (59 bp):
ACCACATGCTAAAAGACAAAACTATAAAAAAAACCAAAAACATAACACAAAGCACATAC
Found at i:1291938 original size:18 final size:17
Alignment explanation
Indices: 1291915--1291963 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
1291905 AAAGCACATA
1291915 CACCACATGAACCACGTG
1 CACCACATG-ACCACGTG
* *
1291933 CACCACATCGATCATGTG
1 CACCACAT-GACCACGTG
1291951 CACCACATG-CCAC
1 CACCACATGACCAC
1291964 CCCAAATCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 2 0.08
17 1 0.04
18 22 0.85
19 1 0.04
ACGTcount: A:0.31, C:0.41, G:0.14, T:0.14
Consensus pattern (17 bp):
CACCACATGACCACGTG
Found at i:1296971 original size:3 final size:3
Alignment explanation
Indices: 1296963--1296991 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1296953 AAACATGCAA
1296963 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1296992 GAGTAGCCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1298596 original size:3 final size:3
Alignment explanation
Indices: 1298584--1298656 Score: 51
Period size: 3 Copynumber: 24.7 Consensus size: 3
1298574 TTAATGTTAT
* * * * *
1298584 TTA TTA -TA TTA TTA TTA -TA ATA TTA TTA TTA TAA TTA TAA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1298630 TAA TAA TTA TTA TTA ATA TATA TTA TT
1 TTA TTA TTA TTA TTA TTA T-TA TTA TT
1298657 TAATATTACA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
2 4 0.07
3 53 0.88
4 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
TTA
Found at i:1298606 original size:14 final size:14
Alignment explanation
Indices: 1298584--1298664 Score: 78
Period size: 14 Copynumber: 5.8 Consensus size: 14
1298574 TTAATGTTAT
*
1298584 TTATTATATTATTA
1 TTATAATATTATTA
1298598 TTATAATATTATTA
1 TTATAATATTATTA
*
1298612 TTAT-A-ATTATAA
1 TTATAATATTATTA
* *
1298624 TAATAATAATAATTA
1 TTATAAT-ATTATTA
1298639 TTATTAATATATATTA
1 TTA-TAATAT-TATTA
1298655 TT-TAATATTA
1 TTATAATATTA
1298665 CAAGCCCAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
12 9 0.16
13 4 0.07
14 23 0.42
15 9 0.16
16 10 0.18
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TTATAATATTATTA
Found at i:1301284 original size:9 final size:9
Alignment explanation
Indices: 1301270--1301294 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1301260 TTACATGTAA
1301270 ATTTAAATT
1 ATTTAAATT
1301279 ATTTAAATT
1 ATTTAAATT
1301288 ATTTAAA
1 ATTTAAA
1301295 AGCATGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (9 bp):
ATTTAAATT
Found at i:1304066 original size:15 final size:15
Alignment explanation
Indices: 1304046--1304077 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1304036 ATCAATACCT
1304046 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1304061 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1304076 TT
1 TT
1304078 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1311414 original size:9 final size:9
Alignment explanation
Indices: 1311400--1311460 Score: 72
Period size: 9 Copynumber: 6.8 Consensus size: 9
1311390 ATGCTTGAAG
1311400 AGAAAAAAA
1 AGAAAAAAA
1311409 AGAAAAAAA
1 AGAAAAAAA
*
1311418 AGAGAGAAAA
1 AGA-AAAAAA
1311428 AG--AAAAA
1 AGAAAAAAA
*
1311435 AGAAAAAAG
1 AGAAAAAAA
1311444 AGAAAAAAGA
1 AGAAAAAA-A
1311454 AGAAAAA
1 AGAAAAA
1311461 GGGGGGTCAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
7 6 0.14
9 24 0.55
10 14 0.32
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Found at i:1311425 original size:13 final size:12
Alignment explanation
Indices: 1311402--1311442 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
1311392 GCTTGAAGAG
1311402 AAAAAAAAGAAA
1 AAAAAAAAGAAA
*
1311414 AAAAAGAGAGAAA
1 AAAAA-AAAGAAA
1311427 AAGAAAAAAGAAA
1 AA-AAAAAAGAAA
1311440 AAA
1 AAA
1311443 GAGAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 6 0.24
13 16 0.64
14 3 0.12
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:1311440 original size:26 final size:23
Alignment explanation
Indices: 1311397--1311459 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
1311387 ATTATGCTTG
*
1311397 AAGAG-AAAAA-AAAGAA-AAAA
1 AAGAGAAAAAAGAAAAAAGAAAA
1311417 AAGAGAGAAAAAGAAAAAAGAAAA
1 AAGAGA-AAAAAGAAAAAAGAAAA
1311441 AAGAGAAAAAAGAAGAAAA
1 AAGAGAAAAAAGAA-AAAA
1311460 AGGGGGGTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
20 5 0.14
22 5 0.14
23 13 0.35
24 14 0.38
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (23 bp):
AAGAGAAAAAAGAAAAAAGAAAA
Found at i:1311454 original size:7 final size:7
Alignment explanation
Indices: 1311404--1311450 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
1311394 TTGAAGAGAA
1311404 AAAAAAG
1 AAAAAAG
1311411 AAAAAA-
1 AAAAAAG
* *
1311417 AAGAGAG
1 AAAAAAG
1311424 -AAAAAG
1 AAAAAAG
1311430 AAAAAAG
1 AAAAAAG
1311437 AAAAAAG
1 AAAAAAG
1311444 AGAAAAA
1 A-AAAAA
1311451 AGAAGAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
6 8 0.24
7 20 0.61
8 5 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:1311459 original size:24 final size:23
Alignment explanation
Indices: 1311397--1311460 Score: 89
Period size: 22 Copynumber: 2.9 Consensus size: 23
1311387 ATTATGCTTG
1311397 AAGAGAAAAAA-AAGAAAAAAAA
1 AAGAGAAAAAAGAAGAAAAAAAA
*
1311419 GAGAG-AAAAAGAA-AAAAGAAAA
1 AAGAGAAAAAAGAAGAAAA-AAAA
1311441 AAGAGAAAAAAGAAGAAAAA
1 AAGAGAAAAAAGAAGAAAAA
1311461 GGGGGGTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
21 9 0.25
22 14 0.39
23 9 0.25
24 4 0.11
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (23 bp):
AAGAGAAAAAAGAAGAAAAAAAA
Found at i:1311460 original size:26 final size:27
Alignment explanation
Indices: 1311400--1311460 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 27
1311390 ATGCTTGAAG
*
1311400 AGAA-AAAAAAGAAAAAAAAGAGAGAA
1 AGAAGAAAAAAGAAAAAAAAGAGAAAA
*
1311426 A-AAGAAAAAAGAAAAAAGAGA-AAAA
1 AGAAGAAAAAAGAAAAAAAAGAGAAAA
1311451 AGAAGAAAAA
1 AGAAGAAAAA
1311461 GGGGGGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 6 0.19
26 25 0.81
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (27 bp):
AGAAGAAAAAAGAAAAAAAAGAGAAAA
Found at i:1312750 original size:84 final size:84
Alignment explanation
Indices: 1312592--1313586 Score: 1616
Period size: 84 Copynumber: 11.8 Consensus size: 84
1312582 GAACAAATGT
* *
1312592 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGGTTTGGTAAAAACCAG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
* * *
1312657 TCATTGAATTTGAAAGATG
66 TTATTGAATTTGGAAGAGG
* * * *
1312676 AATTTGCT-AGTAGAATATTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGTAAAAACCA
1 AATGTGCTCA-TAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCA
1312740 ATTATTGAATTTGGAAGAGG
65 ATTATTGAATTTGGAAGAGG
* *
1312760 AATGTGCTCATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
* * *
1312825 TCATTGAATTTGAAAGATG
66 TTATTGAATTTGGAAGAGG
* * * * *
1312844 AATTTGCTAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTAGTAAAAACCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
1312909 TTATTGAATTTGGAAGAGG
66 TTATTGAATTTGGAAGAGG
1312928 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
1312993 TTATTGAATTTGGAAGAGG
66 TTATTGAATTTGGAAGAGG
1313012 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
1313077 TTATTGAATTTGGAAGAGG
66 TTATTGAATTTGGAAGAGG
1313096 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
* *
1313161 TTATTGAATTTGAAAGATG
66 TTATTGAATTTGGAAGAGG
1313180 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
* *
1313245 TTATTGAATTTGAAAGATG
66 TTATTGAATTTGGAAGAGG
*
1313264 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGT-AAAACCAG
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
1313328 TTATTGAATTTGGAAGAGG
66 TTATTGAATTTGGAAGAGG
1313347 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
* *
1313412 TTATTGAATTTGAAAGATG
66 TTATTGAATTTGGAAGAGG
*
1313431 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATTTGATCTGGTTTGGTATGAACCAC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG--T--A--A-
*
1313496 AGAACCAGTTATTGAATTTGGAAGAGG
59 A-AACCAATTATTGAATTTGGAAGAGG
* *
1313523 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGATATAAAACC
1 AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA-AAAACC
1313587 CAGAAACAAT
Statistics
Matches: 851, Mismatches: 49, Indels: 21
0.92 0.05 0.02
Matches are distributed among these distances:
83 81 0.10
84 683 0.80
85 5 0.01
86 2 0.00
87 1 0.00
88 2 0.00
90 2 0.00
91 1 0.00
92 74 0.09
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (84 bp):
AATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAAACCAA
TTATTGAATTTGGAAGAGG
Found at i:1313591 original size:92 final size:92
Alignment explanation
Indices: 1313322--1313606 Score: 381
Period size: 92 Copynumber: 3.2 Consensus size: 92
1313312 GGTTTGGTAA
* *
1313322 AACCAGTTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
1 AACCAATTATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
1313387 TCTGATCTGGTTTG--GT--A--A-A-
66 TCTGATCTGGTTTGATATAAACCACAG
*
1313406 AACCAATTATTGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
1 AACCAATTATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
* * *
1313471 TTTGATCTGGTTTGGTATGAACCACAG
66 TCTGATCTGGTTTGATATAAACCACAG
* *
1313498 AACCAGTTATTGAATTTGGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
1 AACCAATTATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
*
1313563 TCTGATTTGGTTTGATATAAAACC-CAG
66 TCTGATCTGGTTTGATAT-AAACCACAG
* *
1313590 AAACAATCATTGGAATT
1 AACCAATTATT-GAATT
1313607 AAAAGATGAA
Statistics
Matches: 176, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
84 75 0.43
86 1 0.01
88 1 0.01
90 1 0.01
91 1 0.01
92 88 0.50
93 9 0.05
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (92 bp):
AACCAATTATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTA
TCTGATCTGGTTTGATATAAACCACAG
Found at i:1314015 original size:52 final size:52
Alignment explanation
Indices: 1313953--1314057 Score: 201
Period size: 52 Copynumber: 2.0 Consensus size: 52
1313943 TATCGATATC
1313953 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
*
1314005 TGTGAAATCATCTTGAAAGATCACTTCATATTCAGATGAGTTGTTATCAGAA
1 TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
1314057 T
1 T
1314058 TAACATGTTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.34
Consensus pattern (52 bp):
TGTGAAATCATCTTGAAAGATCACTTCATAATCAGATGAGTTGTTATCAGAA
Found at i:1314432 original size:36 final size:36
Alignment explanation
Indices: 1314385--1314483 Score: 144
Period size: 36 Copynumber: 2.6 Consensus size: 36
1314375 CAGCTTTTCC
1314385 AGAGAAAGTTCATAATGAGAAGAACTCATATGAAGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATATGAAGA
* *
1314421 AGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGA
1 AGAGAAAGTTCATAATGAGAAGAACTCATATGAAGA
1314457 AGGAAGAATAAGTTCATAATGAGAAGA
1 A-G-AG-A-AAGTTCATAATGAGAAGA
1314484 GCTTGTTCAA
Statistics
Matches: 56, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
36 35 0.62
37 1 0.02
38 2 0.04
39 1 0.02
40 17 0.30
ACGTcount: A:0.51, C:0.08, G:0.22, T:0.19
Consensus pattern (36 bp):
AGAGAAAGTTCATAATGAGAAGAACTCATATGAAGA
Found at i:1314440 original size:20 final size:20
Alignment explanation
Indices: 1314385--1314443 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
1314375 CAGCTTTTCC
*
1314385 AGAGAAAGTTCATAATGAG-
1 AGAGAAAGTTCATAATAAGA
*
1314404 A-AG-AA-CTCAT-ATGAAGA
1 AGAGAAAGTTCATAAT-AAGA
1314421 AGAGAAAGTTCATAATAAGA
1 AGAGAAAGTTCATAATAAGA
1314441 AGA
1 AGA
1314444 ACTCATCTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 11
0.69 0.07 0.24
Matches are distributed among these distances:
15 2 0.06
16 6 0.19
17 3 0.10
18 4 0.13
19 3 0.10
20 11 0.35
21 2 0.06
ACGTcount: A:0.53, C:0.07, G:0.22, T:0.19
Consensus pattern (20 bp):
AGAGAAAGTTCATAATAAGA
Found at i:1314444 original size:18 final size:18
Alignment explanation
Indices: 1314387--1314444 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
1314377 GCTTTTCCAG
*
1314387 AGAAAGTTCATAATGAGA
1 AGAAAGTTCATAATAAGA
*
1314405 AG-AA-CTCAT-ATGAAGAA
1 AGAAAGTTCATAAT-AAG-A
1314422 GAGAAAGTTCATAATAAGA
1 -AGAAAGTTCATAATAAGA
1314441 AGAA
1 AGAA
1314445 CTCATCTGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 12
0.67 0.07 0.26
Matches are distributed among these distances:
15 2 0.06
16 6 0.19
17 3 0.10
18 8 0.26
19 3 0.10
20 7 0.23
21 2 0.06
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (18 bp):
AGAAAGTTCATAATAAGA
Found at i:1314619 original size:113 final size:113
Alignment explanation
Indices: 1314421--1314765 Score: 681
Period size: 113 Copynumber: 3.1 Consensus size: 113
1314411 CATATGAAGA
*
1314421 AGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAATAAGTTCATAATGAGAAGAGC
1 AGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1314486 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
1314534 AGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1314599 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
1314647 AGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1 AGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
1314712 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
66 TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
1314760 AGAGAA
1 AGAGAA
1314766 GAACTCATCT
Statistics
Matches: 231, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 231 1.00
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (113 bp):
AGAGAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGC
TTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCC
Found at i:1314834 original size:40 final size:37
Alignment explanation
Indices: 1314761--1314858 Score: 162
Period size: 40 Copynumber: 2.6 Consensus size: 37
1314751 AGCTTTTCCA
1314761 GAGAAGAACTCATCTGAAGAA-GAGAAAGTTCATAAT
1 GAGAAGAACTCATCTGAAGAAGGAGAAAGTTCATAAT
1314797 GAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 GAGAAGAACTCATCTGAAGAAGG-AG-A-AAGTTCATAAT
1314837 GAGAAGAACTCATCTGAAGAAG
1 GAGAAGAACTCATCTGAAGAAG
1314859 AGCTTATTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
36 21 0.36
37 1 0.02
38 2 0.03
39 1 0.02
40 33 0.57
ACGTcount: A:0.47, C:0.11, G:0.24, T:0.17
Consensus pattern (37 bp):
GAGAAGAACTCATCTGAAGAAGGAGAAAGTTCATAAT
Found at i:1315114 original size:3 final size:3
Alignment explanation
Indices: 1315102--1315178 Score: 75
Period size: 3 Copynumber: 25.7 Consensus size: 3
1315092 TTAATGTTAT
* * * *
1315102 TTA TTA -TA TTA TTA TTA TTA TAA TTA TTA TTA TTA TAA TTA TAA TAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
1315149 TAA TAA TAA TTA TTA TTA TTA TATA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TT
1315179 TAATATTACA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
2 2 0.03
3 61 0.92
4 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:1318491 original size:21 final size:20
Alignment explanation
Indices: 1318467--1318508 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
1318457 TTAAGCATCT
1318467 AATAAA-TTAAAATGAAAATAA
1 AATAAACTT-AAATG-AAATAA
1318488 AATAAACTTAAATGAAATAA
1 AATAAACTTAAATGAAATAA
1318508 A
1 A
1318509 GTGTGTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 7 0.35
21 11 0.55
22 2 0.10
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (20 bp):
AATAAACTTAAATGAAATAA
Found at i:1325450 original size:20 final size:20
Alignment explanation
Indices: 1325425--1325472 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1325415 TATCCTTAAA
1325425 AAAAATAAAAGATAATTCCT
1 AAAAATAAAAGATAATTCCT
*
1325445 AAAAATAAGAGATAATTCCT
1 AAAAATAAAAGATAATTCCT
1325465 AAAAATAA
1 AAAAATAA
1325473 TTCTCAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.62, C:0.08, G:0.06, T:0.23
Consensus pattern (20 bp):
AAAAATAAAAGATAATTCCT
Found at i:1326395 original size:27 final size:27
Alignment explanation
Indices: 1326357--1326410 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1326347 GGTAGTTATG
1326357 ATATTGTCCTTAATCATAAATATAAGC
1 ATATTGTCCTTAATCATAAATATAAGC
1326384 ATATTGTCCTTAATCATAAATATAAGC
1 ATATTGTCCTTAATCATAAATATAAGC
1326411 CAAAGATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (27 bp):
ATATTGTCCTTAATCATAAATATAAGC
Found at i:1328221 original size:19 final size:19
Alignment explanation
Indices: 1328197--1328247 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1328187 ACCAACTAAA
*
1328197 TCGCAATGCGATCGATAAT
1 TCGCAACGCGATCGATAAT
1328216 TCGCAACGCGATCGATAAT
1 TCGCAACGCGATCGATAAT
1328235 TCGCAACGCGATC
1 TCGCAACGCGATC
1328248 TGCGGTATCG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (19 bp):
TCGCAACGCGATCGATAAT
Found at i:1328346 original size:21 final size:21
Alignment explanation
Indices: 1328295--1328411 Score: 71
Period size: 20 Copynumber: 5.7 Consensus size: 21
1328285 ATTCTGACTA
* * *
1328295 TCGCATTGCGATTTCCCAAAT
1 TCGCAATGCGATTTACCTAAT
* ** *
1328316 TTGCGTTGCGATTTTCCTAAT
1 TCGCAATGCGATTTACCTAAT
* * *
1328337 TCGCAATGCGA-ATACGTAAA
1 TCGCAATGCGATTTACCTAAT
* *
1328357 TCGCAATGCGA-TTACGTAAA
1 TCGCAATGCGATTTACCTAAT
*
1328377 TCGCAAT-CTGATTTACGTAA-
1 TCGCAATGC-GATTTACCTAAT
*
1328397 TCGCATTGCGATTTA
1 TCGCAATGCGATTTA
1328412 GTAAATCGCA
Statistics
Matches: 80, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
19 1 0.01
20 45 0.56
21 34 0.43
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
TCGCAATGCGATTTACCTAAT
Found at i:1328362 original size:20 final size:21
Alignment explanation
Indices: 1328322--1328422 Score: 113
Period size: 20 Copynumber: 5.0 Consensus size: 21
1328312 AAATTTGCGT
* * *
1328322 TGCGATTTTCCTAATTCGCAA
1 TGCGATTTACGTAAATCGCAA
*
1328343 TGCGA-ATACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
1328363 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
1328383 T-CTGATTTACGT-AATCGCAT
1 TGC-GATTTACGTAAATCGCAA
1328403 TGCGATTTA-GTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
1328423 CGAGATTCTG
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
19 3 0.04
20 54 0.78
21 12 0.17
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:1329310 original size:24 final size:24
Alignment explanation
Indices: 1329283--1329336 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1329273 GTATTCGAAA
1329283 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
1329307 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
1329331 TTTGAT
1 TTTGAT
1329337 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:1331876 original size:20 final size:19
Alignment explanation
Indices: 1331848--1331902 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
1331838 CAATCATCTT
*
1331848 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGC-GA
*
1331868 AATGACTATCGCAATGCGA
1 AATGACTATCGCAACGCGA
**
1331887 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
1331903 AGAGAATCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (19 bp):
AATGACTATCGCAACGCGA
Found at i:1331890 original size:19 final size:20
Alignment explanation
Indices: 1331809--1331902 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
1331799 GGCATTCATT
*
1331809 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* **
1331829 TGACGT-TCGCAATCATC-TTAA
1 TGAC-TATCGCAA-C-GCGGAAA
*
1331850 TGTCTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
1331870 TGACTATCGCAATGC-GAAA
1 TGACTATCGCAACGCGGAAA
**
1331889 TGAAAATCGCAACG
1 TGACTATCGCAACG
1331903 AGAGAATCGC
Statistics
Matches: 57, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
19 16 0.28
20 27 0.47
21 13 0.23
22 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:1331917 original size:33 final size:33
Alignment explanation
Indices: 1331875--1331996 Score: 190
Period size: 33 Copynumber: 3.7 Consensus size: 33
1331865 GGAAATGACT
1331875 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1331908 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1331941 ATCGCAATGCGAAATGAAAATTGCAGCGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1331974 ATCCCAAAGCGAAATGAAAATCG
1 ATCGCAATGCGAAATGAAAATCG
1331997 TAATGTGAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 81 1.00
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1331929 original size:19 final size:18
Alignment explanation
Indices: 1331875--1331961 Score: 55
Period size: 19 Copynumber: 5.1 Consensus size: 18
1331865 GGAAATGACT
1331875 ATCGCAATGCGAAATGAAA
1 ATCGCAATGC-AAATGAAA
* *
1331894 ATCGCAA--C-GA-GAGA
1 ATCGCAATGCAAATGAAA
1331908 ATCGCAATGCAAAATGAAA
1 ATCGCAATGC-AAATGAAA
* *
1331927 ATCGCAA--C-GA-GAGA
1 ATCGCAATGCAAATGAAA
1331941 ATCGCAATGCGAAATGAAA
1 ATCGCAATGC-AAATGAAA
1331960 AT
1 AT
1331962 TGCAGCGAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
14 20 0.40
15 2 0.04
16 2 0.04
17 2 0.04
18 2 0.04
19 22 0.44
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCAAATGAAA
Found at i:1332084 original size:19 final size:19
Alignment explanation
Indices: 1332011--1332076 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
1332001 GTGAATTTAG
*
1332011 TTTCGCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1332030 TTTCGCATTGCGA--TTC-
1 TTTCGCATTGCGATTTTCA
*
1332046 TCTCG--TTGCGATTTTCA
1 TTTCGCATTGCGATTTTCA
1332063 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
1332077 AGTCATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 7 0.18
19 19 0.49
ACGTcount: A:0.12, C:0.23, G:0.20, T:0.45
Consensus pattern (19 bp):
TTTCGCATTGCGATTTTCA
Found at i:1332202 original size:14 final size:14
Alignment explanation
Indices: 1332183--1332219 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1332173 CATCAATTAA
1332183 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1332197 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1332211 ACAAATCAA
1 ACAAATCAA
1332220 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1333635 original size:21 final size:21
Alignment explanation
Indices: 1333569--1333635 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1333559 GTGAATCGGG
*
1333569 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1333589 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1333611 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1333632 CTCT
1 CTCT
1333636 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1333654 original size:42 final size:41
Alignment explanation
Indices: 1333569--1333691 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1333559 GTGAATCGGG
* * * *
1333569 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1333611 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1333653 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1333692 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1334168 original size:19 final size:18
Alignment explanation
Indices: 1334112--1334170 Score: 54
Period size: 19 Copynumber: 3.4 Consensus size: 18
1334102 AAAAATGACT
*
1334112 ATCGCAACGCGAAATGAAA
1 ATCGCAA-GCGGAATGAAA
*
1334131 ATCGCAA-C-G-A-GAGA
1 ATCGCAAGCGGAATGAAA
1334145 ATCGCAATGCGGAATGAAA
1 ATCGCAA-GCGGAATGAAA
1334164 ATCGCAA
1 ATCGCAA
1334171 CGCGATTATT
Statistics
Matches: 32, Mismatches: 3, Indels: 10
0.71 0.07 0.22
Matches are distributed among these distances:
14 10 0.31
15 1 0.03
16 1 0.03
17 2 0.06
18 1 0.03
19 17 0.53
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGGAATGAAA
Found at i:1334206 original size:19 final size:19
Alignment explanation
Indices: 1334172--1334224 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
1334162 AAATCGCAAC
* *
1334172 GCGATTATTGGTTTCGTGTT
1 GCGATT-TTCGTTTCGCGTT
1334192 GCGATTTTCGTTTCGCGTT
1 GCGATTTTCGTTTCGCGTT
*
1334211 GCGATTTTCATTTC
1 GCGATTTTCGTTTC
1334225 AACCAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 24 0.80
20 6 0.20
ACGTcount: A:0.09, C:0.17, G:0.25, T:0.49
Consensus pattern (19 bp):
GCGATTTTCGTTTCGCGTT
Found at i:1334420 original size:94 final size:94
Alignment explanation
Indices: 1334315--1334782 Score: 745
Period size: 94 Copynumber: 5.1 Consensus size: 94
1334305 ATGGATTGCA
* * *
1334315 TTAC-TTCAACCAAAAGAAAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
1334379 TTAGCAGAATTGGCAGCAAACAAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
1334408 TTACTTTCAACCAAAGGACAAAACAAAGATAAATACTAACTTCATAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1334473 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1334502 TTACTTTCAACCAAAAGACAAAACAAAGACAAATAAC-AACTTCACAGTGTTAAAGAATACACAG
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAAT-ACTAACTTCACAGTGTTAAAGAATACACAG
1334566 TTTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
1334596 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
1334661 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
1334690 TTAC-TTCAACCAAAAGACAACA-AAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
1334749 TTAGCAGTATTGGCAGCGACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
1334778 TTACT
1 TTACT
1334783 AAGCAATCTA
Statistics
Matches: 356, Mismatches: 15, Indels: 12
0.93 0.04 0.03
Matches are distributed among these distances:
88 40 0.11
92 27 0.08
93 23 0.06
94 264 0.74
95 2 0.01
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:1336492 original size:20 final size:20
Alignment explanation
Indices: 1336467--1336562 Score: 91
Period size: 20 Copynumber: 5.2 Consensus size: 20
1336457 TTTTGGTTGA
1336467 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
1336487 AATGAAAATCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
1336506 AAATGACTATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
1336525 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
1336540 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
1336560 AAT
1 AAT
1336563 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 8 0.13
16 4 0.06
17 2 0.03
18 1 0.02
19 14 0.23
20 33 0.53
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:1336533 original size:14 final size:14
Alignment explanation
Indices: 1336514--1336569 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1336504 GGAAATGACT
1336514 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1336528 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
1336547 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
1336561 ATCGCAACG
1 ATCGCAACG
1336570 CGAAATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.43, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1336551 original size:33 final size:33
Alignment explanation
Indices: 1336465--1336619 Score: 211
Period size: 33 Copynumber: 4.5 Consensus size: 33
1336455 TCTTTTGGTT
1336465 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-G--AATCGCAACGC
**
1336504 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1336538 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1336571 GAAATTAAAATCTCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1336604 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1336620 TGCGATTTTG
Statistics
Matches: 107, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
33 76 0.71
34 11 0.10
36 1 0.01
37 1 0.01
38 3 0.03
40 15 0.14
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1336653 original size:19 final size:20
Alignment explanation
Indices: 1336631--1336741 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 20
1336621 GCGATTTTGG
1336631 TTTCGCGTTGCGATTTTCA-
1 TTTCGCGTTGCGATTTTCAT
1336650 TTTCGCGTTGCGA--TTC--
1 TTTCGCGTTGCGATTTTCAT
* *
1336666 --TCTCGTTCCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
* **
1336684 TTCTCTCGTTGCGATAGTCAT
1 TT-TCGCGTTGCGATTTTCAT
*
1336705 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATTTTCAT
**
1336725 TTTCATGTTGCGATTTT
1 TTTCGCGTTGCGATTTT
1336742 AAGTTTAGAA
Statistics
Matches: 75, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.12
16 3 0.04
17 3 0.04
19 13 0.17
20 30 0.40
21 17 0.23
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.50
Consensus pattern (20 bp):
TTTCGCGTTGCGATTTTCAT
Found at i:1337315 original size:20 final size:20
Alignment explanation
Indices: 1337269--1337448 Score: 105
Period size: 20 Copynumber: 8.8 Consensus size: 20
1337259 ATGGCGCTAT
*
1337269 GTAAATCGCAATGCGAATTAG
1 GTAAATCGCAATGCG-ATTAC
* *
1337290 GAAAATCGCAATGTGATTAC
1 GTAAATCGCAATGCGATTAC
* *
1337310 GTAAATCACAATGCGAATAC
1 GTAAATCGCAATGCGATTAC
* *
1337330 GT-AATCGCATTGCGATTTTC
1 GTAAATCGCAATGCGA-TTAC
* * *
1337350 CTAATTCGCATTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
*
1337371 GT-AATCGCATTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
* * * *
1337391 GT-ATTCGCATTACGAATTAG
1 GTAAATCGCAATGCG-ATTAC
* * **
1337411 GAAAATCGCAACGCGAATTTG
1 GTAAATCGCAATGCG-ATTAC
*
1337432 GGAAATCGCAATGCGAT
1 GTAAATCGCAATGCGAT
1337449 AGTCAGAATC
Statistics
Matches: 128, Mismatches: 27, Indels: 9
0.78 0.16 0.05
Matches are distributed among these distances:
19 11 0.09
20 60 0.47
21 57 0.45
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.28
Consensus pattern (20 bp):
GTAAATCGCAATGCGATTAC
Found at i:1337418 original size:41 final size:41
Alignment explanation
Indices: 1337323--1337420 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
1337313 AATCACAATG
* * *
1337323 CGAA-TACGTAATCGCATTGCGATTTTCCTAATTCGCATTG
1 CGAATTACGAAATCGCATTGCGATTTACCTAATTCGCATTA
* * *
1337363 CGATTTACGTAATCGCATTGCGATTTACGT-ATTCGCATTA
1 CGAATTACGAAATCGCATTGCGATTTACCTAATTCGCATTA
*
1337403 CGAATTAGGAAAATCGCA
1 CGAATTACG-AAATCGCA
1337421 ACGCGAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 19 0.39
41 30 0.61
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.33
Consensus pattern (41 bp):
CGAATTACGAAATCGCATTGCGATTTACCTAATTCGCATTA
Found at i:1337420 original size:61 final size:60
Alignment explanation
Indices: 1337272--1337426 Score: 141
Period size: 60 Copynumber: 2.6 Consensus size: 60
1337262 GCGCTATGTA
* * *
1337272 AATCGCAATGCGAATTAGGAAAATCGCAATGTGATTACGTAAATCACAATGCGAATACGT
1 AATCGCATTACGAATTAGGAAAATCGCAATGCGATTACGTAAATCACAATGCGAATACGT
* * **** * * * * *
1337332 AATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT-AATCGCATTGCGATTTACGT
1 AATCGCATTACGAATTAGGAAAATCGCAATGCGA-TTACGTAAATCACAATGCGA-ATACGT
* *
1337393 ATTCGCATTACGAATTAGGAAAATCGCAACGCGA
1 AATCGCATTACGAATTAGGAAAATCGCAATGCGA
1337427 ATTTGGGAAA
Statistics
Matches: 71, Mismatches: 22, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
60 36 0.51
61 35 0.49
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (60 bp):
AATCGCATTACGAATTAGGAAAATCGCAATGCGATTACGTAAATCACAATGCGAATACGT
Found at i:1339534 original size:4 final size:4
Alignment explanation
Indices: 1339525--1339557 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1339515 ATATACATAG
1339525 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1339558 TGTCTATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:1341251 original size:20 final size:21
Alignment explanation
Indices: 1341226--1341277 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1341216 TTTTCCCAAT
*
1341226 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
1341246 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
1341267 TCGCAATGCGA
1 TCGCAATGCGA
1341278 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:1341291 original size:20 final size:20
Alignment explanation
Indices: 1341266--1341359 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
1341256 AATTGGGAAA
*
1341266 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
1341286 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
1341307 ATCGCAACGAGATACTAACT
1 ATCGCAACGCGATACTGACT
* *
1341327 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
1341347 TTCGCAACGCGAT
1 ATCGCAACGCGAT
1341360 TTACATAGCG
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.72
21 13 0.21
22 2 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:1341914 original size:19 final size:19
Alignment explanation
Indices: 1341876--1341942 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1341866 TTCGAGAATG
1341876 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
1341896 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
1341915 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
1341934 AAAATCGCA
1 AAAATCGCA
1341943 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:1341984 original size:20 final size:19
Alignment explanation
Indices: 1341938--1342103 Score: 127
Period size: 20 Copynumber: 9.1 Consensus size: 19
1341928 GAAACCAAAA
*
1341938 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1341957 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
*
1341976 TCACGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
1341996 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
1342012 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
1342029 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1342043 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
1342062 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
1342082 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1342102 TC
1 TC
1342104 AACCAAAAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 40 0.34
20 48 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1342028 original size:33 final size:33
Alignment explanation
Indices: 1341991--1342078 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
1341981 GTTGCGATTT
* *
1341991 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
1342024 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
1342057 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
1342079 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:1345531 original size:14 final size:14
Alignment explanation
Indices: 1345512--1345547 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1345502 ATTGTTTAAT
1345512 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
1345526 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
1345540 TGATTTGT
1 TGATTTGT
1345548 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:1345768 original size:33 final size:33
Alignment explanation
Indices: 1345718--1345844 Score: 190
Period size: 33 Copynumber: 3.9 Consensus size: 33
1345708 ATTAAATTTG
1345718 CGTTGCGA-TTTCATTTCGCATTGCGATTACCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTACCT
*
1345750 CGTTGCGATTTTCATTTCGCATTGCGAAATTA--G
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTACCT
1345783 CGTTGCGATTTTCATTTCGCATTGCGATT-CTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTAC-CT
1345816 CGTTGCGATTTTCATTTCGCATTGCGATT
1 CGTTGCGATTTTCATTTCGCATTGCGATT
1345845 GTAATTTCCG
Statistics
Matches: 87, Mismatches: 2, Indels: 11
0.87 0.02 0.11
Matches are distributed among these distances:
31 3 0.03
32 8 0.09
33 72 0.83
35 4 0.05
ACGTcount: A:0.16, C:0.22, G:0.20, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTACCT
Found at i:1345818 original size:66 final size:65
Alignment explanation
Indices: 1345711--1345842 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 65
1345701 TGCGCAAATT
*
1345711 AAATTTGCGTTGCGATTTCATTTCGCATTGCGATTACCTCGTTGCGATTTTCATTTCGCATTGCG
1 AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTACCTCGTTGCGATTTTCATTTCGCATTGCG
1345776 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATT-CTCTCGTTGCGATTTTCATTTCGCATTG
1 AAATTAGCGTTGCGA-TTTCATTTCGCATTGCGATTAC-CTCGTTGCGATTTTCATTTCGCATTG
1345840 CG
64 CG
1345842 A
1 A
1345843 TTGTAATTTC
Statistics
Matches: 64, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
65 15 0.23
66 49 0.77
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.42
Consensus pattern (65 bp):
AAATTAGCGTTGCGATTTCATTTCGCATTGCGATTACCTCGTTGCGATTTTCATTTCGCATTGCG
Found at i:1345862 original size:20 final size:19
Alignment explanation
Indices: 1345816--1345863 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
1345806 GCGATTCTCT
* *
1345816 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTGTAATTTCG
*
1345835 CATTGCGATTGTAATTTCCG
1 CGTTGCGATTGTAATTT-CG
1345855 CGTTGCGAT
1 CGTTGCGAT
1345864 GGACATTAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.15, C:0.21, G:0.23, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTGTAATTTCG
Found at i:1348310 original size:292 final size:291
Alignment explanation
Indices: 1347786--1348368 Score: 1141
Period size: 292 Copynumber: 2.0 Consensus size: 291
1347776 AAAAACTTGG
1347786 GTTCTTGAACATGTATGTTTATCAATAAAAGTCCTAACTTGAACATTGCGCAATCTTTTATCCTC
1 GTTCTTGAACATGTATGTTTATCAATAAAAGTCCTAACTTGAACATTGCGCAATCTTTTATCCTC
1347851 TTTGCAATCATACGCCACGTACAGTTTTTGTCAATCGTACACCTGTTTCGAAACGATCTTTGCTT
66 TTTGCAATCATACGCCACGTACAGTTTTTGTCAATCGTACACCTGTTTCGAAACGATCTTTGCTT
1347916 GATTTGTTAACTTTTAGTTGATAGCCATCTTCCACACATTTCGTATACAAAGCTATCTTCAAGTC
131 GATTTGTTAACTTTTAGTTGATAGCCATCTTCCACACATTTCGTATACAAAGCTATCTTCAAGTC
1347981 TTCCTTTGTATCAAAACAATCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCAACTGCTT
196 TTCCTTTGTATCAAAACAATCATCTTTCTTGATACGAATAACTTTTGTGTAACAATC-ACTGCTT
1348046 TCTTTGCCAACTCTTCTTCCGGTAACTGAAGT
260 TCTTTGCCAACTCTTCTTCCGGTAACTGAAGT
1348078 GTTCTTGAACATGTATGTTTATCAATAAAAGTCCTAACTTGAAACATTGCGCAATC-TTTATCCT
1 GTTCTTGAACATGTATGTTTATCAATAAAAGTCCTAACTTG-AACATTGCGCAATCTTTTATCCT
1348142 CTTTGCAATCATACGCCACGTACAGTTTTTGTCAATCGTACACCTGTTTCGAAACGATCTTTGCT
65 CTTTGCAATCATACGCCACGTACAGTTTTTGTCAATCGTACACCTGTTTCGAAACGATCTTTGCT
1348207 TGATTTGTTAACTTTTAGTTGATAGCCATCTTCCACACATTTCGTATACAAAGCTATCTTCAAGT
130 TGATTTGTTAACTTTTAGTTGATAGCCATCTTCCACACATTTCGTATACAAAGCTATCTTCAAGT
1348272 CTTCCTTTGTATCAAAACAATCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCACTGCTT
195 CTTCCTTTGTATCAAAACAATCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCACTGCTT
1348337 TCTTTGCCAACTCTTCTTCCGGTAACTGAAGT
260 TCTTTGCCAACTCTTCTTCCGGTAACTGAAGT
1348369 AATTCTGGCA
Statistics
Matches: 290, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
291 39 0.13
292 237 0.82
293 14 0.05
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.38
Consensus pattern (291 bp):
GTTCTTGAACATGTATGTTTATCAATAAAAGTCCTAACTTGAACATTGCGCAATCTTTTATCCTC
TTTGCAATCATACGCCACGTACAGTTTTTGTCAATCGTACACCTGTTTCGAAACGATCTTTGCTT
GATTTGTTAACTTTTAGTTGATAGCCATCTTCCACACATTTCGTATACAAAGCTATCTTCAAGTC
TTCCTTTGTATCAAAACAATCATCTTTCTTGATACGAATAACTTTTGTGTAACAATCACTGCTTT
CTTTGCCAACTCTTCTTCCGGTAACTGAAGT
Found at i:1349723 original size:19 final size:20
Alignment explanation
Indices: 1349699--1349756 Score: 82
Period size: 19 Copynumber: 2.9 Consensus size: 20
1349689 ATTCATTTGA
1349699 CTATCGCAACGCGAAAA-GG
1 CTATCGCAACGCGAAAATGG
1349718 CTATCGCAACGCGAAAAATGG
1 CTATCGCAACGCG-AAAATGG
* *
1349739 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
1349757 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 13 0.37
20 9 0.26
21 13 0.37
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:1349745 original size:21 final size:20
Alignment explanation
Indices: 1349699--1349755 Score: 80
Period size: 21 Copynumber: 2.9 Consensus size: 20
1349689 ATTCATTTGA
1349699 CTATCGCAACGCG-AAAAGG
1 CTATCGCAACGCGAAAAAGG
1349718 CTATCGCAACGCGAAAAATGG
1 CTATCGCAACGCGAAAAA-GG
* *
1349739 TTATCGCAACGAGAAAA
1 CTATCGCAACGCGAAAA
1349756 TCGCAATGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.38
20 4 0.12
21 17 0.50
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (20 bp):
CTATCGCAACGCGAAAAAGG
Found at i:1349799 original size:14 final size:14
Alignment explanation
Indices: 1349780--1349833 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
1349770 GAAAATCGCA
1349780 TTGCGATTTTCTCG
1 TTGCGATTTTCTCG
1349794 TTGCGATTTTCATTTCG
1 TTGCGATTTTC---TCG
1349811 CATTGCGATTTTCTCG
1 --TTGCGATTTTCTCG
1349827 TTGCGAT
1 TTGCGAT
1349834 AGCCATTTCG
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
16 3 0.09
17 3 0.09
19 11 0.31
ACGTcount: A:0.11, C:0.20, G:0.20, T:0.48
Consensus pattern (14 bp):
TTGCGATTTTCTCG
Found at i:1349799 original size:33 final size:33
Alignment explanation
Indices: 1349762--1349832 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 33
1349752 AAAATCGCAA
1349762 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
** ** **
1349795 TGCGATTTTCATTTCGCATTGCGATTTTCTCGT
1 TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
1349828 TGCGA
1 TGCGA
1349833 TAGCCATTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (33 bp):
TGCGAAATGAAAATCGCATTGCGATTTTCTCGT
Found at i:1349841 original size:33 final size:33
Alignment explanation
Indices: 1349775--1349852 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
1349765 GAAATGAAAA
***
1349775 TCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1349808 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
**
1349841 TCGTGTTGCGAT
1 TCGCATTGCGAT
1349853 AGTCTGTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:1351843 original size:21 final size:19
Alignment explanation
Indices: 1351807--1351863 Score: 78
Period size: 21 Copynumber: 2.9 Consensus size: 19
1351797 GAAACTTAAA
1351807 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
1351826 ATCGCCAACGCGGAAATGGCT
1 ATCG-CAACGC-GAAATGACT
*
1351847 ATCGCAATGCGAAATGA
1 ATCGCAACGCGAAATGA
1351864 AAATAACGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 10 0.30
20 11 0.33
21 12 0.36
ACGTcount: A:0.35, C:0.25, G:0.25, T:0.16
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:1351952 original size:14 final size:14
Alignment explanation
Indices: 1351929--1351985 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
1351919 TTTTCTTTCG
*
1351929 CGTTGTGATTTTGT
1 CGTTGCGATTTTGT
1351943 CGTTGCGATTCATT-T
1 CGTTGCGATT--TTGT
1351958 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
1351974 CGTTGTGATTTT
1 CGTTGCGATTTT
1351986 CATTTCGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
15 5 0.14
16 5 0.14
17 8 0.22
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:1351959 original size:31 final size:32
Alignment explanation
Indices: 1351920--1352001 Score: 114
Period size: 31 Copynumber: 2.6 Consensus size: 32
1351910 GCATTACGAT
*
1351920 TTTC-TTTCGCGTTGTGATTTTGTCGTTGCGA
1 TTTCATTTCGCATTGTGATTTTGTCGTTGCGA
* *
1351951 -TTCATTTCGCATTGCGATTTTGTCGTTGTGA
1 TTTCATTTCGCATTGTGATTTTGTCGTTGCGA
1351982 TTTTCATTTCGCATTGTGAT
1 -TTTCATTTCGCATTGTGAT
1352002 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
30 3 0.07
31 24 0.55
33 17 0.39
ACGTcount: A:0.11, C:0.16, G:0.22, T:0.51
Consensus pattern (32 bp):
TTTCATTTCGCATTGTGATTTTGTCGTTGCGA
Found at i:1352028 original size:20 final size:19
Alignment explanation
Indices: 1351985--1352040 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
1351975 GTTGTGATTT
* *
1351985 TCATTTCGCATTGTGATAG
1 TCATTTCGCGTTGCGATAG
*
1352004 CCATTTCCGCGTTGCGATAG
1 TCATTT-CGCGTTGCGATAG
*
1352024 TCATTTTCGTGTTGCGA
1 TCA-TTTCGCGTTGCGA
1352041 AAGTAAACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.16, C:0.21, G:0.23, T:0.39
Consensus pattern (19 bp):
TCATTTCGCGTTGCGATAG
Found at i:1352361 original size:17 final size:17
Alignment explanation
Indices: 1352336--1352378 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1352326 GTCGATCAGA
*
1352336 TGATGGCTCTGGTGAGG
1 TGATGGCTCTGGCGAGG
*
1352353 TGATAGCTCTGGCGAGG
1 TGATGGCTCTGGCGAGG
1352370 TGATGGCTC
1 TGATGGCTC
1352379 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.14, C:0.16, G:0.42, T:0.28
Consensus pattern (17 bp):
TGATGGCTCTGGCGAGG
Found at i:1352698 original size:23 final size:24
Alignment explanation
Indices: 1352665--1352713 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
1352655 AGTTTTTATT
1352665 GCATATGTCTTCATGGCGGGAAAG
1 GCATATGTCTTCATGGCGGGAAAG
1352689 GCATA-GTCTTCATGGCGGGAAAG
1 GCATATGTCTTCATGGCGGGAAAG
1352712 GC
1 GC
1352714 CTCAAATATC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.22
Consensus pattern (24 bp):
GCATATGTCTTCATGGCGGGAAAG
Found at i:1354288 original size:21 final size:21
Alignment explanation
Indices: 1354256--1354374 Score: 65
Period size: 21 Copynumber: 5.9 Consensus size: 21
1354246 TGCGAAAGTA
*
1354256 AGTATCG--TTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
1354275 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
1354295 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
1354317 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
1354338 A-T-TCGCATTGCGATTTTCTC
1 AGTATCGCATTGCGATTTT-TC
* *
1354358 AAT-TCGCGTTGCGATTT
1 AGTATCGCATTGCGATTT
1354375 ACTTATTCGC
Statistics
Matches: 78, Mismatches: 13, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
18 1 0.01
19 7 0.09
20 31 0.40
21 35 0.45
22 3 0.04
23 1 0.01
ACGTcount: A:0.18, C:0.20, G:0.19, T:0.42
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:1354302 original size:20 final size:20
Alignment explanation
Indices: 1354198--1354310 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
1354188 TGCTTTGAAA
*
1354198 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
1354219 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
1354239 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
** * *
1354259 ATCG--TTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
1354278 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1354298 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1354311 TTTCCCAATT
Statistics
Matches: 75, Mismatches: 13, Indels: 9
0.77 0.13 0.09
Matches are distributed among these distances:
18 6 0.08
19 9 0.12
20 43 0.57
21 17 0.23
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1354329 original size:41 final size:41
Alignment explanation
Indices: 1354240--1354372 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
1354230 AAAGTCAGTA
* * *
1354240 TCGCGTTGCGAAAGTAAGTATCG--TTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* * *
1354278 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
* **
1354320 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCTCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCTCAAT
1354361 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1354373 TTACTTATTC
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
39 20 0.26
40 3 0.04
41 53 0.68
42 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTCAAT
Found at i:1354343 original size:20 final size:20
Alignment explanation
Indices: 1354299--1354391 Score: 105
Period size: 20 Copynumber: 4.5 Consensus size: 20
1354289 ATAGTCAGTA
* **
1354299 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACTTAT
*
1354320 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
* *
1354340 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-TAT
*
1354361 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTTAT
1354381 TCGCATTGCGA
1 TCGCATTGCGA
1354392 ATTGGGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 33 0.55
21 27 0.45
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (20 bp):
TCGCATTGCGATTTACTTAT
Found at i:1354373 original size:41 final size:41
Alignment explanation
Indices: 1354299--1354391 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
1354289 ATAGTCAGTA
1354299 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
*
1354340 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1354381 TCGCATTGCGA
1 TCGCATTGCGA
1354392 ATTGGGAAAA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.17, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:1359198 original size:17 final size:17
Alignment explanation
Indices: 1359164--1359210 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
1359154 AGTTATTCAA
1359164 TTTTTTTATAAA-AATG
1 TTTTTTTATAAATAATG
**
1359180 TTTTTTTATAAATTTTG
1 TTTTTTTATAAATAATG
*
1359197 TTTTGTTATAAATA
1 TTTTTTTATAAATA
1359211 TAGAATATGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (17 bp):
TTTTTTTATAAATAATG
Found at i:1365642 original size:3 final size:3
Alignment explanation
Indices: 1365634--1365663 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1365624 CCAAGAACAA
*
1365634 AAT AAT AAT AAA AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1365664 TAACTAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1365846 original size:3 final size:3
Alignment explanation
Indices: 1365838--1365885 Score: 55
Period size: 3 Copynumber: 15.7 Consensus size: 3
1365828 AAAATATATC
1365838 ATA ATA AT- ATA ATAA ATA A-A ATTCA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA A-T-A ATA ATA ATA ATA ATA ATA ATA
1365884 AT
1 AT
1365886 GGAAATAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
2 4 0.10
3 30 0.75
4 4 0.10
5 2 0.05
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1367218 original size:25 final size:25
Alignment explanation
Indices: 1367185--1367248 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 25
1367175 ACCTGAAAAG
*
1367185 AAAA-AAAATAAAAATGAAAT-TAAT
1 AAAATAAAATAAAAAAGAAATAT-AT
1367209 AAAATAAAATAAAAAAGAAATATAT
1 AAAATAAAATAAAAAAGAAATATAT
1367234 AATAATAATAATAAA
1 AA-AATAA-AATAAA
1367249 GATCAAATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 4 0.11
25 19 0.54
26 6 0.17
27 6 0.17
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (25 bp):
AAAATAAAATAAAAAAGAAATATAT
Found at i:1367360 original size:29 final size:29
Alignment explanation
Indices: 1367327--1367383 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1367317 ATCATATATT
*
1367327 TTTTGGAAAATGTTTTCAAAACTATATAG
1 TTTTGAAAAATGTTTTCAAAACTATATAG
* *
1367356 TTTTGAAAAATGTTTTTAAAATTATATA
1 TTTTGAAAAATGTTTTCAAAACTATATA
1367384 CTATATAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.11, T:0.46
Consensus pattern (29 bp):
TTTTGAAAAATGTTTTCAAAACTATATAG
Found at i:1367365 original size:66 final size:65
Alignment explanation
Indices: 1367296--1367419 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 65
1367286 ATATTTTCAA
** *
1367296 AAAAAT-ATTTTAAAATTATATA-TCATATATTTTTTGGAAAATG-TTTTCAAAACTATATAGTT
1 AAAAATGATTTTAAAATTATATACT-ATATAAGTTTT-CAAAATGATTTT-AAAACTATATAGTT
1367358 TTG
63 TTG
*
1367361 AAAAATGTTTTTAAAATTATATACTATATAAGTTTTCAAAATGATTTTAAAACTATATA
1 AAAAATGATTTTAAAATTATATACTATATAAGTTTTCAAAATGATTTTAAAACTATATA
1367420 ATATATATGT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
65 23 0.44
66 28 0.54
67 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.44
Consensus pattern (65 bp):
AAAAATGATTTTAAAATTATATACTATATAAGTTTTCAAAATGATTTTAAAACTATATAGTTTTG
Found at i:1367383 original size:102 final size:98
Alignment explanation
Indices: 1367269--1367571 Score: 285
Period size: 102 Copynumber: 3.0 Consensus size: 98
1367259 AACATTTTCC
* *
1367269 AAAAGCCTATATAATATATATTTTCAAAAAAATATTTTAAAATTATATATCATATATTTTTTGGA
1 AAAAG-CTATATAATATATATTTTCAAAAAAATATTTTAAAACTATATAT-ATATATTTTTT-CA
*
1367334 AAATGTTTTCAAAACTATATAGTTTTGAAAAATGTTTTT
63 AAATGTTTTAAAAACTATATA-TTTT-AAAAATG-TTTT
* * *
1367373 AAAA-TTATATACTATATAAGTTTTC---AAAATGATTTTAAAACTATATAATATATATGTTTTC
1 AAAAGCTATATAATATAT-A-TTTTCAAAAAAAT-ATTTTAAAACTATAT-ATATATATTTTTTC
*
1367434 AAAATGTTTTAAAAAACTATATTTATTTTCAAAATGTTTT
62 AAAATGTTTT-AAAAACTATA--TATTTTAAAAATGTTTT
* * ** *
1367474 AAAAGCTACATAATATACATTTTCAAAAACGT-TTTAAAAACTATATAT-TATATTTATTTTCAA
1 AAAAGCTATATAATATATATTTTCAAAAAAATATTTTAAAACTATATATATATA-TT-TTTTCAA
* * * *
1367537 AATGTTTTAAAAATTATATAATATATAAATGTTTT
64 AATGTTTTAAAAACTATATATTTTAAAAATGTTTT
1367572 CAAACATGTT
Statistics
Matches: 166, Mismatches: 20, Indels: 32
0.76 0.09 0.15
Matches are distributed among these distances:
98 13 0.08
99 4 0.02
100 17 0.10
101 52 0.31
102 59 0.36
103 10 0.06
104 11 0.07
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (98 bp):
AAAAGCTATATAATATATATTTTCAAAAAAATATTTTAAAACTATATATATATATTTTTTCAAAA
TGTTTTAAAAACTATATATTTTAAAAATGTTTT
Found at i:1367468 original size:66 final size:65
Alignment explanation
Indices: 1367393--1367599 Score: 213
Period size: 71 Copynumber: 3.0 Consensus size: 65
1367383 ACTATATAAG
1367393 TTTTCAAAATGATTTTAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAAACTATATTT
1 TTTTCAAAATG-TTTTAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAAACTATATTT
1367458 A
65 A
* * * *
1367459 TTTTCAAAATGTTTTAAAAGCTACATAATATACA--TTTTCAAAAACGTTTTAAAAACTATATAT
1 TTTTCAAAATGTTTTAAAA-CTATATAATATATATGTTTTC-AAAATGTTTT--AAA--A-A-AC
1367522 TATATTTA
58 TATATTTA
* *
1367530 TTTTCAAAATGTTTTAAAAATTATATAATATATAAATGTTTTCAAACATGTTTT-CAAAACTATA
1 TTTTCAAAATGTTTT-AAAACTATATAATATAT--ATGTTTTCAAA-ATGTTTTAAAAAACTATA
1367594 TATTA
62 T-TTA
1367599 T
1 T
1367600 ATACATTTTT
Statistics
Matches: 116, Mismatches: 10, Indels: 27
0.76 0.07 0.18
Matches are distributed among these distances:
64 5 0.04
65 17 0.15
66 23 0.20
67 3 0.03
68 6 0.05
69 6 0.05
70 2 0.02
71 34 0.29
72 5 0.04
73 1 0.01
74 3 0.03
75 11 0.09
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (65 bp):
TTTTCAAAATGTTTTAAAACTATATAATATATATGTTTTCAAAATGTTTTAAAAAACTATATTTA
Found at i:1367537 original size:37 final size:37
Alignment explanation
Indices: 1367349--1367639 Score: 234
Period size: 36 Copynumber: 8.1 Consensus size: 37
1367339 TTTTCAAAAC
* * * *
1367349 TATATAGTTTTGAAAAATGTTTTTAAAATTATATACTA
1 TATATA-TTTTCAAAAATGTTTTAAAAACTATATATTA
*
1367387 TATA-AGTTTTC-AAAATGATTTT-AAAACTATATAATA
1 TATATA-TTTTCAAAAATG-TTTTAAAAACTATATATTA
* *
1367423 TATATGTTTTC-AAAATGTTTTAAAAA--A-CTA-TA
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTA
* *
1367455 T-T-TATTTTC-AAAATGTTTTAAAAGCTACATA--A
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTA
* *
1367487 TATACATTTTCAAAAACGTTTTAAAAACTATATATTA
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTA
* *
1367524 TATTTATTTTC-AAAATGTTTTAAAAATTATATAATATA
1 TATATATTTTCAAAAATGTTTTAAAAACTATAT-AT-TA
* * * *
1367562 TAAATGTTTTCAAACATGTTTTCAAAACTATATATTA
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTA
* * * * *
1367599 TATACATTTTTAAAAATATTTT-CAAACTATATAATA
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTA
1367635 TATAT
1 TATAT
1367640 GTATGTATAT
Statistics
Matches: 208, Mismatches: 31, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
30 20 0.10
31 1 0.00
32 6 0.03
33 5 0.02
34 7 0.03
35 23 0.11
36 72 0.35
37 40 0.19
38 16 0.08
39 18 0.09
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (37 bp):
TATATATTTTCAAAAATGTTTTAAAAACTATATATTA
Found at i:1367592 original size:75 final size:73
Alignment explanation
Indices: 1367355--1367638 Score: 270
Period size: 75 Copynumber: 4.0 Consensus size: 73
1367345 AAACTATATA
* * *
1367355 GTTTTGAAAAATGTTTTTAAAATTATATACTATA-TAAGTTTTCAAAATGATTTTAAAACTATAT
1 GTTTTCAAAAATG-TTTTAAAACTATATACTATATTTAGTTTTCAAAATG-TTTTAAAACTATAT
1367419 AATATAT-AT
64 AATATATAAT
*
1367428 GTTTTC-AAAATGTTTT-AAA--A-A-ACTATATTTA-TTTTCAAAATGTTTTAAAAGCTACATA
1 GTTTTCAAAAATGTTTTAAAACTATATACTATATTTAGTTTTCAAAATGTTTTAAAA-CTATATA
*
1367486 ATATA-CA-
65 ATATATAAT
* * *
1367493 -TTTTCAAAAACGTTTTAAAAACTATATATTATATTTA-TTTTCAAAATGTTTTAAAAATTATAT
1 GTTTTCAAAAATGTTTT-AAAACTATATACTATATTTAGTTTTCAAAATGTTTT-AAAACTATAT
1367556 AATATATAAAT
64 AATATAT-AAT
* * ** * * * *
1367567 GTTTTCAAACATGTTTTCAAAACTATATATTATATACATTTTTAAAAATATTTTCAAACTATATA
1 GTTTTCAAAAATGTTTT-AAAACTATATACTATATTTAGTTTTCAAAATGTTTTAAAACTATATA
1367632 ATATATA
65 ATATATA
1367639 TGTATGTATA
Statistics
Matches: 178, Mismatches: 17, Indels: 31
0.79 0.08 0.14
Matches are distributed among these distances:
64 5 0.03
65 17 0.10
66 29 0.16
67 6 0.03
68 1 0.01
69 1 0.01
70 4 0.02
71 38 0.21
72 10 0.06
73 6 0.03
74 1 0.01
75 47 0.26
76 13 0.07
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (73 bp):
GTTTTCAAAAATGTTTTAAAACTATATACTATATTTAGTTTTCAAAATGTTTTAAAACTATATAA
TATATAAT
Found at i:1368315 original size:80 final size:79
Alignment explanation
Indices: 1368202--1369017 Score: 546
Period size: 80 Copynumber: 9.9 Consensus size: 79
1368192 TTGTTGACAG
* * * * * *
1368202 ATAGTCCTTCTTGCATTGAGCTATGTTGTAAATGATGTGCCTTGGAGCTGAGCTTAGTCGAAACT
1 ATAGGCCTTCTAGC-TTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCG-AACT
1368267 CGAAGGTCTTTGGCAT
64 CGAAGGTCTTTGGCAT
* *** * * * * *
1368283 ATAGGTCTTCTAGCCCGAGCTATACCGCAAATGATGTGCCGTT-GAGCTGAGTGTAATCGGACTC
1 ATAGGCCTTCTAGCTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTC
* *
1368347 AAAGGTCTTTTTTGCCAT
65 GAAGGTC---TTTGGCAT
** * * * * * *
1368365 ATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTAGAGTTGAGCGTAGTCGAACTC
1 ATAGGCCTTCTAG-CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
1368430 GAAGGTCTTTGGCAG
65 GAAGGTCTTTGGCAT
* *
1368445 AT-GGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACT
1 ATAGG-CCTTCT-AGCTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
* *
1368509 TGAAGGTCTTTTGGTGACAA
64 CGAAGGTC-TTT-G-G-CAT
** * * * * * * * * *
1368529 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTATTCAAACT
1 ATAGGCCTTCTAG-CTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
** * *
1368594 CGGGGGTCTTTGGTAG
64 CGAAGGTCTTTGGCAT
* * * *
1368610 ATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGTGTAGTCGAACTC
1 ATAGGCCTTCTAG-CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
1368675 GAAGGTCTTTGGTTGGCAG
65 GAAGGTC--T--TTGGCAT
** * * * * * *
1368694 ATAACCCTTCTCTA-CTTAAGTTATGCTGCAAAT-ATTGTGCCCTCGAAGCTGAGTGTAATCAAA
1 ATAGGCC-T-TCTAGCTTAAGCTATGCTGCAAATGA-TGTG-CCTTGGAGCTGAGCGTAGTCGAA
* * *
1368757 CTTGAGGGTCTTTTAGTGGCAG
62 CTCGAAGGTC--TT--TGGCAT
* * *
1368779 ATA-GCACTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTCGAACT
1 ATAGGC-CTTCTAG-CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
* *
1368843 CGAAAGTCTTTGGTGACAG
64 CGAAGGTCTTT-G-G-CAT
** * * * * * * *
1368862 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAGGCCTTCTAG-CTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
* *
1368927 CGAGGGTCTTTGGCAG
64 CGAAGGTCTTTGGCAT
* *
1368943 ATA-GCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGACCTGAGCGTAGTCGAACT
1 ATAGGC-CTTCTAG-CTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
1369007 CGAAGGTCTTT
64 CGAAGGTCTTT
1369018 TGTTGGCAAA
Statistics
Matches: 574, Mismatches: 126, Indels: 71
0.74 0.16 0.09
Matches are distributed among these distances:
79 10 0.02
80 156 0.27
81 84 0.15
82 25 0.04
83 85 0.15
84 122 0.21
85 88 0.15
86 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (79 bp):
ATAGGCCTTCTAGCTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCG
AAGGTCTTTGGCAT
Found at i:1368606 original size:84 final size:84
Alignment explanation
Indices: 1368309--1369037 Score: 601
Period size: 84 Copynumber: 8.8 Consensus size: 84
1368299 GAGCTATACC
* * * ** * ** * *
1368309 GCAAATGATGTGCCGTTG-AGCTGAGTGTAATCGGACTCAAAGGTCTTTTTTGCCATATAACCCT
1 GCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCT
*
1368373 TCTCGACTTAAGTTATGCT
66 TCTAGACTTAAGTTATGCT
* * * * * * * **
1368392 GTAAATGATATGCCTTAG-AGTTGAGCGTAGTCGAACTCGAAGGTCTTT-G-G-CAGATGGCCCT
1 GCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCT
*
1368453 TCTCA-ACTTAAGCTATGCT
66 TCT-AGACTTAAGTTATGCT
* * * * *
1368472 GCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCAAACTTGAAGGTCTTTTGGTGACAAATAACCC
1 GCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTC-TTTGGTGACAGATAACCC
* *
1368536 TTCTAGCCTTGAGTTATGCT
65 TTCTAGACTTAAGTTATGCT
* * * ** *
1368556 GTAAATAATGTGCCCTCGAAGCTGAGTGTATTCAAACTCGGGGGTCTTTGGT---AGATAGCCCT
1 GCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCT
* *
1368618 TCTTGACTTAAGCTATGCT
66 TCTAGACTTAAGTTATGCT
* * * * *
1368637 GCAAATGATGTG-CCTTGGAGTTGAGTGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
1 GCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGG-TGACAGATAACCC
**
1368701 TTCTCTACTTAAGTTATGCT
65 TTCTAGACTTAAGTTATGCT
* * * * * * *
1368721 GCAAAT-ATTGTGCCCTCGAAGCTGAGTGTAATCAAACTTGAGGGTCTTTTAGTGGCAGATAGCA
1 GCAAATGA-TGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTC-TTTGGTGACAGATAACC
* *
1368785 CTTCTTGACTTAAGCTATGCT
64 CTTCTAGACTTAAGTTATGCT
* * ** * *
1368806 GCAAATGATGTGCCTTAG-AGCTGAGCATAGTCGAACTCGAAAGTCTTTGGTGACAGATAACCCT
1 GCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCT
* *
1368870 TCTAGCCTTGAGTTATGCT
66 TCTAGACTTAAGTTATGCT
* * * * * *
1368889 GTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTT-G-G-CAGATAGCTCT
1 GCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCT
* *
1368951 TCTCGACTTAAGCTATGCT
66 TCTAGACTTAAGTTATGCT
* * * * * * * *
1368970 GCAAATGATGTG-CCTTGGACCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCC
1 GCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTC-TTTGGTGACAGATAACCC
1369034 TTCT
65 TTCT
1369038 TGCCTTGAGC
Statistics
Matches: 514, Mismatches: 111, Indels: 41
0.77 0.17 0.06
Matches are distributed among these distances:
79 3 0.01
80 116 0.23
81 76 0.15
82 2 0.00
83 89 0.17
84 129 0.25
85 94 0.18
86 5 0.01
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (84 bp):
GCAAATGATGTGCCCTCGAAGCTGAGTGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAACCCT
TCTAGACTTAAGTTATGCT
Found at i:1368637 original size:165 final size:165
Alignment explanation
Indices: 1368207--1369051 Score: 932
Period size: 165 Copynumber: 5.1 Consensus size: 165
1368197 GACAGATAGT
* * * * * * * *
1368207 CCTTCTTGCATTGAGCTATGTTGTAAATGATGTG-CCTTGGAGCTGAGCT-TAGTCGAAACTCGA
1 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAG-TGTAATC-AAACTCGA
* * ** * *** * *
1368270 AGGTCTTTGGCATATAGGTCTTCTAG-CCCGAGCTATACCGCAAATGATGTGCCGTT-GAGCTGA
64 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGA
* * * * * * *
1368333 GTGTAATCGGACTCAAAGGTCTTTT-TTGCCATATAAC
128 GCGTAGTCGAACTCGAAGGTCTTTTGGTGACAAATAAC
* * * * * * * * * * * *
1368370 CCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTAG-AGTTGAGCGTAGTCGAACTCGAAG
1 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGG
* *
1368434 GTCTTTGGCAGATGGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG
66 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG
* *
1368499 TAGTCAAACTTGAAGGTCTTTTGGTGACAAATAAC
131 TAGTCGAACTCGAAGGTCTTTTGGTGACAAATAAC
* *
1368534 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTATTCAAACTCGGGG
1 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGG
* * * *
1368599 GTCTTTGGTAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGTG
66 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG
* *
1368664 TAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAAC
131 TAGTCGAACTCGAAGGTCTTTTGG-TGACAAATAAC
*** * * * *
1368699 CCTTCTCTACTTAAGTTATGCTGCAAATATTGTGCCCTCGAAGCTGAGTGTAATCAAACTTGAGG
1 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGG
* * *
1368764 GTCTTTTAGTGGCAGATAGCACTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTG
66 GTC--TT--TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTG
* * *
1368829 AGCATAGTCGAACTCGAAAGTC-TTTGGTGACAGATAAC
127 AGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAAATAAC
* *
1368867 CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGG
1 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGG
* *
1368932 GTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGACCTGAGCG
66 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG
* *
1368997 TAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAAC
131 TAGTCGAACTCGAAGGTCTTTTGGTGACAAATAAC
* *
1369032 CCTTCTTGCCTTGAGCTATG
1 CCTTCTAGCCTTGAGTTATG
1369052 TTGCAATTGA
Statistics
Matches: 578, Mismatches: 92, Indels: 22
0.84 0.13 0.03
Matches are distributed among these distances:
162 29 0.05
163 86 0.15
164 122 0.21
165 192 0.33
166 2 0.00
167 2 0.00
168 69 0.12
169 76 0.13
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (165 bp):
CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGG
GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCG
TAGTCGAACTCGAAGGTCTTTTGGTGACAAATAAC
Found at i:1368902 original size:333 final size:328
Alignment explanation
Indices: 1368207--1369037 Score: 1017
Period size: 333 Copynumber: 2.5 Consensus size: 328
1368197 GACAGATAGT
* * * * * * * *
1368207 CCTTCTTGCATTGAGCTATGTTGTAAATGATGTG-CCTTGGAGCTGAGCT-TAGTCGAAACTCGA
1 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAG-TGTAATC-AAACTCGA
* * ** * *** * *
1368270 AGGTCTTTGGCATATAGGTCTTCTAG-CCCGAGCTATACCGCAAATGATGTGCCGTT-GAGCTGA
64 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGA
* * * * * * *
1368333 GTGTAATCGGACTCAAAGGTCTTTTTTGCCATATAACCCTTCTCGACTTAAGTTATGCTGTAAAT
128 GTGTAGTCGAACTCGAAGGTCTTTGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
* * * * * *
1368398 GATATGCCTTAGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGATGGCCCTTCTCAACTTA
193 GATATGCCCTAGAGCTGAGCGTAATCAAACTCGAAGGTCTTTGGCAGATAGCACTTCTCAACTTA
* * * *
1368463 AGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTTGAAGGTCTTTTGGTGACA
258 AGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTCAAACTCGAAAGTCTTTTGGTGACA
1368528 AATAAC
323 AATAAC
* *
1368534 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTATTCAAACTCGGGG
1 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGG
* * *
1368599 GTCTTTGGTAGATAGCCCTTCTTGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGTG
66 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTG
* *
1368664 TAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCTACTTAAGTTATGCTGCAAAT-A
131 TAGTCGAACTCGAAGGTCTTT-GTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAATGA
* * * * * **
1368728 TTGTGCCCTCGAAGCTGAGTGTAATCAAACTTGAGGGTCTTTTAGTGGCAGATAGCACTTCTTGA
195 -TATGCCCTAG-AGCTGAGCGTAATCAAACTCGAAGGTC--TT--TGGCAGATAGCACTTCTCAA
*
1368793 CTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTCGAACTCGAAAGTC-TTTGGT
254 CTTAAGCTATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTCAAACTCGAAAGTCTTTTGGT
*
1368857 GACAGATAAC
319 GACAAATAAC
* *
1368867 CCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGG
1 CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGG
* * *
1368932 GTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGACCTGAGCG
66 GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTG
1368997 TAGTCGAACTCGAAGGTCTTTTGTTGGCAAATAACCCTTCT
131 TAGTCGAACTCGAAGGTC-TTTGTTGGCAAATAACCCTTCT
1369038 TGCCTTGAGC
Statistics
Matches: 433, Mismatches: 59, Indels: 18
0.85 0.12 0.04
Matches are distributed among these distances:
327 59 0.14
328 65 0.15
329 43 0.10
330 21 0.05
332 2 0.00
333 171 0.39
334 72 0.17
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (328 bp):
CCTTCTAGCCTTGAGTTATGCTGTAAATAATGTGCCCTCGAAGCTGAGTGTAATCAAACTCGAGG
GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGTG
TAGTCGAACTCGAAGGTCTTTGTTGGCAAATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
ATGCCCTAGAGCTGAGCGTAATCAAACTCGAAGGTCTTTGGCAGATAGCACTTCTCAACTTAAGC
TATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTCAAACTCGAAAGTCTTTTGGTGACAAAT
AAC
Found at i:1370402 original size:95 final size:94
Alignment explanation
Indices: 1370235--1370430 Score: 286
Period size: 95 Copynumber: 2.1 Consensus size: 94
1370225 GGACAACATA
** * * ** *
1370235 ATATATAAACACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGTCAGGGCGTTTAACCAATTG
1 ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCAGGGCATTTAACCAATTG
*
1370300 CCTTAGAGGGACAGCTCAAGCTTTATTGT
66 CCTTAGAGGGACAACTCAAGCTTTATTGT
*
1370329 ATAGTATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCGGGGCATTTAACCAATT
1 ATA-TATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCAGGGCATTTAACCAATT
1370394 G-CTCTAGAGGGACAACTCAAGCTTTATTGT
65 GCCT-TAGAGGGACAACTCAAGCTTTATTGT
1370424 ATATATA
1 ATATATA
1370431 TAATATTATA
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
94 9 0.10
95 82 0.90
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (94 bp):
ATATATAATTACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCAGGGCATTTAACCAATTG
CCTTAGAGGGACAACTCAAGCTTTATTGT
Found at i:1374048 original size:3 final size:3
Alignment explanation
Indices: 1374040--1374105 Score: 84
Period size: 3 Copynumber: 22.7 Consensus size: 3
1374030 AAAATATATC
* *
1374040 ATA ATA ATA A-A ATAA ATA A-A AT- TTA GTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1374083 ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA AT
1374106 GATGATGATG
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
2 5 0.09
3 48 0.86
4 3 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1374895 original size:34 final size:33
Alignment explanation
Indices: 1374857--1374936 Score: 142
Period size: 34 Copynumber: 2.4 Consensus size: 33
1374847 TTTTCGTTTA
1374857 GTTTTCTCTCGATCTGTTGTTGGCTTTTGTTCTG
1 GTTTTCTCTCGATCTGTTGTTGGCTTTT-TTCTG
1374891 GTTTTCTCTCGATCTGTTGTTGGCTTTTTTCTG
1 GTTTTCTCTCGATCTGTTGTTGGCTTTTTTCTG
*
1374924 GGTTTCTCTCGAT
1 GTTTTCTCTCGAT
1374937 GATGCTTCGT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 17 0.38
34 28 0.62
ACGTcount: A:0.04, C:0.19, G:0.23, T:0.55
Consensus pattern (33 bp):
GTTTTCTCTCGATCTGTTGTTGGCTTTTTTCTG
Found at i:1375604 original size:29 final size:29
Alignment explanation
Indices: 1375571--1375627 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
1375561 ATCATATATT
1375571 TTTTGAAAAATGTTTTCAAAACTATATAG
1 TTTTGAAAAATGTTTTCAAAACTATATAG
*
1375600 TTTTGAAAAATGTTTTTAAAACTATATA
1 TTTTGAAAAATGTTTTCAAAACTATATA
1375628 CTATATAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (29 bp):
TTTTGAAAAATGTTTTCAAAACTATATAG
Found at i:1375609 original size:66 final size:65
Alignment explanation
Indices: 1375540--1375663 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 65
1375530 ATATTTTCAA
* **
1375540 AAAAAT-ATTTTAAAATTATATA-TCATATATTTTTTGAAAAATG-TTTTCAAAACTATATAGTT
1 AAAAATGATTTTAAAACTATATACT-ATATAAGTTTT-AAAAATGATTTTC-AAACTATATAGTT
1375602 TTG
63 TTG
* *
1375605 AAAAATGTTTTTAAAACTATATACTATATAAGTTTTCAAAATGATTTTCAAACTATATA
1 AAAAATGATTTTAAAACTATATACTATATAAGTTTTAAAAATGATTTTCAAACTATATA
1375664 ATATATATGT
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
65 22 0.43
66 28 0.55
67 1 0.02
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (65 bp):
AAAAATGATTTTAAAACTATATACTATATAAGTTTTAAAAATGATTTTCAAACTATATAGTTTTG
Found at i:1375632 original size:36 final size:35
Alignment explanation
Indices: 1375593--1375877 Score: 205
Period size: 36 Copynumber: 8.2 Consensus size: 35
1375583 TTTTCAAAAC
*
1375593 TATATAGTTTTGAAAAATGTTTTTAAAACTATATAC
1 TATATAGTTTT-AAAAATGTTTTTAAAACTATATAA
* * *
1375629 TATATAAGTTTTCAAAATGATTTTCAAACTATATAA
1 TATAT-AGTTTTAAAAATGTTTTTAAAACTATATAA
* *
1375665 TATATATGTTTTCAAAATG--TTTAAAA--AAAT-A
1 TATATA-GTTTTAAAAATGTTTTTAAAACTATATAA
* * * *
1375696 TATTTA-TTTTCAAAATGTTTTAAAAACTACATAA
1 TATATAGTTTTAAAAATGTTTTTAAAACTATATAA
* * *
1375730 TATACA-TTTTCAAAAACGTTTTAAAAACTATAT-A
1 TATATAGTTTT-AAAAATGTTTTTAAAACTATATAA
* * * *
1375764 T-TTTA-TTTTCAAAATGTTTTAAAAATTATATAA
1 TATATAGTTTTAAAAATGTTTTTAAAACTATATAA
* *
1375797 TATATAAACGTTTTCAAACATGTTTTCAAAACTATATATTA
1 TATAT--A-GTTTT-AAAAATGTTTTTAAAACTATATA--A
* * *
1375838 TATACATTTTTAAAAATG-TTTTCAAACTATATAA
1 TATATAGTTTTAAAAATGTTTTTAAAACTATATAA
1375872 TATATA
1 TATATA
1375878 TATATATAAA
Statistics
Matches: 202, Mismatches: 30, Indels: 36
0.75 0.11 0.13
Matches are distributed among these distances:
29 11 0.05
31 12 0.06
32 22 0.11
33 11 0.05
34 25 0.12
35 20 0.10
36 56 0.28
37 12 0.06
38 8 0.04
39 20 0.10
41 5 0.02
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (35 bp):
TATATAGTTTTAAAAATGTTTTTAAAACTATATAA
Found at i:1375698 original size:65 final size:67
Alignment explanation
Indices: 1375593--1375878 Score: 244
Period size: 67 Copynumber: 4.1 Consensus size: 67
1375583 TTTTCAAAAC
* *
1375593 TATATA-GTTTTGAAAAATGTTTTTAAAACTATATACTATATAAGTTTTCAAAATGATTTT-CAA
1 TATATATGTTTT-CAAAATG-TTTTAAAA--ATATA-TATATAA-TTTTCAAAATG-TTTTAAAA
1375656 ACTATATAA
59 ACTATATAA
* * *
1375665 TATATATGTTTTCAAAATG-TTTAAAAAAATATAT-TTATTTTCAAAATGTTTTAAAAACTACAT
1 TATATATGTTTTCAAAATGTTTTAAAAATATATATATAATTTTCAAAATGTTTTAAAAACTATAT
1375728 AA
66 AA
* * * * *
1375730 TATACA--TTTTCAAAAACGTTTTAAAAACTATATATTTTATTTTCAAAATGTTTTAAAAATTAT
1 TATATATGTTTTC-AAAATGTTTTAAAAA-TATATATATAATTTTCAAAATGTTTTAAAAACTAT
1375793 ATAA
64 ATAA
* * *
1375797 TATATAAACGTTTTCAAACATGTTTTCAAAACTATATATTATATACATTTTTAAAAATGTTTT-C
1 TATAT--ATGTTTTCAAA-ATGTTTT-AAAA--ATATA-TATATA-A-TTTTCAAAATGTTTTAA
1375861 AAACTATATAA
57 AAACTATATAA
1375872 TATATAT
1 TATATAT
1375879 ATATATAAAT
Statistics
Matches: 179, Mismatches: 18, Indels: 33
0.78 0.08 0.14
Matches are distributed among these distances:
63 5 0.03
64 9 0.05
65 34 0.19
66 8 0.04
67 36 0.20
68 4 0.02
69 1 0.01
70 10 0.06
71 11 0.06
72 16 0.09
73 10 0.06
74 5 0.03
75 16 0.09
76 14 0.08
ACGTcount: A:0.44, C:0.08, G:0.05, T:0.44
Consensus pattern (67 bp):
TATATATGTTTTCAAAATGTTTTAAAAATATATATATAATTTTCAAAATGTTTTAAAAACTATAT
AA
Found at i:1378484 original size:30 final size:29
Alignment explanation
Indices: 1378444--1378500 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
1378434 GGCATGGTTT
1378444 AAAAAAAAGTAA-AGTTTAGGAACTAAAAC
1 AAAAAAAAGTAATA-TTTAGGAACTAAAAC
*
1378473 AAAAGAAAAGTAATATTTAGGTACTAAA
1 AAAA-AAAAGTAATATTTAGGAACTAAA
1378501 CATATAATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 4 0.16
30 20 0.80
31 1 0.04
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (29 bp):
AAAAAAAAGTAATATTTAGGAACTAAAAC
Found at i:1379011 original size:19 final size:20
Alignment explanation
Indices: 1378970--1379011 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1378960 TTTCTATATT
* *
1378970 TAAAATATCTATTTTTTATA
1 TAAAATATCTATATTTGATA
1378990 TAAAATATCTA-ATTTGATA
1 TAAAATATCTATATTTGATA
1379009 TAA
1 TAA
1379012 TATAAAGTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAAATATCTATATTTGATA
Found at i:1400011 original size:31 final size:33
Alignment explanation
Indices: 1399963--1400041 Score: 90
Period size: 34 Copynumber: 2.4 Consensus size: 33
1399953 TTTAAATAGT
* *
1399963 TATTATATTTTATATT-AAT-ATATTTATGTAAA
1 TATTAT-TTTTTTATTAAATAATATTTATATAAA
*
1399995 TATTATTTTTTTATTAAAATAATATTTATATAAT
1 TATTATTTTTTTATT-AAATAATATTTATATAAA
*
1400029 TATTATTTATTTA
1 TATTATTTTTTTA
1400042 GAATTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.20
32 6 0.15
33 3 0.08
34 23 0.57
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (33 bp):
TATTATTTTTTTATTAAATAATATTTATATAAA
Found at i:1400033 original size:34 final size:31
Alignment explanation
Indices: 1399953--1400041 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
1399943 TTAGTATTTT
* * *
1399953 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
1399985 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
1400019 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
1400042 GAATTATTTA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:1400204 original size:17 final size:17
Alignment explanation
Indices: 1400182--1400235 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
1400172 AATGTTAATA
1400182 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
1400199 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
1400216 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
1400233 TTT
1 TTT
1400236 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:1401796 original size:21 final size:21
Alignment explanation
Indices: 1401766--1401813 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1401756 GCAGGGGTAC
* *
1401766 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
1401787 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
1401808 ATGCCA
1 ATGCCA
1401814 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:1401843 original size:21 final size:20
Alignment explanation
Indices: 1401817--1401889 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 20
1401807 TATGCCATCT
1401817 CCGCAGGGTTACATTCTGAGC
1 CCGCAGGGTTACATTCT-AGC
1401838 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATT-CTAGC
*
1401859 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACAT-TCTAGC
1401880 CCGCAGGGTT
1 CCGCAGGGTT
1401890 TTATACCATA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
20 2 0.04
21 41 0.87
22 4 0.09
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (20 bp):
CCGCAGGGTTACATTCTAGC
Done.