Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008621.1 Hibiscus syriacus cultivar Beakdansim tig00111584_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: 1991651
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1111162 original size:13 final size:13
Alignment explanation
Indices: 1111144--1111214 Score: 72
Period size: 13 Copynumber: 5.5 Consensus size: 13
1111134 TTTTCCTCTA
1111144 TTTTTCTCTTTCT
1 TTTTTCTCTTTCT
1111157 TTTTTCTCTTTCT
1 TTTTTCTCTTTCT
*
1111170 TTTTTCTGTTT-T
1 TTTTTCTCTTTCT
* * *
1111182 TTTCTGTGTTTCT
1 TTTTTCTCTTTCT
* * *
1111195 TTTTTTTTTTTTT
1 TTTTTCTCTTTCT
1111208 TTTTTCT
1 TTTTTCT
1111215 TTTTTTGTGT
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
12 10 0.20
13 39 0.80
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (13 bp):
TTTTTCTCTTTCT
Found at i:1111184 original size:10 final size:9
Alignment explanation
Indices: 1111152--1111220 Score: 61
Period size: 10 Copynumber: 7.2 Consensus size: 9
1111142 TATTTTTCTC
1111152 TTTCTTTTT
1 TTTCTTTTT
*
1111161 TCTCTTTCTTT
1 TTTC-TT-TTT
1111172 TTTCTGTTTT
1 TTTCT-TTTT
1111182 TTTCTGTGTTT
1 TTTCT-T-TTT
1111193 CTTT-TTTTT
1 -TTTCTTTTT
1111202 TTT-TTTTT
1 TTTCTTTTT
1111210 TTTCTTTTT
1 TTTCTTTTT
1111219 TT
1 TT
1111221 GTGTTTTTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
8 11 0.21
9 13 0.25
10 14 0.27
11 11 0.21
12 3 0.06
ACGTcount: A:0.00, C:0.12, G:0.04, T:0.84
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:1111220 original size:13 final size:13
Alignment explanation
Indices: 1111109--1111218 Score: 62
Period size: 13 Copynumber: 8.2 Consensus size: 13
1111099 GATCTGTCTA
1111109 TTTC-TTTTTTTT
1 TTTCTTTTTTTTT
**
1111121 AATCTTTTTTTTCT
1 TTTCTTTTTTTT-T
* * *
1111135 TTTCCTCTATTTT
1 TTTCTTTTTTTTT
* *
1111148 TCTCTTTCTTTTT
1 TTTCTTTTTTTTT
* *
1111161 TCTCTTTCTTTTT
1 TTTCTTTTTTTTT
* *
1111174 TCTGTTTTTTTCTGT
1 TTTCTTTTTTT-T-T
1111189 GTTTCTTTTTTTTT
1 -TTTCTTTTTTTTT
1111203 TTT-TTTTTTTCTT
1 TTTCTTTTTTT-TT
1111216 TTT
1 TTT
1111219 TTGTGTTTTT
Statistics
Matches: 76, Mismatches: 16, Indels: 11
0.74 0.16 0.11
Matches are distributed among these distances:
12 9 0.12
13 46 0.61
14 10 0.13
15 2 0.03
16 9 0.12
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:1111227 original size:10 final size:9
Alignment explanation
Indices: 1111169--1111228 Score: 52
Period size: 8 Copynumber: 6.6 Consensus size: 9
1111159 TTTCTCTTTC
*
1111169 TTTTTTCTG
1 TTTTTTTTG
1111178 TTTTTTTCTG
1 TTTTTTT-TG
*
1111188 TGTTTCTTT-
1 T-TTTTTTTG
1111197 TTTTTTTT-
1 TTTTTTTTG
*
1111205 TTTTTTTTC
1 TTTTTTTTG
1111214 TTTTTTTGTG
1 TTTTTTT-TG
1111224 TTTTT
1 TTTTT
1111229 ATATATCTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 14 0.33
9 14 0.33
10 10 0.23
11 5 0.12
ACGTcount: A:0.00, C:0.07, G:0.08, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1111227 original size:20 final size:20
Alignment explanation
Indices: 1111190--1111228 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1111180 TTTTTCTGTG
* *
1111190 TTTCTTTTTTTTTTTTTTTT
1 TTTCTTTTTTTGTGTTTTTT
1111210 TTTCTTTTTTTGTGTTTTT
1 TTTCTTTTTTTGTGTTTTT
1111229 ATATATCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.05, G:0.05, T:0.90
Consensus pattern (20 bp):
TTTCTTTTTTTGTGTTTTTT
Found at i:1112639 original size:21 final size:23
Alignment explanation
Indices: 1112598--1112648 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
1112588 ATGCACATGC
1112598 AAATG-AAAAGATACAAAAATGG
1 AAATGCAAAAGATACAAAAATGG
* *
1112620 GAATGCAAAA-ATAC-AAAATGT
1 AAATGCAAAAGATACAAAAATGG
1112641 AAATGCAA
1 AAATGCAA
1112649 CAAAGGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 13 0.52
22 8 0.32
23 4 0.16
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (23 bp):
AAATGCAAAAGATACAAAAATGG
Found at i:1117301 original size:13 final size:13
Alignment explanation
Indices: 1117283--1117313 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
1117273 TTATTGATAA
1117283 AAATATTTTTTTT
1 AAATATTTTTTTT
1117296 AAATATTTTTTTT
1 AAATATTTTTTTT
1117309 AAATA
1 AAATA
1117314 ATCGTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (13 bp):
AAATATTTTTTTT
Found at i:1125194 original size:636 final size:636
Alignment explanation
Indices: 1123982--1125258 Score: 2428
Period size: 636 Copynumber: 2.0 Consensus size: 636
1123972 TGCAGGGTTC
1123982 ATATAATCAGGAGCAAGACGAAGTGCCTATGAAGGAATCGACTATTTCCGTTATTGATACCCCTA
1 ATATAATCAGGAGCAAGACGAAGTGCCTATGAAGGAATCGACTATTTCCGTTATTGATACCCCTA
1124047 AACCTAAGGAAATAATAACGGTTCGACGGAGCATAGAAAGGTTTTATATGGACCATGGATGATGG
66 AACCTAAGGAAATAATAACGGTTCGACGGAGCATAGAAAGGTTTTATATGGACCATGGATGATGG
1124112 CAGCTAACCGAAAACGTAGACCAAAAGGCAAGACGCTGCAATATCAACCAGACACGTCAGGTGGT
131 CAGCTAACCGAAAACGTAGACCAAAAGGCAAGACGCTGCAATATCAACCAGACACGTCAGGTGGT
* *
1124177 GGTAGGGGTAACAATTATCGGTTTAATATTCTAGAGATCAGGTACTGACTTAGAGGCTAAGGTTA
196 GGTACGGGTAACAATTATCGGTTTAATATTCTAGAGATCAGGTACTGACTTAGAGGCTAAGATTA
1124242 CTCGGGAAGAAGTAACTATGGAGAATCCGAGAGCTAGTTCAAGAAAGGTGACAACACAAGACCAT
261 CTCGGGAAGAAGTAACTATGGAGAATCCGAGAGCTAGTTCAAGAAAGGTGACAACACAAGACCAT
* *
1124307 TCTCCCCATTTCCAAAATTACAAAGCAAATGGGAAACAATATCTGACGACAGCGGAACAGAGGGG
326 TCTCCCCATTTCCAAAATTACAAAACAAATGGGAAACAATATCTGACGACAGCGGAACAAAGGGG
* *
1124372 AGAATGGAAACAACACAAGACCAGATTTGTCAAGTCAAAGACATCGTTGTTATCTTCTTCTTCAG
391 AGAATGGAAACAACACAAGACCAGATTTGTCAAGTCAAAGACATCATCGTTATCTTCTTCTTCAG
1124437 CTAAAACATATGCATCTGAAGATTACTATTATGCATCTCATACTAGTTTTAATTTTTATACTGCA
456 CTAAAACATATGCATCTGAAGATTACTATTATGCATCTCATACTAGTTTTAATTTTTATACTGCA
1124502 TATTACACTTCAACCGAGACTTAGCCGACTTGGGTTGAACCTTTATGGGATGCAATGCAACACAC
521 TATTACACTTCAACCGAGACTTAGCCGACTTGGGTTGAACCTTTATGGGATGCAATGCAACACAC
*
1124567 TCAAACATCTTCTACAGAACATGCGGGTGAAGGTTAATGGGATCATATCAT
586 TCAAACATCTTCTACAGAACATGCGGGTGAAGGTGAATGGGATCATATCAT
*
1124618 ATATAATCAGGAGCAAGACGAAGTGCCTATGAAGGAATCGACTATTTCCGTTATTGATACCCTTA
1 ATATAATCAGGAGCAAGACGAAGTGCCTATGAAGGAATCGACTATTTCCGTTATTGATACCCCTA
1124683 AACCTAAGGAAATAATAACGGTTCGACGGAGCATAGAAAGGTTTTATATGGACCATGGATGATGG
66 AACCTAAGGAAATAATAACGGTTCGACGGAGCATAGAAAGGTTTTATATGGACCATGGATGATGG
*
1124748 CAGCTAACCGAAAACGTAGACCAAAAGGCAAGACGCTGCAATATCAACCAGACACGTCGGGTGGT
131 CAGCTAACCGAAAACGTAGACCAAAAGGCAAGACGCTGCAATATCAACCAGACACGTCAGGTGGT
*
1124813 GGTACGGGTAACAATTATCGGTTTAATATTCTAGAGATCAGGTACTGACTTGGAGGCTAAGATTA
196 GGTACGGGTAACAATTATCGGTTTAATATTCTAGAGATCAGGTACTGACTTAGAGGCTAAGATTA
1124878 CTCGGGAAGAAGTAACTATGGAGAATCCGAGAGCTAGTTCAAGAAAGGTGACAACACAAGACCAT
261 CTCGGGAAGAAGTAACTATGGAGAATCCGAGAGCTAGTTCAAGAAAGGTGACAACACAAGACCAT
*
1124943 TCTCCCCATTTCCAAAATTACAAAACAAATGGGAAACCATATCTGACGACAGCGGAACAAAGGGG
326 TCTCCCCATTTCCAAAATTACAAAACAAATGGGAAACAATATCTGACGACAGCGGAACAAAGGGG
*
1125008 AGAATGGAAACAACACAAGACCAGATTTGTCAGGTCAAAGACATCATCGTTATCTTCTTCTTCAG
391 AGAATGGAAACAACACAAGACCAGATTTGTCAAGTCAAAGACATCATCGTTATCTTCTTCTTCAG
* *
1125073 CTACAACATCTGCATCTGAAGATTACTATTATGCATCTCATACTAGTTTTAATTTTTATACTGCA
456 CTAAAACATATGCATCTGAAGATTACTATTATGCATCTCATACTAGTTTTAATTTTTATACTGCA
1125138 TATTACACTTCAACCGAGACTTAGCCGACTTGGGTTGAACCTTTATGGGATGCAATGCAACACAC
521 TATTACACTTCAACCGAGACTTAGCCGACTTGGGTTGAACCTTTATGGGATGCAATGCAACACAC
1125203 TCAAACATCTTCTACAGAACATGCGGGTGAAGGTGAATGGGATCATATCAT
586 TCAAACATCTTCTACAGAACATGCGGGTGAAGGTGAATGGGATCATATCAT
1125254 ATATA
1 ATATA
1125259 GTCAACAAGG
Statistics
Matches: 627, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
636 627 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (636 bp):
ATATAATCAGGAGCAAGACGAAGTGCCTATGAAGGAATCGACTATTTCCGTTATTGATACCCCTA
AACCTAAGGAAATAATAACGGTTCGACGGAGCATAGAAAGGTTTTATATGGACCATGGATGATGG
CAGCTAACCGAAAACGTAGACCAAAAGGCAAGACGCTGCAATATCAACCAGACACGTCAGGTGGT
GGTACGGGTAACAATTATCGGTTTAATATTCTAGAGATCAGGTACTGACTTAGAGGCTAAGATTA
CTCGGGAAGAAGTAACTATGGAGAATCCGAGAGCTAGTTCAAGAAAGGTGACAACACAAGACCAT
TCTCCCCATTTCCAAAATTACAAAACAAATGGGAAACAATATCTGACGACAGCGGAACAAAGGGG
AGAATGGAAACAACACAAGACCAGATTTGTCAAGTCAAAGACATCATCGTTATCTTCTTCTTCAG
CTAAAACATATGCATCTGAAGATTACTATTATGCATCTCATACTAGTTTTAATTTTTATACTGCA
TATTACACTTCAACCGAGACTTAGCCGACTTGGGTTGAACCTTTATGGGATGCAATGCAACACAC
TCAAACATCTTCTACAGAACATGCGGGTGAAGGTGAATGGGATCATATCAT
Found at i:1125659 original size:20 final size:20
Alignment explanation
Indices: 1125621--1125668 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1125611 TTTTTTTCAG
*
1125621 TTTTAAAA-TT-AAAATTAT
1 TTTTAAAATTTAAAAAATAT
*
1125639 TTTTACAATTTAAAAAATAT
1 TTTTAAAATTTAAAAAATAT
1125659 TTTTAAAATT
1 TTTTAAAATT
1125669 GACTCGTCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 7 0.28
19 2 0.08
20 16 0.64
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTTAAAATTTAAAAAATAT
Found at i:1132361 original size:18 final size:19
Alignment explanation
Indices: 1132319--1132361 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
1132309 TTGGTTCACA
* *
1132319 GAATATAAGATTATCAGTG
1 GAATAAAAGATTACCAGTG
1132338 GTAATAAAAGATTACCAG-G
1 G-AATAAAAGATTACCAGTG
1132357 GAATA
1 GAATA
1132362 GGATTACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 4 0.19
19 3 0.14
20 14 0.67
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.26
Consensus pattern (19 bp):
GAATAAAAGATTACCAGTG
Found at i:1134032 original size:32 final size:32
Alignment explanation
Indices: 1133988--1134062 Score: 132
Period size: 32 Copynumber: 2.3 Consensus size: 32
1133978 TTACAAAAAT
*
1133988 AAGATTTTAGAGATGTTTAGGTGTTGTGTAAC
1 AAGATTTGAGAGATGTTTAGGTGTTGTGTAAC
*
1134020 AAGATTTGAGAGATGTTTAGGTGTTGTGTAAT
1 AAGATTTGAGAGATGTTTAGGTGTTGTGTAAC
1134052 AAGATTTGAGA
1 AAGATTTGAGA
1134063 AAGTTGTAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.31, C:0.01, G:0.29, T:0.39
Consensus pattern (32 bp):
AAGATTTGAGAGATGTTTAGGTGTTGTGTAAC
Found at i:1134730 original size:21 final size:21
Alignment explanation
Indices: 1134696--1134748 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1134686 ATTCTGACTA
*
1134696 TCGCATTACGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
1134717 TTGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
1134738 TCGCATTGCGA
1 TCGCATTGCGA
1134749 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:1134991 original size:22 final size:22
Alignment explanation
Indices: 1134966--1135027 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
1134956 GGCGACATCC
1134966 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1134988 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
* *
1135006 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
1135028 TTCACGGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:1135383 original size:20 final size:20
Alignment explanation
Indices: 1135358--1135406 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1135348 CAACGAGTGA
*
1135358 ATCGCAACGTGAATTTGACT
1 ATCGCAACGCGAATTTGACT
*
1135378 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAATTTGACT
1135398 ATCGCAACG
1 ATCGCAACG
1135407 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGAATTTGACT
Found at i:1135473 original size:20 final size:20
Alignment explanation
Indices: 1135448--1135497 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1135438 TGCGATTCTT
1135448 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
1135468 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
1135488 GTGTTGCGAT
1 GCGTTGCGAT
1135498 TTTCATTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:1135503 original size:20 final size:20
Alignment explanation
Indices: 1135465--1135519 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
1135455 GATAGTCAAA
* **
1135465 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
1135485 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
1135505 TTCGTGTTGCGATTT
1 TTCGTGTTGCGATTT
1135520 AAAGTTTCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.11, C:0.16, G:0.24, T:0.49
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:1135527 original size:20 final size:20
Alignment explanation
Indices: 1135484--1135527 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1135474 CGATAGTCAT
** *
1135484 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
1135504 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
1135524 TTTC
1 TTTC
1135528 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:1137368 original size:20 final size:20
Alignment explanation
Indices: 1137345--1137448 Score: 94
Period size: 20 Copynumber: 5.5 Consensus size: 20
1137335 AGAATAGTTT
*
1137345 ACTATCGCAATGCGAAAATT
1 ACTATCGCAATGCGAAAATG
***
1137365 ACTATCGCAACATGAAAATG
1 ACTATCGCAATGCGAAAATG
*
1137385 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
*
1137401 A--ATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
**
1137419 ACTATCGCAATGCGAATTTG
1 ACTATCGCAATGCGAAAATG
1137439 ACTATCGCAA
1 ACTATCGCAA
1137449 CGAAAGAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
14 6 0.09
16 4 0.06
17 4 0.06
18 3 0.04
20 50 0.75
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:1137441 original size:54 final size:54
Alignment explanation
Indices: 1137352--1137486 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 54
1137342 TTTACTATCG
* *** *
1137352 CAATGCGAAAATTACTATCGCAACATGAAAATGACTATCGCAACGAGAGAATCA
1 CAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCA
** *
1137406 CAATGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAAAGAATCG
1 CAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCA
** *
1137460 CAATGCG-AAATGAAAATCGCATTGCGA
1 CAATGCGAAAATGACTATCGCAATGCGA
1137487 TTCTCTCGTT
Statistics
Matches: 70, Mismatches: 11, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
53 17 0.24
54 53 0.76
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.19
Consensus pattern (54 bp):
CAATGCGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCA
Found at i:1137523 original size:20 final size:20
Alignment explanation
Indices: 1137495--1137581 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
1137485 GATTCTCTCG
**
1137495 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
1137515 TTACGATAGTCATTTTCGTA
1 TTGCGATAGTCATTTTCGCA
1137535 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
1137555 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
1137575 TTGCGAT
1 TTGCGAT
1137582 TTTAAGTTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:1138156 original size:21 final size:21
Alignment explanation
Indices: 1138065--1138169 Score: 95
Period size: 21 Copynumber: 5.0 Consensus size: 21
1138055 GACTCACCTG
*
1138065 TCATCGTTCAAGAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
1138087 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
1138107 TCATCCATCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
1138128 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
1138149 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
1138170 CCAACATTCT
Statistics
Matches: 63, Mismatches: 19, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
20 3 0.05
21 59 0.94
22 1 0.02
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.23
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:1138162 original size:42 final size:42
Alignment explanation
Indices: 1138062--1138172 Score: 118
Period size: 42 Copynumber: 2.6 Consensus size: 42
1138052 CCTGACTCAC
* * * *
1138062 CTGTCATCGTTCAAGAGGCCTCC-CCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGTCC-CCTCCCACCGTTCAAGAGGCCA
* **
1138104 CTATCATCCATCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
*
1138146 CTGTCATCGTTGAAGAGGT-CCCTCCCA
1 CTGTCATCGTTCAAGA-GTCCCCTCCCA
1138173 ACATTCTAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
41 2 0.04
42 52 0.93
43 2 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGTCCCCTCCCACCGTTCAAGAGGCCA
Found at i:1139417 original size:24 final size:24
Alignment explanation
Indices: 1139383--1139436 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1139373 CTGAAAAATC
1139383 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1139407 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1139431 ATCAAA
1 ATCAAA
1139437 TTTCGAATAC
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:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1139450 original size:24 final size:24
Alignment explanation
Indices: 1139383--1139450 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1139373 CTGAAAAATC
* * *
1139383 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1139407 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1139431 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1139451 TGGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1140314 original size:20 final size:20
Alignment explanation
Indices: 1140298--1140363 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
1140288 CAGAATCTCG
1140298 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* *
1140318 TTGCGATTTTCGTATTCGCA
1 TTGCGATTTACGTAATCGCA
*
1140338 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
1140358 TTGCGA
1 TTGCGA
1140364 ATTAGGAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:1140324 original size:40 final size:39
Alignment explanation
Indices: 1140277--1140363 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 39
1140267 GGAATTCAGT
1140277 ATTGCGATAGTCAGAATCTCG-TTGCGATTTACGTAATCGC
1 ATTGCGATAGTC-GAAT-TCGATTGCGATTTACGTAATCGC
** * *
1140317 ATTGCGATTTTCGTATTCGCATTGCGATTTACGTATTCGC
1 ATTGCGATAGTCGAATTCG-ATTGCGATTTACGTAATCGC
1140357 ATTGCGA
1 ATTGCGA
1140364 ATTAGGAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 3 0.07
39 3 0.07
40 35 0.85
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (39 bp):
ATTGCGATAGTCGAATTCGATTGCGATTTACGTAATCGC
Found at i:1140384 original size:21 final size:21
Alignment explanation
Indices: 1140360--1140405 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1140350 TATTCGCATT
1140360 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
1140381 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
1140402 GCGA
1 GCGA
1140406 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:1141979 original size:16 final size:16
Alignment explanation
Indices: 1141958--1141988 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1141948 GTATCCAAGA
1141958 AATCATTAAATAAATT
1 AATCATTAAATAAATT
*
1141974 AATCATTTAATAAAT
1 AATCATTAAATAAAT
1141989 ATTTCTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
AATCATTAAATAAATT
Found at i:1147397 original size:30 final size:31
Alignment explanation
Indices: 1147361--1147423 Score: 110
Period size: 30 Copynumber: 2.0 Consensus size: 31
1147351 CTGGTAAATC
1147361 TAAACTATTTTATGACTC-AGTGTCTGATGA
1 TAAACTATTTTATGACTCAAGTGTCTGATGA
1147391 TAAACTATTTTATGACTCAAAGTGTCTGATGA
1 TAAACTATTTTATGACTC-AAGTGTCTGATGA
1147423 T
1 T
1147424 TAACCGATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 18 0.58
32 13 0.42
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.40
Consensus pattern (31 bp):
TAAACTATTTTATGACTCAAGTGTCTGATGA
Found at i:1150220 original size:15 final size:14
Alignment explanation
Indices: 1150200--1150244 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 14
1150190 GGACATGAAC
1150200 AATAAAAATAAAATT
1 AATAAAAATAAAA-T
1150215 AATAAAAATAATAAT
1 AATAAAAATAA-AAT
1150230 AATACTAAAATAAAA
1 AATA--AAAATAAAA
1150245 AAAATGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 16 0.59
16 4 0.15
17 7 0.26
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAAAAATAAAAT
Found at i:1150439 original size:38 final size:37
Alignment explanation
Indices: 1150390--1150541 Score: 163
Period size: 38 Copynumber: 4.1 Consensus size: 37
1150380 AATTATATGT
1150390 TATATGTTTTCAAAAATGATTTCAAAAACTATATAATA
1 TATATGTTTTC-AAAATGATTTCAAAAACTATATAATA
* *
1150428 TATATTTTTTCAAAAATGTTTTCAAAAACTATAT-AT-
1 TATATGTTTTC-AAAATGATTTCAAAAACTATATAATA
* * * *
1150464 TATATATTTTCAAAATGTTTTTAAAAAAAAC-ATATATTA
1 TATATGTTTTCAAAATG-ATTT--CAAAAACTATATAATA
1150503 TATA-GTTTTCAAAATGATTTC--AAACTATATAATA
1 TATATGTTTTCAAAATGATTTCAAAAACTATATAATA
1150537 TATAT
1 TATAT
1150542 ATATATAAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
33 4 0.04
34 11 0.11
35 6 0.06
36 14 0.14
37 9 0.09
38 50 0.51
39 4 0.04
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.43
Consensus pattern (37 bp):
TATATGTTTTCAAAATGATTTCAAAAACTATATAATA
Found at i:1150543 original size:38 final size:37
Alignment explanation
Indices: 1150363--1150545 Score: 134
Period size: 38 Copynumber: 5.0 Consensus size: 37
1150353 AAACTCATAG
* * * *
1150363 TTTCAAAAATGTTTTGAAAT-TAT-ATGT-TATATGT
1 TTTCAAAAATGATTTCAAATATATAATATATATATAT
1150397 TTTCAAAAATGATTTCAAAAACTATATAATATATAT-T-T
1 TTTCAAAAATGATTTC--AAA-TATATAATATATATATAT
* *
1150435 TTTCAAAAATGTTTTCAAAAACTAT-ATAT-TATATAT
1 TTTCAAAAATGATTTCAAATA-TATAATATATATATAT
* * * *
1150471 TTTC-AAAATGTTTTTAAA-AAAAACATATATTATATAGT
1 TTTCAAAAATGATTTCAAATATATA-ATATA-TATATA-T
1150509 TTTC-AAAATGATTTCAAACTATATAATATATATATAT
1 TTTCAAAAATGATTTCAAA-TATATAATATATATATAT
1150546 ATAAATAATA
Statistics
Matches: 121, Mismatches: 12, Indels: 29
0.75 0.07 0.18
Matches are distributed among these distances:
33 1 0.01
34 18 0.15
35 23 0.19
36 14 0.12
37 8 0.07
38 42 0.35
39 9 0.07
40 6 0.05
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (37 bp):
TTTCAAAAATGATTTCAAATATATAATATATATATAT
Found at i:1151224 original size:84 final size:84
Alignment explanation
Indices: 1151130--1151524 Score: 532
Period size: 84 Copynumber: 4.8 Consensus size: 84
1151120 TTTTGTAAAT
*
1151130 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAAAACCCTTCTC
1 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
1151195 GACTTAAGTTATGCTGCAA
66 GACTTAAGTTATGCTGCAA
* * * *
1151214 ATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACTCTTCTA
1 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
* * * * *
1151278 GCCATGAGTTATTCTGTAA
66 GACTTAAGTTATGCTGCAA
* * * * ** ** *
1151297 ATGATGTGCCCTCGAAGCTGAGTGTAATCGAGTTCGGGGGTC--T--TTGGCAGATAGCCCTTCT
1 ATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
*
1151358 CGACTTAAGCTATGCTGCAA
65 CGACTTAAGTTATGCTGCAA
1151378 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
1 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
1151443 GACTTAAGTTATGCTGCAA
66 GACTTAAGTTATGCTGCAA
* * *
1151462 ATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAACTCTTCT
1 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCT
1151525 GGCCTTGAGC
Statistics
Matches: 263, Mismatches: 42, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
80 25 0.10
81 35 0.13
82 2 0.01
83 50 0.19
84 151 0.57
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (84 bp):
ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTC
GACTTAAGTTATGCTGCAA
Found at i:1151505 original size:164 final size:163
Alignment explanation
Indices: 1151130--1151507 Score: 513
Period size: 164 Copynumber: 2.3 Consensus size: 163
1151120 TTTTGTAAAT
1151130 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAAAACCCTTCTC
1 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC--T--TTGGCAGAAAACCCTTCTC
*
1151195 GACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
62 GACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * *
1151260 TGACAGATAACTCTTCTAGCCATGAGTTATTCTGTAA
127 TGACAGATAACCCTTCTAGACATAAGTTATGCTGCAA
* * * * ** ** * *
1151297 ATGATGTGCCCTCGAAGCTGAGTGTAATCGAGTTCGGGGGTCTTTGGCAGATAGCCCTTCTCGAC
1 ATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGAAAACCCTTCTCGAC
*
1151362 TTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTG
65 TTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TG
* * *
1151427 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAA
129 ACAGATAACCCTTCTAGACATAAGTTATGCTGCAA
*
1151462 ATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
1 ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
1151508 TGACAGATAA
Statistics
Matches: 180, Mismatches: 29, Indels: 7
0.83 0.13 0.03
Matches are distributed among these distances:
164 110 0.61
165 36 0.20
166 1 0.01
167 8 0.04
168 25 0.14
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (163 bp):
ATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGCAGAAAACCCTTCTCGACT
TAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGAC
AGATAACCCTTCTAGACATAAGTTATGCTGCAA
Found at i:1154953 original size:18 final size:19
Alignment explanation
Indices: 1154912--1154956 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
1154902 AGTTAATGTG
1154912 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
1154931 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
1154949 AATGCAAA
1 AATGCAAA
1154957 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:1158066 original size:15 final size:14
Alignment explanation
Indices: 1158046--1158090 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 14
1158036 GGACATGAAC
1158046 AATAAAAATAAAATT
1 AATAAAAATAAAA-T
1158061 AATAAAAATAATAAT
1 AATAAAAATAA-AAT
1158076 AATACTAAAATAAAA
1 AATA--AAAATAAAA
1158091 AAAATGACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 16 0.59
16 4 0.15
17 7 0.26
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAAAAATAAAAT
Found at i:1158285 original size:38 final size:37
Alignment explanation
Indices: 1158236--1158388 Score: 156
Period size: 38 Copynumber: 4.1 Consensus size: 37
1158226 AATTATATGT
1158236 TATATGTTTTCAAAAATGATTTCAAAAACTATATAATA
1 TATATGTTTTC-AAAATGATTTCAAAAACTATATAATA
* *
1158274 TATATTTTTTCAAAAATGTTTTCAAAAACTATAT-AT-
1 TATATGTTTTC-AAAATGATTTCAAAAACTATATAATA
* * * *
1158310 TATATATTTTCAAAATGTTTTAAAAAAAAAAC-ATATATTA
1 TATATGTTTTCAAAATGATTT----CAAAAACTATATAATA
1158350 TATA-GTTTTCAAAATGATTTC--AAACTATATAATA
1 TATATGTTTTCAAAATGATTTCAAAAACTATATAATA
1158384 TATAT
1 TATAT
1158389 ATATATAAAT
Statistics
Matches: 98, Mismatches: 9, Indels: 19
0.78 0.07 0.15
Matches are distributed among these distances:
33 4 0.04
34 11 0.11
35 10 0.10
36 10 0.10
37 2 0.02
38 36 0.37
39 21 0.21
40 4 0.04
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.42
Consensus pattern (37 bp):
TATATGTTTTCAAAATGATTTCAAAAACTATATAATA
Found at i:1158337 original size:74 final size:71
Alignment explanation
Indices: 1158205--1158388 Score: 187
Period size: 72 Copynumber: 2.5 Consensus size: 71
1158195 TTTCAAACTC
* * * * *
1158205 ATAG-TTTCAAAAATGTTTTGAAATTATATGTTATATGTTTTCAAAAATGATTT-CAAAAACTAT
1 ATAGTTTTCAAAAATGTTTTCAAACTATATATTATATATTTTCAAAAATGATTTAAAAAAAC-AT
1158268 ATAATAT
65 ATAATAT
* *
1158275 ATATTTTTTCAAAAATGTTTTCAAAAACTATATATTATATATTTTC-AAAATGTTTTAAAAAAAA
1 ATA-GTTTTCAAAAATGTTTTC--AAACTATATATTATATATTTTCAAAAATGATTT---AAAAA
*
1158339 AACATATATTAT
60 AACATATAATAT
* *
1158351 ATAGTTTTC-AAAATGATTTCAAACTATATAATATATAT
1 ATAGTTTTCAAAAATGTTTTCAAACTATATATTATATAT
1158389 ATATATAAAT
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
70 3 0.03
72 32 0.34
73 9 0.09
74 29 0.31
75 5 0.05
76 11 0.12
77 6 0.06
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (71 bp):
ATAGTTTTCAAAAATGTTTTCAAACTATATATTATATATTTTCAAAAATGATTTAAAAAAACATA
TAATAT
Found at i:1161776 original size:2 final size:2
Alignment explanation
Indices: 1161769--1161800 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1161759 AGGGTCCATA
1161769 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1161801 CATAATACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1164806 original size:24 final size:25
Alignment explanation
Indices: 1164749--1164807 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
1164739 AGGGGAAGTA
* * *
1164749 ATTGTATCTCACACGTACCAGGTAG
1 ATTGCATCTCTCACCTACCAGGTAG
1164774 ATTGC-TCTCTCACCTACCAGGTAG
1 ATTGCATCTCTCACCTACCAGGTAG
1164798 ATT-CATCTCT
1 ATTGCATCTCT
1164808 GTAATAAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.03
24 25 0.83
25 4 0.13
ACGTcount: A:0.24, C:0.29, G:0.15, T:0.32
Consensus pattern (25 bp):
ATTGCATCTCTCACCTACCAGGTAG
Found at i:1165554 original size:2 final size:2
Alignment explanation
Indices: 1165547--1165584 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1165537 ATTTCATCTT
1165547 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1165585 GAAACAAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1168438 original size:25 final size:25
Alignment explanation
Indices: 1168404--1168453 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
1168394 TAGAATAATC
*
1168404 ACCCAACTATAAGGCATTTGATATT
1 ACCCAACTATAAGGCATTTAATATT
1168429 ACCCAACTATAAGGCATTTAATATT
1 ACCCAACTATAAGGCATTTAATATT
1168454 TATATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (25 bp):
ACCCAACTATAAGGCATTTAATATT
Found at i:1174912 original size:24 final size:24
Alignment explanation
Indices: 1174876--1174922 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1174866 CGTTAGTCCA
1174876 GCTAACGTACACCCAGAGAAACTT
1 GCTAACGTACACCCAGAGAAACTT
* *
1174900 GCTATCGTGCACCCAGAGAAACT
1 GCTAACGTACACCCAGAGAAACT
1174923 GTCAGGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.30, G:0.19, T:0.17
Consensus pattern (24 bp):
GCTAACGTACACCCAGAGAAACTT
Found at i:1178240 original size:23 final size:24
Alignment explanation
Indices: 1178184--1178240 Score: 57
Period size: 23 Copynumber: 2.4 Consensus size: 24
1178174 ATTTAAATTC
1178184 AAAATATAAA-AATACTCAAAAACT
1 AAAAT-TAAATAATACTCAAAAACT
* *
1178208 TAAATAAAATAATAC-CAAAAA-T
1 AAAATTAAATAATACTCAAAAACT
1178230 AAAAATTAAAT
1 -AAAATTAAAT
1178241 TACTAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
22 1 0.04
23 17 0.63
24 9 0.33
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (24 bp):
AAAATTAAATAATACTCAAAAACT
Found at i:1178836 original size:21 final size:23
Alignment explanation
Indices: 1178794--1178839 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
1178784 ATAAAAAATT
1178794 AATAATATATATTTTTAAATTTTG
1 AATAATATATATTTTT-AATTTTG
* *
1178818 AATAATTTA-ATTTTTATTTTTG
1 AATAATATATATTTTTAATTTTG
1178840 GTATTATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (23 bp):
AATAATATATATTTTTAATTTTG
Found at i:1182601 original size:35 final size:35
Alignment explanation
Indices: 1182560--1182631 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
1182550 TTTAAAACGG
1182560 GAAGCTTCATCAAATAAATTTCAATCATCCTAAAA
1 GAAGCTTCATCAAATAAATTTCAATCATCCTAAAA
1182595 GAAGCTTCATCAAATAAATTTCAATCATCCTAAAA
1 GAAGCTTCATCAAATAAATTTCAATCATCCTAAAA
1182630 GA
1 GA
1182632 TCTCGGAGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (35 bp):
GAAGCTTCATCAAATAAATTTCAATCATCCTAAAA
Found at i:1186528 original size:61 final size:61
Alignment explanation
Indices: 1186433--1186555 Score: 176
Period size: 61 Copynumber: 2.0 Consensus size: 61
1186423 TAACATCCAT
* * *
1186433 GAAACTTGAAAGCAAACAATAAGGGATTGTAGAGCAAACAAATTCATTCAATCAAACACAA
1 GAAACTTGAAAGCAAACAACAAGGGATTGTAGAGCAAACAAATACACTCAATCAAACACAA
* * *
1186494 GAAACTTGAAAGCAAACAACAATGGG-TTGTAGAGCTAATAAATACACTCAATCAAATACAA
1 GAAACTTGAAAGCAAACAACAA-GGGATTGTAGAGCAAACAAATACACTCAATCAAACACAA
1186555 G
1 G
1186556 TTCAAGTCGG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
61 52 0.95
62 3 0.05
ACGTcount: A:0.50, C:0.16, G:0.15, T:0.19
Consensus pattern (61 bp):
GAAACTTGAAAGCAAACAACAAGGGATTGTAGAGCAAACAAATACACTCAATCAAACACAA
Found at i:1189160 original size:29 final size:30
Alignment explanation
Indices: 1189090--1189148 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1189080 CAATTTAAGG
1189090 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
1189121 CAAAATGTTTTTGGACTT-AATTGAATTT
1 CAAAATGTTTTTGGACTTGAATTGAATTT
1189149 TTTCAAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 10 0.36
30 12 0.43
31 6 0.21
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1189255 original size:21 final size:20
Alignment explanation
Indices: 1189229--1189327 Score: 128
Period size: 21 Copynumber: 4.8 Consensus size: 20
1189219 AGAATGTCAA
1189229 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCA-CCCTGC
1189250 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCA-CCCTGC
1189271 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCACCCTG--C
* *
1189292 TAGTGCATCGATGCACCATGC
1 -AGTGCATCCATGCACCCTGC
1189313 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
1189328 TCAAACACTG
Statistics
Matches: 70, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.06
20 14 0.20
21 36 0.51
22 13 0.19
23 3 0.04
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.21
Consensus pattern (20 bp):
AGTGCATCCATGCACCCTGC
Found at i:1189263 original size:13 final size:14
Alignment explanation
Indices: 1189260--1189327 Score: 54
Period size: 13 Copynumber: 4.9 Consensus size: 14
1189250 AGTGCATCCA
*
1189260 TGCATCCCTGCA-G
1 TGCATCCATGCACG
*
1189273 TGCATCCATGCACC
1 TGCATCCATGCACG
*
1189287 TGCA-CTAGTGCATCG
1 TGCATCCA-TGCA-CG
1189302 ATGCA-CCATGCA-G
1 -TGCATCCATGCACG
1189315 TGCATCCATGCAC
1 TGCATCCATGCAC
1189328 TCAAACACTG
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
12 4 0.09
13 21 0.48
14 8 0.18
15 5 0.11
16 6 0.14
ACGTcount: A:0.22, C:0.35, G:0.21, T:0.22
Consensus pattern (14 bp):
TGCATCCATGCACG
Found at i:1189373 original size:20 final size:20
Alignment explanation
Indices: 1189348--1189421 Score: 87
Period size: 20 Copynumber: 3.6 Consensus size: 20
1189338 AATACAATTA
1189348 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
**
1189368 GTGCATCGATGCATCAAGGT-T
1 GTGCATCGATGCATC--CTTCT
*
1189389 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTTCT
*
1189409 GTGCATCCATGCA
1 GTGCATCGATGCA
1189422 CGAAGGCTGC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
20 28 0.62
21 16 0.36
22 1 0.02
ACGTcount: A:0.19, C:0.27, G:0.24, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:1189572 original size:20 final size:22
Alignment explanation
Indices: 1189534--1189573 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
1189524 TTTGAGTAGA
1189534 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
1189556 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
1189574 ATATACAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:1190744 original size:19 final size:19
Alignment explanation
Indices: 1190711--1190757 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1190701 AATGATTTTC
*
1190711 TTTTGAAAACAAAAT-AGA
1 TTTTGAAAACAAAATGAAA
*
1190729 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAA-ACAAAATGAAA
1190749 TTTTGAAAA
1 TTTTGAAAA
1190758 ATGATTTAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.33
19 6 0.25
20 10 0.42
ACGTcount: A:0.51, C:0.06, G:0.13, T:0.30
Consensus pattern (19 bp):
TTTTGAAAACAAAATGAAA
Found at i:1192097 original size:29 final size:30
Alignment explanation
Indices: 1192027--1192086 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
1192017 CAATATAAGG
1192027 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
1192058 CAAAATTTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
1192087 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:1192192 original size:21 final size:21
Alignment explanation
Indices: 1192166--1192208 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1192156 AGAATGTCAA
1192166 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
1192187 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
1192208 A
1 A
1192209 CCTGTACTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.40, G:0.19, T:0.21
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:1193242 original size:2 final size:2
Alignment explanation
Indices: 1193235--1193260 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1193225 AAAATCCTAA
1193235 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
1193261 TCTGTAAAAA
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:1194161 original size:16 final size:16
Alignment explanation
Indices: 1194120--1194153 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1194110 TTTTCGTTCA
*
1194120 CTTCAGACGAGTTCTT
1 CTTCAGATGAGTTCTT
1194136 CTTCAGATGAGTTCTT
1 CTTCAGATGAGTTCTT
1194152 CT
1 CT
1194154 CATTATGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (16 bp):
CTTCAGATGAGTTCTT
Found at i:1194384 original size:137 final size:136
Alignment explanation
Indices: 1194218--1194577 Score: 424
Period size: 137 Copynumber: 2.6 Consensus size: 136
1194208 AGTCGAGCAA
* ** * *
1194218 AAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAA
*
1194283 GAACTCTATCTGGAAATGCTGATCCTCGAAAGAGACGTTGTTAATTCAACTTCA-TAT-GTA-A-
66 GAACTCT-TCTGGAAATGCTGATCCTC--AAGAGACGTTATT-ATTCAA-TTCATTATCGTAGAT
*
1194344 TGAATTAAGAC-
126 TGAATCAA-ACT
* * *
1194355 AAGGTTAAACAAGTTCTTCTCATTATGAACATCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAA
* * * * * ** *
1194420 GAACTTCCTCTGAAAATGTTGATCCTCAAGTGAGGTTATTATTTTATTCATTTTCGTAGATGTTG
66 GAAC-TCTTCTGGAAATGCTGATCCTCAAGAGACGTTATTATTCAATTCATTATCGTAGA--TTG
*
1194485 AATCAATCT
128 AATCAAACT
*
1194494 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAA
1194559 GAACTCTTCTGGAAATGCT
66 GAACTCTTCTGGAAATGCT
1194578 AATGATGCTC
Statistics
Matches: 189, Mismatches: 26, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
133 4 0.02
134 6 0.03
135 13 0.07
136 1 0.01
137 78 0.41
138 15 0.08
139 72 0.38
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (136 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAA
GAACTCTTCTGGAAATGCTGATCCTCAAGAGACGTTATTATTCAATTCATTATCGTAGATTGAAT
CAAACT
Found at i:1194530 original size:139 final size:136
Alignment explanation
Indices: 1194218--1194577 Score: 401
Period size: 139 Copynumber: 2.6 Consensus size: 136
1194208 AGTCGAGCAA
* ** * *
1194218 AAGGTTGAATAAGTTCTTCAGATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAA
* * *
1194283 GAAC-TCTATCTGGAAATGCTGATCCTCGAAAGAGACGTTGTTAATTCAACTTCATATGTAATGA
66 GAACTTCTATCTGAAAATGCTGATCCTC-AAAGAGACGTTATTAATTCAACTTCAGATGT-ATGA
*
1194347 ATTAAGAC
129 ATCAAGAC
* * *
1194355 AAGGTTAAACAAGTTCTTCTCATTATGAACATCTTCTTCCTCTTCAGATAAGTTCTTCTCATTAA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAA
* * * * **
1194420 GAACTTC-CTCTGAAAATGTTGATCCTC-AAGTGAGGTTATTATTTTATTCATTTTCGTAGATGT
66 GAACTTCTATCTGAAAATGCTGATCCTCAAAGAGACGTTATTA----ATTCAACTTC--AGATGT
*
1194483 -TGAATCAA-TC
125 ATGAATCAAGAC
1194493 TAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 -AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* *
1194558 TGAAC-TCT-TCTGGAAATGCT
65 AGAACTTCTATCTGAAAATGCT
1194578 AATGATGCTC
Statistics
Matches: 189, Mismatches: 25, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
135 11 0.06
137 78 0.41
138 15 0.08
139 80 0.42
141 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (136 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAA
GAACTTCTATCTGAAAATGCTGATCCTCAAAGAGACGTTATTAATTCAACTTCAGATGTATGAAT
CAAGAC
Found at i:1195190 original size:123 final size:123
Alignment explanation
Indices: 1194494--1195190 Score: 1094
Period size: 123 Copynumber: 5.7 Consensus size: 123
1194484 GAATCAATCT
* ** * * * *
1194494 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
* * *
1194559 GAAC-TCTTCTGGAAATG-CTAATGA-TGCTCTATCTCATTCTGCGATAGAATCAAGCAA
66 GAACTTCTTCTGGAAATGAC-GAT-ACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAA
*
1194616 AAGGTTGAATAAGTTCTTCAGATTATGAATTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
1 AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
* * * *
1194681 GAACTTCTTCTAGAAATAACGACACTGCTCTATATCCTTCTGCGATAGAGTCAAGCAA
66 GAACTTCTTCTGGAAATGACGATACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAA
* *
1194739 AAGTTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTTAGACGAGTTCTTCTTATTAC
1 AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
1194804 GAACTTCTTCTGGAAATGACGATACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAA
66 GAACTTCTTCTGGAAATGACGATACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAA
*
1194862 AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGATGAGTTCTTCTTATTAC
1 AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
* * * * *
1194927 GAACTTCTTCTGGAAATAATGATATTACTCTATCTTCTTCTGCGATAGAGTCAAGCAA
66 GAACTTCTTCTGGAAATGACGATACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAA
1194985 AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
1 AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
* *
1195050 GAACTTCTTCTAGAAATGACGATACTGCTCTATCTCCTTCTGCGATAGAGTCAAGTAA
66 GAACTTCTTCTGGAAATGACGATACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAA
* * *
1195108 AACGTTGAATAAGTTTTTAAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
1 AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
*
1195173 AAACTTCTTCTGGAAATG
66 GAACTTCTTCTGGAAATG
1195191 TTAATCCATC
Statistics
Matches: 529, Mismatches: 43, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
122 62 0.12
123 466 0.88
124 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (123 bp):
AAGGTTGAATAAGTTCTTCAGATTATGAACTTTTTCTTCCTCTTCAGACGAGTTCTTCTTATTAC
GAACTTCTTCTGGAAATGACGATACTGCTCTATCTCCTTCTGCGATAGAGTCAAGCAA
Found at i:1200517 original size:22 final size:22
Alignment explanation
Indices: 1200489--1200549 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
1200479 TCAAGGGTAT
*
1200489 AGTGGTCCTTCGGGACATATCC
1 AGTGGTCCTTCGAGACATATCC
*
1200511 AGTGGTCCTTCGAGACGTATCC
1 AGTGGTCCTTCGAGACATATCC
*
1200533 AGTGGTCCTTTGAGACA
1 AGTGGTCCTTCGAGACA
1200550 AATATTCACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.28, T:0.28
Consensus pattern (22 bp):
AGTGGTCCTTCGAGACATATCC
Found at i:1205695 original size:15 final size:15
Alignment explanation
Indices: 1205675--1205706 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1205665 TGCAATGAAT
1205675 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
1205690 AATGAATTTATGCAA
1 AATGAATGTATGCAA
1205705 AA
1 AA
1205707 GGTATTGATC
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:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:1209569 original size:27 final size:26
Alignment explanation
Indices: 1209539--1209596 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
1209529 AATTTCAAGA
*
1209539 AAATATATTAA-TTTTTATATTTTTAAT
1 AAATATA-TAATTTTTTAAATTTTT-AT
1209566 AAATATATAATTTTTTAAATTTTTAT
1 AAATATATAATTTTTTAAATTTTTAT
1209592 AAATA
1 AAATA
1209597 AGATATTTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
AAATATATAATTTTTTAAATTTTTAT
Found at i:1209588 original size:26 final size:27
Alignment explanation
Indices: 1209539--1209596 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
1209529 AATTTCAAGA
*
1209539 AAATATATTAATTTTTATATTTTTAAT
1 AAATATATTAATTTTTATAATTTTAAT
*
1209566 AAATATA-TAATTTTT-TAAATTTTTAT
1 AAATATATTAATTTTTAT-AATTTTAAT
1209592 AAATA
1 AAATA
1209597 AGATATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 1 0.04
26 20 0.71
27 7 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AAATATATTAATTTTTATAATTTTAAT
Found at i:1209609 original size:27 final size:27
Alignment explanation
Indices: 1209550--1209609 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
1209540 AATATATTAA
* *
1209550 TTTTTATATTTTTAATAAATATATAAT
1 TTTTTAAATTTTTAATAAATAGATAAT
1209577 TTTTTAAATTTTT-ATAAATAAGAT-AT
1 TTTTTAAATTTTTAATAAAT-AGATAAT
1209603 TTATTTA
1 TT-TTTA
1209610 CTTAGAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.34
27 19 0.66
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (27 bp):
TTTTTAAATTTTTAATAAATAGATAAT
Found at i:1209937 original size:2 final size:2
Alignment explanation
Indices: 1209930--1209958 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1209920 CATAATGAAT
1209930 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1209959 TCATGTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1213538 original size:23 final size:23
Alignment explanation
Indices: 1213512--1213566 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
1213502 TCTGATTTTA
*
1213512 TGATATATTTTTTGTCATTTGGT
1 TGATATATTTTTGGTCATTTGGT
1213535 TGATATATTTTTGGTCATTTGGT
1 TGATATATTTTTGGTCATTTGGT
1213558 TG-T-TATTTT
1 TGATATATTTT
1213567 AGTTTATCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 6 0.19
22 1 0.03
23 24 0.77
ACGTcount: A:0.16, C:0.04, G:0.18, T:0.62
Consensus pattern (23 bp):
TGATATATTTTTGGTCATTTGGT
Found at i:1226235 original size:42 final size:42
Alignment explanation
Indices: 1226188--1226281 Score: 188
Period size: 42 Copynumber: 2.2 Consensus size: 42
1226178 GTTCGAGCCC
1226188 AATTACAACAACTCACTAAGCCTGTTTACAAAGCAAGACCCA
1 AATTACAACAACTCACTAAGCCTGTTTACAAAGCAAGACCCA
1226230 AATTACAACAACTCACTAAGCCTGTTTACAAAGCAAGACCCA
1 AATTACAACAACTCACTAAGCCTGTTTACAAAGCAAGACCCA
1226272 AATTACAACA
1 AATTACAACA
1226282 TCAACCCAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.45, C:0.28, G:0.09, T:0.19
Consensus pattern (42 bp):
AATTACAACAACTCACTAAGCCTGTTTACAAAGCAAGACCCA
Found at i:1227657 original size:54 final size:56
Alignment explanation
Indices: 1227596--1227737 Score: 139
Period size: 54 Copynumber: 2.6 Consensus size: 56
1227586 GGAGGTGCTT
* * * *
1227596 GATTTTAGATTGTAGCATAGAGGTGCTCAATCA-TTCT-AATGCACAGAGGTGACA
1 GATTTTAGACTGAAGCACAAAGGTGCTCAATCATTTCTGAATGCACAGAGGTGACA
* * * *
1227650 GATTTTAGACTGAAGCACAAAGGTGCTCAGTCATTTTTGACTGCACAGAGGTGTCA
1 GATTTTAGACTGAAGCACAAAGGTGCTCAATCATTTCTGAATGCACAGAGGTGACA
* ** *
1227706 G-TCCTT-GGTTGAAGCACATAGGTGCTCAATCA
1 GAT-TTTAGACTGAAGCACAAAGGTGCTCAATCA
1227738 GTCTTAGCTA
Statistics
Matches: 72, Mismatches: 13, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
54 28 0.39
55 26 0.36
56 18 0.25
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.29
Consensus pattern (56 bp):
GATTTTAGACTGAAGCACAAAGGTGCTCAATCATTTCTGAATGCACAGAGGTGACA
Found at i:1227722 original size:27 final size:27
Alignment explanation
Indices: 1227660--1227733 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
1227650 GATTTTAGAC
*
1227660 TGAAGCACAAAGGTGCTCAGTCATTTT
1 TGAAGCACAAAGGTGCTCAGTCATTGT
* * *
1227687 TGACTGCACAGAGGTG-TCAGTCCTTGGT
1 TGA-AGCACAAAGGTGCTCAGTCATT-GT
*
1227715 TGAAGCACATAGGTGCTCA
1 TGAAGCACAAAGGTGCTCA
1227734 ATCAGTCTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (27 bp):
TGAAGCACAAAGGTGCTCAGTCATTGT
Found at i:1227729 original size:55 final size:55
Alignment explanation
Indices: 1227603--1227905 Score: 238
Period size: 55 Copynumber: 5.5 Consensus size: 55
1227593 CTTGATTTTA
* * * * * * ** *
1227603 GATTGTAGCATAGAGGTGCTCAATCA-TTCTA-ATGCACAGAGGTGACAGATTTTA
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-TCCTC
* * * * *
1227657 GACTGAAGCACAAAGGTGCTCAGTCATTTTT-GACTGCACAGAGGTGTCAGTCCTT
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAG-CTACACAGAGGTGTCAGTCCTC
* * * *
1227712 GGTTGAAGCACATAGGTGCTCAATCAGTCTTAGCTACACAGAGGTGTCAGCTCCT-
1 GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAG-TCCTC
* * * * *
1227767 GATTGAAGCACAGAGGTACTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTC
1 GATTGAAGCACAGAGGTGCTCAATCA---TTTTTAGCTACACAGAGGTGTCAGTCCTC
* * * * * *
1227825 GATTGATGCATATAAGTGCTCAATCCCTTTTTAGCTAAACAGAGGTGTCAG-CTCTC
1 GATTGAAGCACAGAGGTGCTCAAT-CATTTTTAGCTACACAGAGGTGTCAGTC-CTC
1227881 GATTGAAGCACAGAGGTGCTCAATC
1 GATTGAAGCACAGAGGTGCTCAATC
1227906 GTTAATTCAA
Statistics
Matches: 196, Mismatches: 42, Indels: 21
0.76 0.16 0.08
Matches are distributed among these distances:
54 21 0.11
55 69 0.35
56 64 0.33
57 3 0.02
58 38 0.19
59 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (55 bp):
GATTGAAGCACAGAGGTGCTCAATCATTTTTAGCTACACAGAGGTGTCAGTCCTC
Found at i:1227818 original size:113 final size:111
Alignment explanation
Indices: 1227660--1227902 Score: 319
Period size: 113 Copynumber: 2.2 Consensus size: 111
1227650 GATTTTAGAC
* * * *
1227660 TGAAGCACAAAGGTGCTCAGTCATTTTTGACTGCACAGAGGTGTCAGTCCTTGGTTGAAGCACAT
1 TGAAGCACAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAT
* *
1227725 AGGTGCTCAAT-CAGTCTTAGCTACACAGAGGTGTCAGCTC-CTGAT
66 AAGTGCTCAATCCAGTCTTAGCTAAACAGAGGTGTCAGCTCTC-GAT
* * *
1227770 TGAAGCACAGAGGTACTCAGTCATTTTTTTTAACTGCACAGAGGTGTCAGTTCTCGATTGATGCA
1 TGAAGCACAGAGGTGCTCAGTCA---TTTTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCA
* ** *
1227835 TATAAGTGCTCAATCCCTTTTTAGCTAAACAGAGGTGTCAGCTCTCGAT
63 CATAAGTGCTCAATCCAGTCTTAGCTAAACAGAGGTGTCAGCTCTCGAT
1227884 TGAAGCACAGAGGTGCTCA
1 TGAAGCACAGAGGTGCTCA
1227903 ATCGTTAATT
Statistics
Matches: 114, Mismatches: 14, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
110 21 0.18
113 46 0.40
114 46 0.40
115 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (111 bp):
TGAAGCACAGAGGTGCTCAGTCATTTTTAACTGCACAGAGGTGTCAGTCCTCGATTGAAGCACAT
AAGTGCTCAATCCAGTCTTAGCTAAACAGAGGTGTCAGCTCTCGAT
Found at i:1228155 original size:81 final size:81
Alignment explanation
Indices: 1228020--1228173 Score: 204
Period size: 81 Copynumber: 1.9 Consensus size: 81
1228010 GCAAGTTACA
* * *
1228020 GAGAATGGTTCGCACAAGAAACGGTGGAGTAACAACCTCTCATAGAGGTGTAGAGCCA-GAAGTT
1 GAGAATGGTTCGCACAAGAAACGGCGGAGTAACAACCTCTCACAGAGGTGTAGAG-CAGGAAGCT
*
1228084 ACTGAGCCGATTGTACC
65 ACGGAGCCGATTGTACC
* * * *
1228101 GAGAATGGTTCGCACACGAAATGGCGGA-TCGACAAGCTCTCACAGAGGTGTAGAGCAGGAAGCT
1 GAGAATGGTTCGCACAAGAAACGGCGGAGT-AACAACCTCTCACAGAGGTGTAGAGCAGGAAGCT
1228165 ACGGAGCCG
65 ACGGAGCCG
1228174 GTGGTGCAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 3 0.05
81 60 0.95
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (81 bp):
GAGAATGGTTCGCACAAGAAACGGCGGAGTAACAACCTCTCACAGAGGTGTAGAGCAGGAAGCTA
CGGAGCCGATTGTACC
Found at i:1233822 original size:29 final size:29
Alignment explanation
Indices: 1233789--1233873 Score: 71
Period size: 30 Copynumber: 2.9 Consensus size: 29
1233779 TATGTTAATA
1233789 CTATTTAATCCTTTAATTTTCTGTTTGTG
1 CTATTTAATCCTTTAATTTTCTGTTTGTG
* * * * * * *
1233818 TTATTTTAGTACTTTATTTTTTTTTTTTTG
1 CTA-TTTAATCCTTTAATTTTCTGTTTGTG
* **
1233848 CTATTTAATCCCTTACGTTTCTGTTT
1 CTATTTAATCCTTTAATTTTCTGTTT
1233874 TTCTCTTGCA
Statistics
Matches: 40, Mismatches: 15, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
29 18 0.45
30 22 0.55
ACGTcount: A:0.15, C:0.13, G:0.08, T:0.64
Consensus pattern (29 bp):
CTATTTAATCCTTTAATTTTCTGTTTGTG
Found at i:1243802 original size:22 final size:22
Alignment explanation
Indices: 1243774--1243824 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1243764 CAAAGCACAG
1243774 AGGAAATGACGAATCTGTCTTA
1 AGGAAATGACGAATCTGTCTTA
1243796 AGGAAATGACGAATCTGTCTTA
1 AGGAAATGACGAATCTGTCTTA
1243818 AGGAAAT
1 AGGAAAT
1243825 TATTCATACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.25
Consensus pattern (22 bp):
AGGAAATGACGAATCTGTCTTA
Found at i:1245446 original size:21 final size:20
Alignment explanation
Indices: 1245360--1245517 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
1245350 AAATGACCAA
**
1245360 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1245379 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1245399 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1245419 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1245440 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1245461 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
1245481 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1245502 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1245518 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1245508 original size:20 final size:20
Alignment explanation
Indices: 1245484--1245733 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
1245474 CGATTTTCCA
** *
1245484 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
1245504 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
1245524 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
1245544 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
1245564 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
1245584 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1245604 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1245624 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1245644 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1245664 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1245684 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1245704 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
1245724 AAATCACAAC
1 AAATCGCAAC
1245734 ACTGAAATTT
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:1246455 original size:24 final size:23
Alignment explanation
Indices: 1246417--1246461 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
1246407 AATTTGGTCT
1246417 TGGTCAATATCCGGACTTTGATAC
1 TGGTCAATATCCGGA-TTTGATAC
1246441 TGGTCAATA-CACGGATTTGAT
1 TGGTCAATATC-CGGATTTGAT
1246462 GATGTTTCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (23 bp):
TGGTCAATATCCGGATTTGATAC
Found at i:1249030 original size:19 final size:19
Alignment explanation
Indices: 1248990--1249088 Score: 136
Period size: 19 Copynumber: 5.4 Consensus size: 19
1248980 GATTCTCTCG
1248990 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1249010 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1249029 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
1249043 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1249062 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1249081 TTGCGATT
1 TTGCGATT
1249089 CTCTCGTTGC
Statistics
Matches: 70, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1249084 original size:52 final size:53
Alignment explanation
Indices: 1248971--1249098 Score: 240
Period size: 52 Copynumber: 2.4 Consensus size: 53
1248961 GAAATGAAAA
*
1248971 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCAATTTTCATTTCCGCATTGCGATTTTCATT
1249024 TCGCATTGCGATTCTCTCGTTGCAATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCAATTTTCATTTCCGCATTGCGATTTTCATT
1249076 TCGCATTGCGATTCTCTCGTTGC
1 TCGCATTGCGATTCTCTCGTTGC
1249099 GATAGTCAAA
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
52 41 0.55
53 33 0.45
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCAATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1249099 original size:33 final size:33
Alignment explanation
Indices: 1248971--1249101 Score: 99
Period size: 33 Copynumber: 3.8 Consensus size: 33
1248961 GAAATGAAAA
1248971 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
* *
1249004 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC-GT
1 T-CGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TCATT
* * *
1249044 T-GCAATTTTC-ATT-TCGCATTGCGATTTTCATT
1 TCGC-A-TTGCGATTCTCTCGTTGCGATTTTCATT
1249076 TCGCATTGCGATTCTCTCGTTGCGAT
1 TCGCATTGCGATTCTCTCGTTGCGAT
1249102 AGTCAAATGC
Statistics
Matches: 74, Mismatches: 10, Indels: 28
0.66 0.09 0.25
Matches are distributed among these distances:
31 5 0.07
32 7 0.09
33 21 0.28
34 10 0.14
35 2 0.03
36 3 0.04
37 6 0.08
38 2 0.03
39 10 0.14
40 6 0.08
41 2 0.03
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (33 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1249138 original size:14 final size:14
Alignment explanation
Indices: 1249121--1249175 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1249111 CGGAAATGAA
1249121 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1249135 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1249154 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1249168 AATCGCAA
1 AATCGCAA
1249176 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1249151 original size:33 final size:33
Alignment explanation
Indices: 1249107--1249194 Score: 167
Period size: 33 Copynumber: 2.6 Consensus size: 33
1249097 GCGATAGTCA
1249107 AATGCGGAAATGAAAATCGCAACGAGAGAATCGC
1 AATGC-GAAATGAAAATCGCAACGAGAGAATCGC
1249141 AATGCGAAATGAAAATCGCAACGAGAGAATCGC
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGC
1249174 AATGCGAAATGAAAATCGCAA
1 AATGCGAAATGAAAATCGCAA
1249195 TGCGAAATGA
Statistics
Matches: 54, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 49 0.91
34 5 0.09
ACGTcount: A:0.47, C:0.17, G:0.24, T:0.12
Consensus pattern (33 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGC
Found at i:1249194 original size:52 final size:52
Alignment explanation
Indices: 1249135--1249251 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
1249125 GCAACGAGAG
1249135 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
1249187 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
*
1249239 AATCGCATTGCGA
1 AATCGCAATGCGA
1249252 TTCTCCCATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.44, C:0.18, G:0.21, T:0.16
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1249300 original size:19 final size:19
Alignment explanation
Indices: 1249258--1249357 Score: 156
Period size: 19 Copynumber: 5.5 Consensus size: 19
1249248 GCGATTCTCC
1249258 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
1249278 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1249297 CATTGCGA--TTC-TTTCG
1 CATTGCGATTTTCATTTCG
1249313 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1249330 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1249349 CATTGCGAT
1 CATTGCGAT
1249358 AGTCAATTTT
Statistics
Matches: 75, Mismatches: 0, Indels: 11
0.87 0.00 0.13
Matches are distributed among these distances:
14 6 0.08
16 8 0.11
17 8 0.11
19 36 0.48
20 17 0.23
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:1249354 original size:52 final size:53
Alignment explanation
Indices: 1249241--1249357 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
1249231 GAAATTAAAA
1249241 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
** *
1249294 TCGCATTGCGATTCTTTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1249346 TCGCATTGCGAT
1 TCGCATTGCGAT
1249358 AGTCAATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 30 0.49
53 31 0.51
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1249491 original size:13 final size:14
Alignment explanation
Indices: 1249464--1249499 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1249454 CATCAATTAC
1249464 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1249478 ACAAATCATC-TTT
1 ACAAATCAACTTTT
1249491 ACAAATCAA
1 ACAAATCAA
1249500 TTAAACAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1251505 original size:33 final size:33
Alignment explanation
Indices: 1251459--1251551 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1251449 GCGAAACCAA
* *
1251459 AATCGCAACGCGAAATGAAAATCGCAACGACAT
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1251492 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1251525 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1251552 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1251516 original size:19 final size:19
Alignment explanation
Indices: 1251422--1251556 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1251412 TAGTTTACTT
* *
1251422 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1251442 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1251461 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1251480 TCGCAA--CGACAT---AA
1 TCGCAACGCGAAATGAAAA
*
1251494 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1251513 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1251527 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1251546 TCGCAATGCGA
1 TCGCAACGCGA
1251557 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1251530 original size:14 final size:14
Alignment explanation
Indices: 1251478--1251534 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1251468 GCGAAATGAA
* *
1251478 AATCGCAACGACAT
1 AATCGCAACGAAAG
1251492 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1251509 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1251525 AATCGCAACG
1 AATCGCAACG
1251535 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 18 0.50
16 5 0.14
17 5 0.14
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1251574 original size:19 final size:19
Alignment explanation
Indices: 1251552--1251680 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
1251542 AAAATCGCAA
1251552 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1251571 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
*
1251585 TGCGATTATGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1251604 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1251618 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1251637 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1251656 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1251676 TGCGA
1 TGCGA
1251681 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.54
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1251597 original size:33 final size:33
Alignment explanation
Indices: 1251552--1251643 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
1251542 AAAATCGCAA
1251552 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
*
1251585 TGCGATTATGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1251618 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1251644 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.09, C:0.18, G:0.28, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1251955 original size:94 final size:93
Alignment explanation
Indices: 1251724--1252104 Score: 728
Period size: 93 Copynumber: 4.1 Consensus size: 93
1251714 TTGAATGGAT
*
1251724 AAATTTACTTTCAACCAAAAGACAAAAC-AAGGCAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1251788 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1251816 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1251881 AGTTTAGCAGAATTGGCAGCAAACCGAAC
66 AGTTTAGCAGAATTGGCAGC-AACCGAAC
1251910 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1251975 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1252003 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1252068 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1252096 AAATTTACT
1 AAATTTACT
1252105 AAGCAATCTA
Statistics
Matches: 285, Mismatches: 2, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 28 0.10
93 164 0.58
94 93 0.33
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1252038 original size:187 final size:185
Alignment explanation
Indices: 1251724--1252104 Score: 726
Period size: 187 Copynumber: 2.0 Consensus size: 185
1251714 TTGAATGGAT
*
1251724 AAATTTACTTTCAACCAAAAGACAAAACAAGGCAAATACTATTTCACAGTGTTAAAGAATACACA
1 AAATTTACTTTCAACCAAAAGACAAAACAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
1251789 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
66 GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
1251854 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAAACCGAAC
131 ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGC-AACCGAAC
1251910 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1251975 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
65 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
1252040 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
130 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1252096 AAATTTACT
1 AAATTTACT
1252105 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
186 44 0.23
187 148 0.77
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAGACAAATACTATTTCACAGTGTTAAAGAATACACA
GTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAAT
ACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1253821 original size:14 final size:14
Alignment explanation
Indices: 1253802--1253891 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1253792 TTGAAATGAA
1253802 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1253816 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1253833 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1253849 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1253868 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1253882 AATCGCAACG
1 AATCGCAACG
1253892 CGAAATAAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1253839 original size:33 final size:33
Alignment explanation
Indices: 1253794--1253908 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
1253784 TCTTTTGGTT
1253794 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1253827 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1253860 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
1253893 GAAATAAAAATCGCAA
1 GAAATGAAAATCGCAA
1253909 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1253840 original size:19 final size:18
Alignment explanation
Indices: 1253801--1253913 Score: 79
Period size: 19 Copynumber: 6.8 Consensus size: 18
1253791 GTTGAAATGA
1253801 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1253816 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1253833 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1253849 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1253866 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
* *
1253882 -AATCGCAACGCGAAATAA
1 AAATCGCAACGCGAGAT-G
*
1253900 AAATCGCAATGCGA
1 AAATCGCAACGCGA
1253914 TTTTGGTTTC
Statistics
Matches: 78, Mismatches: 5, Indels: 26
0.72 0.05 0.24
Matches are distributed among these distances:
14 24 0.31
16 15 0.19
17 11 0.14
19 28 0.36
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1253957 original size:33 final size:37
Alignment explanation
Indices: 1253909--1253994 Score: 108
Period size: 39 Copynumber: 2.4 Consensus size: 37
1253899 AAAATCGCAA
**
1253909 TGCGATTTTGGTTTCGCGTT-G-C-G-ATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTCGACAGCATTCTCTCGT
1253942 TGCGATTTTCATTTCGCGTTGCGACAGTCATTCTCTCGT
1 TGCGATTTTCATTTCGCGTT-CGACAG-CATTCTCTCGT
1253981 TGCGATTTTCATTT
1 TGCGATTTTCATTT
1253995 ATCTCGTTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
33 18 0.40
35 1 0.02
36 1 0.02
37 1 0.02
39 24 0.53
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (37 bp):
TGCGATTTTCATTTCGCGTTCGACAGCATTCTCTCGT
Found at i:1253983 original size:20 final size:20
Alignment explanation
Indices: 1253932--1253985 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
1253922 TCGCGTTGCG
***
1253932 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGACAGTC
*
1253952 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGACAGTC
1253971 ATTCTCTCGTTGCGA
1 ATTCTCTCGTTGCGA
1253986 TTTTCATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.13, C:0.26, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCTCTCGTTGCGACAGTC
Found at i:1253992 original size:20 final size:20
Alignment explanation
Indices: 1253932--1254006 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1253922 TCGCGTTGCG
1253932 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
* ***
1253952 ATT-TCGCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1253971 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1253991 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1254007 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 15 0.34
20 16 0.36
21 13 0.30
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1254128 original size:33 final size:33
Alignment explanation
Indices: 1254086--1254156 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
1254076 AATACTAACT
1254086 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
1254119 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1254152 TGAAA
1 TGAAA
1254157 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:1254367 original size:25 final size:25
Alignment explanation
Indices: 1254339--1254391 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 25
1254329 TGTGAGGGAT
1254339 TTCGCCGGAGATGGGGACGGAAATC
1 TTCGCCGGAGATGGGGACGGAAATC
**
1254364 TT---C-GAGATGGGGACGGATTTC
1 TTCGCCGGAGATGGGGACGGAAATC
1254385 TTCGCCG
1 TTCGCCG
1254392 TAGAGAGAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 8
0.69 0.06 0.25
Matches are distributed among these distances:
21 18 0.82
22 1 0.05
24 1 0.05
25 2 0.09
ACGTcount: A:0.19, C:0.21, G:0.38, T:0.23
Consensus pattern (25 bp):
TTCGCCGGAGATGGGGACGGAAATC
Found at i:1255216 original size:33 final size:33
Alignment explanation
Indices: 1255171--1255247 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
1255161 GGGCATTGGT
*
1255171 CAAATCTATCTGCCCTCGCTTTCTTAATTTTAA
1 CAAATCTCTCTGCCCTCGCTTTCTTAATTTTAA
*
1255204 CAAATCTCTCTGCCCTCGCTTTCTTATTTTTAA
1 CAAATCTCTCTGCCCTCGCTTTCTTAATTTTAA
1255237 CAAATCTCTCT
1 CAAATCTCTCT
1255248 TTATGCAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.22, C:0.30, G:0.05, T:0.43
Consensus pattern (33 bp):
CAAATCTCTCTGCCCTCGCTTTCTTAATTTTAA
Found at i:1259882 original size:15 final size:16
Alignment explanation
Indices: 1259862--1259892 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1259852 AAAATACAAC
1259862 ATTCCC-AGTAATCTT
1 ATTCCCTAGTAATCTT
1259877 ATTCCCTAGTAATCTT
1 ATTCCCTAGTAATCTT
1259893 TTATTCCCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.26, C:0.26, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTCCCTAGTAATCTT
Found at i:1260988 original size:2 final size:2
Alignment explanation
Indices: 1260981--1261010 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1260971 ACTAGAAAAC
1260981 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1261011 ATGTTAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1261264 original size:32 final size:32
Alignment explanation
Indices: 1261205--1261265 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
1261195 ATGTATAAAG
* *
1261205 TGATGGCATGACACATATCACATGTACATTAA
1 TGATGACATGACACATATCACAAGTACATTAA
* *
1261237 TGATGACATGACACATGTCATAAGTACAT
1 TGATGACATGACACATATCACAAGTACAT
1261266 AAGTGATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (32 bp):
TGATGACATGACACATATCACAAGTACATTAA
Found at i:1261734 original size:31 final size:31
Alignment explanation
Indices: 1261697--1261756 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1261687 TGTGTAAAGT
1261697 GATATGATATATGTCACGTGT-TCAAAATGAC
1 GATATGATATATGTCACGTGTCT-AAAATGAC
*
1261728 GATATGATATATGTCATGTGTCTAAAATG
1 GATATGATATATGTCACGTGTCTAAAATG
1261757 GTGATGTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (31 bp):
GATATGATATATGTCACGTGTCTAAAATGAC
Found at i:1261767 original size:31 final size:31
Alignment explanation
Indices: 1261695--1261767 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
1261685 CATGTGTAAA
1261695 GTGATATGATATATGTCACGTGTTCAAAATG
1 GTGATATGATATATGTCACGTGTTCAAAATG
** *
1261726 ACGATATGATATATGTCATGTG-TCTAAAATG
1 GTGATATGATATATGTCACGTGTTC-AAAATG
*
1261757 GTGATGTGATA
1 GTGATATGATA
1261768 CATATTATTT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 2 0.06
31 33 0.94
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (31 bp):
GTGATATGATATATGTCACGTGTTCAAAATG
Found at i:1263446 original size:15 final size:15
Alignment explanation
Indices: 1263426--1263461 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1263416 GTTGTTTGTC
1263426 TTCTTAAAATAATAT
1 TTCTTAAAATAATAT
*
1263441 TTCTTAAAATAATTT
1 TTCTTAAAATAATAT
1263456 TTCTTA
1 TTCTTA
1263462 TTGTTTGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCTTAAAATAATAT
Found at i:1269356 original size:176 final size:176
Alignment explanation
Indices: 1269057--1269402 Score: 575
Period size: 176 Copynumber: 2.0 Consensus size: 176
1269047 AAAACTATAG
* * *
1269057 ATTGTATTTTCATTTGCTATGTAGAACATAACAATGCATATCGGTTTCTTGTGTATGAATCAAAG
1 ATTGCATTTTCATTGGCTATGTAGAACATAACAATGCATACCGGTTTCTTGTGTATGAATCAAAG
* *
1269122 AATCCTGAGATTCATAAGAACATGATAATAAAATCAAAGAATGAATAATTATTTGAAGATATATT
66 AATCCTAAGATTCATAAGAACACGATAATAAAATCAAAGAATGAATAATTATTTGAAGATATATT
* **
1269187 CCCTTACAAGTTTAGGGTGGTTGATCATAGTACAATAAAATTGTGA
131 CCCTTACAAGTCTAAAGTGGTTGATCATAGTACAATAAAATTGTGA
*
1269233 ATTGCATTTTCATTGGCTATGTAGAACATAACAATGCATACCGGTTTCTTGTGTATGAATTAAAG
1 ATTGCATTTTCATTGGCTATGTAGAACATAACAATGCATACCGGTTTCTTGTGTATGAATCAAAG
* * * *
1269298 AATCTTAAGATTCATAAGAACACGATAATAAAATCAAAGAATGCATTATTCTTTGAAGATATATT
66 AATCCTAAGATTCATAAGAACACGATAATAAAATCAAAGAATGAATAATTATTTGAAGATATATT
1269363 CCCTTACAAGTCTAAAGTGGTTGATCATAGTACAATAAAA
131 CCCTTACAAGTCTAAAGTGGTTGATCATAGTACAATAAAA
1269403 ACAAACTTTG
Statistics
Matches: 157, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
176 157 1.00
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (176 bp):
ATTGCATTTTCATTGGCTATGTAGAACATAACAATGCATACCGGTTTCTTGTGTATGAATCAAAG
AATCCTAAGATTCATAAGAACACGATAATAAAATCAAAGAATGAATAATTATTTGAAGATATATT
CCCTTACAAGTCTAAAGTGGTTGATCATAGTACAATAAAATTGTGA
Found at i:1271325 original size:6 final size:6
Alignment explanation
Indices: 1271320--1271360 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
1271310 AAAAATGAAA
*
1271320 ACGAAA ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC ACGAA
1 ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC ACGAAC ACGAA
1271361 AACTTGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.54, C:0.29, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGAAC
Found at i:1271326 original size:12 final size:12
Alignment explanation
Indices: 1271311--1271363 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
1271301 ACTTAAAATA
*
1271311 AAAATGAAAACG
1 AAAACGAAAACG
*
1271323 AAAACGAACACG
1 AAAACGAAAACG
* *
1271335 AACACGAACACG
1 AAAACGAAAACG
* *
1271347 AACACGAACACG
1 AAAACGAAAACG
1271359 AAAAC
1 AAAAC
1271364 TTGAAAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.58, C:0.25, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAACGAAAACG
Found at i:1273323 original size:15 final size:15
Alignment explanation
Indices: 1273303--1273333 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1273293 AACTGTGCAG
1273303 GGGGTATAAATCGAA
1 GGGGTATAAATCGAA
1273318 GGGGTATAAATCGAA
1 GGGGTATAAATCGAA
1273333 G
1 G
1273334 CCCGCCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.35, T:0.19
Consensus pattern (15 bp):
GGGGTATAAATCGAA
Found at i:1287753 original size:21 final size:20
Alignment explanation
Indices: 1287667--1287824 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1287657 AAATGACCAA
**
1287667 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1287686 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1287706 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1287726 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1287747 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1287768 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1287788 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1287809 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1287825 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1287886 original size:20 final size:20
Alignment explanation
Indices: 1287792--1288020 Score: 239
Period size: 20 Copynumber: 11.4 Consensus size: 20
1287782 GATTTTCCAG
* ** *
1287792 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1287812 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1287832 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1287852 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1287872 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1287892 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1287912 TATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1287932 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1287952 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1287972 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1287992 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1288012 AATCACAAC
1 AATCGCAAC
1288021 ACTGAAATTT
Statistics
Matches: 179, Mismatches: 24, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
19 2 0.01
20 175 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1288752 original size:24 final size:24
Alignment explanation
Indices: 1288713--1288759 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1288703 AAATTTGGTC
1288713 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1288737 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1288760 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1291311 original size:53 final size:49
Alignment explanation
Indices: 1291234--1291432 Score: 231
Period size: 53 Copynumber: 3.8 Consensus size: 49
1291224 CGGAAATTAC
* *
1291234 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA-C-ATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAAGCAATGAA
1291281 AATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAAAATCGCAATGCGAAATGAAAATCGCAA-GC--AATGAA
*
1291339 AATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGC-GAAATGAAAATCGCAA-GC--AATGAA
*
1291392 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAA
1291433 CGAGAGAATC
Statistics
Matches: 137, Mismatches: 3, Indels: 19
0.86 0.02 0.12
Matches are distributed among these distances:
47 8 0.06
49 1 0.01
50 1 0.01
52 30 0.22
53 81 0.59
55 2 0.01
56 1 0.01
58 13 0.09
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (49 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAAGCAATGAA
Found at i:1291341 original size:72 final size:72
Alignment explanation
Indices: 1291248--1291399 Score: 270
Period size: 72 Copynumber: 2.1 Consensus size: 72
1291238 GCAACGAGAG
1291248 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAATGC
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAAAATCGCAATGCGGAAATGAAAATCGCAATGC
1291312 GAAATGAA
65 GAAATGAA
* *
1291320 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCAATGCG
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
1291385 AAATGAA
66 AAATGAA
1291392 AATCGCAA
1 AATCGCAA
1291400 CGAGAGAATC
Statistics
Matches: 77, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
72 76 0.99
73 1 0.01
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (72 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAAAATCGCAATGCGGAAATGAAAATCGCAATGCG
AAATGAA
Found at i:1291411 original size:14 final size:14
Alignment explanation
Indices: 1291392--1291446 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1291382 GCGAAATGAA
1291392 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1291406 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1291425 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1291439 AATCGCAA
1 AATCGCAA
1291447 TGCGAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1291415 original size:33 final size:33
Alignment explanation
Indices: 1291373--1291464 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
1291363 CGGAAATGAA
1291373 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1291406 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
1291439 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
1291465 TTGCGATTCT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Done.