Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006374.1 Hibiscus syriacus cultivar Beakdansim tig00015335_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: 750659
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:420500 original size:31 final size:31
Alignment explanation
Indices: 420462--420544 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
420452 CGGGTCAACG
420462 GGTCGGGTCAACGGGTCGGGTAAACGGGTCA
1 GGTCGGGTCAACGGGTCGGGTAAACGGGTCA
* *
420493 GGTCGGGTCAACGGGTCAGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCGGGTAAACGGGTCA
*
420524 GGTCGGGTCAATGGGTCGGGT
1 GGTCGGGTCAACGGGTCGGGT
420545 CGGGTTGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.17, C:0.18, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCGGGTCAACGGGTCGGGTAAACGGGTCA
Found at i:422652 original size:35 final size:35
Alignment explanation
Indices: 422581--422653 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
422571 TCACGAACAA
* **
422581 TAAGGTCCTGAGCACACAGCCGAGGAACCGGTAAG
1 TAAGGCCCTGAGCACACAGCCGAGGAACCGCCAAG
* *
422616 TAAGGCCCTGAGCACACAGCCTAGGAACCTCCAAG
1 TAAGGCCCTGAGCACACAGCCGAGGAACCGCCAAG
422651 TAA
1 TAA
422654 TCTTCCTCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.29, G:0.26, T:0.12
Consensus pattern (35 bp):
TAAGGCCCTGAGCACACAGCCGAGGAACCGCCAAG
Found at i:422763 original size:24 final size:23
Alignment explanation
Indices: 422735--422821 Score: 120
Period size: 24 Copynumber: 3.7 Consensus size: 23
422725 ATTCAAATCG
422735 AGTATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* *
422758 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCATATCAGAATCCAGGTC
*
422782 AATATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
*
422805 AGGTATCATAACAGAAT
1 A-GTATCATATCAGAAT
422822 TCAAATTTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
23 21 0.38
24 34 0.62
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAGGTC
Found at i:423978 original size:18 final size:18
Alignment explanation
Indices: 423957--423992 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
423947 TTACCATCTG
*
423957 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
423975 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
423993 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:425308 original size:8 final size:8
Alignment explanation
Indices: 425278--425359 Score: 61
Period size: 8 Copynumber: 10.6 Consensus size: 8
425268 GGTCAACAAT
425278 GGTCAACG
1 GGTCAACG
425286 CCGGTCAAC-
1 --GGTCAACG
425295 GGTCAACG
1 GGTCAACG
425303 GGTCAACG
1 GGTCAACG
425311 GGT---CG
1 GGTCAACG
425316 GGTCAACG
1 GGTCAACG
425324 GGT---CG
1 GGTCAACG
*
425329 GGTAAACG
1 GGTCAACG
*
425337 GGTCAGGTCG
1 GGTCA--ACG
425347 GGTCAACG
1 GGTCAACG
425355 GGTCA
1 GGTCA
425360 GGTAAACGGG
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
5 10 0.17
7 7 0.12
8 29 0.48
10 14 0.23
ACGTcount: A:0.21, C:0.24, G:0.40, T:0.15
Consensus pattern (8 bp):
GGTCAACG
Found at i:425308 original size:15 final size:16
Alignment explanation
Indices: 425278--425311 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
425268 GGTCAACAAT
425278 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
425295 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
425310 GG
1 GG
425312 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:425319 original size:13 final size:13
Alignment explanation
Indices: 425301--425376 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
425291 CAACGGTCAA
425301 CGGGTCAACGGGT
1 CGGGTCAACGGGT
425314 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
425327 CGGGTAAACGGGTCAGGT
1 CGGGTCAAC--G---GGT
425345 CGGGTCAACGGGT
1 CGGGTCAACGGGT
* *
425358 CAGGTAAACGGGT
1 CGGGTCAACGGGT
425371 CGGGTC
1 CGGGTC
425377 GGGTCAATGG
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
13 39 0.75
15 1 0.02
16 1 0.02
18 11 0.21
ACGTcount: A:0.18, C:0.21, G:0.45, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:425345 original size:18 final size:18
Alignment explanation
Indices: 425324--425398 Score: 70
Period size: 18 Copynumber: 4.4 Consensus size: 18
425314 CGGGTCAACG
425324 GGTCGGGTAAACGGGTCA
1 GGTCGGGTAAACGGGTCA
*
425342 GGTCGGGTCAACGGGTCA
1 GGTCGGGTAAACGGGTCA
*
425360 -----GGTAAACGGGTCG
1 GGTCGGGTAAACGGGTCA
* * *
425373 GGTCGGGTCAATGGGTCG
1 GGTCGGGTAAACGGGTCA
425391 GGTCGGGT
1 GGTCGGGT
425399 TGTGACCGGT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
13 11 0.23
18 36 0.77
ACGTcount: A:0.16, C:0.17, G:0.48, T:0.19
Consensus pattern (18 bp):
GGTCGGGTAAACGGGTCA
Found at i:425349 original size:31 final size:31
Alignment explanation
Indices: 425311--425393 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
425301 CGGGTCAACG
425311 GGTCGGGTCAACGGGTCGGGTAAACGGGTCA
1 GGTCGGGTCAACGGGTCGGGTAAACGGGTCA
* *
425342 GGTCGGGTCAACGGGTCAGGTAAACGGGTCG
1 GGTCGGGTCAACGGGTCGGGTAAACGGGTCA
*
425373 GGTCGGGTCAATGGGTCGGGT
1 GGTCGGGTCAACGGGTCGGGT
425394 CGGGTTGTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.17, C:0.18, G:0.47, T:0.18
Consensus pattern (31 bp):
GGTCGGGTCAACGGGTCGGGTAAACGGGTCA
Found at i:427501 original size:35 final size:35
Alignment explanation
Indices: 427430--427502 Score: 101
Period size: 35 Copynumber: 2.1 Consensus size: 35
427420 TCACGAACAA
* **
427430 TAAGGTCCTGAGCACACAGCCGAGGAACCGGTAAG
1 TAAGGCCCTGAGCACACAGCCGAGGAACCGCCAAG
* *
427465 TAAGGCCCTGAGCACACAGCCTAGGAACCTCCAAG
1 TAAGGCCCTGAGCACACAGCCGAGGAACCGCCAAG
427500 TAA
1 TAA
427503 TCTTCCTCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.33, C:0.29, G:0.26, T:0.12
Consensus pattern (35 bp):
TAAGGCCCTGAGCACACAGCCGAGGAACCGCCAAG
Found at i:427612 original size:24 final size:23
Alignment explanation
Indices: 427584--427670 Score: 120
Period size: 24 Copynumber: 3.7 Consensus size: 23
427574 ATTCAAATCG
427584 AGTATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* *
427607 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCATATCAGAATCCAGGTC
*
427631 AATATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
*
427654 AGGTATCATAACAGAAT
1 A-GTATCATATCAGAAT
427671 TCAAATTTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
23 21 0.38
24 34 0.62
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAGGTC
Found at i:428829 original size:18 final size:18
Alignment explanation
Indices: 428806--428841 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
428796 CTACCATCCG
*
428806 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
428824 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
428842 GTCCTTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:430158 original size:8 final size:8
Alignment explanation
Indices: 430128--430177 Score: 54
Period size: 8 Copynumber: 6.5 Consensus size: 8
430118 GGTCAACAAT
430128 GGTCAACG
1 GGTCAACG
430136 CCGGTCAAC-
1 --GGTCAACG
430145 GGTCAACG
1 GGTCAACG
430153 GGTCAACG
1 GGTCAACG
430161 GGT---CG
1 GGTCAACG
430166 GGTCAACG
1 GGTCAACG
430174 GGTC
1 GGTC
430178 GGGTAAACGG
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.14
7 7 0.19
8 17 0.47
10 7 0.19
ACGTcount: A:0.20, C:0.28, G:0.38, T:0.14
Consensus pattern (8 bp):
GGTCAACG
Found at i:430158 original size:15 final size:16
Alignment explanation
Indices: 430128--430161 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
430118 GGTCAACAAT
430128 GGTCAACGCCGGTCAAC
1 GGTCAACG-CGGTCAAC
430145 GGTCAACG-GGTCAAC
1 GGTCAACGCGGTCAAC
430160 GG
1 GG
430162 GTCGGGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
17 8 0.47
ACGTcount: A:0.24, C:0.29, G:0.35, T:0.12
Consensus pattern (16 bp):
GGTCAACGCGGTCAAC
Found at i:430169 original size:13 final size:13
Alignment explanation
Indices: 430151--430208 Score: 89
Period size: 13 Copynumber: 4.5 Consensus size: 13
430141 CAACGGTCAA
430151 CGGGTCAACGGGT
1 CGGGTCAACGGGT
430164 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
430177 CGGGTAAACGGGT
1 CGGGTCAACGGGT
* *
430190 CAGGTAAACGGGT
1 CGGGTCAACGGGT
430203 CGGGTC
1 CGGGTC
430209 GGGTCGGGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.19, C:0.21, G:0.45, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:432320 original size:35 final size:36
Alignment explanation
Indices: 432248--432321 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
432238 TCACGAACAA
* **
432248 TAAGGTCCTGAGCACACAGCCCGAGGAACCGGTAAG
1 TAAGGCCCTGAGCACACAGCCCGAGGAACCGCCAAG
* *
432284 TAAGGCCCTGAGCACACAG-CCTAGGAACCTCCAAG
1 TAAGGCCCTGAGCACACAGCCCGAGGAACCGCCAAG
432319 TAA
1 TAA
432322 TCTTCCTCCA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
35 15 0.45
36 18 0.55
ACGTcount: A:0.32, C:0.30, G:0.26, T:0.12
Consensus pattern (36 bp):
TAAGGCCCTGAGCACACAGCCCGAGGAACCGCCAAG
Found at i:432431 original size:24 final size:23
Alignment explanation
Indices: 432403--432489 Score: 120
Period size: 24 Copynumber: 3.7 Consensus size: 23
432393 ATTCAAATCG
432403 AGTATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* *
432426 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCATATCAGAATCCAGGTC
*
432450 AATATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
*
432473 AGGTATCATAACAGAAT
1 A-GTATCATATCAGAAT
432490 TCAAATTTGA
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
23 21 0.38
24 34 0.62
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAGGTC
Found at i:433650 original size:18 final size:18
Alignment explanation
Indices: 433627--433662 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
433617 CTACCATCCG
*
433627 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
433645 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
433663 GTCCTTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:434986 original size:18 final size:18
Alignment explanation
Indices: 434965--435027 Score: 64
Period size: 18 Copynumber: 3.8 Consensus size: 18
434955 CGCCGGTCAA
434965 CGGGTCAACAGGTCGGGT
1 CGGGTCAACAGGTCGGGT
434983 CGGGTC-A-A---CGGGT
1 CGGGTCAACAGGTCGGGT
* *
434996 CGGGTAAACGGGTCGGGT
1 CGGGTCAACAGGTCGGGT
*
435014 CGGGTCAACGGGTC
1 CGGGTCAACAGGTC
435028 AGGTAAACGG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
16 1 0.03
17 1 0.03
18 24 0.65
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (18 bp):
CGGGTCAACAGGTCGGGT
Found at i:435010 original size:31 final size:31
Alignment explanation
Indices: 434965--435062 Score: 151
Period size: 31 Copynumber: 3.2 Consensus size: 31
434955 CGCCGGTCAA
* *
434965 CGGGTCAACAGGTCGGGTCGGGTCAACGGGT
1 CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
434996 CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
1 CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
* * *
435027 CAGGTAAACGGGTTGGGTCGGGTCAATGGGT
1 CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
435058 CGGGT
1 CGGGT
435063 CGGGTTGTGA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.16, C:0.18, G:0.47, T:0.18
Consensus pattern (31 bp):
CGGGTAAACGGGTCGGGTCGGGTCAACGGGT
Found at i:435027 original size:13 final size:13
Alignment explanation
Indices: 434978--435014 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
434968 GTCAACAGGT
434978 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
*
434991 CGGGTCGGGTAAA
1 CGGGTCGGGTCAA
435004 CGGGTCGGGTC
1 CGGGTCGGGTC
435015 GGGTCAACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.14, C:0.22, G:0.49, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:446594 original size:18 final size:18
Alignment explanation
Indices: 446560--446596 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
446550 GGCTAGAAGT
*
446560 ACATAACTTAATGAATGC
1 ACATAACTTAATAAATGC
*
446578 ACATAACTTATTAAATGC
1 ACATAACTTAATAAATGC
446596 A
1 A
446597 TGCATGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (18 bp):
ACATAACTTAATAAATGC
Found at i:452980 original size:20 final size:20
Alignment explanation
Indices: 452953--453008 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
452943 GAAACCCCTT
452953 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
*
452973 TTAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
452992 TGAAAATACATGCTTTT
1 TGAAAATACATGATTTT
453009 GGCTGAATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:456258 original size:24 final size:24
Alignment explanation
Indices: 456213--456268 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
456203 TTCTTTTATT
* * *
456213 TTTTCTTTTTTTTGGGTGCTTGCAA
1 TTTTC-TTCTTTTGAGTACTTGCAA
456238 TTTTCTTCTTTTGAGTACTTGCAA
1 TTTTCTTCTTTTGAGTACTTGCAA
456262 -TTTCTTC
1 TTTTCTTC
456269 GCTGATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 7 0.25
24 16 0.57
25 5 0.18
ACGTcount: A:0.11, C:0.16, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTTCTTCTTTTGAGTACTTGCAA
Found at i:460665 original size:24 final size:24
Alignment explanation
Indices: 460603--460648 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
460593 AACAAAATGG
*
460603 TGGAGTTAAAAATGATGAAAACAC
1 TGGAGTTGAAAATGATGAAAACAC
460627 TGGAGTTGAAAATGATGAAAAC
1 TGGAGTTGAAAATGATGAAAAC
460649 GTTGGGGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.24, T:0.22
Consensus pattern (24 bp):
TGGAGTTGAAAATGATGAAAACAC
Found at i:460844 original size:24 final size:24
Alignment explanation
Indices: 460788--460833 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
460778 TTTGTGGACC
460788 AAAAGATGTGACACTTGAAGTTCG
1 AAAAGATGTGACACTTGAAGTTCG
*
460812 AAAAGATGTGTCACTTGAAGTT
1 AAAAGATGTGACACTTGAAGTT
460834 TCAAGTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (24 bp):
AAAAGATGTGACACTTGAAGTTCG
Found at i:466014 original size:13 final size:13
Alignment explanation
Indices: 465996--466035 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
465986 AATAGCTGGA
465996 TTGAGCTAAAGAT
1 TTGAGCTAAAGAT
* *
466009 TTGAGCTGACGAT
1 TTGAGCTAAAGAT
466022 TTGAGCTAGAAGAT
1 TTGAGCTA-AAGAT
466036 GACTTCATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 18 0.82
14 4 0.18
ACGTcount: A:0.33, C:0.10, G:0.28, T:0.30
Consensus pattern (13 bp):
TTGAGCTAAAGAT
Found at i:474173 original size:25 final size:24
Alignment explanation
Indices: 474133--474180 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
474123 AGTTGTTTCG
474133 AATTAATAAATAAAATAT-CATTT
1 AATTAATAAATAAAATATACATTT
*
474156 AATTAATTCAAATTAAATATACATT
1 AATTAA-T-AAATAAAATATACATT
474181 AAAGACTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 6 0.29
24 1 0.05
25 10 0.48
26 4 0.19
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (24 bp):
AATTAATAAATAAAATATACATTT
Found at i:490982 original size:18 final size:18
Alignment explanation
Indices: 490959--490997 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
490949 CACATGCATT
490959 CATTTAATAAGTTATGTA
1 CATTTAATAAGTTATGTA
*
490977 CATTTATTAAGTTATGTA
1 CATTTAATAAGTTATGTA
490995 CAT
1 CAT
490998 CTAAACAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (18 bp):
CATTTAATAAGTTATGTA
Found at i:499244 original size:21 final size:21
Alignment explanation
Indices: 499215--499257 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
499205 TCATCCTTAC
499215 AAGAATTCATGGCCTCGATAA
1 AAGAATTCATGGCCTCGATAA
* * *
499236 AAGATTTCATGGCTTCTATAA
1 AAGAATTCATGGCCTCGATAA
499257 A
1 A
499258 GACCTAGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (21 bp):
AAGAATTCATGGCCTCGATAA
Found at i:513703 original size:54 final size:53
Alignment explanation
Indices: 513644--513766 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 53
513634 TTCTCTAGGG
* *
513644 TGCACACGTAGTGCCGATACGGTCT-TTCATCAACATATAATGAATT-CTTTGGGT
1 TGCACACTTAGTGCCG-TACGGT-TGTTCATCAACATATAATGAATTAC-GTGGGT
* * * *
513698 TGCACACTTAGTGCATGTATGGTTGTTCATCAATATATGATGAATTACGTGGGT
1 TGCACACTTAGTGC-CGTACGGTTGTTCATCAACATATAATGAATTACGTGGGT
513752 TGCACACTTAGTGCC
1 TGCACACTTAGTGCC
513767 TATAGTACAC
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
53 1 0.02
54 56 0.95
55 2 0.03
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (53 bp):
TGCACACTTAGTGCCGTACGGTTGTTCATCAACATATAATGAATTACGTGGGT
Found at i:516488 original size:21 final size:20
Alignment explanation
Indices: 516450--516488 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
516440 CTAATATTAA
* *
516450 AATTAAATCTTAGCTTTTTT
1 AATTAAACCTTAGATTTTTT
516470 AATTAAAACCTTAGATTTT
1 AATT-AAACCTTAGATTTT
516489 AAGTTGTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (20 bp):
AATTAAACCTTAGATTTTTT
Found at i:517342 original size:13 final size:12
Alignment explanation
Indices: 517295--517422 Score: 61
Period size: 13 Copynumber: 10.6 Consensus size: 12
517285 CCGACCTTAG
*
517295 TTATATAATATA
1 TTATATATTATA
517307 TT-T-T-TTATA
1 TTATATATTATA
**
517316 TTATATAAACATA
1 TTATAT-ATTATA
517329 TTATATGATTATA
1 TTATAT-ATTATA
*
517342 TATTTATATTAT-
1 T-TATATATTATA
*
517354 TTATGATGCTTAT-
1 TTAT-AT-ATTATA
**
517367 TTATATGGTATA
1 TTATATATTATA
*
517379 -TACATATTATA
1 TTATATATTATA
517390 TTATATATTTATA
1 TTATATA-TTATA
* *
517403 ATATATACTTACA
1 TTATATA-TTATA
517416 TTATATA
1 TTATATA
517423 ATGTGTATAT
Statistics
Matches: 87, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
9 6 0.07
10 2 0.02
11 15 0.17
12 12 0.14
13 48 0.55
14 4 0.05
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.53
Consensus pattern (12 bp):
TTATATATTATA
Found at i:519137 original size:21 final size:21
Alignment explanation
Indices: 519111--519158 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
519101 TGACTTAGTT
519111 ATGGCCGAGGAGATTATAGAA
1 ATGGCCGAGGAGATTATAGAA
519132 ATGGCCGAGGAGATTATAGAA
1 ATGGCCGAGGAGATTATAGAA
519153 ATGGCC
1 ATGGCC
519159 ATAAAACAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.35, C:0.12, G:0.33, T:0.19
Consensus pattern (21 bp):
ATGGCCGAGGAGATTATAGAA
Found at i:529352 original size:66 final size:66
Alignment explanation
Indices: 529244--529376 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
529234 TGAGTGAGAT
* *
529244 GAAGGAGGTAAATGTGTCGATATTAAATTATATAGGTTAATGATTGGTTCTTTACTTTATCTTAC
1 GAAGGAGGTAAATGTGTCGATATTAAATTATATAGGTCAATGATTGGTTCTTTACTTTATCTAAC
529309 C
66 C
*
529310 GAAGGAGGTAAATGTGTCGATATTAAATTATATTGGTCAATGATTGGTTCTTTACTTTATCTAAC
1 GAAGGAGGTAAATGTGTCGATATTAAATTATATAGGTCAATGATTGGTTCTTTACTTTATCTAAC
529375 C
66 C
529376 G
1 G
529377 CAAGTAGACT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (66 bp):
GAAGGAGGTAAATGTGTCGATATTAAATTATATAGGTCAATGATTGGTTCTTTACTTTATCTAAC
C
Found at i:532267 original size:20 final size:20
Alignment explanation
Indices: 532242--532282 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
532232 AACATTTTGA
532242 TTTGAATAGTTGGATGTTTT
1 TTTGAATAGTTGGATGTTTT
* *
532262 TTTGAATATTTGGTTGTTTT
1 TTTGAATAGTTGGATGTTTT
532282 T
1 T
532283 AGATTTTTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.22, T:0.61
Consensus pattern (20 bp):
TTTGAATAGTTGGATGTTTT
Found at i:534557 original size:72 final size:73
Alignment explanation
Indices: 534431--534588 Score: 210
Period size: 72 Copynumber: 2.2 Consensus size: 73
534421 AATTCATCTA
** ** **
534431 GACTCAACTTCACAACGAAAAAAATCACCCATGATTTTGACTTCACAACGAAGGATATCGTACCC
1 GACTCAACTTCACAACGAAAAAAATCACCCACAATTTAAACTTCACAAAAAAGGATATCGTACCC
*
534496 AAAAGATT
66 AAAAGATC
* * *
534504 GACTCAACTTCACAACG-AAAGAGTCACCCACAATTTAAACTTCACAAAAAAGGATATCGTACTC
1 GACTCAACTTCACAACGAAAAAAATCACCCACAATTTAAACTTCACAAAAAAGGATATCGTACCC
534568 AAAAGATC
66 AAAAGATC
*
534576 GACTAAACTTCAC
1 GACTCAACTTCAC
534589 GATGATGGAG
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
72 57 0.77
73 17 0.23
ACGTcount: A:0.42, C:0.25, G:0.11, T:0.21
Consensus pattern (73 bp):
GACTCAACTTCACAACGAAAAAAATCACCCACAATTTAAACTTCACAAAAAAGGATATCGTACCC
AAAAGATC
Found at i:536321 original size:18 final size:17
Alignment explanation
Indices: 536292--536345 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
536282 TTATATTCAC
536292 ATGTAT-TATATATTAT
1 ATGTATGTATATATTAT
* *
536308 ATTTATAGTATATAGTAT
1 ATGTAT-GTATATATTAT
*
536326 ATGTATGTGTATCATTAT
1 ATGTATGTATAT-ATTAT
536344 AT
1 AT
536346 ATTTATATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
16 5 0.17
17 5 0.17
18 20 0.67
ACGTcount: A:0.35, C:0.02, G:0.11, T:0.52
Consensus pattern (17 bp):
ATGTATGTATATATTAT
Found at i:536735 original size:32 final size:33
Alignment explanation
Indices: 536686--536753 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
536676 TGTAAATCTA
*
536686 AATTAAAAAAAATAGGATGATCGAGAGGAAAAC
1 AATTAAAAAAAATAGGATGACCGAGAGGAAAAC
*
536719 AATTAAAAAGAA-AGGATGACCGAGAGGAAAAC
1 AATTAAAAAAAATAGGATGACCGAGAGGAAAAC
536751 AAT
1 AAT
536754 ATTTGTAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.57, C:0.07, G:0.22, T:0.13
Consensus pattern (33 bp):
AATTAAAAAAAATAGGATGACCGAGAGGAAAAC
Found at i:537505 original size:19 final size:19
Alignment explanation
Indices: 537464--537512 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
537454 CCGATAAGTT
* * *
537464 TTATTTACTTTTTATTTTTA
1 TTATTT-CTTTTTAATCTAA
537484 TTATTTCTTTTTAATCTAA
1 TTATTTCTTTTTAATCTAA
537503 TTAATTTCTT
1 TT-ATTTCTT
537513 GTCTTTGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.22, C:0.08, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATTTCTTTTTAATCTAA
Found at i:537578 original size:17 final size:18
Alignment explanation
Indices: 537556--537596 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
537546 TTCTTTTTTA
537556 TTTTTAATTTA-ATTGA-C
1 TTTTTAATTTACATT-ATC
*
537573 TTTTTATTTTACATTATC
1 TTTTTAATTTACATTATC
537591 TTTTTA
1 TTTTTA
537597 TCACTTTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.66
Consensus pattern (18 bp):
TTTTTAATTTACATTATC
Found at i:542517 original size:10 final size:10
Alignment explanation
Indices: 542502--542526 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
542492 ACCACCATTA
542502 ATGCAACTAT
1 ATGCAACTAT
542512 ATGCAACTAT
1 ATGCAACTAT
542522 ATGCA
1 ATGCA
542527 TCTAAAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (10 bp):
ATGCAACTAT
Found at i:561526 original size:22 final size:22
Alignment explanation
Indices: 561498--561539 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
561488 CTGGAAGGGG
561498 GTATCGATACCATAGTAGGGTA
1 GTATCGATACCATAGTAGGGTA
561520 GTATCGATACCATAGTAGGG
1 GTATCGATACCATAGTAGGG
561540 GTATCTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (22 bp):
GTATCGATACCATAGTAGGGTA
Found at i:561549 original size:20 final size:20
Alignment explanation
Indices: 561495--561549 Score: 83
Period size: 22 Copynumber: 2.6 Consensus size: 20
561485 ATACTGGAAG
561495 GGGGTATCGATACCATAGTA
1 GGGGTATCGATACCATAGTA
561515 GGGTAGTATCGATACCATAGTA
1 GGG--GTATCGATACCATAGTA
*
561537 GGGGTATCTATAC
1 GGGGTATCGATAC
561550 TGAAGGGCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 12 0.38
22 20 0.62
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (20 bp):
GGGGTATCGATACCATAGTA
Found at i:562042 original size:45 final size:45
Alignment explanation
Indices: 561992--562298 Score: 368
Period size: 45 Copynumber: 6.9 Consensus size: 45
561982 AAAGGGTGCC
* **
561992 ATAGTTGAAATGTATATGGGTACATTATCAATAGAAAAACATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
562037 TTAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * * *
562082 AGAGTTTAAAT-TCATATGGGTGCATTATCAACATAAAAGTATGCC
1 ATAGTTGAAATGT-ATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
562127 AGAGTTGAAATGCATATGGGTGCATTATCAACAGTAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
562172 AGAGTTGAAATATATATGGGTACATTATCAACAG-AAAG-GTACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
562215 ATGGTTGAAATGTATATAGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
562260 ATAGTTGAAATGCATAGGGGTGCATTATCAACAGAAAAG
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAG
562299 ATGTTATAGT
Statistics
Matches: 227, Mismatches: 31, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
43 33 0.15
44 9 0.04
45 185 0.81
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:562201 original size:135 final size:134
Alignment explanation
Indices: 561955--562298 Score: 408
Period size: 135 Copynumber: 2.6 Consensus size: 134
561945 ATGAAATACT
*** * ** * *
561955 AATG-CATATGGGTGCATTATTGGCATGAAAGGGTGCCATAGTTGAAATGTATATGGGTACATTA
1 AATGTCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTA
* * ** *
562019 TCAATAGAAAAACATACTTTAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCTA-
66 TCAACAGAAAAGCATACTAGAGTTGAAATATATATGGGTACATTATCAACAGAAAAGTA--CTAT
*
562083 GAGTTTA
129 G-GTTGA
*
562090 AAT-TCATATGGGTGCATTATCAACATAAAAGTATGCCAGAGTTGAAATGCATATGGGTGCATTA
1 AATGTCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTA
* * * *
562154 TCAACAGTAAAGTATGCTAGAGTTGAAATATATATGGGTACATTATCAACAGAAAGGTACTATGG
66 TCAACAGAAAAGCATACTAGAGTTGAAATATATATGGGTACATTATCAACAGAAAAGTACTATGG
562219 TTGA
131 TTGA
* * * * * *
562223 AATGT-ATATAGGTACATTATCAACAGAAAAGTATACTATAGTTGAAATGCATAGGGGTGCATTA
1 AATGTCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTA
562287 TCAACAGAAAAG
66 TCAACAGAAAAG
562299 ATGTTATAGT
Statistics
Matches: 179, Mismatches: 27, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
133 73 0.41
134 2 0.01
135 104 0.58
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (134 bp):
AATGTCATATGGGTGCATTATCAACATAAAAGTATGCCATAGTTGAAATGCATATGGGTGCATTA
TCAACAGAAAAGCATACTAGAGTTGAAATATATATGGGTACATTATCAACAGAAAAGTACTATGG
TTGA
Found at i:562332 original size:45 final size:45
Alignment explanation
Indices: 561992--562337 Score: 241
Period size: 45 Copynumber: 7.7 Consensus size: 45
561982 AAAGGGTGCC
* ** * * **
561992 ATAGTTGAAATGTATATGGGTACATTATCAATAGAAAAACATACT
1 ATAGTTGAAATGAATAAAGGTGCATTATCAACAGAAAAGTATACT
* * ** * *
562037 TTAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATGCT
1 ATAGTTGAAATGAATAAAGGTGCATTATCAACAGAAAAGTATACT
* * ** ** * * *
562082 AGAGTTTAAATTCATATGGGTGCATTATCAACATAAAAGTATGCC
1 ATAGTTGAAATGAATAAAGGTGCATTATCAACAGAAAAGTATACT
* * ** * *
562127 AGAGTTGAAATGCATATGGGTGCATTATCAACAGTAAAGTATGCT
1 ATAGTTGAAATGAATAAAGGTGCATTATCAACAGAAAAGTATACT
* ** * *
562172 AGAGTTGAAAT-ATATATGGGTACATTATCAACAG-AAAG-GTACT
1 ATAGTTGAAATGA-ATAAAGGTGCATTATCAACAGAAAAGTATACT
* * * *
562215 ATGGTTGAAATGTATATAGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGAATAAAGGTGCATTATCAACAGAAAAGTATACT
* ** **
562260 ATAGTTGAAATGCATAGGGGTGCATTATCAACAGAAAAG-ATGTT
1 ATAGTTGAAATGAATAAAGGTGCATTATCAACAGAAAAGTATACT
* * *
562304 ATAGTTTAAAGTGAATAAAGGTGTATTATAAACA
1 ATAGTTGAAA-TGAATAAAGGTGCATTATCAACA
562338 TAAATGGAGG
Statistics
Matches: 256, Mismatches: 40, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
43 32 0.12
44 20 0.08
45 204 0.80
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.30
Consensus pattern (45 bp):
ATAGTTGAAATGAATAAAGGTGCATTATCAACAGAAAAGTATACT
Found at i:562332 original size:133 final size:134
Alignment explanation
Indices: 561994--562298 Score: 346
Period size: 133 Copynumber: 2.3 Consensus size: 134
561984 AGGGTGCCAT
* * * * ** * ** * **
561994 AGTTGAAATGTATATGGGTACATTATCAATAGAAAAACATACTTTAGTTGAAATGTATATGGGTA
1 AGTTGAAATGCATAGGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATATATAAAGGTA
* * * *
562059 CATTATCAACAGAAAAGTATGCTAGAGTTTAAATTCATATGGGTGCATTATCAACATAAAAGTAT
66 CATTATCAACAGAAAAGTA-GCTAGAGTTGAAATTCATATAGGTACATTATCAACAGAAAAGTAT
*
562124 GCCAG
130 ACCAG
* * **
562129 AGTTGAAATGCATATGGGTGCATTATCAACAGTAAAGTATGCTAGAGTTGAAATATATATGGGTA
1 AGTTGAAATGCATAGGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATATATAAAGGTA
*
562194 CATTATCAACAGAAAGGTA-CTATG-GTTGAAATGT-ATATAGGTACATTATCAACAGAAAAGTA
66 CATTATCAACAGAAAAGTAGCTA-GAGTTGAAAT-TCATATAGGTACATTATCAACAGAAAAGTA
* *
562256 TACTAT
129 TACCAG
562262 AGTTGAAATGCATAGGGGTGCATTATCAACAGAAAAG
1 AGTTGAAATGCATAGGGGTGCATTATCAACAGAAAAG
562299 ATGTTATAGT
Statistics
Matches: 148, Mismatches: 20, Indels: 6
0.85 0.11 0.03
Matches are distributed among these distances:
133 73 0.49
134 2 0.01
135 73 0.49
ACGTcount: A:0.40, C:0.10, G:0.20, T:0.30
Consensus pattern (134 bp):
AGTTGAAATGCATAGGGGTGCATTATCAACAGAAAAGTATGCTAGAGTTGAAATATATAAAGGTA
CATTATCAACAGAAAAGTAGCTAGAGTTGAAATTCATATAGGTACATTATCAACAGAAAAGTATA
CCAG
Found at i:567524 original size:47 final size:47
Alignment explanation
Indices: 567471--567603 Score: 185
Period size: 49 Copynumber: 2.8 Consensus size: 47
567461 AACCAACCTA
567471 AAATGAATTAGATTCTTATTCTTTTGATGAGTTGTAACTTCTAACTC
1 AAATGAATTAGATTCTTATTCTTTTGATGAGTTGTAACTTCTAACTC
** * * * *
567518 AAATGAATTAGATTCTTATTCAAGTAGATTCAATGGTAACTTCTAACTC
1 AAATGAATTAGATTCTTATTC-TTTTGA-TGAGTTGTAACTTCTAACTC
*
567567 AAATGAATTTGATTCTTATTCTTTTGATGAGTTGTAA
1 AAATGAATTAGATTCTTATTCTTTTGATGAGTTGTAA
567604 GTTGTTTATA
Statistics
Matches: 71, Mismatches: 13, Indels: 4
0.81 0.15 0.05
Matches are distributed among these distances:
47 28 0.39
48 6 0.08
49 37 0.52
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (47 bp):
AAATGAATTAGATTCTTATTCTTTTGATGAGTTGTAACTTCTAACTC
Found at i:570224 original size:18 final size:18
Alignment explanation
Indices: 570187--570237 Score: 75
Period size: 18 Copynumber: 2.7 Consensus size: 18
570177 GTCGGTTAAC
570187 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCG
570208 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
570226 GGTCAACGGGTC
1 GGTCAACGGGTC
570238 TACTGGTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 19 0.63
21 11 0.37
ACGTcount: A:0.16, C:0.24, G:0.45, T:0.16
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:570237 original size:13 final size:13
Alignment explanation
Indices: 570193--570224 Score: 64
Period size: 13 Copynumber: 2.5 Consensus size: 13
570183 TAACGGTCAA
570193 CGGGTCAACGGGT
1 CGGGTCAACGGGT
570206 CGGGTCAACGGGT
1 CGGGTCAACGGGT
570219 CGGGTC
1 CGGGTC
570225 GGGTCAACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.12, C:0.25, G:0.47, T:0.16
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:581926 original size:15 final size:16
Alignment explanation
Indices: 581889--581921 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
581879 ACTAATACTA
*
581889 TTAAG-TATGGAAAAT
1 TTAAGATATGAAAAAT
581904 TTAAGATATGAAAAAT
1 TTAAGATATGAAAAAT
581920 TT
1 TT
581922 TGATAGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (16 bp):
TTAAGATATGAAAAAT
Found at i:582565 original size:111 final size:111
Alignment explanation
Indices: 582409--582615 Score: 281
Period size: 111 Copynumber: 1.9 Consensus size: 111
582399 GGTGTCACTA
* * *
582409 ATGAAAGCTATCGATCGATTTTGTGTAATGCATAACGGTGTATTTTCGGCATAACAA-GTGCCAC
1 ATGAAAGCTATCGATCAATTTTGTGTAATGCATAACGGTGCATTTTCGGAATAA-AAGGTGCCAC
* * * * *
582473 CCATTGTATTCATAAAAGGTGAGTTACCATTTCGACATACTTCGTGT
65 CAATGGTATTCATAAAAGATGAATGACCATTTCGACATACTTCGTGT
* * * **
582520 ATGAAAGTTATCGATCAATTTTGTGTAATGTATAATGGTGCATTTTCGGAATAAAAGGTGCCATT
1 ATGAAAGCTATCGATCAATTTTGTGTAATGCATAACGGTGCATTTTCGGAATAAAAGGTGCCACC
582585 AATGGTATTCATAAAAGATGAATGACCATTT
66 AATGGTATTCATAAAAGATGAATGACCATTT
582616 TGGAACTTTG
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
110 2 0.02
111 80 0.98
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (111 bp):
ATGAAAGCTATCGATCAATTTTGTGTAATGCATAACGGTGCATTTTCGGAATAAAAGGTGCCACC
AATGGTATTCATAAAAGATGAATGACCATTTCGACATACTTCGTGT
Found at i:595002 original size:8 final size:9
Alignment explanation
Indices: 594980--595008 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
594970 AACGTTGAGC
594980 ACCAAAATG
1 ACCAAAATG
594989 ACCAAAAT-
1 ACCAAAATG
594997 ACCAAAATG
1 ACCAAAATG
595006 ACC
1 ACC
595009 TAGAATAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.55, C:0.28, G:0.07, T:0.10
Consensus pattern (9 bp):
ACCAAAATG
Found at i:600397 original size:20 final size:20
Alignment explanation
Indices: 600372--600416 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
600362 GCAAAATGCT
600372 CACATTACCATTTTCATGGC
1 CACATTACCATTTTCATGGC
* *
600392 CACATTTCCATTTTCATGGT
1 CACATTACCATTTTCATGGC
600412 CACAT
1 CACAT
600417 GGAACATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.09, T:0.38
Consensus pattern (20 bp):
CACATTACCATTTTCATGGC
Found at i:608498 original size:267 final size:267
Alignment explanation
Indices: 607984--608466 Score: 687
Period size: 267 Copynumber: 1.8 Consensus size: 267
607974 GGGTAAGGCC
* * *
607984 TGAGCCTGGTTTAACAAAGCAATGATCACCTCTCACTCGTTGTAGTGGAATGATTACAAGCCTAC
1 TGAGCCTGGTTTAACAAAGCAACGATCACCTCTCACTCGTTGTAGTGGAAGGATTACAAACCTAC
* ** * *
608049 TCCACATGAACTCAATGTGGCACGATGGGTCAACCTAAGTTGGACTAGAATATTTTTCCTTTTTC
66 TCCACAAGAACTCAACATGGCACAATGGCTCAACCTAAGTTGGACTAGAATATTTTTCCTTTTTC
* *
608114 AGCAATGCAAAAATCCTAGAATTTTTTCATGATGCCTTGAAGGCTTGAAAAGAATTTTAAATTCT
131 AGCAACGCAAAAATCCTAGAATTTTTTCATGATGCCTTGAAGGCTTGAAAAGAATTTTAAATTAT
* *
608179 AAATGAGTTACTCGAAAAATACTTATGAAGATTTTTTGAAGCATGCCAAATAACTTCATAGAGTG
196 AAATGAATTACACGAAAAATACTTATGAAGATTTTTTGAAGCATGCCAAATAACTTCATAGAGTG
608244 TAATGCG
261 TAATGCG
* * * * *
608251 TGAGCCTGGTTTAACAGAGCAACGATCACCTCTCGCTCTTTGTGGTGGAAGGATTACAAACCTAT
1 TGAGCCTGGTTTAACAAAGCAACGATCACCTCTCACTCGTTGTAGTGGAAGGATTACAAACCTAC
* * * * *
608316 TTCACAAGAACTCAACATGGCATAATGGCTCGACTTAAGTTGGGCTAGAATATTTTTCCTTTTTC
66 TCCACAAGAACTCAACATGGCACAATGGCTCAACCTAAGTTGGACTAGAATATTTTTCCTTTTTC
* * * ** *
608381 TGTAACGTAAAAATCCTTTAGTTTTTTTTCATGATGCCTTGAAGGCTTGAAAATAATTTTAAATT
131 AGCAACGCAAAAATCC--TAGAATTTTTTCATGATGCCTTGAAGGCTTGAAAAGAATTTTAAATT
*
608446 ATACATGAATTACACGAAAAA
194 ATAAATGAATTACACGAAAAA
608467 CTTTTATGAA
Statistics
Matches: 185, Mismatches: 29, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
267 124 0.67
269 61 0.33
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (267 bp):
TGAGCCTGGTTTAACAAAGCAACGATCACCTCTCACTCGTTGTAGTGGAAGGATTACAAACCTAC
TCCACAAGAACTCAACATGGCACAATGGCTCAACCTAAGTTGGACTAGAATATTTTTCCTTTTTC
AGCAACGCAAAAATCCTAGAATTTTTTCATGATGCCTTGAAGGCTTGAAAAGAATTTTAAATTAT
AAATGAATTACACGAAAAATACTTATGAAGATTTTTTGAAGCATGCCAAATAACTTCATAGAGTG
TAATGCG
Found at i:611646 original size:37 final size:37
Alignment explanation
Indices: 611596--611669 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
611586 AATAGAATTA
611596 CAATATTACAAGGTTGATACGATGTTGATACTTTACG
1 CAATATTACAAGGTTGATACGATGTTGATACTTTACG
611633 CAATATTACAAGGTTGATACGATGTTGATACTTTACG
1 CAATATTACAAGGTTGATACGATGTTGATACTTTACG
611670 AATTCACTCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (37 bp):
CAATATTACAAGGTTGATACGATGTTGATACTTTACG
Found at i:613246 original size:32 final size:32
Alignment explanation
Indices: 613210--613288 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 32
613200 TTATAAATTG
** *
613210 TTATTTTGATTAAATAAATTTTTCACAATTTT
1 TTATTTTGATTAAATAAATTTGACACAACTTT
** *
613242 TTATTTTGACAAAATAAATTTGACATAACTTT
1 TTATTTTGATTAAATAAATTTGACACAACTTT
*
613274 TTACTTTGATTAAAT
1 TTATTTTGATTAAAT
613289 TTAACGTGTT
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.51
Consensus pattern (32 bp):
TTATTTTGATTAAATAAATTTGACACAACTTT
Found at i:613275 original size:97 final size:97
Alignment explanation
Indices: 613095--613417 Score: 237
Period size: 98 Copynumber: 3.4 Consensus size: 97
613085 TTCGTCACTA
613095 AATATTTCTTATAACATTTTACTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAAGAATA
1 AATATTTCTTATAACATTTTACTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAAGAATA
* *
613160 TTATTTGTCACAAATTTTTATAATGAGAAATT
66 TAATTTGACACAAATTTTTATAATGAGAAATT
* * * * * *
613192 AATATTTGTTATAA-ATTGTTATTTTGATTAAATAAATTT-TTCACAATTTTTTATTTTGACAA-
1 AATATTTCTTATAACATT-TTACTGTGACTAAAT-AATTTGTT-ACAATTTGTTATTGTGA-AAG
* * *
613254 AATA-AATTTGACATAACTTTTTACT--T-TG--ATT
62 AATATAATTTGACACAAATTTTTA-TAATGAGAAATT
* * * * * *
613285 AA-A----TT-TAACGTGTTATTGTGACTAAATCATTTTGTTACAATTTGTTATTGTGAAATATT
1 AATATTTCTTATAACATTTTACTGTGACTAAAT-AATTTGTTACAATTTGTTATTGTGAAAGAAT
* * * *
613344 ATTATTTGTCACAATTTTTTATATTGAGAAATT
65 ATAATTTGACACAAATTTTTATAATGAGAAATT
* * * *
613377 AATATTTGTTATAA-ATTATTATTTTGATTAAATAAATTTGT
1 AATATTTCTTATAACATT-TTACTGTGACTAAAT-AATTTGT
613418 AAAAAAAATA
Statistics
Matches: 174, Mismatches: 31, Indels: 41
0.71 0.13 0.17
Matches are distributed among these distances:
86 2 0.01
87 39 0.22
88 20 0.11
89 1 0.01
90 1 0.01
92 6 0.03
93 6 0.03
95 1 0.01
96 4 0.02
97 45 0.26
98 47 0.27
99 2 0.01
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.49
Consensus pattern (97 bp):
AATATTTCTTATAACATTTTACTGTGACTAAATAATTTGTTACAATTTGTTATTGTGAAAGAATA
TAATTTGACACAAATTTTTATAATGAGAAATT
Found at i:613383 original size:33 final size:33
Alignment explanation
Indices: 613315--613385 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
613305 ACTAAATCAT
* *
613315 TTTGTTACAATTTGTTATTGTGAAATATTATTA
1 TTTGTCACAATTTGTTATTGTGAAATATTAATA
*
613348 TTTGTCACAATTTTTTATAT-TGAGAA-ATTAATA
1 TTTGTCACAATTTGTTAT-TGTGA-AATATTAATA
613381 TTTGT
1 TTTGT
613386 TATAAATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 30 0.91
34 3 0.09
ACGTcount: A:0.31, C:0.04, G:0.11, T:0.54
Consensus pattern (33 bp):
TTTGTCACAATTTGTTATTGTGAAATATTAATA
Found at i:613459 original size:14 final size:13
Alignment explanation
Indices: 613423--613461 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
613413 TTTGTAAAAA
613423 AAATATTTTGACT
1 AAATATTTTGACT
613436 AAATATTTTGACT
1 AAATATTTTGACT
613449 AAATAATTTTGAC
1 AAAT-ATTTTGAC
613462 ATAATTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
AAATATTTTGACT
Found at i:618029 original size:181 final size:177
Alignment explanation
Indices: 617582--618087 Score: 474
Period size: 179 Copynumber: 2.8 Consensus size: 177
617572 AAAATAGTTA
** * * * * *
617582 TGACAATATATGCTATCACTATAGTTAAAATTTGTAACTACAAATATAATTTGTCACAAAAACAT
1 TGACAATATATTTTGTCACTATAATTAAAATATATAACTACAAA-AAAATTTGTCACAAAAACAT
* * *
617647 GAATAGCATTATTTTTTGTGAC-ACTGTTTTTTGTAATAATTATTAACACTTATAGTTACAAAAT
65 GAATATCATTATTTGTTGTGACAACT-TTTTTTGTAATAATTATTAACACTTATAGTTACAAAAA
* *
617711 TTGTCACTATATGACTTTTTTGGCGATAAAAATATGGAGGGAAATCTTTG
129 ATGTCACTATATGACTTTTTTGACGATAAAAATATGGA-GGAAATCTTTG
* * * * * * *
617761 TGACAATATATTTTGTCGCTATAATTAAAACATATAACGACAAAAATTATTTTTTACTAAAAACT
1 TGACAATATATTTTGTCACTATAATTAAAATATATAACTACAAAAA-AATTTGTCAC-AAAAACA
* * *
617826 TGAATCTCATTATTTGTTGTGACAACTTTTTTTGTAA-CATTAGTTATA-GCTTATAGTTACAAA
64 TGAATATCATTATTTGTTGTGACAACTTTTTTTGTAATAATTA-TTA-ACACTTATAGTTACAAA
*
617889 AAATGTCACTATATGATTTTGTTTTTGTAC-A-AAAAAT-TGGA-GATAATCATTTG
127 AAATGTCACTATATGA--CT-TTTTTG-ACGATAAAAATATGGAGGA-AATC-TTTG
* * *
617942 TGACTATATGTTTTGTCACTATAATTAAAATATATAATTACAAACAAAATTTGTCACAACAAATC
1 TGACAATATATTTTGTCACTATAATTAAAATATATAACTACAAA-AAAATTTGTCACAA-AAA-C
* * * * * * *
618007 -TAAATATTATTATTTGTTGTGACAA--TTTTTTGTCATAATTACTAAAACTTTTAATTACAAAA
63 ATGAATATCATTATTTGTTGTGACAACTTTTTTTGTAATAATTATTAACACTTATAGTTACAAAA
** *
618069 TTTGTCACTATATGCCTTT
128 AATGTCACTATATGACTTT
618088 AATTTGGCGC
Statistics
Matches: 266, Mismatches: 45, Indels: 35
0.77 0.13 0.10
Matches are distributed among these distances:
176 2 0.01
177 1 0.00
178 2 0.01
179 84 0.32
180 77 0.29
181 82 0.31
182 10 0.04
183 7 0.03
184 1 0.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (177 bp):
TGACAATATATTTTGTCACTATAATTAAAATATATAACTACAAAAAAATTTGTCACAAAAACATG
AATATCATTATTTGTTGTGACAACTTTTTTTGTAATAATTATTAACACTTATAGTTACAAAAAAT
GTCACTATATGACTTTTTTGACGATAAAAATATGGAGGAAATCTTTG
Found at i:618926 original size:14 final size:14
Alignment explanation
Indices: 618909--618940 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
618899 TACACTTACA
618909 ATATTACATGGTTG
1 ATATTACATGGTTG
618923 ATATTACATGGTTG
1 ATATTACATGGTTG
618937 ATAT
1 ATAT
618941 GTTGTTGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.06, G:0.19, T:0.44
Consensus pattern (14 bp):
ATATTACATGGTTG
Found at i:628689 original size:40 final size:40
Alignment explanation
Indices: 628645--628727 Score: 114
Period size: 40 Copynumber: 2.1 Consensus size: 40
628635 TTATTAATAA
* *
628645 TTGTGACGAATAAGT-TTTGTCATTAGTCTTAGTTGGTGAT
1 TTGTGACG-ATAAGTGTTTGTCATTAGTCCTAGTTGGGGAT
* *
628685 TTGTGACGATAATTGTTTGTCCTTAGTCCTAGTTGGGGAT
1 TTGTGACGATAAGTGTTTGTCATTAGTCCTAGTTGGGGAT
628725 TTG
1 TTG
628728 CACGACAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 5 0.13
40 33 0.87
ACGTcount: A:0.19, C:0.10, G:0.27, T:0.45
Consensus pattern (40 bp):
TTGTGACGATAAGTGTTTGTCATTAGTCCTAGTTGGGGAT
Found at i:640737 original size:153 final size:154
Alignment explanation
Indices: 640550--640854 Score: 587
Period size: 153 Copynumber: 2.0 Consensus size: 154
640540 TGTTATTTCG
640550 GGTATGAATTGCCCAATGTTAAATTATCATAATATTCTTTTTCATGGATAAAAAATATACTATAT
1 GGTATGAATTGCCCAATGTTAAATTATCATAATATTCTTTTTCATGGATAAAAAATATACTATAT
640615 ACCCAAGTAAGTCATTAAGGGACAGGGTATAGTCGGCATGCCATAGATTATAGCACACTGCAGTT
66 ACCCAAGTAAGTCATTAAGGGACAGGGTATAGTCGGCATGCCATAGATTATAGCAC-CTGCAGTT
640680 TTATATTGGCACTAGT-TGTAAGTC
130 TTATATTGGCACTAGTGTGTAAGTC
640704 GGTATGAATTG-CCAATGTTAAATTATCATAATATTCTTTTTCATGGATAAAAAATATACTATAT
1 GGTATGAATTGCCCAATGTTAAATTATCATAATATTCTTTTTCATGGATAAAAAATATACTATAT
640768 ACCCAAGTAAGTCATTAAGGGACAGGGTATAGTCGGCATGCCATAGATTATAGCACCTGCAGTTT
66 ACCCAAGTAAGTCATTAAGGGACAGGGTATAGTCGGCATGCCATAGATTATAGCACCTGCAGTTT
640833 TATATTGGCACTAGTGTGTAAG
131 TATATTGGCACTAGTGTGTAAG
640855 GACACTAAGT
Statistics
Matches: 150, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
152 24 0.16
153 115 0.77
154 11 0.07
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (154 bp):
GGTATGAATTGCCCAATGTTAAATTATCATAATATTCTTTTTCATGGATAAAAAATATACTATAT
ACCCAAGTAAGTCATTAAGGGACAGGGTATAGTCGGCATGCCATAGATTATAGCACCTGCAGTTT
TATATTGGCACTAGTGTGTAAGTC
Found at i:641727 original size:14 final size:14
Alignment explanation
Indices: 641705--641764 Score: 102
Period size: 14 Copynumber: 4.3 Consensus size: 14
641695 AGAGTTTTTA
*
641705 CAATTACCTAAATG
1 CAATCACCTAAATG
*
641719 CAATCACCTAAATA
1 CAATCACCTAAATG
641733 CAATCACCTAAATG
1 CAATCACCTAAATG
641747 CAATCACCTAAATG
1 CAATCACCTAAATG
641761 CAAT
1 CAAT
641765 TTAATTCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 43 1.00
ACGTcount: A:0.45, C:0.27, G:0.05, T:0.23
Consensus pattern (14 bp):
CAATCACCTAAATG
Found at i:642558 original size:17 final size:17
Alignment explanation
Indices: 642507--642559 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
642497 AATTAAGAGT
*
642507 TAGTCTAATAAATGAAC
1 TAGTTTAATAAATGAAC
* * *
642524 TAGTTTGATGAATTAAC
1 TAGTTTAATAAATGAAC
*
642541 TAGTTTAATTAATGAAC
1 TAGTTTAATAAATGAAC
642558 TA
1 TA
642560 ACTTTATTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:651644 original size:9 final size:9
Alignment explanation
Indices: 651630--651654 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
651620 AAAGAATGAG
651630 GAAAATTAT
1 GAAAATTAT
651639 GAAAATTAT
1 GAAAATTAT
651648 GAAAATT
1 GAAAATT
651655 GTAAAAATGA
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:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (9 bp):
GAAAATTAT
Found at i:669268 original size:21 final size:19
Alignment explanation
Indices: 669230--669275 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
669220 AATTAATCCT
669230 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
669250 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
669271 A-TAAT
1 ACTAAT
669276 GATTCAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:679600 original size:21 final size:19
Alignment explanation
Indices: 679562--679607 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
679552 AAATAATCCT
679562 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
679582 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
679603 A-TAAT
1 ACTAAT
679608 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:681667 original size:6 final size:6
Alignment explanation
Indices: 681656--681724 Score: 59
Period size: 6 Copynumber: 10.8 Consensus size: 6
681646 ATGCTTGAAG
*
681656 AAAAGA AAAAGAA AAAAGA AAATAAA AAAGAGA AAAGAGAA AAAAGA AAAAG-
1 AAAAGA AAAAG-A AAAAGA AAA-AGA AAA-AGA AAA-AG-A AAAAGA AAAAGA
* *
681708 TAAATA AAAAGA AAAAG
1 AAAAGA AAAAGA AAAAG
681725 GGGTTTAAGG
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
5 3 0.06
6 24 0.46
7 21 0.40
8 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:681689 original size:14 final size:14
Alignment explanation
Indices: 681656--681705 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
681646 ATGCTTGAAG
681656 AAAAGAAAA-AGAA
1 AAAAGAAAAGAGAA
*
681669 AAAAGAAAATA-AA
1 AAAAGAAAAGAGAA
681682 AAAGAGAAAAGAGAA
1 AAA-AGAAAAGAGAA
681697 AAAAGAAAA
1 AAAAGAAAA
681706 AGTAAATAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
13 14 0.42
14 14 0.42
15 5 0.15
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAGAGAA
Found at i:681699 original size:17 final size:15
Alignment explanation
Indices: 681656--681724 Score: 60
Period size: 17 Copynumber: 4.7 Consensus size: 15
681646 ATGCTTGAAG
681656 AAAAGAAAAAG--AA
1 AAAAGAAAAAGTAAA
681669 AAAAG-AAAA-T-AA
1 AAAAGAAAAAGTAAA
681681 AAAAGAGAAAAG-AGAA
1 AAAAGA-AAAAGTA-AA
681697 AAAAGAAAAAGTAAATA
1 AAAAGAAAAAGT-AA-A
681714 AAAAGAAAAAG
1 AAAAGAAAAAG
681725 GGGTTTAAGG
Statistics
Matches: 47, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
12 11 0.23
13 5 0.11
14 4 0.09
15 5 0.11
16 9 0.19
17 13 0.28
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (15 bp):
AAAAGAAAAAGTAAA
Found at i:681706 original size:34 final size:33
Alignment explanation
Indices: 681661--681724 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 33
681651 TGAAGAAAAG
681661 AAAAAGAAAAAAGAAAATAAAAAAGAGAAAAGAGA
1 AAAAAGAAAAAAGAAAAT-AAAAAGA-AAAAGAGA
*
681696 AAAAAG-AAAAAGTAAATAAAAAGAAAAAG
1 AAAAAGAAAAAAGAAAATAAAAAGAAAAAG
681725 GGGTTTAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 5 0.18
33 7 0.25
34 10 0.36
35 6 0.21
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.05
Consensus pattern (33 bp):
AAAAAGAAAAAAGAAAATAAAAAGAAAAAGAGA
Found at i:681723 original size:7 final size:7
Alignment explanation
Indices: 681656--681706 Score: 61
Period size: 7 Copynumber: 7.4 Consensus size: 7
681646 ATGCTTGAAG
681656 AAAAG-A
1 AAAAGAA
681662 AAAAGAA
1 AAAAGAA
681669 AAAAGAA
1 AAAAGAA
681676 AATAA-AA
1 AA-AAGAA
*
681683 AAGAGAA
1 AAAAGAA
*
681690 AAGAGAA
1 AAAAGAA
681697 AAAAGAA
1 AAAAGAA
681704 AAA
1 AAA
681707 GTAAATAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 6 0.15
7 32 0.80
8 2 0.05
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (7 bp):
AAAAGAA
Found at i:682435 original size:18 final size:17
Alignment explanation
Indices: 682407--682445 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 17
682397 AGAAAAAGGA
682407 AAAACAAGGAAAACAAAAG
1 AAAACAAGG-AAA-AAAAG
682426 AAAA-AAGGAAAAAAAG
1 AAAACAAGGAAAAAAAG
682442 AAAA
1 AAAA
682446 TATGAACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 3 0.15
18 4 0.20
19 4 0.20
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAACAAGGAAAAAAAG
Found at i:682438 original size:9 final size:9
Alignment explanation
Indices: 682399--682445 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
682389 GAATAAGAAG
682399 AAAAAGGAA
1 AAAAAGGAA
682408 AAACAAGGAA
1 AAA-AAGGAA
*
682418 AACAAAAG-A
1 AA-AAAGGAA
682427 AAAAAGGAA
1 AAAAAGGAA
682436 AAAAA-GAA
1 AAAAAGGAA
682444 AA
1 AA
682446 TATGAACCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
8 9 0.27
9 12 0.36
10 11 0.33
11 1 0.03
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (9 bp):
AAAAAGGAA
Found at i:700551 original size:3 final size:3
Alignment explanation
Indices: 700526--700579 Score: 58
Period size: 3 Copynumber: 18.3 Consensus size: 3
700516 TAAATAGTTG
* * *
700526 TAA TAAA TAT TAA TAA GAA TAA TAA TAA TAA TCA T-A TAA T-A TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
700570 TAA TAA TAA T
1 TAA TAA TAA T
700580 TATTATTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
2 4 0.09
3 36 0.84
4 3 0.07
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:700859 original size:53 final size:53
Alignment explanation
Indices: 700775--701145 Score: 349
Period size: 53 Copynumber: 6.9 Consensus size: 53
700765 ATTTCGACTA
** * *
700775 ACGGGTTCTTTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * * ** * *
700828 ACAGGTTCACTCCCTCTTGCTTCAGAAAGTAGAACTCGAATAATCTTCTGTCT
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * * * *
700881 ATGGGTTTGCTCCCTCTTTCTTAAGGAAGTAGAACTCAAACAATCTTCTGCCT
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
* * * *
700934 ACGGGTTTGCTCCCTCTTTCTTTAGGGAGTAAAGAACTC-TATAATCTTCTG-CT
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGT--AGAACTCGAACAATCTTCTGCCT
*
700987 AACGGGTTCGCTCCCTCTTTCTTTCAGGGAGTATAGAACTCGAAC-ATCTTCTTCCT
1 -ACGGGTTCGCTCCCTCTTTC-TTCAGGGAG--TAGAACTCGAACAATCTTCTGCCT
* *
701043 ACGGGTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCGAAC-ATCTTCTTTCC-
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTA--GAACTCGAACAATCTTC-TGCCT
* * * * *
701097 AAGGGTTCGCCCCCTATTTCTTTAGGGAGTATAAATCTCGAAC-ATCTTC
1 ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTA-GAA-CTCGAACAATCTTC
701146 AACAACCGTG
Statistics
Matches: 272, Mismatches: 34, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
52 2 0.01
53 119 0.44
54 94 0.35
55 53 0.19
56 3 0.01
57 1 0.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.34
Consensus pattern (53 bp):
ACGGGTTCGCTCCCTCTTTCTTCAGGGAGTAGAACTCGAACAATCTTCTGCCT
Found at i:701217 original size:55 final size:55
Alignment explanation
Indices: 701108--701419 Score: 432
Period size: 55 Copynumber: 5.7 Consensus size: 55
701098 AGGGTTCGCC
* * * * *
701108 CCCTATTTCTTTAGGGAGTATAA-ATCTCGAAC-ATCTTCAACAACCGTGTATGCT
1 CCCTATTCCTTCAGAGAGTATAAGA-CTCGAACAATCTTCAACAATCGTGTCTGCT
* * *
701162 CTCTATTCCTACAGAGAGTATAAGACTTGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
701217 CCATATTCTTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
1 CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* * * *
701272 CCCTATTCCTTCAGAGATTATAAGACTCGAATAATCTTCAACAATTGTGTCCGCT
1 CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
701327 CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCACCAATCATGTCTGCT
1 CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
* *
701382 CCCTAATCCTTCAGAGAGTATAAGGCTCGAAC-ATCTTC
1 CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTC
701420 TTCAACGGGT
Statistics
Matches: 229, Mismatches: 27, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
54 30 0.13
55 199 0.87
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (55 bp):
CCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCT
Found at i:701484 original size:55 final size:54
Alignment explanation
Indices: 701414--701569 Score: 233
Period size: 54 Copynumber: 2.9 Consensus size: 54
701404 AGGCTCGAAC
* ** * *
701414 ATCTTCTTC-AACGGGTTCGCTCTTTCTTTCTTTAAGGAGTATGGAACTCAAACA
1 ATCTTCTACAAACGGGTTCGCTCACTCTTT-TTTAGGGAGTATAGAACTCAAACA
* *
701468 ATCTTCTACAAACGGGTTCGCTCCCTCTTTTTTAGGGAGAATAGAACTCAAACA
1 ATCTTCTACAAACGGGTTCGCTCACTCTTTTTTAGGGAGTATAGAACTCAAACA
701522 ATCTTCTACAAACGGGTTCGCTCACTCTTTTTTAGGGAGTATAGAACT
1 ATCTTCTACAAACGGGTTCGCTCACTCTTTTTTAGGGAGTATAGAACT
701570 TGAACATCTT
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
54 75 0.81
55 18 0.19
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (54 bp):
ATCTTCTACAAACGGGTTCGCTCACTCTTTTTTAGGGAGTATAGAACTCAAACA
Found at i:701963 original size:37 final size:38
Alignment explanation
Indices: 701922--702002 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 38
701912 TTTACTCCAA
*
701922 TACTCTTTC-GAGAAGGCTTAAAATGGATTTGCTTCAC
1 TACTCTTTCAGAGAAGCCTTAAAATGGATTTGCTTCAC
* * *
701959 TACTC-TTCAGTGAAGCCTTAAGATGGATTTGTTTCAC
1 TACTCTTTCAGAGAAGCCTTAAAATGGATTTGCTTCAC
701996 TACTCTT
1 TACTCTT
702003 CGGTGAAGAC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
36 3 0.08
37 34 0.89
38 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (38 bp):
TACTCTTTCAGAGAAGCCTTAAAATGGATTTGCTTCAC
Found at i:702003 original size:37 final size:37
Alignment explanation
Indices: 701933--702101 Score: 164
Period size: 37 Copynumber: 4.6 Consensus size: 37
701923 ACTCTTTCGA
* * *
701933 GAAGGCTTAAAATGGATTTGCTTCACTACTCTTCAGT
1 GAAGGCTTAAGATGGATTTGTTTCACTACTCTTCGGT
*
701970 GAAGCCTTAAGATGGATTTGTTTCACTACTCTTCGGT
1 GAAGGCTTAAGATGGATTTGTTTCACTACTCTTCGGT
* * * * * *
702007 GAAGACTTAGGATAGA-TCGCTTT-ATTATTCTTCGGT
1 GAAGGCTTAAGATGGATTTG-TTTCACTACTCTTCGGT
* * *
702043 GAAGGCATAAGATGGATTT-TCTTCACTATTCTTTGGT
1 GAAGGCTTAAGATGGATTTGT-TTCACTACTCTTCGGT
*
702080 GAAGGCTTAAGATTGACTTTGT
1 GAAGGCTTAAGATGGA-TTTGT
702102 CCCAATCTCC
Statistics
Matches: 107, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
35 1 0.01
36 27 0.25
37 75 0.70
38 3 0.03
39 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (37 bp):
GAAGGCTTAAGATGGATTTGTTTCACTACTCTTCGGT
Found at i:707643 original size:55 final size:55
Alignment explanation
Indices: 707581--707723 Score: 178
Period size: 55 Copynumber: 2.6 Consensus size: 55
707571 CAACTTCAAA
* * * * * * *
707581 CTTCATTCATCAGATGTCTTTCTTCATGGATCGGTCTTCAATCAGTTTTAGATTT
1 CTTCATTCATCGGATGTCCTTCTTCATGAATCAGTCTTCAATCAGGTTCAAATTT
* * * *
707636 CTTCATTCATTGGATATCCATCTTCATGAATCATTCTTCAATCAGGTTCAAATTT
1 CTTCATTCATCGGATGTCCTTCTTCATGAATCAGTCTTCAATCAGGTTCAAATTT
*
707691 CTTCATTCATCGGATGTCCTTCTTAATGAATCA
1 CTTCATTCATCGGATGTCCTTCTTCATGAATCA
707724 CTTGAATGTC
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 73 1.00
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.43
Consensus pattern (55 bp):
CTTCATTCATCGGATGTCCTTCTTCATGAATCAGTCTTCAATCAGGTTCAAATTT
Found at i:710112 original size:2 final size:2
Alignment explanation
Indices: 710105--710145 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
710095 TATACTTTAA
*
710105 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
710146 CGATATAGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:713683 original size:4 final size:4
Alignment explanation
Indices: 713674--713703 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
713664 CATGTTCTGA
*
713674 GATT GATT GATT GATT GATT GATT CATT GA
1 GATT GATT GATT GATT GATT GATT GATT GA
713704 ACTGAGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (4 bp):
GATT
Found at i:717961 original size:16 final size:16
Alignment explanation
Indices: 717940--717973 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
717930 CGCGTTCTGA
* *
717940 GATTGATTGATTCACT
1 GATTGATTCATTAACT
717956 GATTGATTCATTAACT
1 GATTGATTCATTAACT
717972 GA
1 GA
717974 GATTTGTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (16 bp):
GATTGATTCATTAACT
Found at i:727898 original size:59 final size:58
Alignment explanation
Indices: 727825--727950 Score: 207
Period size: 59 Copynumber: 2.2 Consensus size: 58
727815 CAGCAGGCTG
* *
727825 CATATTCGGGATTGTACTTAAGTATACATAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCAGGATTGTACTTAAGGATACATAGTACAGATGGTGG-CACGACCTTATGTGT
*
727884 CATATTCAGGATTGTACTTAAGGATACCTAGTACAGATGGTGGCACGACCTTATGTGT
1 CATATTCAGGATTGTACTTAAGGATACATAGTACAGATGGTGGCACGACCTTATGTGT
*
727942 CATACTCAG
1 CATATTCAG
727951 ATTAGCACTA
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 23 0.37
59 40 0.63
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (58 bp):
CATATTCAGGATTGTACTTAAGGATACATAGTACAGATGGTGGCACGACCTTATGTGT
Found at i:730908 original size:16 final size:19
Alignment explanation
Indices: 730885--730927 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 19
730875 ATCATGACAG
730885 CATG-TATTCAT-TCAT-T
1 CATGTTATTCATCTCATGT
730901 CAT-TTATT-ATCTCATGT
1 CATGTTATTCATCTCATGT
730918 CATGTTATTC
1 CATGTTATTC
730928 TAGCTGATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.09
16 11 0.50
17 4 0.18
18 5 0.23
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.51
Consensus pattern (19 bp):
CATGTTATTCATCTCATGT
Found at i:731827 original size:20 final size:19
Alignment explanation
Indices: 731787--731827 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
731777 AGCATGTATC
* *
731787 TTCATTAAAATCATGTGTT
1 TTCATTAAAATCATATATT
731806 TTCATTAAAAATCATATATT
1 TTCATT-AAAATCATATATT
731826 TT
1 TT
731828 TAAAGGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.37, C:0.10, G:0.05, T:0.49
Consensus pattern (19 bp):
TTCATTAAAATCATATATT
Found at i:734792 original size:19 final size:20
Alignment explanation
Indices: 734768--734810 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
734758 AACATTTATC
*
734768 TTCATT-AAAATCATGTATT
1 TTCATTAAAAATCATATATT
734787 TTCATTAAAAATCATATATT
1 TTCATTAAAAATCATATATT
734807 TTCA
1 TTCA
734811 AAGGCTCAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.47
Consensus pattern (20 bp):
TTCATTAAAAATCATATATT
Found at i:735575 original size:13 final size:12
Alignment explanation
Indices: 735556--735595 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
735546 GTGCTACAAC
735556 AAAAAGAAAAAG
1 AAAAAGAAAAAG
*
735568 AAAGAAGAAAAAC
1 AAA-AAGAAAAAG
735581 AAAAAGAAAAGAG
1 AAAAAGAAAA-AG
735594 AA
1 AA
735596 GAAATCCTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:735595 original size:7 final size:6
Alignment explanation
Indices: 735556--735595 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
735546 GTGCTACAAC
*
735556 AAAAAG AAAAAG AAAGAAG AAAAAC AAAAAG AAAAGAG AA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAA-AG AA
735596 GAAATCCTAC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 20 0.67
7 10 0.33
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Done.