Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006564.1 Hibiscus syriacus cultivar Beakdansim tig00016065_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: 1886890
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 8
Found at i:771 original size:13 final size:11
Alignment explanation
Indices: 753--869 Score: 78
Period size: 11 Copynumber: 9.8 Consensus size: 11
743 TAGGCGTTTA
753 ATGGTGATGGACT
1 ATGGTGAT-GA-T
766 ATGGTGATGAT
1 ATGGTGATGAT
*
777 ATAGGCG-TGAT
1 AT-GGTGATGAT
788 AATGGTGATGGAAT
1 -ATGGTGAT-G-AT
802 ATGGTGATGAT
1 ATGGTGATGAT
*
813 ATAGGCG-TGAT
1 AT-GGTGATGAT
824 AATGGTGATGGACT
1 -ATGGTGAT-GA-T
838 ATGGTGATGAT
1 ATGGTGATGAT
*
849 ATAGGCG-TGAT
1 AT-GGTGATGAT
860 AATGGTGATG
1 -ATGGTGATG
870 GACAGATTGT
Statistics
Matches: 85, Mismatches: 6, Indels: 27
0.72 0.05 0.23
Matches are distributed among these distances:
11 31 0.36
12 24 0.28
13 27 0.32
14 3 0.04
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.31
Consensus pattern (11 bp):
ATGGTGATGAT
Found at i:796 original size:23 final size:24
Alignment explanation
Indices: 755--869 Score: 82
Period size: 23 Copynumber: 4.8 Consensus size: 24
745 GGCGTTTAAT
755 GGTGATGGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
*
781 GCGTGAT-A-ATGGTGATGGA-ATAT
1 G-GTGATGATATGGTGAT-GATATAG
* *
804 GGTGATGATATAGGCG-TGATA-AT
1 GGTGATGATAT-GGTGATGATATAG
827 GGTGATGGACTATGGTGATGATATAG
1 GGTGAT-GA-TATGGTGATGATATAG
853 GCGTGAT-A-ATGGTGATG
1 G-GTGATGATATGGTGATG
870 GACAGATTGT
Statistics
Matches: 74, Mismatches: 4, Indels: 25
0.72 0.04 0.24
Matches are distributed among these distances:
22 5 0.07
23 32 0.43
24 11 0.15
25 13 0.18
26 3 0.04
27 10 0.14
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.30
Consensus pattern (24 bp):
GGTGATGATATGGTGATGATATAG
Found at i:798 original size:36 final size:36
Alignment explanation
Indices: 730--872 Score: 261
Period size: 36 Copynumber: 4.0 Consensus size: 36
720 ATAGGCGTGA
*
730 TATGGTGATGATATAGGCGT-TTAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
765 TATGGTGATGATATAGGCGTGATAATGGTGATGGAA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
801 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
837 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
873 AGATTGTATC
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.19
36 84 0.81
ACGTcount: A:0.28, C:0.05, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:1254 original size:19 final size:20
Alignment explanation
Indices: 1207--1257 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
1197 GAAATCCCTT
**
1207 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
1227 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
1246 TGAAGATACATG
1 TGAAAATACATG
1258 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:4438 original size:13 final size:11
Alignment explanation
Indices: 4418--4574 Score: 106
Period size: 11 Copynumber: 13.2 Consensus size: 11
4408 AATATAGGCG
4418 TGATATGGTGA
1 TGATATGGTGA
4429 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
4442 TGATATAGGCG-
1 TGATAT-GGTGA
4453 TGATAATGGTGA
1 TGAT-ATGGTGA
4465 TGGATTATGGTGA
1 T-GA-TATGGTGA
*
4478 TGATATAGGCG-
1 TGATAT-GGTGA
4489 TGATAATGGTGA
1 TGAT-ATGGTGA
4501 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
4514 TGATATAGGCG-
1 TGATAT-GGTGA
4525 TGATAATGGTGA
1 TGAT-ATGGTGA
4537 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
4550 TGATATAGGCG-
1 TGATAT-GGTGA
4561 TGATAATGGTGA
1 TGAT-ATGGTGA
4573 TG
1 TG
4575 GACAGATTGT
Statistics
Matches: 118, Mismatches: 8, Indels: 39
0.72 0.05 0.24
Matches are distributed among these distances:
11 43 0.36
12 32 0.27
13 39 0.33
14 4 0.03
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:4570 original size:23 final size:24
Alignment explanation
Indices: 4401--4574 Score: 102
Period size: 23 Copynumber: 7.3 Consensus size: 24
4391 ATTTATAAGT
* *
4401 TGGTGATAATATA-GGCG-TGATA
1 TGGTGATGATATAGGGTGATGATA
*
4423 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
4447 TAGGCG-TGATA-ATGGTGATGGATTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
4472 TGGTGATGATATAGGCGTGAT-A-A
1 TGGTGATGATATAGG-GTGATGATA
*
4495 TGGTGATGGA-ATATGGTGATGATA
1 TGGTGAT-GATATAGGGTGATGATA
* *
4519 TAGGCG-TGATA-ATGGTGATGGACTA
1 T-GGTGATGATATAGGGTGAT-GA-TA
4544 TGGTGATGATATAGGCGTGAT-A-A
1 TGGTGATGATATAGG-GTGATGATA
4567 TGGTGATG
1 TGGTGATG
4575 GACAGATTGT
Statistics
Matches: 123, Mismatches: 9, Indels: 39
0.72 0.05 0.23
Matches are distributed among these distances:
22 15 0.12
23 46 0.37
24 24 0.20
25 24 0.20
26 4 0.03
27 10 0.08
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.32
Consensus pattern (24 bp):
TGGTGATGATATAGGGTGATGATA
Found at i:4577 original size:36 final size:36
Alignment explanation
Indices: 4401--4576 Score: 318
Period size: 36 Copynumber: 4.9 Consensus size: 36
4391 ATTTATAAGT
*
4401 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
4436 TGGTGATGATATAGGCGTGATAATGGTGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
4472 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
*
4508 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
4544 TGGTGATGATATAGGCGTGATAATGGTGATGGA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGA
4577 CAGATTGTAT
Statistics
Matches: 136, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.15
36 116 0.85
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.31
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGAATA
Found at i:8444 original size:22 final size:23
Alignment explanation
Indices: 8416--8467 Score: 88
Period size: 22 Copynumber: 2.3 Consensus size: 23
8406 ATTTATAAGT
8416 TGGTGATAATATAGGCGTGAT-A
1 TGGTGATAATATAGGCGTGATAA
*
8438 TGGTGATGATATAGGCGTGATAA
1 TGGTGATAATATAGGCGTGATAA
8461 TGGTGAT
1 TGGTGAT
8468 GGACTATGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 20 0.71
23 8 0.29
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.33
Consensus pattern (23 bp):
TGGTGATAATATAGGCGTGATAA
Found at i:8459 original size:36 final size:36
Alignment explanation
Indices: 8436--8579 Score: 270
Period size: 36 Copynumber: 4.0 Consensus size: 36
8426 ATAGGCGTGA
8436 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
8472 TATGGTGATGATATAGGCGTGATAATGGTGATGGAA
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
8508 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
*
8544 TATGGTGATGATATAGGTGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
8580 AGATTGTATC
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 105 1.00
ACGTcount: A:0.28, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
Found at i:8478 original size:13 final size:11
Alignment explanation
Indices: 8433--8576 Score: 107
Period size: 11 Copynumber: 12.2 Consensus size: 11
8423 AATATAGGCG
8433 TGATATGGTGA
1 TGATATGGTGA
*
8444 TGATATAGGCG-
1 TGATAT-GGTGA
8455 TGATAATGGTGA
1 TGAT-ATGGTGA
8467 TGGACTATGGTGA
1 T-GA-TATGGTGA
*
8480 TGATATAGGCG-
1 TGATAT-GGTGA
8491 TGATAATGGTGA
1 TGAT-ATGGTGA
8503 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
8516 TGATATAGGCG-
1 TGATAT-GGTGA
8527 TGATAATGGTGA
1 TGAT-ATGGTGA
8539 TGGACTATGGTGA
1 T-GA-TATGGTGA
8552 TGATATAGGTG-
1 TGATAT-GGTGA
8563 TGATAATGGTGA
1 TGAT-ATGGTGA
8575 TG
1 TG
8577 GACAGATTGT
Statistics
Matches: 109, Mismatches: 6, Indels: 35
0.73 0.04 0.23
Matches are distributed among these distances:
11 45 0.41
12 31 0.28
13 29 0.27
14 4 0.04
ACGTcount: A:0.28, C:0.03, G:0.36, T:0.32
Consensus pattern (11 bp):
TGATATGGTGA
Found at i:8575 original size:23 final size:24
Alignment explanation
Indices: 8435--8576 Score: 113
Period size: 23 Copynumber: 5.9 Consensus size: 24
8425 TATAGGCGTG
*
8435 ATATGGTGATGATATAGGCG-TGAT
1 ATATGGTGATGATAT-GGTGATGAT
8459 A-ATGGTGATGGACTATGGTGATGAT
1 ATATGGTGAT-GA-TATGGTGATGAT
*
8484 ATA-GGCG-TGATAATGGTGATGGA-
1 ATATGGTGATGAT-ATGGTGAT-GAT
*
8507 ATATGGTGATGATATAGGCG-TGAT
1 ATATGGTGATGATAT-GGTGATGAT
8531 A-ATGGTGATGGACTATGGTGATGAT
1 ATATGGTGAT-GA-TATGGTGATGAT
8556 ATA-GGTG-TGATAATGGTGATG
1 ATATGGTGATGAT-ATGGTGATG
8577 GACAGATTGT
Statistics
Matches: 98, Mismatches: 5, Indels: 31
0.73 0.04 0.23
Matches are distributed among these distances:
22 2 0.02
23 42 0.43
24 22 0.22
25 30 0.31
26 2 0.02
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.32
Consensus pattern (24 bp):
ATATGGTGATGATATGGTGATGAT
Found at i:13536 original size:35 final size:37
Alignment explanation
Indices: 13467--13546 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
13457 ATACTATTTC
* * *
13467 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCAGTATCACACCTATAT
*
13504 CATCACCATAGTCCATC-ACC-GTATCACACCTATAT
1 CATCACCATAATCCATCTACCAGTATCACACCTATAT
13539 CATCACCA
1 CATCACCA
13547 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 21 0.54
36 2 0.05
37 16 0.41
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCAGTATCACACCTATAT
Found at i:14019 original size:14 final size:15
Alignment explanation
Indices: 13984--14031 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
13974 AAATTTGGAG
13984 AGCAAAAGAAAGAAA
1 AGCAAAAGAAAGAAA
*
13999 AGAAAAAG-AAGAAA
1 AGCAAAAGAAAGAAA
*
14013 ATCAAAAGCAAAAGAAA
1 AGCAAAAG--AAAGAAA
14030 AG
1 AG
14032 TGAAGCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.46
15 7 0.27
17 7 0.27
ACGTcount: A:0.73, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
AGCAAAAGAAAGAAA
Found at i:14415 original size:29 final size:29
Alignment explanation
Indices: 14373--14436 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
14363 CGAGAGGGTG
14373 AGATCAGAAGGGGGATCCGAAAAAGCCAA
1 AGATCAGAAGGGGGATCCGAAAAAGCCAA
*
14402 AGATCAGAAGGGGGATCCGAAATAGCCAA
1 AGATCAGAAGGGGGATCCGAAAAAGCCAA
*
14431 GGATCA
1 AGATCA
14437 TATCCTCGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.42, C:0.17, G:0.31, T:0.09
Consensus pattern (29 bp):
AGATCAGAAGGGGGATCCGAAAAAGCCAA
Found at i:18173 original size:22 final size:22
Alignment explanation
Indices: 18140--18192 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
18130 TTGGAGGAGA
18140 CACATG-CACGCCTAAGAAGAAG
1 CACATGAC-CGCCTAAGAAGAAG
18162 CACATGACCGCCTAAGAAGAAG
1 CACATGACCGCCTAAGAAGAAG
18184 CACATGACC
1 CACATGACC
18193 AGCCATCATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 29 0.97
23 1 0.03
ACGTcount: A:0.40, C:0.30, G:0.21, T:0.09
Consensus pattern (22 bp):
CACATGACCGCCTAAGAAGAAG
Found at i:19129 original size:23 final size:24
Alignment explanation
Indices: 19103--19155 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
19093 AAATCAAGCA
19103 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAGCACTCGAAAAG
* *
19126 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATCAAAGCACTCGAAAAG
19150 AAGAAA
1 AAGAAA
19156 CAGAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.60, C:0.13, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCGAAAAG
Found at i:19161 original size:24 final size:23
Alignment explanation
Indices: 19112--19162 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
19102 AAAGAAAATC
**
19112 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAACAG
19135 AAAGCACTCGAAAAGAAGAAACAG
1 AAAGCACTC-AAAAGAAGAAACAG
19159 AAAG
1 AAAG
19163 AAAGAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.59, C:0.14, G:0.20, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAACAG
Found at i:20448 original size:24 final size:25
Alignment explanation
Indices: 20402--20456 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
20392 ACAGTTATGC
*
20402 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
20426 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
20451 CA-TTGA
1 CACTTGA
20457 GGCTCTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:22994 original size:23 final size:24
Alignment explanation
Indices: 22968--23020 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
22958 AAATCCAGCA
22968 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAGCACTCGAAAAG
* *
22991 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATCAAAGCACTCGAAAAG
23015 AAGAAA
1 AAGAAA
23021 CAGAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.60, C:0.13, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCGAAAAG
Found at i:23026 original size:24 final size:23
Alignment explanation
Indices: 22977--23027 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
22967 AAAGAAAATC
**
22977 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAACAG
23000 AAAGCACTCGAAAAGAAGAAACAG
1 AAAGCACTC-AAAAGAAGAAACAG
23024 AAAG
1 AAAG
23028 AAAGAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.59, C:0.14, G:0.20, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAACAG
Found at i:24314 original size:24 final size:25
Alignment explanation
Indices: 24268--24322 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
24258 ACAGTTATGC
*
24268 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
24292 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
24317 CA-TTGA
1 CACTTGA
24323 GGCTCTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:26859 original size:23 final size:24
Alignment explanation
Indices: 26833--26885 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
26823 AAATCCAGCA
26833 AAGAAAATCAAAGCACTC-AAAAG
1 AAGAAAATCAAAGCACTCGAAAAG
* *
26856 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATCAAAGCACTCGAAAAG
26880 AAGAAA
1 AAGAAA
26886 CAGAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.60, C:0.13, G:0.17, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCGAAAAG
Found at i:26891 original size:24 final size:23
Alignment explanation
Indices: 26842--26892 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
26832 AAAGAAAATC
**
26842 AAAGCACTCAAAAGAAGAAATTG
1 AAAGCACTCAAAAGAAGAAACAG
26865 AAAGCACTCGAAAAGAAGAAACAG
1 AAAGCACTC-AAAAGAAGAAACAG
26889 AAAG
1 AAAG
26893 AAAGAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.59, C:0.14, G:0.20, T:0.08
Consensus pattern (23 bp):
AAAGCACTCAAAAGAAGAAACAG
Found at i:28179 original size:24 final size:25
Alignment explanation
Indices: 28133--28187 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
28123 ACAGTTATTC
*
28133 CACTTGAAGTTCAAAAAGATGTG-T
1 CACTTGAAGTGCAAAAAGATGTGAT
* * *
28157 CACTTGAAGTGCCACAAGTTGTGAT
1 CACTTGAAGTGCAAAAAGATGTGAT
28182 CA-TTGA
1 CACTTGA
28188 GGCTCCAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 23 0.88
25 3 0.12
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (25 bp):
CACTTGAAGTGCAAAAAGATGTGAT
Found at i:35757 original size:15 final size:16
Alignment explanation
Indices: 35730--35766 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
35720 CTTTATTATC
35730 TTATTTCATCTTTCGT
1 TTATTTCATCTTTCGT
*
35746 TTATTT-ATCTTTTGT
1 TTATTTCATCTTTCGT
35761 TTATTT
1 TTATTT
35767 TATTCTAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.14, C:0.11, G:0.05, T:0.70
Consensus pattern (16 bp):
TTATTTCATCTTTCGT
Found at i:36134 original size:8 final size:8
Alignment explanation
Indices: 36120--36187 Score: 73
Period size: 8 Copynumber: 8.0 Consensus size: 8
36110 TTTTTTTTTT
36120 CAAAAAAA
1 CAAAAAAA
*
36128 TAAAAAAA
1 CAAAAAAA
*
36136 CAAAACAA
1 CAAAAAAA
*
36144 CAAAAAAGG
1 CAAAAAA-A
36153 CAAAAAAA
1 CAAAAAAA
36161 CAAAAAAAA
1 C-AAAAAAA
36170 GGCAAAAAAA
1 --CAAAAAAA
36180 CAAAAAAA
1 CAAAAAAA
36188 GAGCCAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
8 28 0.56
9 14 0.28
10 7 0.14
11 1 0.02
ACGTcount: A:0.81, C:0.12, G:0.06, T:0.01
Consensus pattern (8 bp):
CAAAAAAA
Found at i:36156 original size:17 final size:17
Alignment explanation
Indices: 36120--36186 Score: 82
Period size: 19 Copynumber: 3.9 Consensus size: 17
36110 TTTTTTTTTT
* *
36120 CAAAAAAATAAAAAA-A
1 CAAAAAAACAAAAAAGG
*
36136 CAAAACAACAAAAAAGG
1 CAAAAAAACAAAAAAGG
36153 CAAAAAAACAAAAAAAAGG
1 CAAAAAAAC--AAAAAAGG
36172 CAAAAAAACAAAAAA
1 CAAAAAAACAAAAAA
36187 AGAGCCAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
16 13 0.30
17 14 0.32
19 17 0.39
ACGTcount: A:0.81, C:0.12, G:0.06, T:0.01
Consensus pattern (17 bp):
CAAAAAAACAAAAAAGG
Found at i:36167 original size:19 final size:19
Alignment explanation
Indices: 36137--36198 Score: 97
Period size: 19 Copynumber: 3.2 Consensus size: 19
36127 ATAAAAAAAC
36137 AAAACAACAAAAAAGGCAAA
1 AAAACAA-AAAAAAGGCAAA
36157 AAAACAAAAAAAAGGCAAA
1 AAAACAAAAAAAAGGCAAA
*
36176 AAAACAAAAAAAGAGCCAAA
1 AAAACAAAAAAA-AGGCAAA
36196 AAA
1 AAA
36199 GCCAAAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
19 24 0.60
20 16 0.40
ACGTcount: A:0.77, C:0.13, G:0.10, T:0.00
Consensus pattern (19 bp):
AAAACAAAAAAAAGGCAAA
Found at i:36205 original size:20 final size:18
Alignment explanation
Indices: 36144--36205 Score: 54
Period size: 20 Copynumber: 3.3 Consensus size: 18
36134 AACAAAACAA
*
36144 CAAAAAAG-GCAAAAAAA
1 CAAAAAAGAGCAAAAAAC
*
36161 CAAAAAAAAGGCAAAAAAAC
1 CAAAAAAGA-GC-AAAAAAC
*
36181 AAAAAAAGAGCCAAAAAAGC
1 CAAAAAAGAG-CAAAAAA-C
36201 CAAAA
1 CAAAA
36206 TTTCAAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 7 0.20
19 9 0.26
20 19 0.54
ACGTcount: A:0.74, C:0.15, G:0.11, T:0.00
Consensus pattern (18 bp):
CAAAAAAGAGCAAAAAAC
Found at i:45097 original size:35 final size:37
Alignment explanation
Indices: 45028--45107 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
45018 ATATTATTTC
* *
45028 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
45065 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
45100 CATCACCA
1 CATCACCA
45108 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.38, G:0.03, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:45101 original size:11 final size:11
Alignment explanation
Indices: 45061--45107 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
45051 TATCACGCCT
45061 ATATCATCACC
1 ATATCATCACC
45072 ATAGTCCATCACC
1 ATA-T-CATCACC
45085 ATATCA-CACC
1 ATATCATCACC
45095 TATATCATCACC
1 -ATATCATCACC
45107 A
1 A
45108 AATTCTCAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 12 0.38
12 6 0.19
13 10 0.31
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:45105 original size:22 final size:24
Alignment explanation
Indices: 45061--45107 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
45051 TATCACGCCT
45061 ATATCATCACCATAGTCCATCACC
1 ATATCATCACCATAGTCCATCACC
45085 ATATCA-CACCTATA-T-CATCACC
1 ATATCATCACC-ATAGTCCATCACC
45107 A
1 A
45108 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.36
23 5 0.23
24 9 0.41
ACGTcount: A:0.36, C:0.36, G:0.02, T:0.26
Consensus pattern (24 bp):
ATATCATCACCATAGTCCATCACC
Found at i:47886 original size:31 final size:31
Alignment explanation
Indices: 47820--47887 Score: 86
Period size: 31 Copynumber: 2.2 Consensus size: 31
47810 TGGAAAGATA
* *
47820 AAAGAAATGATTTAAGGAAATGAATTAAACG
1 AAAGAAATGATTTAAGGAAAAGAATGAAACG
47851 AAAGAAATGATTTAA-GAAACAGAATGAAA-G
1 AAAGAAATGATTTAAGGAAA-AGAATGAAACG
47881 CAAAGAA
1 -AAAGAA
47888 GGAATAGGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 5 0.15
31 28 0.85
ACGTcount: A:0.59, C:0.04, G:0.19, T:0.18
Consensus pattern (31 bp):
AAAGAAATGATTTAAGGAAAAGAATGAAACG
Found at i:62576 original size:35 final size:37
Alignment explanation
Indices: 62507--62586 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
62497 ATACTATTTC
* *
62507 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
* *
62544 CATCACGATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
62579 CATCACCA
1 CATCACCA
62587 AATTCTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 20 0.53
36 3 0.08
37 15 0.39
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:62580 original size:11 final size:11
Alignment explanation
Indices: 62540--62586 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
62530 TATCACGCCT
*
62540 ATATCATCACG
1 ATATCATCACC
62551 ATAGTCCATCACC
1 ATA-T-CATCACC
62564 ATATCA-CACC
1 ATATCATCACC
62574 TATATCATCACC
1 -ATATCATCACC
62586 A
1 A
62587 AATTCTCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
10 4 0.13
11 12 0.39
12 6 0.19
13 9 0.29
ACGTcount: A:0.36, C:0.34, G:0.04, T:0.26
Consensus pattern (11 bp):
ATATCATCACC
Found at i:68261 original size:35 final size:37
Alignment explanation
Indices: 68192--68271 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
68182 ATACTATTTC
* *
68192 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
68229 CATCACCATAGTCCATC-ACCA-TATCACACCTATAT
1 CATCACCATAATCCATCTACCATTATCACACCTATAT
*
68264 TATCACCA
1 CATCACCA
68272 AATTCTCAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 3 0.08
37 16 0.41
ACGTcount: A:0.33, C:0.36, G:0.03, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACACCTATAT
Found at i:78091 original size:24 final size:24
Alignment explanation
Indices: 78051--78097 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
78041 AAAGTGCTAC
78051 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
78076 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
78098 CTCCTACATC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:78142 original size:11 final size:10
Alignment explanation
Indices: 78121--78171 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
78111 TTTGGAGTGC
78121 AAAAGAAAAA
1 AAAAGAAAAA
78131 AAAAGAAAAA
1 AAAAGAAAAA
*
78141 AAAA-AAGAAG
1 AAAAGAA-AAA
*
78151 AAAAGCAAAAGC
1 AAAAG-AAAA-A
78163 AAAAGAAAA
1 AAAAGAAAA
78172 GTGAAGCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
9 2 0.06
10 20 0.57
11 6 0.17
12 7 0.20
ACGTcount: A:0.82, C:0.04, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:78143 original size:12 final size:13
Alignment explanation
Indices: 78123--78154 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
78113 TGGAGTGCAA
78123 AAGAAAAAAAAAG
1 AAGAAAAAAAAAG
78136 AA-AAAAAAAAAG
1 AAGAAAAAAAAAG
78148 AAGAAAA
1 AAGAAAA
78155 GCAAAAGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAAAAG
Found at i:78144 original size:15 final size:15
Alignment explanation
Indices: 78121--78154 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
78111 TTTGGAGTGC
*
78121 AAAAGAAAAAAAAAG
1 AAAAAAAAAAAAAAG
*
78136 AAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAAG
78151 AAAA
1 AAAA
78155 GCAAAAGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAAG
Found at i:78160 original size:15 final size:15
Alignment explanation
Indices: 78121--78172 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 15
78111 TTTGGAGTGC
78121 AAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAG
78136 AAAA-AAAAAAAGAAG
1 AAAAGAAAAAAA-AAG
*
78151 AAAAGCAAAAGCAAAAG
1 AAAAG-AAAA-AAAAAG
78168 AAAAG
1 AAAAG
78173 TGAAGCAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 7 0.22
15 11 0.34
17 12 0.38
18 2 0.06
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:83281 original size:30 final size:31
Alignment explanation
Indices: 83229--83288 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
83219 CTTAGCTTTA
**
83229 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
83259 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
83289 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:84222 original size:19 final size:20
Alignment explanation
Indices: 84198--84248 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
84188 CGGCCAAGAG
* *
84198 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
84217 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
84237 CATGTATTTTCA
1 CATGTATTTTCA
84249 AAGGGGTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:93590 original size:25 final size:25
Alignment explanation
Indices: 93541--93591 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
93531 AGACAAAAAG
93541 AAGAAAAAAATTCAGAAAAGAAGAA
1 AAGAAAAAAATTCAGAAAAGAAGAA
93566 AAGAAAAAGAATTTCA-AAAAG-AGAA
1 AAGAAAAA-AA-TTCAGAAAAGAAGAA
93591 A
1 A
93592 GCAAGCCAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 13 0.54
26 7 0.29
27 4 0.17
ACGTcount: A:0.71, C:0.04, G:0.16, T:0.10
Consensus pattern (25 bp):
AAGAAAAAAATTCAGAAAAGAAGAA
Found at i:97679 original size:28 final size:27
Alignment explanation
Indices: 97648--97713 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
97638 CAAAAAGAAA
97648 AGAAAAGACA-AAAAGAATAAAAAAATTC
1 AGAAAAGA-AGAAAAGAA-AAAAAAATTC
* *
97676 AGAAAAGAAGAAAAGAAAAAGAATTTC
1 AGAAAAGAAGAAAAGAAAAAAAAATTC
97703 A-AAAAG-AGAAA
1 AGAAAAGAAGAAA
97714 GCAAGCCAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 5 0.14
26 5 0.14
27 10 0.29
28 15 0.43
ACGTcount: A:0.71, C:0.05, G:0.15, T:0.09
Consensus pattern (27 bp):
AGAAAAGAAGAAAAGAAAAAAAAATTC
Found at i:97929 original size:17 final size:18
Alignment explanation
Indices: 97907--97942 Score: 56
Period size: 17 Copynumber: 2.0 Consensus size: 18
97897 CCTTAATTCC
97907 TTTCTTCTA-CCTTTCTA
1 TTTCTTCTATCCTTTCTA
97924 TTTCTTCTATTCCTTTCTA
1 TTTCTTCTA-TCCTTTCTA
97943 CCCTAACCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
19 8 0.47
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTCTTCTATCCTTTCTA
Found at i:103439 original size:42 final size:41
Alignment explanation
Indices: 103392--103476 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 41
103382 TTTGTTGCAC
* *
103392 GTTGCTTCTTCCACCAAAACTCTAATTATCGCTTGATGTAAG
1 GTTGCTTCTTCCACCAAAACTCTAA-TACCACTTGATGTAAG
* *
103434 GTTGCTTCTTCCACCAAAGCTCTGATACCACTTGATGTAAG
1 GTTGCTTCTTCCACCAAAACTCTAATACCACTTGATGTAAG
103475 GT
1 GT
103477 CGTTGGGGTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 16 0.41
42 23 0.59
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.34
Consensus pattern (41 bp):
GTTGCTTCTTCCACCAAAACTCTAATACCACTTGATGTAAG
Found at i:106691 original size:65 final size:65
Alignment explanation
Indices: 106612--106737 Score: 234
Period size: 65 Copynumber: 1.9 Consensus size: 65
106602 CTTGGCTGAA
106612 ATTCTTCCCCCTTGTGTGAACATGACAATTTGGCATCTTGCATGAATATGCATGAATGGATTAAC
1 ATTCTTCCCCCTTGTGTGAACATGACAATTTGGCATCTTGCATGAATATGCATGAATGGATTAAC
* *
106677 ATTCTTCCCCCTTGTGTGAACATGACTATTTGGCTTCTTGCATGAATATGCATGAATGGAT
1 ATTCTTCCCCCTTGTGTGAACATGACAATTTGGCATCTTGCATGAATATGCATGAATGGAT
106738 GAAATTAAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (65 bp):
ATTCTTCCCCCTTGTGTGAACATGACAATTTGGCATCTTGCATGAATATGCATGAATGGATTAAC
Found at i:108211 original size:11 final size:11
Alignment explanation
Indices: 108189--108235 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
108179 TTTGAGAATT
108189 TGGTGATGATA
1 TGGTGATGATA
108200 TAGGTG-TGATA
1 T-GGTGATGATA
108211 TGGTGATGGACTA
1 TGGTGAT-GA-TA
108224 TGGTGATGATA
1 TGGTGATGATA
108235 T
1 T
108236 AGGCGTGATA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.12
11 11 0.34
12 8 0.25
13 9 0.28
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (11 bp):
TGGTGATGATA
Found at i:108217 original size:22 final size:24
Alignment explanation
Indices: 108189--108235 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
108179 TTTGAGAATT
108189 TGGTGAT-GA-TATAGGTG-TGATA
1 TGGTGATGGACTAT-GGTGATGATA
108211 TGGTGATGGACTATGGTGATGATA
1 TGGTGATGGACTATGGTGATGATA
108235 T
1 T
108236 AGGCGTGATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.32
23 6 0.27
24 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.36, T:0.36
Consensus pattern (24 bp):
TGGTGATGGACTATGGTGATGATA
Found at i:108235 original size:35 final size:37
Alignment explanation
Indices: 108189--108268 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
108179 TTTGAGAATT
* *
108189 TGGTGATGATATAGGTGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
108224 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
108261 TGGTGATG
1 TGGTGATG
108269 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 20 0.50
36 4 0.10
37 16 0.40
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:108654 original size:19 final size:20
Alignment explanation
Indices: 108607--108657 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
108597 GAAACCCCTT
**
108607 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
108627 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
108646 TGAAGATACATG
1 TGAAAATACATG
108658 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:112360 original size:11 final size:12
Alignment explanation
Indices: 112339--112387 Score: 59
Period size: 11 Copynumber: 4.2 Consensus size: 12
112329 TTGAGAATTT
112339 GGTGATGATATA
1 GGTGATGATATA
112351 GGTG-TGATAT-
1 GGTGATGATATA
112361 GGTGATGA-ACTA
1 GGTGATGATA-TA
112373 TGGTGATGATATA
1 -GGTGATGATATA
112386 GG
1 GG
112388 CGTGATAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
10 5 0.16
11 10 0.31
12 6 0.19
13 10 0.31
14 1 0.03
ACGTcount: A:0.29, C:0.02, G:0.37, T:0.33
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:112384 original size:35 final size:37
Alignment explanation
Indices: 112338--112417 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 37
112328 TTTGAGAATT
* *
112338 TGGTGATGATATAGGTGTGAT-ATGG-TGATGAACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
* *
112373 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
112410 TGGTGATG
1 TGGTGATG
112418 GAAATAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
35 20 0.51
36 4 0.10
37 15 0.38
ACGTcount: A:0.29, C:0.03, G:0.36, T:0.33
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGAACTA
Found at i:119521 original size:55 final size:53
Alignment explanation
Indices: 119448--119552 Score: 147
Period size: 55 Copynumber: 1.9 Consensus size: 53
119438 GTATCTTGGT
* *
119448 TGAAATTCTCCCCCTTGTGTGAAAATGACTATTTTCCATCTTGCATGAATGGA
1 TGAAATTCTCCCCCTTGTGCGAAAATGACTATTTGCCATCTTGCATGAATGGA
* * *
119501 TGAACATTCTTCCCCCTTGTGCGAACATGACTATTTGGCTTCTTGCATGAAT
1 TGAA-ATTC-TCCCCCTTGTGCGAAAATGACTATTTGCCATCTTGCATGAAT
119553 ATGCATTAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
53 4 0.09
54 4 0.09
55 37 0.82
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (53 bp):
TGAAATTCTCCCCCTTGTGCGAAAATGACTATTTGCCATCTTGCATGAATGGA
Found at i:132175 original size:17 final size:16
Alignment explanation
Indices: 132155--132193 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
132145 TTTTTTGAAA
*
132155 TTTTGGCTTTTTTTGTT
1 TTTTGGCTCTTTTT-TT
*
132172 TTTTGCCTCTTTTTTT
1 TTTTGGCTCTTTTTTT
132188 TTTTGG
1 TTTTGG
132194 AAAAAATAGC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.00, C:0.10, G:0.15, T:0.74
Consensus pattern (16 bp):
TTTTGGCTCTTTTTTT
Found at i:134431 original size:19 final size:20
Alignment explanation
Indices: 134384--134434 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
134374 GAAACCCCTT
**
134384 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTAAA
134404 TGAAAATACATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
134423 TGAAGATACATG
1 TGAAAATACATG
134435 CTCTTGCCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:139254 original size:12 final size:13
Alignment explanation
Indices: 139231--139255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
139221 ACATACAACG
139231 AAAATACAAAAAA
1 AAAATACAAAAAA
139244 AAAATACAAAAA
1 AAAATACAAAAA
139256 GAAGTTCAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAATACAAAAAA
Found at i:154844 original size:24 final size:24
Alignment explanation
Indices: 154800--154851 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
154790 TCCTTTCCAA
*
154800 TTGAAGATCCACAAGCGATGTCTT
1 TTGAAGATCCACAAGCGATGTCTC
**
154824 TTGAAGATCCA-ATAGTTATGTCTC
1 TTGAAGATCCACA-AGCGATGTCTC
154848 TTGA
1 TTGA
154852 TATTTCTAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 23 0.96
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (24 bp):
TTGAAGATCCACAAGCGATGTCTC
Found at i:158946 original size:19 final size:20
Alignment explanation
Indices: 158905--158955 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
158895 GAAACCCCTT
*
158905 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
158925 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
158944 TGAAGATACATG
1 TGAAAATACATG
158956 CTCTTGGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:162262 original size:18 final size:18
Alignment explanation
Indices: 162241--162293 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
162231 CTTTTTTGAA
162241 CTTTTCTTTTCTTTTCTT
1 CTTTTCTTTTCTTTTCTT
*
162259 CTTTTCTGATTTTTTTCTCTT
1 CTTTTCT--TTTCTTT-TCTT
*
162280 TTTTTC-TTTCTTTT
1 CTTTTCTTTTCTTTT
162294 TTTGCACTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
17 1 0.03
18 13 0.45
20 6 0.21
21 9 0.31
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (18 bp):
CTTTTCTTTTCTTTTCTT
Found at i:162279 original size:21 final size:21
Alignment explanation
Indices: 162247--162286 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
162237 TGAACTTTTC
162247 TTTTCTTTTCTTCTTTTCTGA
1 TTTTCTTTTCTTCTTTTCTGA
*
162268 TTTT-TTTCTCTTTTTTTCT
1 TTTTCTTT-TCTTCTTTTCT
162287 TTCTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTCTTCTTTTCTGA
Found at i:163056 original size:19 final size:20
Alignment explanation
Indices: 163015--163065 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
163005 GAAACCCCTT
*
163015 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
163035 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
163054 TGAAGATACATG
1 TGAAAATACATG
163066 CTCGTGGCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:165387 original size:24 final size:21
Alignment explanation
Indices: 165353--165395 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
165343 TGCACAAGAT
*
165353 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
165375 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
165396 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:167972 original size:17 final size:16
Alignment explanation
Indices: 167948--167982 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
167938 TCCGAAAATT
167948 AAAAAAAAAAAAAAAG
1 AAAAAAAAAAAAAAAG
*
167964 AAAAGAAAAAGAAAAAG
1 AAAA-AAAAAAAAAAAG
167981 AA
1 AA
167983 TTCTGGTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAAAG
Found at i:177080 original size:2 final size:2
Alignment explanation
Indices: 177073--177117 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
177063 CTATCACCAT
177073 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
177115 TA T
1 TA T
177118 GCTTCCATAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:185847 original size:35 final size:36
Alignment explanation
Indices: 185791--185858 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
185781 ATACAATCTG
185791 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
185827 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
185859 ACTTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:186341 original size:14 final size:15
Alignment explanation
Indices: 186307--186353 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
186297 AATTTGGAGT
186307 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
186322 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
186336 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
186353 G
1 G
186354 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:189777 original size:35 final size:36
Alignment explanation
Indices: 189721--189788 Score: 120
Period size: 35 Copynumber: 1.9 Consensus size: 36
189711 ATACAATCTG
189721 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
189757 TCCATCACCA-TATCACGCCTATATTATCACCA
1 TCCATCACCATTATCACGCCTATATCATCACCA
189789 ACTTATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 21 0.68
36 10 0.32
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:192158 original size:32 final size:33
Alignment explanation
Indices: 192117--192189 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 33
192107 CAACTCCTTG
*
192117 TGAAAAGGTACCTCTTGGAATG-GAACTATTCA
1 TGAAAAGGTACCTCTTGGAATGTCAACTATTCA
* *
192149 TGAAAAGGTAGCTCTTGGAATGTCAACTATTCG
1 TGAAAAGGTACCTCTTGGAATGTCAACTATTCA
192182 TGAAAAGG
1 TGAAAAGG
192190 CACCATTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 21 0.57
33 16 0.43
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (33 bp):
TGAAAAGGTACCTCTTGGAATGTCAACTATTCA
Found at i:194534 original size:27 final size:25
Alignment explanation
Indices: 194484--194534 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
194474 TATATCAAAT
* *
194484 GTCTATTTATAAAATGAATGGACTA
1 GTCTATTTAAAAAATGAAGGGACTA
194509 GTCTATTTAAAGAAATTGAAGGGACT
1 GTCTATTTAAA-AAA-TGAAGGGACT
194535 TGGCCAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 10 0.45
26 3 0.14
27 9 0.41
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.33
Consensus pattern (25 bp):
GTCTATTTAAAAAATGAAGGGACTA
Found at i:206732 original size:97 final size:97
Alignment explanation
Indices: 206619--206809 Score: 382
Period size: 97 Copynumber: 2.0 Consensus size: 97
206609 GAGTTAAAAT
206619 ATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCCCTATATA
1 ATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCCCTATATA
206684 AAGGAGGCTTCATTCAACTTTGTAAATCAAAC
66 AAGGAGGCTTCATTCAACTTTGTAAATCAAAC
206716 ATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCCCTATATA
1 ATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCCCTATATA
206781 AAGGAGGCTTCATTCAACTTTGTAAATCA
66 AAGGAGGCTTCATTCAACTTTGTAAATCA
206810 GATTTCTTTG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 94 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (97 bp):
ATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCCCTATATA
AAGGAGGCTTCATTCAACTTTGTAAATCAAAC
Found at i:207846 original size:13 final size:13
Alignment explanation
Indices: 207827--207871 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 13
207817 GCTTGCTTTC
*
207827 TCTTTTTTTTCTTT
1 TCTTTTTTTT-TTG
207841 TCTTTTTTTTTTG
1 TCTTTTTTTTTTG
207854 TC--TTTTTTTTG
1 TCTTTTTTTTTTG
207865 TCTTTTT
1 TCTTTTT
207872 GTACTCCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 11 0.39
13 7 0.25
14 10 0.36
ACGTcount: A:0.00, C:0.11, G:0.04, T:0.84
Consensus pattern (13 bp):
TCTTTTTTTTTTG
Found at i:207852 original size:18 final size:17
Alignment explanation
Indices: 207829--207873 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 17
207819 TTGCTTTCTC
207829 TTTTTTT-TCTTTTCTTT
1 TTTTTTTGTCTTTT-TTT
207846 TTTTTTTGTCTTTTTTT
1 TTTTTTTGTCTTTTTTT
207863 TGTCTTTTTGT
1 T-T-TTTTTGT
207874 ACTCCAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 11 0.44
18 7 0.28
19 7 0.28
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (17 bp):
TTTTTTTGTCTTTTTTT
Found at i:208193 original size:22 final size:21
Alignment explanation
Indices: 208165--208206 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
208155 GGTTGCAGAA
208165 TTGATGGTCTTGATGGATGAAG
1 TTGATGGTCTTGAT-GATGAAG
*
208187 TTGATGGTGTTGATGATGAA
1 TTGATGGTCTTGATGATGAA
208207 ATGGAGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGAAG
Found at i:212151 original size:14 final size:16
Alignment explanation
Indices: 212125--212159 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
212115 TCTAAAGGTC
212125 CAAAATAACTAACAAA
1 CAAAATAACTAACAAA
212141 -AAAATAA-TAACAAA
1 CAAAATAACTAACAAA
212155 CAAAA
1 CAAAA
212160 ATGTCTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.11
Consensus pattern (16 bp):
CAAAATAACTAACAAA
Found at i:214836 original size:20 final size:21
Alignment explanation
Indices: 214811--214858 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
214801 TCTTTGATAA
214811 CATTTCTATCCATTT-CATTT
1 CATTTCTATCCATTTCCATTT
*
214831 CATTTCTTTCCATTTCCATTT
1 CATTTCTATCCATTTCCATTT
*
214852 CCTTTCT
1 CATTTCT
214859 TAATTATCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.15, C:0.29, G:0.00, T:0.56
Consensus pattern (21 bp):
CATTTCTATCCATTTCCATTT
Found at i:218518 original size:34 final size:32
Alignment explanation
Indices: 218477--218551 Score: 98
Period size: 34 Copynumber: 2.3 Consensus size: 32
218467 ATTCATCTTG
*
218477 AAAAAAAAGAAAAA-AAGAATTCTGAAAATTTAA
1 AAAAAAAAGAAAAACAA-AATTCCGAAAA-TTAA
*
218510 AAACAAAAACAAAAACAAAATTCCGAAAATTAA
1 AAA-AAAAAGAAAAACAAAATTCCGAAAATTAA
218543 AAAAAAAAG
1 AAAAAAAAG
218552 TTATGGTCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 5 0.14
33 10 0.27
34 20 0.54
35 2 0.05
ACGTcount: A:0.72, C:0.08, G:0.07, T:0.13
Consensus pattern (32 bp):
AAAAAAAAGAAAAACAAAATTCCGAAAATTAA
Found at i:223794 original size:51 final size:55
Alignment explanation
Indices: 223690--223796 Score: 150
Period size: 56 Copynumber: 2.0 Consensus size: 55
223680 CATTCTGTCA
* *
223690 TTCAAGTACATTCACATTCAAACAACATGGTATCATTTATTTTCTTTTTAATTCAC
1 TTCAAGTACATTCACATTCAAACAACAT-GTATCATTCATTTTATTTTTAATTCAC
*
223746 TTCACGTACATTCACATTCAAACAACAT-TAT-A-TCA-TTTATTTTTAATTCAC
1 TTCAAGTACATTCACATTCAAACAACATGTATCATTCATTTTATTTTTAATTCAC
223797 ACATGGCATT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
51 15 0.31
52 2 0.04
53 1 0.02
54 3 0.06
56 27 0.56
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (55 bp):
TTCAAGTACATTCACATTCAAACAACATGTATCATTCATTTTATTTTTAATTCAC
Found at i:227445 original size:16 final size:16
Alignment explanation
Indices: 227424--227461 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
227414 CATTTCCTTT
227424 CTTAATTATCCAGTTA
1 CTTAATTATCCAGTTA
227440 CTTAATTATCCAGTTA
1 CTTAATTATCCAGTTA
227456 CTTAAT
1 CTTAAT
227462 CATTTCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (16 bp):
CTTAATTATCCAGTTA
Found at i:230057 original size:15 final size:15
Alignment explanation
Indices: 230037--230073 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
230027 TCTTTGATAA
230037 CATTTCTATCCATTT
1 CATTTCTATCCATTT
*
230052 CATTTCTTTCCATTT
1 CATTTCTATCCATTT
230067 CGATTTC
1 C-ATTTC
230074 CTTTCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.16, C:0.27, G:0.03, T:0.54
Consensus pattern (15 bp):
CATTTCTATCCATTT
Found at i:242699 original size:16 final size:16
Alignment explanation
Indices: 242667--242714 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
242657 ATGGTAATGA
242667 AATAAGAAAAGATGAAAG
1 AATAA-AAAA-ATGAAAG
* *
242685 AATAAAGAAATGAAAT
1 AATAAAAAAATGAAAG
242701 AATAAAAAAATGAA
1 AATAAAAAAATGAA
242715 TATAACTTAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (16 bp):
AATAAAAAAATGAAAG
Found at i:242945 original size:23 final size:20
Alignment explanation
Indices: 242902--242948 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
242892 TGTAGGAGTC
*
242902 TTTTTCTTTTCTTTTTGTTT
1 TTTTTCTTTTCTTGTTGTTT
242922 TTTTTCTTCTTTCTTGTTGCTTT
1 TTTTTC-T-TTTCTTGTTG-TTT
242945 TTTT
1 TTTT
242949 GTTGTAGCAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 6 0.26
21 1 0.04
22 9 0.39
23 7 0.30
ACGTcount: A:0.00, C:0.13, G:0.06, T:0.81
Consensus pattern (20 bp):
TTTTTCTTTTCTTGTTGTTT
Found at i:245143 original size:15 final size:16
Alignment explanation
Indices: 245123--245159 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
245113 TCTTTGATAA
245123 CATTTCTATCCATTT-
1 CATTTCTATCCATTTC
*
245138 CATTTCTTTCCATTTC
1 CATTTCTATCCATTTC
245154 CATTTC
1 CATTTC
245160 CTTTCTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.54
Consensus pattern (16 bp):
CATTTCTATCCATTTC
Found at i:247814 original size:12 final size:12
Alignment explanation
Indices: 247797--247824 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
247787 ATTGATTCAA
247797 GTGTAGCATTTG
1 GTGTAGCATTTG
247809 GTGTAGCATTTG
1 GTGTAGCATTTG
247821 GTGT
1 GTGT
247825 CTCTCCTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.07, G:0.36, T:0.43
Consensus pattern (12 bp):
GTGTAGCATTTG
Found at i:254422 original size:18 final size:18
Alignment explanation
Indices: 254399--254437 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
254389 TTGTTTGTAA
254399 TTTTTGAATTTTTGAATT
1 TTTTTGAATTTTTGAATT
** *
254417 TTTTTGGCTTTTTTAATT
1 TTTTTGAATTTTTGAATT
254435 TTT
1 TTT
254438 CGACCTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.15, C:0.03, G:0.10, T:0.72
Consensus pattern (18 bp):
TTTTTGAATTTTTGAATT
Found at i:254917 original size:59 final size:59
Alignment explanation
Indices: 254804--254924 Score: 154
Period size: 59 Copynumber: 2.1 Consensus size: 59
254794 AATAGATGGA
* * *** *
254804 TAAGTGTCCTATCAAACCCTCCTAGTCGCAATGAAAAGGAAAAGTTGGTAATATGGCTC
1 TAAGTGTCCCATCAAACCCTCATAGTCGCAATGAAAAGGAAAACACGATAATATGGCTC
* *
254863 TAAGTGTCCCATCGAACCCTCATAGTCGCAATGAAAA-GACAAACACGATCATATGGCTC
1 TAAGTGTCCCATCAAACCCTCATAGTCGCAATGAAAAGGA-AAACACGATAATATGGCTC
254922 TAA
1 TAA
254925 CAAACCCTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
58 2 0.04
59 51 0.96
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (59 bp):
TAAGTGTCCCATCAAACCCTCATAGTCGCAATGAAAAGGAAAACACGATAATATGGCTC
Found at i:256357 original size:93 final size:93
Alignment explanation
Indices: 256099--256890 Score: 661
Period size: 93 Copynumber: 8.5 Consensus size: 93
256089 ATTTTAGCTA
* * * * * ** **
256099 ATTTCAACGCTATTCTATCTTCAATTCATTGTTGTAACAACTTTAATAAGTTAACCTCTTTAGTC
1 ATTTCAACACTATTCAAACTTCCATCCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTC
* * * *
256164 CATAAACATCAAAGTGTTAAATGAAGGC
66 CATAAACATCAAAGTGTTTAGTTAAGAC
** * * * *
256192 ATTTCAATGCTACTT-AAAATTTCATCCATTAAGGTAACAACTTGGACAAGTTAACCTCTTTTA-
1 ATTTCAACACTA-TTCAAACTTCCATCCATTAATGTAACAACTTGGATAAGTTAACCTC-TTTAG
**** * * **
256255 TTTGGAAATATCAAAGTGTTTAGATAAGTT
64 TCCATAAACATCAAAGTGTTTAGTTAAGAC
* *
256285 ATTTCAAC-CATATTCAAACATCCACCCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGT
1 ATTTCAACAC-TATTCAAACTTCCATCCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGT
* * * *
256349 CCGTAAATATAAAAGTGTTCAGTTAAGAC
65 CCATAAACATCAAAGTGTTTAGTTAAGAC
* * ** * * * *
256378 ATTTCAATACTATTTAAACTTTTATCCACTAATGTAGA-AACTTAGATAAGTTAACATCTATAGT
1 ATTTCAACACTATTCAAACTTCCATCCATTAATGTA-ACAACTTGGATAAGTTAACCTCTTTAGT
*
256442 CCATAAACATCAAAGTATTTAGTTAAGAC
65 CCATAAACATCAAAGTGTTTAGTTAAGAC
* * * * * * * * * *
256471 ATTTCAGCACTATTCAAACTTCTATCCATTAATGTTATAACATGAATATGTTATCTTATTTAG-C
1 ATTTCAACACTATTCAAACTTCCATCCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTC
* * *
256535 CTGTAAA-AGTCAAAGTGATTAGTTAAGGC
66 C-ATAAACA-TCAAAGTGTTTAGTTAAGAC
* * *
256564 ATTTCAATACTATTGAAA-TTACCATCTATTAATGTAACAA---GGATAAGTTAACCTCTTTAGT
1 ATTTCAACACTATTCAAACTT-CCATCCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGT
* *
256625 TCGTAAACATCAAAGTGTTTAGTTAAGAC
65 CCATAAACATCAAAGTGTTTAGTTAAGAC
*** * * * * * * * *
256654 ATTTCATTTCTATTCAAACTACCAACCATTATTGTGACAACATGGATATGTTAAACTCCTTAGTC
1 ATTTCAACACTATTCAAACTTCCATCCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTC
* * *
256719 CATAATCATCAAAATGTTTATTTAAGAC
66 CATAAACATCAAAGTGTTTAGTTAAGAC
* * * * * *
256747 ATGTCAACACTATTCAAACTTCTATCCATTAATGGAACAACTTGCATAAGTTAACCTCCTTAGTT
1 ATTTCAACACTATTCAAACTTCCATCCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTC
*
256812 TATAAACATCAAAGTGTTTAGTTAAGAC
66 CATAAACATCAAAGTGTTTAGTTAAGAC
** * * *
256840 ATTTCAATTCTATTCAAACATT-CATCCCTCAATCTAACAACTTGGATAAGT
1 ATTTCAACACTATTCAAAC-TTCCATCCATTAATGTAACAACTTGGATAAGT
256891 GATGTGATCC
Statistics
Matches: 550, Mismatches: 131, Indels: 36
0.77 0.18 0.05
Matches are distributed among these distances:
90 68 0.12
91 3 0.01
92 13 0.02
93 456 0.83
94 10 0.02
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (93 bp):
ATTTCAACACTATTCAAACTTCCATCCATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTC
CATAAACATCAAAGTGTTTAGTTAAGAC
Found at i:256826 original size:276 final size:277
Alignment explanation
Indices: 256312--256853 Score: 653
Period size: 276 Copynumber: 2.0 Consensus size: 277
256302 ACATCCACCC
*
256312 ATTAATGTAACAACTTGGATAAGTTAACCTCTTTAGTCCGTAAATATAAAAGTGTTCAGTTAAGA
1 ATTAATGTAACAA--TGGATAAGTTAACCTCTTTAGTCCGTAAACATAAAAGTGTTCAGTTAAGA
* *** * *
256377 CATTTCAATACTATTTAAACTTTTATCCACTAATGTAGAAACTTAGATAAGTTAACATCTATAGT
64 CATTTCAATACTATTCAAACTACCAACCACTAATGTAGAAACATAGATAAGTTAACATCTATAGT
* * * **
256442 CCATAAACATCAAAGTATTTAGTTAAGACATTTCAGCACTATTCAAACTTCTATCCATTAATGTT
129 CCATAAACATCAAAATATTTAGTTAAGACATGTCAACACTATTCAAACTTCTATCCATTAATGGA
* * * * * * *
256507 ATAACATGAATATGTTATCTTATTTAGCCTGTAAAAGTCAAAGTGATTAGTTAAGGCATTTCAAT
194 ACAACATGAATAAGTTAACCTACTTAGCCTATAAAAGTCAAAGTGATTAGTTAAGACATTTCAAT
256572 ACTATTGAAATTACCATCT
259 ACTATTGAAATTACCATCT
* * *
256591 ATTAATGTAACAA-GGATAAGTTAACCTCTTTAGTTCGTAAACATCAAAGTGTTTAGTTAAGACA
1 ATTAATGTAACAATGGATAAGTTAACCTCTTTAGTCCGTAAACATAAAAGTGTTCAGTTAAGACA
* * * * * *
256655 TTTCATTTCTATTCAAACTACCAACCATTATTGT-GACAACATGGATATGTTAA-ACTCCT-TAG
66 TTTCAATACTATTCAAACTACCAACCACTAATGTAGA-AACATAGATAAGTTAACA-T-CTATAG
* * *
256717 TCCATAATCATCAAAATGTTTATTTAAGACATGTCAACACTATTCAAACTTCTATCCATTAATGG
128 TCCATAAACATCAAAATATTTAGTTAAGACATGTCAACACTATTCAAACTTCTATCCATTAATGG
* * * ** *
256782 AACAACTTGCATAAGTTAACCTCCTTAGTTTATAAACA-TCAAAGTGTTTAGTTAAGACATTTCA
193 AACAACATGAATAAGTTAACCTACTTAGCCTATAAA-AGTCAAAGTGATTAGTTAAGACATTTCA
*
256846 ATTCTATT
257 ATACTATT
256854 CAAACATTCA
Statistics
Matches: 221, Mismatches: 38, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
275 3 0.01
276 202 0.91
277 3 0.01
279 13 0.06
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.36
Consensus pattern (277 bp):
ATTAATGTAACAATGGATAAGTTAACCTCTTTAGTCCGTAAACATAAAAGTGTTCAGTTAAGACA
TTTCAATACTATTCAAACTACCAACCACTAATGTAGAAACATAGATAAGTTAACATCTATAGTCC
ATAAACATCAAAATATTTAGTTAAGACATGTCAACACTATTCAAACTTCTATCCATTAATGGAAC
AACATGAATAAGTTAACCTACTTAGCCTATAAAAGTCAAAGTGATTAGTTAAGACATTTCAATAC
TATTGAAATTACCATCT
Found at i:264435 original size:93 final size:93
Alignment explanation
Indices: 264204--264549 Score: 241
Period size: 93 Copynumber: 3.7 Consensus size: 93
264194 AATTGTATTA
* * * * ** * * * * *
264204 ATAAGTTAACCTCCTTATTCCATAAACATGAAAGTGTTTAGTTAAGACATTTCAACGCTATTCAA
1 ATAACTTAACATCCTTAGTCTATAAACAACAAAATGTTTAGTTAAGACTTTTCAATGTTATACAA
* * * * * *
264269 ACATCAATCCCTCAATTTAATAACTTGG
66 ACATCCATCCATTAATATAACAACTTAG
* * * * * * * * *
264297 ATAAGTTAA-ACTCCTTGGT-TCATAAATATCGACATGTTCAATTAAGACTTTTCAATGATATAC
1 ATAACTTAACA-TCCTTAGTCT-ATAAACAACAAAATGTTTAGTTAAGACTTTTCAATGTTATAC
** * * *
264360 ATTCTTTCATCCATTAATATAACAGA-TTGG
64 AAACATCCATCCATTAATATAACA-ACTTAG
* * * * * *
264390 ATAAGTTAACATCTTTAGTCTATAAACATCAAAGTGTTTAGTTAAGA-TAATTCAATGTTATTCA
1 ATAACTTAACATCCTTAGTCTATAAACAACAAAATGTTTAGTTAAGACT-TTTCAATGTTATACA
*
264454 AACATCCATCCATTAATATAACAACTTAT
65 AACATCCATCCATTAATATAACAACTTAG
* * * * *
264483 TTAACTTAACCTCCTTAGTCTATAAGCAACAAAATGTTTAGTTAAGACATTTCAACGTTATACAA
1 ATAACTTAACATCCTTAGTCTATAAACAACAAAATGTTTAGTTAAGACTTTTCAATGTTATACAA
264548 AC
66 AC
264550 TACCATTTAT
Statistics
Matches: 193, Mismatches: 52, Indels: 16
0.74 0.20 0.06
Matches are distributed among these distances:
92 2 0.01
93 188 0.97
94 3 0.02
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (93 bp):
ATAACTTAACATCCTTAGTCTATAAACAACAAAATGTTTAGTTAAGACTTTTCAATGTTATACAA
ACATCCATCCATTAATATAACAACTTAG
Found at i:264530 original size:186 final size:186
Alignment explanation
Indices: 264204--264546 Score: 400
Period size: 186 Copynumber: 1.8 Consensus size: 186
264194 AATTGTATTA
* * * *
264204 ATAAGTTAACCTCCTTATTCCATAAACATGAAAGTGTTTAGTTAAGACATTTCAACGCTATTCAA
1 ATAAGTTAACATCCTTAGTCCATAAACATCAAAGTGTTTAGTTAAGACAATTCAACGCTATTCAA
* * * * * * * * * *
264269 ACATCAATCCCTCAATTTAATAACTTGGATAAGTTAAACTCCTTGGTTCATAAATATCGACATGT
66 ACATCAATCCATCAATATAACAACTTAGATAACTTAAACTCCTTAGTTCATAAACAACAAAATGT
* *
264334 TCAATTAAGACTTTTCAATGATATACATTCTTTCATCCATTAATATAACAGATTGG
131 TCAATTAAGACATTTCAACGATATACATTCTTTCATCCATTAATATAACAGATTGG
* * * * *
264390 ATAAGTTAACATCTTTAGTCTATAAACATCAAAGTGTTTAGTTAAGATAATTCAATGTTATTCAA
1 ATAAGTTAACATCCTTAGTCCATAAACATCAAAGTGTTTAGTTAAGACAATTCAACGCTATTCAA
* * ** * *
264455 ACATCCATCCATTAATATAACAACTTATTTAACTTAACCTCCTTAG-TCTATAAGCAACAAAATG
66 ACATCAATCCATCAATATAACAACTTAGATAACTTAAACTCCTTAGTTC-ATAAACAACAAAATG
* * *
264519 TTTAGTTAAGACATTTCAACGTTATACA
130 TTCAATTAAGACATTTCAACGATATACA
264547 AACTACCATT
Statistics
Matches: 126, Mismatches: 30, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
185 2 0.02
186 124 0.98
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (186 bp):
ATAAGTTAACATCCTTAGTCCATAAACATCAAAGTGTTTAGTTAAGACAATTCAACGCTATTCAA
ACATCAATCCATCAATATAACAACTTAGATAACTTAAACTCCTTAGTTCATAAACAACAAAATGT
TCAATTAAGACATTTCAACGATATACATTCTTTCATCCATTAATATAACAGATTGG
Found at i:264569 original size:93 final size:93
Alignment explanation
Indices: 264395--264573 Score: 225
Period size: 93 Copynumber: 1.9 Consensus size: 93
264385 ATTGGATAAG
* * * * * *
264395 TTAACATCTTTAGTCTATAAACATCAAAGTGTTTAGTTAAGATAATTCAATGTTATTCAAACATC
1 TTAACATCCTTAGTCTATAAACAACAAAATGTTTAGTTAAGACAATTCAACGTTATACAAACATC
*
264460 CATCCATTAATATAACAACTTATTTAAC
66 CATCCATCAATATAACAACTTATTTAAC
* * *
264488 TTAACCTCCTTAGTCTATAAGCAACAAAATGTTTAGTTAAGACATTTCAACGTTATACAAAC-TA
1 TTAACATCCTTAGTCTATAAACAACAAAATGTTTAGTTAAGACAATTCAACGTTATACAAACAT-
** *
264552 CCATTTATCAATGTAACAACTT
65 CCATCCATCAATATAACAACTT
264574 GAATAAGTTA
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 1 0.01
93 71 0.99
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (93 bp):
TTAACATCCTTAGTCTATAAACAACAAAATGTTTAGTTAAGACAATTCAACGTTATACAAACATC
CATCCATCAATATAACAACTTATTTAAC
Found at i:270370 original size:19 final size:19
Alignment explanation
Indices: 270335--270387 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
270325 CCATTTGGCC
* * *
270335 AAAAGCATGTATCTTCATT
1 AAAATCATGTATTTTCATA
* *
270354 TAAATCTTGTATTTTCATA
1 AAAATCATGTATTTTCATA
270373 AAAATCATGTATTTT
1 AAAATCATGTATTTT
270388 TAAAGGGGTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.45
Consensus pattern (19 bp):
AAAATCATGTATTTTCATA
Found at i:270776 original size:36 final size:35
Alignment explanation
Indices: 270728--270844 Score: 180
Period size: 36 Copynumber: 3.3 Consensus size: 35
270718 TACTATCTGT
270728 TCATCACCATCTTCCATCACCATTTTCACGCCTATA
1 TCATCACCATCTTCCATCACCA-TTTCACGCCTATA
* * *
270764 ACATCACCATCTTCCATCTCCAGTTGCACGCCTATA
1 TCATCACCATCTTCCATCACCA-TTTCACGCCTATA
*
270800 TCATCACCATCTTCTATCACCATTTCACGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
270835 TCATCACCAT
1 TCATCACCAT
270845 TCCCTTACCA
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
35 22 0.30
36 51 0.70
ACGTcount: A:0.26, C:0.38, G:0.04, T:0.32
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTTCACGCCTATA
Found at i:273685 original size:44 final size:44
Alignment explanation
Indices: 273635--273755 Score: 181
Period size: 44 Copynumber: 2.7 Consensus size: 44
273625 ATAAGTATGC
273635 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTATA-TGGTA
* * *
273679 AAATAAGCTTACGAGCTTATGGTATAAATTGTAAGTATATGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTATATGGTA
273723 AAATAAGCTTACGAGCTTATGGTTAATAAATGG
1 AAATAAGCTTACGAGCTTATGG--AATAAATGG
273756 TAAAATATTG
Statistics
Matches: 69, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
44 51 0.74
45 11 0.16
46 7 0.10
ACGTcount: A:0.39, C:0.08, G:0.21, T:0.31
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGCAAGTATATGGTA
Found at i:273702 original size:24 final size:24
Alignment explanation
Indices: 273674--273745 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
273664 GCAAGTATAT
273674 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
*
273698 TGGTATAAAT-TG--TA--AG-TATA
1 TGGTA-AAATAAGCTTACGAGCT-TA
273718 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTACGAGCTTA
273742 TGGT
1 TGGT
273746 TAATAAATGG
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
19 5 0.13
20 10 0.26
22 4 0.11
24 14 0.37
25 5 0.13
ACGTcount: A:0.36, C:0.08, G:0.22, T:0.33
Consensus pattern (24 bp):
TGGTAAAATAAGCTTACGAGCTTA
Found at i:280731 original size:44 final size:45
Alignment explanation
Indices: 280683--280851 Score: 243
Period size: 44 Copynumber: 3.8 Consensus size: 45
280673 GTAAGTATGC
* **
280683 AAATAAGCTTATGAGCTTATGGAAT-AATGACAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
280727 AAATAAGCTTATGAGCTTATGGTATAAATGGTAAGTATA-TGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
280771 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
280816 AAATAAGCTTACGAGCTTATGGTTAATAAATGGTAA
1 AAATAAGCTTACGAGCTTATGG--AATAAATGGTAA
280852 AATATTAGAT
Statistics
Matches: 114, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
44 65 0.57
45 38 0.33
47 11 0.10
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:280750 original size:24 final size:23
Alignment explanation
Indices: 280722--280838 Score: 63
Period size: 24 Copynumber: 5.2 Consensus size: 23
280712 ACAAGTATAT
280722 TGGTAAAATAAGCTTATGAGCTTA
1 TGGTAAAATAAGCTTA-GAGCTTA
*
280746 TGGTATAAAT--G-GTA-AG-TATA
1 TGGTA-AAATAAGCTTAGAGCT-TA
280766 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTA-GAGCTTA
* * * *
280790 TGGGATAAAT--G-GTA-AGTATTT
1 TGGTA-AAATAAGCTTAGAG-CTTA
280811 TGGTAAAATAAGCTTACGAGCTTA
1 TGGTAAAATAAGCTTA-GAGCTTA
280835 TGGT
1 TGGT
280839 TAATAAATGG
Statistics
Matches: 68, Mismatches: 10, Indels: 30
0.63 0.09 0.28
Matches are distributed among these distances:
19 5 0.07
20 15 0.22
21 7 0.10
22 7 0.10
23 4 0.06
24 19 0.28
25 11 0.16
ACGTcount: A:0.36, C:0.07, G:0.24, T:0.33
Consensus pattern (23 bp):
TGGTAAAATAAGCTTAGAGCTTA
Found at i:280824 original size:89 final size:90
Alignment explanation
Indices: 280660--280851 Score: 270
Period size: 89 Copynumber: 2.2 Consensus size: 90
280650 TATGGTTTAT
* *
280660 TGGTTAATAAATGGTAAG--TAT-G-CAAATAAGCTTATGAGCTTATGGAATAATGACAAGTATA
1 TGGTTAATAAATGGTAAGTATATGGTAAAATAAGCTTACGAGCTTATGGAATAATGACAAGTATA
*
280721 TTGGTAAAATAAGCTTATGAGCTTA
66 TTGGTAAAATAAGCTTACGAGCTTA
* **
280746 TGG-T-ATAAATGGTAAGTATATGGTAAAATAAGCTTACGAGCTTATGGGATAAATGGTAAGTAT
1 TGGTTAATAAATGGTAAGTATATGGTAAAATAAGCTTACGAGCTTATGGAAT-AATGACAAGTAT
*
280809 TTTGGTAAAATAAGCTTACGAGCTTA
65 ATTGGTAAAATAAGCTTACGAGCTTA
280835 TGGTTAATAAATGGTAA
1 TGGTTAATAAATGGTAA
280852 AATATTAGAT
Statistics
Matches: 92, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
84 12 0.13
85 1 0.01
86 6 0.07
87 1 0.01
88 23 0.25
89 37 0.40
90 1 0.01
91 11 0.12
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (90 bp):
TGGTTAATAAATGGTAAGTATATGGTAAAATAAGCTTACGAGCTTATGGAATAATGACAAGTATA
TTGGTAAAATAAGCTTACGAGCTTA
Found at i:290979 original size:19 final size:19
Alignment explanation
Indices: 290943--290981 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
290933 GAACCGGTCT
*
290943 GACCCAACCCGACTCGACC
1 GACCCAACCCGACCCGACC
* *
290962 GACCCGACCTGACCCGACC
1 GACCCAACCCGACCCGACC
290981 G
1 G
290982 CTGACCCGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.51, G:0.21, T:0.05
Consensus pattern (19 bp):
GACCCAACCCGACCCGACC
Found at i:290996 original size:17 final size:17
Alignment explanation
Indices: 290949--291004 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
290939 GTCTGACCCA
*
290949 ACCCGACTCGACCGACCCG
1 ACCCGACTCGACCG--CTG
* *
290968 ACCTGACCCGACCGCTG
1 ACCCGACTCGACCGCTG
*
290985 ACCCGACTCGACCGTTG
1 ACCCGACTCGACCGCTG
291002 ACC
1 ACC
291005 GTTGACAGTG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
17 19 0.61
19 12 0.39
ACGTcount: A:0.20, C:0.48, G:0.21, T:0.11
Consensus pattern (17 bp):
ACCCGACTCGACCGCTG
Found at i:298180 original size:5 final size:5
Alignment explanation
Indices: 298170--298220 Score: 84
Period size: 5 Copynumber: 9.8 Consensus size: 5
298160 GAACCAGTCT
298170 GACCC GACCC GACCC GACCC GACCC GACCGC TGACCC GACCC GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACC-C -GACCC GACCC GACCC GACC
298221 GTTGACCGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 38 0.86
6 2 0.05
7 4 0.09
ACGTcount: A:0.20, C:0.57, G:0.22, T:0.02
Consensus pattern (5 bp):
GACCC
Found at i:298208 original size:22 final size:22
Alignment explanation
Indices: 298170--298227 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
298160 GAACCAGTCT
298170 GACCCGACC-C-GACCCGACCC
1 GACCCGACCGCTGACCCGACCC
298190 GACCCGACCGCTGACCCGACCC
1 GACCCGACCGCTGACCCGACCC
*
298212 GACCCGACCGTTGACC
1 GACCCGACCGCTGACC
298228 GTTGACTTTC
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 9 0.26
21 1 0.03
22 25 0.71
ACGTcount: A:0.19, C:0.53, G:0.22, T:0.05
Consensus pattern (22 bp):
GACCCGACCGCTGACCCGACCC
Found at i:302384 original size:24 final size:21
Alignment explanation
Indices: 302349--302391 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
302339 GGCACATTCT
*
302349 TTTGAATTTCAAGAGGTACATCA
1 TTTGAATGTCAA-AGG-ACATCA
302372 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
302392 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCA
Found at i:305036 original size:9 final size:9
Alignment explanation
Indices: 304999--305075 Score: 83
Period size: 9 Copynumber: 8.8 Consensus size: 9
304989 TTGGATTGCA
304999 AAAAGAAAAG
1 AAAA-AAAAG
305009 AAAAGACAAA-
1 AAAA-A-AAAG
*
305019 AAGAAAAAG
1 AAAAAAAAG
305028 AAAAAAAAG
1 AAAAAAAAG
305037 AAAAAAAAG
1 AAAAAAAAG
305046 ---AAAAAG
1 AAAAAAAAG
305052 AAAAAAAAG
1 AAAAAAAAG
305061 -AAAAAAAG
1 AAAAAAAAG
305069 AAAAAAA
1 AAAAAAA
305076 GCAAAAGAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
6 6 0.10
8 11 0.19
9 30 0.51
10 9 0.15
11 3 0.05
ACGTcount: A:0.86, C:0.01, G:0.13, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:305045 original size:32 final size:32
Alignment explanation
Indices: 304998--305085 Score: 117
Period size: 33 Copynumber: 2.8 Consensus size: 32
304988 ATTGGATTGC
* *
304998 AAAAAGAAAAGAAAAGACAAA-AAGAAAAAGAAA
1 AAAAAGAAAA-AAAAGAAAAAGAAAAAAAAG-AA
305031 AAAAAGAAAAAAAAGAAAAAGAAAAAAAAGAA
1 AAAAAGAAAAAAAAGAAAAAGAAAAAAAAGAA
*
305063 AAAAAG-AAAAAAAGCAAAAGAAA
1 AAAAAGAAAAAAAAGAAAAAGAAA
305086 TTAAAAAAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
31 16 0.31
32 17 0.33
33 18 0.35
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (32 bp):
AAAAAGAAAAAAAAGAAAAAGAAAAAAAAGAA
Found at i:305073 original size:18 final size:18
Alignment explanation
Indices: 304998--305095 Score: 83
Period size: 18 Copynumber: 5.4 Consensus size: 18
304988 ATTGGATTGC
* *
304998 AAAAAGAAAAGAAAAGAC
1 AAAAAGAAAAAAAAAGAA
305016 AAAAAGAAAAAGAAAA-AA
1 AAAAAGAAAAA-AAAAGAA
*
305034 AAGAAAAAAAAGAAAAAGAA
1 AA-AAAGAAAA-AAAAAGAA
*
305054 AAAAA-AGAAAAAAAGAA
1 AAAAAGAAAAAAAAAGAA
* * **
305071 AAAAAGCAAAAGAAATTA
1 AAAAAGAAAAAAAAAGAA
305089 AAAAAGA
1 AAAAAGA
305096 GAAAGCAAGA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
17 13 0.20
18 29 0.45
19 18 0.28
20 5 0.08
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAGAA
Found at i:305081 original size:9 final size:8
Alignment explanation
Indices: 304998--305095 Score: 92
Period size: 8 Copynumber: 11.9 Consensus size: 8
304988 ATTGGATTGC
304998 AAAAAGAAA
1 AAAAAG-AA
*
305007 AGAAAAGAC
1 A-AAAAGAA
305016 AAAAAGAA
1 AAAAAGAA
*
305024 AAAGA-AA
1 AAAAAGAA
305031 AAAAAGAA
1 AAAAAGAA
*
305039 AAAAA-AG
1 AAAAAGAA
305046 AAAAAGAAA
1 AAAAAG-AA
305055 AAAAAGAA
1 AAAAAGAA
305063 AAAAAGAA
1 AAAAAGAA
305071 AAAAAGCAA
1 AAAAAG-AA
**
305080 AAGAAATTA
1 AA-AAAGAA
305089 AAAAAGA
1 AAAAAGA
305096 GAAAGCAAGA
Statistics
Matches: 73, Mismatches: 10, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
7 12 0.16
8 36 0.49
9 17 0.23
10 8 0.11
ACGTcount: A:0.83, C:0.02, G:0.13, T:0.02
Consensus pattern (8 bp):
AAAAAGAA
Found at i:305091 original size:24 final size:23
Alignment explanation
Indices: 304998--305073 Score: 125
Period size: 24 Copynumber: 3.2 Consensus size: 23
304988 ATTGGATTGC
*
304998 AAAAAGAAAAGAAAAGACAAAAAG
1 AAAAAGAAAA-AAAAGAAAAAAAG
305022 AAAAAGAAAAAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG-AAAAAAAG
305046 AAAAAGAAAAAAAAGAAAAAAAG
1 AAAAAGAAAAAAAAGAAAAAAAG
305069 AAAAA
1 AAAAA
305074 AAGCAAAAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 3
0.93 0.02 0.06
Matches are distributed among these distances:
23 18 0.36
24 32 0.64
ACGTcount: A:0.86, C:0.01, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAAAAAAGAAAAAAAG
Found at i:305093 original size:1 final size:1
Alignment explanation
Indices: 305016--305075 Score: 57
Period size: 1 Copynumber: 60.0 Consensus size: 1
305006 AAGAAAAGAC
* * * * * * *
305016 AAAAAGAAAAAGAAAAAAAAGAAAAAAAAGAAAAAGAAAAAAAAGAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
305076 GCAAAAGAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:310443 original size:8 final size:8
Alignment explanation
Indices: 310430--310472 Score: 61
Period size: 8 Copynumber: 5.4 Consensus size: 8
310420 ATTGGAGTAC
310430 AAAAAGAA
1 AAAAAGAA
310438 AAAAAGACA
1 AAAAAGA-A
310447 AAAAA-AA
1 AAAAAGAA
*
310454 GAAAAGAA
1 AAAAAGAA
310462 AAAAAGAA
1 AAAAAGAA
310470 AAA
1 AAA
310473 GAAATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 5 0.16
8 20 0.65
9 6 0.19
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:310452 original size:13 final size:12
Alignment explanation
Indices: 310431--310472 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
310421 TTGGAGTACA
310431 AAAAGAAAAAAAG
1 AAAA-AAAAAAAG
*
310444 -ACAAAAAAAAG
1 AAAAAAAAAAAG
310455 AAAAGAAAAAAAG
1 AAAA-AAAAAAAG
310468 AAAAA
1 AAAAA
310473 GAAATTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 8 0.32
12 5 0.20
13 12 0.48
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:310452 original size:19 final size:19
Alignment explanation
Indices: 310430--310476 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
310420 ATTGGAGTAC
310430 AAAAAGAAAA-AAAGACAAA-
1 AAAAAGAAAAGAAA-A-AAAG
310449 AAAAAGAAAAGAAAAAAAG
1 AAAAAGAAAAGAAAAAAAG
310468 AAAAAGAAA
1 AAAAAGAAA
310477 TTTAAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.12
19 20 0.77
20 3 0.12
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAAAAG
Found at i:321168 original size:26 final size:26
Alignment explanation
Indices: 321134--321208 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
321124 TATCCCTTCT
321134 TTATTTCATTTCATTTCTTATCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
*
321160 TTATTTCATTT-A-TTCTT-CCTTTA
1 TTATTTCATTTCATTTCTTATCTTTA
* *
321183 TTA-ATCATCTTCCTTTTCTTATCTTT
1 TTATTTCAT-TT-CATTTCTTATCTTT
321209 GTTGCAGACA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
22 4 0.10
23 10 0.25
24 5 0.12
25 1 0.03
26 16 0.40
27 4 0.10
ACGTcount: A:0.17, C:0.19, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTTCATTTCATTTCTTATCTTTA
Found at i:321635 original size:23 final size:23
Alignment explanation
Indices: 321616--321669 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
321606 TTTTGCTTTT
321616 TTTTCTTCTTTTTGAATGCTTTAA
1 TTTTCTTC-TTTTGAATGCTTTAA
* * *
321640 ATTTCTTCTTTTGAGTGCTTTGA
1 TTTTCTTCTTTTGAATGCTTTAA
321663 TTTTCTT
1 TTTTCTT
321670 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.13, C:0.13, G:0.11, T:0.63
Consensus pattern (23 bp):
TTTTCTTCTTTTGAATGCTTTAA
Found at i:323187 original size:19 final size:19
Alignment explanation
Indices: 323145--323199 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
323135 CTATTCGACC
* * *
323145 AAAAGTATGTATCTTCATT
1 AAAATTATGTATTTTCATA
*
323164 TAAATTATGTATTTTCATA
1 AAAATTATGTATTTTCATA
*
323183 AAAATCATGTATTTTCA
1 AAAATTATGTATTTTCA
323200 AAGGGGTTCC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (19 bp):
AAAATTATGTATTTTCATA
Found at i:334454 original size:12 final size:11
Alignment explanation
Indices: 334433--334462 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
334423 AAATTTTGGC
334433 TTTTTTTGCTT
1 TTTTTTTGCTT
334444 TTTTCTTTGCTT
1 TTTT-TTTGCTT
334456 TTTTTTT
1 TTTTTTT
334463 TTGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:338192 original size:10 final size:10
Alignment explanation
Indices: 338179--338212 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
338169 GGAGTTCAAA
*
338179 AAAAAAAAAG
1 AAAAAAGAAG
338189 -AAAAAGAAG
1 AAAAAAGAAG
338198 AAAAAAGAAG
1 AAAAAAGAAG
338208 AAAAA
1 AAAAA
338213 TAATTTCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:345912 original size:17 final size:17
Alignment explanation
Indices: 345890--345922 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
345880 GAGTTAAAAC
345890 ATTATT-TTTTAGTTATT
1 ATTATTATTTTA-TTATT
345907 ATTATTATTTTATTAT
1 ATTATTATTTTATTAT
345923 GAATTAGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTATTATTTTATTATT
Found at i:362335 original size:19 final size:20
Alignment explanation
Indices: 362311--362355 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
362301 CGGCCAAGAG
*
362311 CATGTAGCTTCAT-TAAAAT
1 CATGTAGCTTCATCAAAAAT
**
362330 CATGTATTTTCATCAAAAAT
1 CATGTAGCTTCATCAAAAAT
362350 CATGTA
1 CATGTA
362356 TTTTCAAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 11 0.50
20 11 0.50
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (20 bp):
CATGTAGCTTCATCAAAAAT
Done.