Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008094.1 Hibiscus syriacus cultivar Beakdansim tig00110610_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: 9952466
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 41 of 43
Found at i:9013624 original size:15 final size:15
Alignment explanation
Indices: 9013604--9013650 Score: 94
Period size: 15 Copynumber: 3.1 Consensus size: 15
9013594 TTGATAACAT
9013604 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
9013619 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
9013634 TTCTTTCCATTTCAA
1 TTCTTTCCATTTCAA
9013649 TT
1 TT
9013651 TCCTTTCTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.55
Consensus pattern (15 bp):
TTCTTTCCATTTCAA
Found at i:9014570 original size:6 final size:6
Alignment explanation
Indices: 9014551--9014583 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
9014541 ATTAAATTAA
*
9014551 GAAAT- GAAAAG GAAATG GAAATG GAAATG GAAA
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAA
9014584 GAATTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
5 4 0.16
6 21 0.84
ACGTcount: A:0.58, C:0.00, G:0.30, T:0.12
Consensus pattern (6 bp):
GAAATG
Found at i:9014810 original size:35 final size:36
Alignment explanation
Indices: 9014761--9014847 Score: 140
Period size: 36 Copynumber: 2.4 Consensus size: 36
9014751 TAGGCATGAA
* * *
9014761 ATGGTGATGATATAGGCGTG-CAATGGTTATGGAAG
1 ATGGTGATGTTATAGGCGTGAAAATGGTGATGGAAG
9014796 ATGGTGATGTTATAGGCGTGAAAATGGTGATGGAAG
1 ATGGTGATGTTATAGGCGTGAAAATGGTGATGGAAG
9014832 ATGGTGATGTTATAGG
1 ATGGTGATGTTATAGG
9014848 TAGTATCTTA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
35 19 0.40
36 29 0.60
ACGTcount: A:0.29, C:0.03, G:0.38, T:0.30
Consensus pattern (36 bp):
ATGGTGATGTTATAGGCGTGAAAATGGTGATGGAAG
Found at i:9015297 original size:2 final size:2
Alignment explanation
Indices: 9015290--9015318 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9015280 AGTTATTTTC
9015290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9015319 ATACCTATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9015298 original size:23 final size:23
Alignment explanation
Indices: 9015253--9015298 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
9015243 TTATACCTAT
*
9015253 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
9015276 AGATAGTTATTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
9015299 TATATATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:9016944 original size:13 final size:12
Alignment explanation
Indices: 9016926--9016994 Score: 68
Period size: 13 Copynumber: 5.5 Consensus size: 12
9016916 GTGCAAAAAG
9016926 AAAGAAAAGACAA
1 AAAGAAAAGA-AA
*
9016939 AAAGAAGAGAAA
1 AAAGAAAAGAAA
**
9016951 AAA-ATCAGAAA
1 AAAGAAAAGAAA
9016962 AGAAGAAAAGAAGA
1 A-AAGAAAAGAA-A
9016976 AAAGAAAAGAAA
1 AAAGAAAAGAAA
9016988 AAGAGAA
1 AA-AGAA
9016995 GTTCAAAAAG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
11 7 0.15
12 10 0.21
13 28 0.60
14 2 0.04
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.01
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:9016961 original size:29 final size:29
Alignment explanation
Indices: 9016928--9016983 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 29
9016918 GCAAAAAGAA
9016928 AGAAAAGACA-AAAAGAAGAGAAA-AAAATC
1 AGAAAAGA-AGAAAAGAAGA-AAAGAAAATC
9016957 AGAAAAGAAGAAAAGAAGAAAAGAAAA
1 AGAAAAGAAGAAAAGAAGAAAAGAAAA
9016984 GAAAAAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 4 0.16
29 21 0.84
ACGTcount: A:0.75, C:0.04, G:0.20, T:0.02
Consensus pattern (29 bp):
AGAAAAGAAGAAAAGAAGAAAAGAAAATC
Found at i:9016968 original size:8 final size:8
Alignment explanation
Indices: 9016957--9016981 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
9016947 GAAAAAAATC
9016957 AGAAAAGA
1 AGAAAAGA
9016965 AGAAAAGA
1 AGAAAAGA
9016973 AGAAAAGA
1 AGAAAAGA
9016981 A
1 A
9016982 AAGAAAAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:9016981 original size:21 final size:20
Alignment explanation
Indices: 9016921--9016986 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
9016911 TTGGAGTGCA
9016921 AAAAGAAAGAAAAGACAAAAAG
1 AAAAG-AAGAAAAGA-AAAAAG
**
9016943 --AAG-AGAAAA-AAATCAG
1 AAAAGAAGAAAAGAAAAAAG
9016959 AAAAGAAGAAAAGAAGAAAAG
1 AAAAGAAGAAAAGAA-AAAAG
9016980 AAAAGAA
1 AAAAGAA
9016987 AAAGAGAAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 11
0.70 0.08 0.22
Matches are distributed among these distances:
16 4 0.11
17 1 0.03
18 9 0.26
19 6 0.17
20 5 0.14
21 10 0.29
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAGAAGAAAAGAAAAAAG
Found at i:9016991 original size:16 final size:15
Alignment explanation
Indices: 9016920--9016991 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 15
9016910 ATTGGAGTGC
*
9016920 AAAAAGAAAGAAAAG
1 AAAAAAAAAGAAAAG
* *
9016935 --ACAAAAAGAAGAG
1 AAAAAAAAAGAAAAG
*
9016948 AAAAAAATCAGAAAAG
1 AAAAAAA-AAGAAAAG
*
9016964 AAGAAAAGAAGAAAAG
1 AA-AAAAAAAGAAAAG
9016980 AAAAGAAAAAGA
1 AAAA-AAAAAGA
9016992 GAAGTTCAAA
Statistics
Matches: 43, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
13 10 0.23
15 6 0.14
16 23 0.53
17 4 0.09
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:9019890 original size:23 final size:22
Alignment explanation
Indices: 9019855--9019899 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
9019845 TTATACCTAT
* *
9019855 AGATACTTATTTCTTATGTATA
1 AGATACTTATTTCATATATATA
*
9019877 AGATAGTTATTTTCATATATATA
1 AGATACTTA-TTTCATATATATA
9019900 TATAATACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (22 bp):
AGATACTTATTTCATATATATA
Found at i:9021517 original size:13 final size:12
Alignment explanation
Indices: 9021499--9021568 Score: 70
Period size: 13 Copynumber: 5.5 Consensus size: 12
9021489 GTGCAAAAAG
9021499 AAAGAAAAGACAA
1 AAAGAAAAGA-AA
*
9021512 AAAGAAGAGAAA
1 AAAGAAAAGAAA
*
9021524 AAA-AATCAGAAA
1 AAAGAA-AAGAAA
9021536 AGAAGAAAAGAAGA
1 A-AAGAAAAGAA-A
9021550 AAAGAAAAGAAA
1 AAAGAAAAGAAA
9021562 AAGAGAA
1 AA-AGAA
9021569 GTTCAAAAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
11 2 0.04
12 14 0.29
13 29 0.59
14 4 0.08
ACGTcount: A:0.76, C:0.03, G:0.20, T:0.01
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:9021523 original size:22 final size:23
Alignment explanation
Indices: 9021497--9021560 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 23
9021487 GAGTGCAAAA
9021497 AGAAAGAAAAGA-CA-AAAAGAAG
1 AGAAAGAAAA-ATCAGAAAAGAAG
9021519 AGAAA-AAAAATCAGAAAAGAAG
1 AGAAAGAAAAATCAGAAAAGAAG
9021541 A-AAAGAAGAAA--AGAAAAGAA
1 AGAAAGAA-AAATCAGAAAAGAA
9021561 AAAGAGAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
20 1 0.03
21 18 0.47
22 16 0.42
23 3 0.08
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.02
Consensus pattern (23 bp):
AGAAAGAAAAATCAGAAAAGAAG
Found at i:9021527 original size:30 final size:29
Alignment explanation
Indices: 9021493--9021569 Score: 79
Period size: 30 Copynumber: 2.6 Consensus size: 29
9021483 AATAGAGTGC
9021493 AAAAAGAAAGAAAAGACA-AAAAGAAGAGAA
1 AAAAAGAAAGAAAAGA-AGAAAAGAAGA-AA
*
9021523 AAAAA-ATCAGAAAAGAAGAAAAGAAGAAA
1 AAAAAGA-AAGAAAAGAAGAAAAGAAGAAA
*
9021552 AGAAAAGAAA-AAGAGAAG
1 A-AAAAGAAAGAAAAGAAG
9021570 TTCAAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
29 12 0.30
30 27 0.68
31 1 0.03
ACGTcount: A:0.75, C:0.03, G:0.21, T:0.01
Consensus pattern (29 bp):
AAAAAGAAAGAAAAGAAGAAAAGAAGAAA
Found at i:9021542 original size:8 final size:8
Alignment explanation
Indices: 9021494--9021555 Score: 58
Period size: 8 Copynumber: 7.9 Consensus size: 8
9021484 ATAGAGTGCA
9021494 AAAAGAAAG
1 AAAAG-AAG
9021503 AAAAGACA-
1 AAAAGA-AG
9021511 AAAAGAAG
1 AAAAGAAG
*
9021519 AGAA-AA-
1 AAAAGAAG
**
9021525 AAAATCAG
1 AAAAGAAG
9021533 AAAAGAAG
1 AAAAGAAG
9021541 AAAAGAAG
1 AAAAGAAG
9021549 AAAAGAA
1 AAAAGAA
9021556 AAGAAAAAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
6 3 0.07
7 4 0.09
8 31 0.70
9 6 0.14
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (8 bp):
AAAAGAAG
Found at i:9036988 original size:23 final size:23
Alignment explanation
Indices: 9036971--9037015 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
9036961 TTATACCTAT
9036971 AGATACTTA-TTTCATATATATA
1 AGATACTTATTTTCATATATATA
*
9036993 AGATAGTTATTTTCATATATATA
1 AGATACTTATTTTCATATATATA
9037016 TATAATACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (23 bp):
AGATACTTATTTTCATATATATA
Found at i:9038798 original size:20 final size:20
Alignment explanation
Indices: 9038773--9038814 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
9038763 AAGAGAAGAT
9038773 AACCTTATTGTTTTCTTGAG
1 AACCTTATTGTTTTCTTGAG
9038793 AACCTTATTGTTTTCTTGAG
1 AACCTTATTGTTTTCTTGAG
9038813 AA
1 AA
9038815 AGGTTGCAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.48
Consensus pattern (20 bp):
AACCTTATTGTTTTCTTGAG
Found at i:9041636 original size:23 final size:22
Alignment explanation
Indices: 9041601--9041645 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
9041591 TTATACCTAT
*
9041601 AGATATTTATTTCATATATATA
1 AGATAGTTATTTCATATATATA
9041623 AGATAGTTATTTTCATATATATA
1 AGATAGTTA-TTTCATATATATA
9041646 TATAATACCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (22 bp):
AGATAGTTATTTCATATATATA
Found at i:9046986 original size:35 final size:35
Alignment explanation
Indices: 9046908--9047012 Score: 138
Period size: 35 Copynumber: 3.0 Consensus size: 35
9046898 CTACCTAAAT
* *
9046908 ATCACCATCTTCCATCACTATTTTCACGCCTATAAC
1 ATCACCATCTTCCATCACCA-TTTCACGCCTATATC
* *
9046944 ATCACCATCTTCCATTACCATTGCACGCCTATATC
1 ATCACCATCTTCCATCACCATTTCACGCCTATATC
* * *
9046979 ATTACCATCTACTATCACCATTTCACGCCTATAT
1 ATCACCATCTTCCATCACCATTTCACGCCTATAT
9047013 AACCACCAAT
Statistics
Matches: 60, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 42 0.70
36 18 0.30
ACGTcount: A:0.28, C:0.35, G:0.04, T:0.33
Consensus pattern (35 bp):
ATCACCATCTTCCATCACCATTTCACGCCTATATC
Found at i:9048394 original size:36 final size:35
Alignment explanation
Indices: 9048284--9048393 Score: 150
Period size: 34 Copynumber: 3.1 Consensus size: 35
9048274 TTGGTTGTTG
* * * *
9048284 TATAGACGTGAAATGGGGATAGAAGATTGTGATGA
1 TATAGACGTGAAATGGTGATGGAAGATGGTGATGT
*
9048319 TATAGACGTGCAATGGT-ATGGAAGATGGTGATGT
1 TATAGACGTGAAATGGTGATGGAAGATGGTGATGT
*
9048353 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGACGTG-AAATGGTGATGGAAGATGGTGATGT
9048389 TATAG
1 TATAG
9048394 GTAGTATCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
34 23 0.35
35 21 0.32
36 22 0.33
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (35 bp):
TATAGACGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:9061476 original size:18 final size:18
Alignment explanation
Indices: 9061453--9061490 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
9061443 ATGGGTTGAT
9061453 ATATCAATGGACTTTGTG
1 ATATCAATGGACTTTGTG
9061471 ATATCAATGGACTTTGTG
1 ATATCAATGGACTTTGTG
9061489 AT
1 AT
9061491 GGGACTACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (18 bp):
ATATCAATGGACTTTGTG
Found at i:9063781 original size:20 final size:20
Alignment explanation
Indices: 9063756--9063796 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
9063746 TATCATTTCT
9063756 TTATTTCATTTTCATT-CTTA
1 TTATTTC-TTTTCATTACTTA
9063776 TTATTTCTTTTCATTACTTA
1 TTATTTCTTTTCATTACTTA
9063796 T
1 T
9063797 ATTATTATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTCTTTTCATTACTTA
Found at i:9063799 original size:19 final size:19
Alignment explanation
Indices: 9063752--9063799 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
9063742 TCTCTATCAT
9063752 TTCTT-TATTTCATTTTCA
1 TTCTTATATTTCATTTTCA
9063770 TTCTTATTATTTC-TTTTCA
1 TTCTTA-TATTTCATTTTCA
9063789 TTACTTATATT
1 TT-CTTATATT
9063800 ATTATTCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 5 0.19
19 12 0.44
20 10 0.37
ACGTcount: A:0.19, C:0.15, G:0.00, T:0.67
Consensus pattern (19 bp):
TTCTTATATTTCATTTTCA
Found at i:9069309 original size:25 final size:24
Alignment explanation
Indices: 9069281--9069328 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
9069271 CCACCAAAGC
*
9069281 TCTGATTACCGCTTGATGTAAGGCT
1 TCTGA-TACCACTTGATGTAAGGCT
*
9069306 TCTGATGCCACTTGATGTAAGGC
1 TCTGATACCACTTGATGTAAGGC
9069329 ACTTGTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (24 bp):
TCTGATACCACTTGATGTAAGGCT
Found at i:9072536 original size:13 final size:13
Alignment explanation
Indices: 9072518--9072575 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
9072508 ACTACCTAAA
9072518 CATCACCATCTTC
1 CATCACCATCTTC
*
9072531 CATCACCAT-TTT
1 CATCACCATCTTC
* **
9072543 CA-CACC-TATAA
1 CATCACCATCTTC
9072554 CATCACCATCTTC
1 CATCACCATCTTC
*
9072567 CATTACCAT
1 CATCACCAT
9072576 TGCACGCCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
10 1 0.03
11 7 0.20
12 8 0.23
13 19 0.54
ACGTcount: A:0.29, C:0.40, G:0.00, T:0.31
Consensus pattern (13 bp):
CATCACCATCTTC
Found at i:9072557 original size:36 final size:35
Alignment explanation
Indices: 9072511--9072622 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 35
9072501 ATAAGATACT
9072511 ACCTA-AACATCACCATCTTCCATCACCATTTTCAC
1 ACCTATAACATCACCATCTTCCATCACCA-TTTCAC
* *
9072546 ACCTATAACATCACCATCTTCCATTACCATTGCAC
1 ACCTATAACATCACCATCTTCCATCACCATTTCAC
* * * *
9072581 GCCTATATCATTACCATCTTCTATCACCATTTCAC
1 ACCTATAACATCACCATCTTCCATCACCATTTCAC
9072616 ACCTATA
1 ACCTATA
9072623 TAACCACCAA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 45 0.67
36 22 0.33
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.31
Consensus pattern (35 bp):
ACCTATAACATCACCATCTTCCATCACCATTTCAC
Found at i:9073405 original size:19 final size:20
Alignment explanation
Indices: 9073364--9073414 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
9073354 GAAACCCCTT
*
9073364 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
9073384 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
9073403 TGAAGATACATG
1 TGAAAATACATG
9073415 CTCTTGGCCG
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:9076450 original size:19 final size:20
Alignment explanation
Indices: 9076402--9076456 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
9076392 TAAGAAAAGG
9076402 ATAAGGAAATGAAATAAGCAA
1 ATAA-GAAATGAAATAAGCAA
* *
9076423 ATATG-AATGACATAAG-AA
1 ATAAGAAATGAAATAAGCAA
9076441 ATAAGAAATGAAATAA
1 ATAAGAAATGAAATAA
9076457 TAAGAAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.21
19 19 0.66
20 1 0.03
21 3 0.10
ACGTcount: A:0.62, C:0.04, G:0.16, T:0.18
Consensus pattern (20 bp):
ATAAGAAATGAAATAAGCAA
Found at i:9078286 original size:13 final size:12
Alignment explanation
Indices: 9078267--9078352 Score: 58
Period size: 11 Copynumber: 7.2 Consensus size: 12
9078257 ATATAGGCGT
9078267 GATATGGTGATG
1 GATATGGTGATG
9078279 GAATATGGTGAT-
1 G-ATATGGTGATG
*
9078291 GATATAGGCG-T-
1 GATAT-GGTGATG
9078302 GATAATGGTGATG
1 GAT-ATGGTGATG
9078315 GACTATGGTGAT-
1 GA-TATGGTGATG
*
9078327 GATATAGGCG-T-
1 GATAT-GGTGATG
9078338 GATAGTGGTGATG
1 GATA-TGGTGATG
9078351 GA
1 GA
9078353 CAGATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 22 0.37
12 15 0.25
13 22 0.37
14 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.38, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:9078322 original size:36 final size:36
Alignment explanation
Indices: 9078249--9078353 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
9078239 ATTTATAAGT
* *
9078249 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
9078284 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
*
9078320 TGGTGATGATATAGGCGTGATAGTGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
9078354 AGATTGTATC
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 20 0.30
36 46 0.70
ACGTcount: A:0.28, C:0.05, G:0.37, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:9082275 original size:17 final size:19
Alignment explanation
Indices: 9082253--9082296 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
9082243 GTAGGAGTCT
9082253 TTTTCTTTTCTCTT-TT-C
1 TTTTCTTTTCTCTTGTTGC
*
9082270 TTTTCTTCTCTCTTGTTGC
1 TTTTCTTTTCTCTTGTTGC
9082289 TTTT-TTTT
1 TTTTCTTTT
9082297 TTAGCACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 13 0.57
18 5 0.22
19 5 0.22
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.75
Consensus pattern (19 bp):
TTTTCTTTTCTCTTGTTGC
Found at i:9082701 original size:13 final size:12
Alignment explanation
Indices: 9082682--9082767 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
9082672 ATATAGGCGT
9082682 GATATGGTGATG
1 GATATGGTGATG
9082694 GAATATGGTGAT-
1 G-ATATGGTGATG
*
9082706 GATATAGGCG-T-
1 GATAT-GGTGATG
9082717 GATAATGGTGATG
1 GAT-ATGGTGATG
9082730 GACTATGGTGAT-
1 GA-TATGGTGATG
*
9082742 GATATAGGCG-T-
1 GATAT-GGTGATG
9082753 GATAATGGTGATG
1 GAT-ATGGTGATG
9082766 GA
1 GA
9082768 CATATTGTAT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 21 0.35
12 16 0.27
13 22 0.37
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.37, T:0.30
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:9082737 original size:36 final size:36
Alignment explanation
Indices: 9082664--9082768 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
9082654 ATTTATAAGT
* *
9082664 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
9082699 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
9082735 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TGGTGATGATATAGGCGTGATAATGGTGATGGAC
9082769 ATATTGTATC
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 20 0.30
36 47 0.70
ACGTcount: A:0.29, C:0.05, G:0.36, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGCGTGATAATGGTGATGGACTA
Found at i:9089072 original size:19 final size:20
Alignment explanation
Indices: 9089039--9089086 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
9089029 ACCGCTTTGG
*
9089039 AAATACATGATTTTTGATGA
1 AAATACATGATTTTTAATGA
*
9089059 AAATACATTA-TTTTAATGA
1 AAATACATGATTTTTAATGA
*
9089078 AGATACATG
1 AAATACATG
9089087 CTCCTTGGCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (20 bp):
AAATACATGATTTTTAATGA
Found at i:9094594 original size:13 final size:11
Alignment explanation
Indices: 9094553--9094637 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
9094543 ACAATCTGTC
9094553 CATCACCATTAT
1 CATCACCA-TAT
*
9094565 CA-CGCCTATAT
1 CATCACC-ATAT
9094576 CATCACCATAGT
1 CATCACCATA-T
9094588 CCATCACCATTAT
1 -CATCACCA-TAT
*
9094601 CA-CGCCTATAT
1 CATCACC-ATAT
9094612 CATCACCATATT
1 CATCACCATA-T
9094624 CCATCACCATAT
1 -CATCACCATAT
9094636 CA
1 CA
9094638 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:9094597 original size:36 final size:36
Alignment explanation
Indices: 9094550--9094654 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
9094540 GATACAATCT
9094550 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
9094586 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
9094622 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
9094655 ATTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:9104231 original size:11 final size:13
Alignment explanation
Indices: 9104199--9104228 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9104189 TGGCCAAAGA
9104199 TGAAAAGGTATGT
1 TGAAAAGGTATGT
9104212 TGAAAAGGTATG-
1 TGAAAAGGTATGT
9104224 TGAAA
1 TGAAA
9104229 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:9109757 original size:36 final size:36
Alignment explanation
Indices: 9109707--9109811 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
9109697 GATACAATCT
9109707 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
9109743 GTCCATCACAATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
9109779 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
9109812 ACTTATAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:9125789 original size:35 final size:37
Alignment explanation
Indices: 9125743--9125823 Score: 130
Period size: 35 Copynumber: 2.2 Consensus size: 37
9125733 TTTGAGAATT
*
9125743 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
9125778 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
9125815 TGGTGATGA
1 TGGTGATGA
9125824 AAATAGTATC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.50
36 4 0.10
37 17 0.40
ACGTcount: A:0.28, C:0.04, G:0.37, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:9126707 original size:19 final size:20
Alignment explanation
Indices: 9126683--9126725 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
9126673 AGCATTTATC
*
9126683 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
9126702 TTCATTAAAAATCATGTATT
1 TTCATTAAAAATCATGTATT
9126722 TTCA
1 TTCA
9126726 AAGGGGTTTC
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:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:9127260 original size:15 final size:14
Alignment explanation
Indices: 9127240--9127287 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 14
9127230 TACTTTGATA
9127240 TCATTTCTTTCCATT
1 TCATTTCTTT-CATT
*
9127255 TCATTTCTTATTAATT
1 TCATTTC-T-TTCATT
9127271 TCCATTTCTTTCATT
1 T-CATTTCTTTCATT
9127286 TC
1 TC
9127288 TTATTTCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
14 1 0.04
15 13 0.46
16 6 0.21
17 8 0.29
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (14 bp):
TCATTTCTTTCATT
Found at i:9127301 original size:33 final size:32
Alignment explanation
Indices: 9127241--9127302 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
9127231 ACTTTGATAT
**
9127241 CATTTCTTTCCATTTCATTTCTTATTAATTTC
1 CATTTCTTTCCATTTCATTTCCAATTAATTTC
9127273 CATTTCTTT-CATTTCTTATTTCCAATTAAT
1 CATTTCTTTCCATTTC--ATTTCCAATTAAT
9127303 CATTTTCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 6 0.23
32 9 0.35
33 11 0.42
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (32 bp):
CATTTCTTTCCATTTCATTTCCAATTAATTTC
Found at i:9132214 original size:81 final size:81
Alignment explanation
Indices: 9132079--9132304 Score: 353
Period size: 81 Copynumber: 2.8 Consensus size: 81
9132069 TTCTTAAAAT
* * * *
9132079 AAAAGATTAATTGCCTAGATGTGCATTTGGTAGAAAGGTGCCAATATTGCAAGTTAGATAAAAGA
1 AAAAGATTAATTGCATAGTTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGA
*
9132144 CTAAATTCCTTTGAGA
66 CTAAATGCCTTTGAGA
* * * *
9132160 AAAAGATTAATTGCGTAGTTGTGCATTTGCCAGAAATGTGCCAATATTGCAAGTTAAATGAAAGA
1 AAAAGATTAATTGCATAGTTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGA
*
9132225 CTAAATGCCTTTGAGT
66 CTAAATGCCTTTGAGA
*
9132241 ATAAGATTAATTGCATAGTTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
1 AAAAGATTAATTGCATAGTTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAG
9132305 CAACAATAAG
Statistics
Matches: 131, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 131 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (81 bp):
AAAAGATTAATTGCATAGTTGTGCATTTGGCAGAAAGGTGCCAATATTGCAAGTTAGATGAAAGA
CTAAATGCCTTTGAGA
Found at i:9136212 original size:59 final size:59
Alignment explanation
Indices: 9136092--9136205 Score: 165
Period size: 59 Copynumber: 1.9 Consensus size: 59
9136082 AATAGATGGA
* ** *
9136092 TAAGTGTCCTATCAAACCCTCCTAGTCTTAATGAAAAAGAAAACTCGATAATATGGATC
1 TAAGTGTCCTATCAAACCCTCCTAATCGCAATGAAAAAGAAAACTCCATAATATGGATC
* * *
9136151 TAAGTGTCCTATCGAACCCTCCTAATCGCAATGAAAAGGCAAACTCCATAATATG
1 TAAGTGTCCTATCAAACCCTCCTAATCGCAATGAAAAAGAAAACTCCATAATATG
9136206 ACTCTAACCA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (59 bp):
TAAGTGTCCTATCAAACCCTCCTAATCGCAATGAAAAAGAAAACTCCATAATATGGATC
Found at i:9142328 original size:3 final size:3
Alignment explanation
Indices: 9142320--9142346 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9142310 TTTGGTATTT
9142320 TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG
9142347 CACGTTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:9145979 original size:90 final size:91
Alignment explanation
Indices: 9145825--9146006 Score: 260
Period size: 90 Copynumber: 2.0 Consensus size: 91
9145815 CCTAGAACAC
*
9145825 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
* *
9145890 AAG-AGTTCTCTCTCTATTCGGCCAAG
66 AAGAACTT-TCTCCCTATTCGGCCAAG
** * * * *
9145916 CCATGTGTTTTGCATGTGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
9145980 AAGAACTTTCTCCCTATTCGGCCAAG
66 AAGAACTTTCTCCCTATTCGGCCAAG
9146006 C
1 C
9146007 ATCATTTCCC
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
90 59 0.73
91 22 0.27
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
AAGAACTTTCTCCCTATTCGGCCAAG
Found at i:9158771 original size:11 final size:11
Alignment explanation
Indices: 9158757--9158785 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
9158747 TTCAAAAAAA
9158757 CAAAAAAAAGC
1 CAAAAAAAAGC
9158768 CAAAAAAAAGC
1 CAAAAAAAAGC
9158779 CAAAAAA
1 CAAAAAA
9158786 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.76, C:0.17, G:0.07, T:0.00
Consensus pattern (11 bp):
CAAAAAAAAGC
Found at i:9158775 original size:20 final size:20
Alignment explanation
Indices: 9158750--9158792 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
9158740 ATTTTTTTTC
9158750 AAAAAAA-CAAAAAAAAGCCA
1 AAAAAAAGC-AAAAAAAGCCA
*
9158770 AAAAAAAGCCAAAAAAGCCA
1 AAAAAAAGCAAAAAAAGCCA
9158790 AAA
1 AAA
9158793 TTTCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.77, C:0.16, G:0.07, T:0.00
Consensus pattern (20 bp):
AAAAAAAGCAAAAAAAGCCA
Found at i:9166142 original size:11 final size:11
Alignment explanation
Indices: 9166074--9166157 Score: 64
Period size: 11 Copynumber: 7.2 Consensus size: 11
9166064 ATAAGATGTC
9166074 CATCACCATTAT
1 CATCACCA-TAT
*
9166086 CA-CGCCTATAT
1 CATCACC-ATAT
9166097 CATCACCATAGT
1 CATCACCATA-T
*
9166109 AATCACCATTAT
1 CATCACCA-TAT
*
9166121 CA-CGCCTATAT
1 CATCACC-ATAT
9166132 CATCACCATATT
1 CATCACCATA-T
9166144 CCATCACCATAT
1 -CATCACCATAT
9166156 CA
1 CA
9166158 CGCCTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
11 24 0.41
12 22 0.38
13 12 0.21
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:9166174 original size:35 final size:36
Alignment explanation
Indices: 9166071--9166166 Score: 160
Period size: 35 Copynumber: 2.7 Consensus size: 36
9166061 TTTATAAGAT
9166071 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
9166107 GT-AATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
9166142 TTCCATCACCA-TATCACGCCTATAT
1 GTCCATCACCATTATCACGCCTATAT
9166167 TAACACCAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
35 47 0.84
36 9 0.16
ACGTcount: A:0.31, C:0.34, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:9166641 original size:14 final size:15
Alignment explanation
Indices: 9166607--9166653 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
9166597 AATTTTGAGT
9166607 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
9166622 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
9166636 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
9166653 G
1 G
9166654 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:9175716 original size:11 final size:11
Alignment explanation
Indices: 9175702--9175757 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
9175692 TCTTTTTGAA
9175702 TTCTTTTTCTT
1 TTCTTTTTCTT
9175713 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
9175726 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
9175739 TGTCTTTTTCTT
1 T-TCTTTTTCTT
9175751 TT-TTTTT
1 TTCTTTTT
9175758 TTGCACTCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 5 0.13
11 4 0.11
12 10 0.26
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.80
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:9175726 original size:19 final size:18
Alignment explanation
Indices: 9175702--9175758 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 18
9175692 TCTTTTTGAA
9175702 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
9175720 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
9175739 TGTCTTTTTCTTTT-TTTT
1 T-TCTTTTTCTTTTCTTTT
9175757 TT
1 TT
9175759 TGCACTCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
17 1 0.03
18 13 0.37
19 14 0.40
20 7 0.20
ACGTcount: A:0.00, C:0.18, G:0.02, T:0.81
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Found at i:9179040 original size:11 final size:11
Alignment explanation
Indices: 9178972--9179055 Score: 64
Period size: 11 Copynumber: 7.2 Consensus size: 11
9178962 ACAATCTGTC
9178972 CATCACCATTAT
1 CATCACCA-TAT
*
9178984 CA-CGCCTATAT
1 CATCACC-ATAT
9178995 CATCACCATAGT
1 CATCACCATA-T
*
9179007 AATCACCATTAT
1 CATCACCA-TAT
*
9179019 CA-CGCCTATAT
1 CATCACC-ATAT
9179030 CATCACCATATT
1 CATCACCATA-T
9179042 CCATCACCATAT
1 -CATCACCATAT
9179054 CA
1 CA
9179056 CGCCTATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
11 24 0.41
12 22 0.38
13 12 0.21
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:9179072 original size:35 final size:36
Alignment explanation
Indices: 9178969--9179064 Score: 160
Period size: 35 Copynumber: 2.7 Consensus size: 36
9178959 GATACAATCT
9178969 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
9179005 GT-AATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
9179040 TTCCATCACCA-TATCACGCCTATAT
1 GTCCATCACCATTATCACGCCTATAT
9179065 TAACACCAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
35 47 0.84
36 9 0.16
ACGTcount: A:0.31, C:0.34, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:9186679 original size:25 final size:26
Alignment explanation
Indices: 9186621--9186679 Score: 68
Period size: 24 Copynumber: 2.3 Consensus size: 26
9186611 CCTTTCTTTG
* * *
9186621 CTTTTTCTTCTTTTTTGAGTTCTTGA
1 CTTTTTCTTCTTTTTGGAGTGCTTAA
*
9186647 C-TTCTCTTC-TTTTGGAGTGCTTAA
1 CTTTTTCTTCTTTTTGGAGTGCTTAA
9186671 CTTTTTCTT
1 CTTTTTCTT
9186680 TGCTGATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
24 13 0.48
25 13 0.48
26 1 0.04
ACGTcount: A:0.08, C:0.19, G:0.12, T:0.61
Consensus pattern (26 bp):
CTTTTTCTTCTTTTTGGAGTGCTTAA
Found at i:9186716 original size:18 final size:18
Alignment explanation
Indices: 9186672--9186710 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
9186662 AGTGCTTAAC
9186672 TTTTTC-TTTGCTGATTT
1 TTTTTCATTTGCTGATTT
9186689 TTTTTCATTTG-TGATTCT
1 TTTTTCATTTGCTGATT-T
9186707 TTTT
1 TTTT
9186711 GTATTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.08, C:0.10, G:0.10, T:0.72
Consensus pattern (18 bp):
TTTTTCATTTGCTGATTT
Found at i:9187817 original size:30 final size:30
Alignment explanation
Indices: 9187782--9187861 Score: 99
Period size: 30 Copynumber: 2.7 Consensus size: 30
9187772 TCCAAAACTT
9187782 TCCTCCAGCTAAGTT-ATGCTACATGCTAGC
1 TCCTCCAGCTAAGTTCA-GCTACATGCTAGC
** *
9187812 TCCTCCAGAAAAGTTCAGCTACATGGTAGC
1 TCCTCCAGCTAAGTTCAGCTACATGCTAGC
* *
9187842 TCATCCAGCTAAGTTGAGCT
1 TCCTCCAGCTAAGTTCAGCT
9187862 TTCCTTAGTG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
30 41 0.98
31 1 0.02
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.28
Consensus pattern (30 bp):
TCCTCCAGCTAAGTTCAGCTACATGCTAGC
Found at i:9192307 original size:90 final size:91
Alignment explanation
Indices: 9192154--9192335 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 91
9192144 GGGAAATGAT
* **
9192154 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGTGCCTAAATAAACCACATGCAAGGCACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATG
*
9192218 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * * *
9192244 GCTTGGCCGAATAGGGAGAGAACTCTTTATCTTGGCACCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATG
* **
9192309 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
9192335 G
1 G
9192336 GTGTTCTAGG
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 57 0.71
91 23 0.29
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCACCTAAATAAACCACATGCAAGGCACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:9201383 original size:2 final size:2
Alignment explanation
Indices: 9201372--9201401 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9201362 TAACTATAGG
9201372 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9201402 GAAAATAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9204368 original size:20 final size:17
Alignment explanation
Indices: 9204300--9204381 Score: 62
Period size: 17 Copynumber: 4.8 Consensus size: 17
9204290 CCTTGGCTTG
*
9204300 CTTTCTTTTTGAATTTAT
1 CTTTCTTTTTGTATTT-T
* *
9204318 TTTTCTTTTCT-TCTTTT
1 CTTTCTTTT-TGTATTTT
* *
9204335 CTTT-TTCTTCT-TTTT
1 CTTTCTTTTTGTATTTT
9204350 CTTCTTCTTTTTGTATTTT
1 C-T-TTCTTTTTGTATTTT
9204369 CTTTCTTTTTGTA
1 CTTTCTTTTTGTA
9204382 CTCCAATTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
15 6 0.12
16 5 0.10
17 17 0.33
18 17 0.33
19 6 0.12
ACGTcount: A:0.06, C:0.16, G:0.04, T:0.74
Consensus pattern (17 bp):
CTTTCTTTTTGTATTTT
Found at i:9204368 original size:29 final size:28
Alignment explanation
Indices: 9204317--9204378 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 28
9204307 TTTGAATTTA
*
9204317 TTTTTCTTTTCTTCTTTTCTTTT-TCTTC
1 TTTTTCTTTTCTTCTTTTATTTTCT-TTC
9204345 TTTTTCTTCTTCTT-TTTGTATTTTCTTTC
1 TTTTTCTT-TTCTTCTTT-TATTTTCTTTC
9204374 TTTTT
1 TTTTT
9204379 GTACTCCAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 11 0.37
29 18 0.60
30 1 0.03
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (28 bp):
TTTTTCTTTTCTTCTTTTATTTTCTTTC
Found at i:9204373 original size:23 final size:21
Alignment explanation
Indices: 9204317--9204377 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
9204307 TTTGAATTTA
9204317 TTTTTC-TTTTC-TTCTTTTC
1 TTTTTCTTTTTCTTTCTTTTC
*
9204336 TTTTTCTTCTT-TTTCTTCTTC
1 TTTTTCTTTTTCTTTCTT-TTC
*
9204357 TTTTTGTATTTTCTTTCTTTT
1 TTTTTCT-TTTTCTTTCTTTT
9204378 TGTACTCCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
19 6 0.18
20 8 0.24
21 9 0.26
22 5 0.15
23 6 0.18
ACGTcount: A:0.02, C:0.18, G:0.02, T:0.79
Consensus pattern (21 bp):
TTTTTCTTTTTCTTTCTTTTC
Found at i:9222166 original size:25 final size:25
Alignment explanation
Indices: 9222114--9222172 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
9222104 TTCTTTGTTT
* * *
9222114 TTTTC-TTCTTTTTGAGTGCTGGAT
1 TTTTCTTTCTTTTGGAGTGCTGCAA
*
9222138 TTTTCTTTCTTTTGGAGTGCTTCAA
1 TTTTCTTTCTTTTGGAGTGCTGCAA
*
9222163 TTTTTTTTCT
1 TTTTCTTTCT
9222173 GATTTTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 5 0.17
25 24 0.83
ACGTcount: A:0.08, C:0.14, G:0.15, T:0.63
Consensus pattern (25 bp):
TTTTCTTTCTTTTGGAGTGCTGCAA
Found at i:9223855 original size:16 final size:17
Alignment explanation
Indices: 9223814--9223866 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 17
9223804 ATAAACATGT
* *
9223814 TGATATGTCATAT-GCA
1 TGATATATCATATAACA
9223830 TGA-ATATCATATAACA
1 TGATATATCATATAACA
9223846 TGATAT-TCATAATAA-A
1 TGATATATCAT-ATAACA
9223862 TGATA
1 TGATA
9223867 AATGGAAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 8 0.25
16 18 0.56
17 6 0.19
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.36
Consensus pattern (17 bp):
TGATATATCATATAACA
Found at i:9230100 original size:30 final size:29
Alignment explanation
Indices: 9230065--9230132 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
9230055 TGGCTTTGCT
* *
9230065 TTCTTTTTGAATTCTTTTTC-TTTTCTTTTC
1 TTCTTTTTG-ATT-TTTCTCTTTTTCTCTTC
9230095 TTCTTTTCTGATTTTTCTCTTTTTCTCTTC
1 TTCTTTT-TGATTTTTCTCTTTTTCTCTTC
*
9230125 TTTTTTTT
1 TTCTTTTT
9230133 TTTTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
29 6 0.18
30 25 0.76
31 2 0.06
ACGTcount: A:0.04, C:0.18, G:0.03, T:0.75
Consensus pattern (29 bp):
TTCTTTTTGATTTTTCTCTTTTTCTCTTC
Found at i:9230131 original size:22 final size:22
Alignment explanation
Indices: 9230080--9230137 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
9230070 TTTGAATTCT
*
9230080 TTTTCTTTTCTTTTCTTCTTTTC
1 TTTT-TTTTCTTTTCTTCTCTTC
**
9230103 TGATTTTTCTCTTT-TTCTCTTC
1 TTTTTTTTCT-TTTCTTCTCTTC
*
9230125 TTTTTTTTTTTTT
1 TTTTTTTTCTTTT
9230138 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
21 3 0.11
22 20 0.71
23 5 0.18
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTTTTTCTTTTCTTCTCTTC
Found at i:9235120 original size:14 final size:14
Alignment explanation
Indices: 9235101--9235141 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
9235091 AAGATACTAC
9235101 CTTTCCATCACCAT
1 CTTTCCATCACCAT
9235115 CTTTCCATCACCAT
1 CTTTCCATCACCAT
* *
9235129 -TCTCTATCACCAT
1 CTTTCCATCACCAT
9235142 TCACGCCTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 11 0.44
14 14 0.56
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.37
Consensus pattern (14 bp):
CTTTCCATCACCAT
Found at i:9235139 original size:13 final size:13
Alignment explanation
Indices: 9235104--9235143 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
9235094 ATACTACCTT
*
9235104 TCCATCACCATCTT
1 TCCATCACCAT-TC
9235118 TCCATCACCATTC
1 TCCATCACCATTC
*
9235131 TCTATCACCATTC
1 TCCATCACCATTC
9235144 ACGCCTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.23, C:0.42, G:0.00, T:0.35
Consensus pattern (13 bp):
TCCATCACCATTC
Found at i:9237345 original size:20 final size:22
Alignment explanation
Indices: 9237320--9237359 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9237310 GTATAAGACC
9237320 TATGAGCT-A-AAATGAATGCA
1 TATGAGCTAACAAATGAATGCA
9237340 TATGAGCTAACAAATGAATG
1 TATGAGCTAACAAATGAATG
9237360 ATTAAGCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (22 bp):
TATGAGCTAACAAATGAATGCA
Found at i:9243006 original size:90 final size:91
Alignment explanation
Indices: 9242861--9243033 Score: 240
Period size: 90 Copynumber: 1.9 Consensus size: 91
9242851 CCCATGTGCC
* * ** *
9242861 TTGCATATGACCAGCCCCCGTGTGCCTTTTATGAGGATCATTTAGGCACCAAGATGAAGAGTTCT
1 TTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATGAAGAGCTCT
* *
9242926 CTCCCTATTCGGCCAAGCCATGGGTT
66 CTCCCTAGTCGGACAAGCCATGGGTT
* * * *
9242952 TTGCATATGAACAG-CCCCATGTGCCTTGCATGTGGTTTATTTAGGCTCCAAGATGAAGAGCTCT
1 TTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATGAAGAGCTCT
9243016 CTCCCTAGTCGGACAAGC
66 CTCCCTAGTCGGACAAGC
9243034 ATCATTTCCC
Statistics
Matches: 71, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
90 58 0.82
91 13 0.18
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (91 bp):
TTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCACCAAGATGAAGAGCTCT
CTCCCTAGTCGGACAAGCCATGGGTT
Found at i:9247412 original size:90 final size:91
Alignment explanation
Indices: 9247267--9247439 Score: 269
Period size: 90 Copynumber: 1.9 Consensus size: 91
9247257 CCCATGTGCC
* *
9247267 TTGCATATGACCAGCACCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGAACAGCACCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
9247332 CTCCCTATTCGACCAAGCCATGTATT
66 CTCCCTATTCGACCAAGCCATGTATT
* * *
9247358 TTGCATATGAACAGC-CCCATGTGCCTTGTAT-ATGGTTTATTTAGGCGCCAAGATGAAGAGCTC
1 TTGCATATGAACAGCACCCATGTGCCTTGCATGA-GGATCATTTAGGCGCCAAGATGAAGAGCTC
*
9247421 TCTCCCTATTCGGCCAAGC
65 TCTCCCTATTCGACCAAGC
9247440 ATCATTTCCC
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
89 1 0.01
90 60 0.80
91 14 0.19
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.28
Consensus pattern (91 bp):
TTGCATATGAACAGCACCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGCTCT
CTCCCTATTCGACCAAGCCATGTATT
Found at i:9250141 original size:32 final size:32
Alignment explanation
Indices: 9250105--9250201 Score: 185
Period size: 32 Copynumber: 3.0 Consensus size: 32
9250095 ATGTAGTTAA
9250105 ATACTATATGCTTTTATAATACATTTTATGAT
1 ATACTATATGCTTTTATAATACATTTTATGAT
9250137 ATACTATATGCTTTTATAATACATTTTATGAT
1 ATACTATATGCTTTTATAATACATTTTATGAT
*
9250169 ATACTACATGCTTTTATAATACATTTTATGAT
1 ATACTATATGCTTTTATAATACATTTTATGAT
9250201 A
1 A
9250202 AGAATTCTTG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.35, C:0.10, G:0.06, T:0.48
Consensus pattern (32 bp):
ATACTATATGCTTTTATAATACATTTTATGAT
Found at i:9253583 original size:13 final size:13
Alignment explanation
Indices: 9253559--9253590 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
9253549 ATACTAAACA
9253559 CTTTTC-ACATAC
1 CTTTTCAACATAC
9253571 CTTTTCAACATAC
1 CTTTTCAACATAC
9253584 CTTTTCA
1 CTTTTCA
9253591 TCTTTGGCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (13 bp):
CTTTTCAACATAC
Found at i:9257341 original size:90 final size:91
Alignment explanation
Indices: 9257188--9257367 Score: 254
Period size: 90 Copynumber: 2.0 Consensus size: 91
9257178 GAAATGATGC
* * *
9257188 TTGGCTGAATAGGGAGAGAGCTCTTCATCTTGGTGCCTAAATAAACCACATGCAAGGCACAT-GG
1 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATGGG
*
9257252 GGCTGTTCACATGCAAAACACATGGT
66 GGCTGGTCACATGCAAAACACATGGT
* * * *
9257278 TTGGCCGAATAGGGAGATAACTCTTCATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATGGG
1 TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATGGG
* **
9257343 GGCTGGTCATATGCAAGGCACATGG
66 GGCTGGTCACATGCAAAACACATGG
9257368 GTGTTCTAGG
Statistics
Matches: 78, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 55 0.71
91 23 0.29
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (91 bp):
TTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGCACATGGG
GGCTGGTCACATGCAAAACACATGGT
Found at i:9264101 original size:17 final size:17
Alignment explanation
Indices: 9264024--9264095 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
9264014 ATTCATGCAT
9264024 CTAGTTCATTGAA-TAAA
1 CTAGTTCATT-AATTAAA
*
9264041 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAATTAAA
* *
9264059 CTAGTTCATTCATCAAA
1 CTAGTTCATTAATTAAA
*
9264076 CTAGTTCATTTATTAAA
1 CTAGTTCATTAATTAAA
9264093 CTA
1 CTA
9264096 AATCATAACT
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 34 0.72
18 13 0.28
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (17 bp):
CTAGTTCATTAATTAAA
Found at i:9264686 original size:16 final size:18
Alignment explanation
Indices: 9264649--9264690 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
9264639 TAGTGATGAT
9264649 ATAAGAAATGGAAAATAA
1 ATAAGAAATGGAAAATAA
*
9264667 ATAAGTAAT-GAAAA-AA
1 ATAAGAAATGGAAAATAA
9264683 ATAAGAAA
1 ATAAGAAA
9264691 AGAGATGGCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 9 0.41
17 5 0.23
18 8 0.36
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (18 bp):
ATAAGAAATGGAAAATAA
Found at i:9266006 original size:2 final size:2
Alignment explanation
Indices: 9265999--9266053 Score: 76
Period size: 2 Copynumber: 27.5 Consensus size: 2
9265989 CATTATAGCC
*
9265999 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GA- AT AT AG
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT
*
9266041 CT AT AT AT AT AT A
1 AT AT AT AT AT AT A
9266054 ATGAATAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 1 0.02
2 45 0.96
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:9270590 original size:30 final size:33
Alignment explanation
Indices: 9270554--9270614 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
9270544 AATGATTAAG
9270554 ATGGAAAT-ATAA-ATAA-GAAATGGA-AGAAGA
1 ATGGAAATGATAAGA-AATGAAATGGATAGAAGA
9270584 ATGGAAATGATAAGAAATGAAATGGATAGAA
1 ATGGAAATGATAAGAAATGAAATGGATAGAA
9270615 ATGTTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.30
31 6 0.22
32 9 0.33
33 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.25, T:0.18
Consensus pattern (33 bp):
ATGGAAATGATAAGAAATGAAATGGATAGAAGA
Found at i:9270799 original size:13 final size:13
Alignment explanation
Indices: 9270781--9270849 Score: 54
Period size: 13 Copynumber: 5.5 Consensus size: 13
9270771 TTGGCATGAA
**
9270781 GGTGATGGACTAT
1 GGTGATGGAAGAT
9270794 GGTGATGGAAGAT
1 GGTGATGGAAGAT
** *
9270807 GGTGATGTTATA-
1 GGTGATGGAAGAT
* *
9270819 GGCG-T-GAAAAT
1 GGTGATGGAAGAT
9270830 GGTGATGGAAGAT
1 GGTGATGGAAGAT
9270843 GGTGATG
1 GGTGATG
9270850 TTATAGGTAG
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
10 2 0.05
11 4 0.10
12 4 0.10
13 32 0.76
ACGTcount: A:0.28, C:0.03, G:0.42, T:0.28
Consensus pattern (13 bp):
GGTGATGGAAGAT
Found at i:9274553 original size:22 final size:23
Alignment explanation
Indices: 9274526--9274568 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
9274516 TGTAGGAGTC
9274526 TTTTCTT-TCTCTTTTTTTTTGT
1 TTTTCTTCTCTCTTTTTTTTTGT
*
9274548 TTTTCTTCTTTCTTTTTTTTT
1 TTTTCTTCTCTCTTTTTTTTT
9274569 TCTTTTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 7 0.37
23 12 0.63
ACGTcount: A:0.00, C:0.14, G:0.02, T:0.84
Consensus pattern (23 bp):
TTTTCTTCTCTCTTTTTTTTTGT
Found at i:9274563 original size:18 final size:17
Alignment explanation
Indices: 9274524--9274575 Score: 61
Period size: 18 Copynumber: 3.1 Consensus size: 17
9274514 GTTGTAGGAG
*
9274524 TCTTTTCTTTCTCTTTT
1 TCTTTTCTTTTTCTTTT
*
9274541 T-TTTTGTTTTTCTTCTT
1 TCTTTTCTTTTTCTT-TT
*
9274558 TCTTTTTTTTTTCTTTT
1 TCTTTTCTTTTTCTTTT
9274575 T
1 T
9274576 GTTGCTTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 11 0.37
17 7 0.23
18 12 0.40
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (17 bp):
TCTTTTCTTTTTCTTTT
Found at i:9274583 original size:25 final size:25
Alignment explanation
Indices: 9274528--9274575 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
9274518 TAGGAGTCTT
*
9274528 TTCTTTCTCTTTTTTTTTGTTTTTC
1 TTCTTTCTCTTTTTTTTTCTTTTTC
9274553 TTCTTTCT-TTTTTTTTTCTTTTT
1 TTCTTTCTCTTTTTTTTTCTTTTT
9274576 GTTGCTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 14 0.64
25 8 0.36
ACGTcount: A:0.00, C:0.15, G:0.02, T:0.83
Consensus pattern (25 bp):
TTCTTTCTCTTTTTTTTTCTTTTTC
Found at i:9274803 original size:30 final size:33
Alignment explanation
Indices: 9274767--9274827 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
9274757 AATGATTAAG
9274767 ATGGAAAT-ATAA-ATAA-GAAATGGA-AGAAGA
1 ATGGAAATGATAAGA-AAGGAAATGGATAGAAGA
9274797 ATGGAAATGATAAGAAAGGAAATGGATAGAA
1 ATGGAAATGATAAGAAAGGAAATGGATAGAA
9274828 ATGTTATCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 8 0.30
31 6 0.22
32 9 0.33
33 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.26, T:0.16
Consensus pattern (33 bp):
ATGGAAATGATAAGAAAGGAAATGGATAGAAGA
Found at i:9279276 original size:90 final size:91
Alignment explanation
Indices: 9279154--9279319 Score: 253
Period size: 90 Copynumber: 1.8 Consensus size: 91
9279144 CCCATGTGCC
* *
9279154 TTGCATATGACCAGCCCCCATGTGCCTTGTATGAGGATCATTTACGCACCAAGATGAAGAGTTCT
1 TTGCATATGAACAGCCCCCATGTGCCTTGTATGAGGATCATTTACGCACCAAGATGAAGAGCTCT
9279219 CTCCCTATTCGATCAAGCGATGTGTT
66 CTCCCTATTCGATCAAGCGATGTGTT
* * * * * *
9279245 TTGCATGTGAACAG-CCCCATGTGCCTTGTATGTGGTTTATTTAGGCGCCAAGATGAAGAGCTCT
1 TTGCATATGAACAGCCCCCATGTGCCTTGTATGAGGATCATTTACGCACCAAGATGAAGAGCTCT
9279309 CTCCCTATTCG
66 CTCCCTATTCG
9279320 GCCAAGCATC
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 55 0.82
91 12 0.18
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (91 bp):
TTGCATATGAACAGCCCCCATGTGCCTTGTATGAGGATCATTTACGCACCAAGATGAAGAGCTCT
CTCCCTATTCGATCAAGCGATGTGTT
Found at i:9280102 original size:16 final size:16
Alignment explanation
Indices: 9280083--9280115 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
9280073 TGCAAAAGTG
9280083 AAACAAAGCAAAA-AAA
1 AAACAAAG-AAAACAAA
9280099 AAACAAAGAAAACAAA
1 AAACAAAGAAAACAAA
9280115 A
1 A
9280116 GCACTCAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.82, C:0.12, G:0.06, T:0.00
Consensus pattern (16 bp):
AAACAAAGAAAACAAA
Found at i:9284515 original size:15 final size:16
Alignment explanation
Indices: 9284495--9284537 Score: 61
Period size: 15 Copynumber: 2.7 Consensus size: 16
9284485 GATAACATTC
9284495 CTTTCCATTTCAATT-
1 CTTTCCATTTCAATTA
*
9284510 CTTTCCATTTCCATTTA
1 CTTTCCATTT-CAATTA
9284527 CTTTCCATTTC
1 CTTTCCATTTC
9284538 TTAATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 10 0.40
16 5 0.20
17 10 0.40
ACGTcount: A:0.16, C:0.30, G:0.00, T:0.53
Consensus pattern (16 bp):
CTTTCCATTTCAATTA
Found at i:9284756 original size:12 final size:11
Alignment explanation
Indices: 9284729--9284772 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 11
9284719 AAAGTGCTAA
9284729 AAAAAGCAACAAG
1 AAAAAG-AA-AAG
9284742 AAAGAAGAAAAG
1 AAA-AAGAAAAG
9284754 AAAAAAGAAAAG
1 -AAAAAGAAAAG
9284766 AAAAAGA
1 AAAAAGA
9284773 CTACTACATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.24
12 11 0.38
13 8 0.28
14 3 0.10
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:9284828 original size:14 final size:15
Alignment explanation
Indices: 9284794--9284840 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
9284784 AATTTGGAGT
9284794 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
9284809 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
9284823 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
9284840 G
1 G
9284841 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:9301238 original size:23 final size:23
Alignment explanation
Indices: 9301193--9301238 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
9301183 TTATACCTAT
* *
9301193 AGATACTTATTTCATATGTTATA
1 AGATAATTATTTCATATGATATA
9301216 AGATAATTATTTTCATAT-ATATA
1 AGATAATTA-TTTCATATGATATA
9301239 TATATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (23 bp):
AGATAATTATTTCATATGATATA
Found at i:9302892 original size:13 final size:13
Alignment explanation
Indices: 9302874--9302911 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
9302864 GAGAAAAATC
*
9302874 AGAAAAGAAGAAA
1 AGAAAAAAAGAAA
9302887 AGAAAAAAAGAAA
1 AGAAAAAAAGAAA
*
9302900 AGAAAAAGAGAA
1 AGAAAAAAAGAA
9302912 GTTCAAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AGAAAAAAAGAAA
Found at i:9305842 original size:23 final size:23
Alignment explanation
Indices: 9305797--9305842 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
9305787 TTATACCTAT
*
9305797 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
9305820 AGATAGTTACTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
9305843 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:9310427 original size:23 final size:23
Alignment explanation
Indices: 9310382--9310427 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
9310372 TTATACCTAT
*
9310382 AGATACTTATTTCATATGTTATA
1 AGATACTTATTTCATATGATATA
*
9310405 AGATAGTTACTTTCATAT-ATATA
1 AGATACTTA-TTTCATATGATATA
9310428 TATTATACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (23 bp):
AGATACTTATTTCATATGATATA
Found at i:9312274 original size:20 final size:19
Alignment explanation
Indices: 9312230--9312284 Score: 76
Period size: 18 Copynumber: 2.9 Consensus size: 19
9312220 CTATTCGTCC
* *
9312230 AAAAGCATGTACTTTCATT
1 AAAATCATGTATTTTCATT
9312249 -AAATCATGTATTTTCATT
1 AAAATCATGTATTTTCATT
9312267 AAAAATCATGTATTTTCA
1 -AAAATCATGTATTTTCA
9312285 AAGGGGTTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 16 0.50
20 16 0.50
ACGTcount: A:0.38, C:0.13, G:0.07, T:0.42
Consensus pattern (19 bp):
AAAATCATGTATTTTCATT
Found at i:9321591 original size:24 final size:21
Alignment explanation
Indices: 9321557--9321599 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
9321547 TCCACAAGAT
*
9321557 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
9321579 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
9321600 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:9329517 original size:10 final size:10
Alignment explanation
Indices: 9329504--9329568 Score: 96
Period size: 10 Copynumber: 6.5 Consensus size: 10
9329494 AAATTTTGGC
9329504 TTTTTTGTTT
1 TTTTTTGTTT
9329514 TTTTTTGTTT
1 TTTTTTGTTT
9329524 TTTTTTG-TT
1 TTTTTTGTTT
*
9329533 TTTTTTGCTT
1 TTTTTTGTTT
*
9329543 TTTTTTGCCTT
1 TTTTTTG-TTT
9329554 TTTTTTGTTT
1 TTTTTTGTTT
9329564 TTTTT
1 TTTTT
9329569 GAAAAAAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
9 9 0.17
10 33 0.63
11 10 0.19
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:9329519 original size:19 final size:19
Alignment explanation
Indices: 9329497--9329546 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
9329487 TTTTTTGAAA
*
9329497 TTTTGGCTTTTTTGTT-TT
1 TTTTTGCTTTTTTGTTGTT
*
9329515 TTTTTG-TTTTTTTTTGTTT
1 TTTTTGCTTTTTTGTTG-TT
9329534 TTTTTGCTTTTTT
1 TTTTTGCTTTTTT
9329547 TTGCCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 8 0.30
18 5 0.19
19 8 0.30
20 6 0.22
ACGTcount: A:0.00, C:0.04, G:0.12, T:0.84
Consensus pattern (19 bp):
TTTTTGCTTTTTTGTTGTT
Found at i:9329527 original size:20 final size:19
Alignment explanation
Indices: 9329504--9329568 Score: 94
Period size: 19 Copynumber: 3.3 Consensus size: 19
9329494 AAATTTTGGC
9329504 TTTTTTGTTTTTTTTTGTTT
1 TTTTTTG-TTTTTTTTGTTT
*
9329524 TTTTTTGTTTTTTTTGCTT
1 TTTTTTGTTTTTTTTGTTT
9329543 TTTTTTGCCTTTTTTTTGTTT
1 TTTTTTG--TTTTTTTTGTTT
9329564 TTTTT
1 TTTTT
9329569 GAAAAAAATA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.44
20 7 0.17
21 16 0.39
ACGTcount: A:0.00, C:0.05, G:0.09, T:0.86
Consensus pattern (19 bp):
TTTTTTGTTTTTTTTGTTT
Found at i:9329761 original size:17 final size:17
Alignment explanation
Indices: 9329739--9329773 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
9329729 CCCAAATCTG
9329739 ATACCAATTGATAGGGA
1 ATACCAATTGATAGGGA
9329756 ATACCAATTGATAGGGA
1 ATACCAATTGATAGGGA
9329773 A
1 A
9329774 GCAGTGGCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (17 bp):
ATACCAATTGATAGGGA
Found at i:9332139 original size:36 final size:35
Alignment explanation
Indices: 9332088--9332198 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
9332078 TAAGATACTA
9332088 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * *
9332123 CCTATAACATCACCATCTTCCATTACCATTGCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * *
9332158 CCTATATCCTTACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
9332193 CCTATA
1 CCTATA
9332199 TAACCACCAA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
35 43 0.66
36 22 0.34
ACGTcount: A:0.27, C:0.37, G:0.04, T:0.32
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:9332879 original size:15 final size:16
Alignment explanation
Indices: 9332823--9332880 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
9332813 GAGTTGTAAG
9332823 TTATCTTCACTTTC-TTA
1 TTAT-TTCA-TTTCTTTA
*
9332840 CTATTTCATTTCTTTA
1 TTATTTCATTTCTTTA
*
9332856 TTCTTTCATATT-TTT-
1 TTATTTCAT-TTCTTTA
9332871 TTATTTCATT
1 TTATTTCATT
9332881 ACCATATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
14 1 0.03
15 12 0.34
16 17 0.49
17 5 0.14
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATTTCATTTCTTTA
Found at i:9336727 original size:35 final size:36
Alignment explanation
Indices: 9336623--9336730 Score: 121
Period size: 35 Copynumber: 3.0 Consensus size: 36
9336613 TACTACCTAA
*
9336623 ACATCACCATCTTCCATCACCATTTTCATGCCTATA-
1 ACATCACCATCTTCCATCACCA-TTTCACGCCTATAT
* ** *
9336659 ACATCACCATCTTCCATTACCATTGAACACCTATAT
1 ACATCACCATCTTCCATCACCATTTCACGCCTATAT
* * *
9336695 TC-TTACCATCTTCTATCACCATTTCACGCCTATAT
1 ACATCACCATCTTCCATCACCATTTCACGCCTATAT
9336730 A
1 A
9336731 ACCACCAATC
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
35 36 0.62
36 22 0.38
ACGTcount: A:0.29, C:0.34, G:0.03, T:0.34
Consensus pattern (36 bp):
ACATCACCATCTTCCATCACCATTTCACGCCTATAT
Found at i:9336912 original size:16 final size:15
Alignment explanation
Indices: 9336874--9336912 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
9336864 TCTTTGATAA
9336874 CATTTCTTTCCATTT
1 CATTTCTTTCCATTT
**
9336889 CAAGTCTTTCCATTTT
1 CATTTCTTTCCA-TTT
9336905 CATTTCTT
1 CATTTCTT
9336913 AATTATCAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.15, C:0.26, G:0.03, T:0.56
Consensus pattern (15 bp):
CATTTCTTTCCATTT
Found at i:9340894 original size:598 final size:591
Alignment explanation
Indices: 9339759--9340937 Score: 1622
Period size: 598 Copynumber: 2.0 Consensus size: 591
9339749 AGTGATATGG
* * * * *
9339759 TCACACCTACCCCAGATCCGGAAGTCATGCCACAAGGTCTCATTACTAGGTCAAGGGCCAAACAA
1 TCACACCTACACCAGATCCGAAAGTCATGCCACAAGGTCCCATTACTAGATCAAGAGCCAAACAA
9339824 TTCAGGGAAGTTATCCTAACTAAGTGTCTTGAAGCTTTTGATTCATTTGATAACTTAACACCCTC
66 TTCAGGGAAGTTATCCTAACTAAGTGTCTTGAAGCTTTTGATTCATTTGATAACTTAACACCCTC
* *
9339889 CAATGTTATGTTATATAATGTTTTAATAGTTAAAGAATAACTTAGTATGAACACAACATGCACAT
131 CAATGTTAAGTTATATAATGTTTTAATAGATAAAGAATAACTTAGTATGAACACAACATGCACAT
* *
9339954 TGATATTTAAGCATGTTAGGATAGTCTTATAATCATATTAAGCATGATTATCATATATACATCAA
196 TGATATTTAAGCATGTTAGGATAGTCTTATAAT-ATATTAAGCATGATTATAACATATACATCAA
*
9340019 GGCAGCATCATTATAAATCATTTAATTAGTTCATATGCATTCATTTTAGCTCTTAAGCTTCATGC
260 GGCAGCATCATTATAAATCATTTAATTAGTTCATATGCATTCATATTAGCTCTTAAGCTTCATGC
* * * *
9340084 ATAATCTTACACATATTATGAGATGATATAATTAGCTCATGACCTTTAAACATAGCTCACATTAC
325 ATAACCTTACACATATTAGGAGATGATATAATTAGCTCATGACATTCAAACATAGCTCACATTAC
* *
9340149 CAATATCATACATGGCAGCAAGGTATTTAGCTCATAACAACTCAATATCATGGACTTACCTTGTT
390 CAATATCATACATGACAGCAAGGTATTTAGCTCATAACAACTCAATACCATGGACTTACCTTGTT
** * ** ** *
9340214 TCCTTGCACATATAGGTACATTGGAGTGTGATGCACGTTGATTTAGATTGGTGAATGATTTGGAC
455 TCCTTGCACATATAGGTACATTGGAGAATAATAAACGTTGAGATAGATTGGTGAATAATTTGGAC
* * *
9340279 GTCATATGTATCTCACAAAT-AGCTCACAAAGTACATGCCAGCTCATGGAACACT-AAGGAAAGC
520 GTCATATGCAGCTCAC-AATCAGCTCACAAAGTACAAGCCAGCTCATGGAACACTAAAGGAAAGC
9340342 TGATATAA
584 TGATATAA
*
9340350 TCACACCTACACCAGATCCGAAAGTCATGCCACATGGTCCCATTACTAGATCAAGAGCCAAACAA
1 TCACACCTACACCAGATCCGAAAGTCATGCCACAAGGTCCCATTACTAGATCAAGAGCCAAACAA
* *
9340415 TTCAGGGAAGTTCTCTTAACTAAGTGT-TTAGAAGCTTTTGATTCAATTT-ATAACTTAACACCC
66 TTCAGGGAAGTTATCCTAACTAAGTGTCTT-GAAGCTTTTGATTC-ATTTGATAACTTAACACCC
* * * *
9340478 TCCTATGTTAAGTTATATAATGTTTTAATAGATAAAGAATAACTTAGTATGAATACATCTTGCAC
129 TCCAATGTTAAGTTATATAATGTTTTAATAGATAAAGAATAACTTAGTATGAACACAACATGCAC
*
9340543 ATTGTTATTTTGTTATGTTAAGCATGTTAGGATAG-CTATATAAT-TATTATGCATGATTATAAC
194 ATTG--A------TAT-TTAAGCATGTTAGGATAGTCT-TATAATATATTAAGCATGATTATAAC
* *
9340606 ATATACATCAAGGCAGCAT-ACTTAT-AATGCATTTCATTAGTTCATTTGCATTCATATTAGCTC
249 ATATACATCAAGGCAGCATCA-TTATAAAT-CATTTAATTAGTTCATATGCATTCATATTAGCTC
* * * *
9340669 TTAGGCTTTATATC-TTACCTTACACATATTAGGAGATGATATAATTAGCTCATGACATTCAAAC
312 TTAAGCTTCAT-GCATAACCTTACACATATTAGGAGATGATATAATTAGCTCATGACATTCAAAC
* * * * * * * *
9340733 TTAGCTTACATTAGC-ATATTCATGCTTGACAGCAAGGTATTTAGCTCATATCAGCTCAATGCCA
376 ATAGCTCACATTACCAATA-TCATACATGACAGCAAGGTATTTAGCTCATAACAACTCAATACCA
* * * *
9340797 TGGACTTACCTTGTTTTCTTGCACATGTAGGTACATTGGAGAATAATAAATGTTGAGATAGCTTG
440 TGGACTTACCTTGTTTCCTTGCACATATAGGTACATTGGAGAATAATAAACGTTGAGATAGATTG
* * *
9340862 GTGAATAATTTGGACTTCATATGCAGCTCACAATCAGCTTACAAAGTACAAGGCAGCTCATGGAA
505 GTGAATAATTTGGACGTCATATGCAGCTCACAATCAGCTCACAAAGTACAAGCCAGCTCATGGAA
9340927 CACTAAAGGAA
570 CACTAAAGGAA
9340938 GCTCGGTTCA
Statistics
Matches: 514, Mismatches: 56, Indels: 28
0.86 0.09 0.05
Matches are distributed among these distances:
590 2 0.00
591 175 0.34
592 4 0.01
593 1 0.00
597 10 0.02
598 286 0.56
599 12 0.02
600 24 0.05
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (591 bp):
TCACACCTACACCAGATCCGAAAGTCATGCCACAAGGTCCCATTACTAGATCAAGAGCCAAACAA
TTCAGGGAAGTTATCCTAACTAAGTGTCTTGAAGCTTTTGATTCATTTGATAACTTAACACCCTC
CAATGTTAAGTTATATAATGTTTTAATAGATAAAGAATAACTTAGTATGAACACAACATGCACAT
TGATATTTAAGCATGTTAGGATAGTCTTATAATATATTAAGCATGATTATAACATATACATCAAG
GCAGCATCATTATAAATCATTTAATTAGTTCATATGCATTCATATTAGCTCTTAAGCTTCATGCA
TAACCTTACACATATTAGGAGATGATATAATTAGCTCATGACATTCAAACATAGCTCACATTACC
AATATCATACATGACAGCAAGGTATTTAGCTCATAACAACTCAATACCATGGACTTACCTTGTTT
CCTTGCACATATAGGTACATTGGAGAATAATAAACGTTGAGATAGATTGGTGAATAATTTGGACG
TCATATGCAGCTCACAATCAGCTCACAAAGTACAAGCCAGCTCATGGAACACTAAAGGAAAGCTG
ATATAA
Found at i:9341378 original size:90 final size:91
Alignment explanation
Indices: 9341224--9341405 Score: 267
Period size: 90 Copynumber: 2.0 Consensus size: 91
9341214 CCTAGAACAC
* *
9341224 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCAAAGATG
*
9341289 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
** * * * * *
9341315 CCATGTGTTTTGCATGTGAACAG-CCCCATGTTCCTTGCATGTGGTTTATTTAGGCGCAAAGATG
1 CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCAAAGATG
9341379 AAGAGCTCTCTCCCTATTCGGCCAAG
66 AAGAGCTCTCTCCCTATTCGGCCAAG
9341405 C
1 C
9341406 ATCATTTCCC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 62 0.77
91 19 0.23
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGAACAGCCCCCATGTGCCTTGCATGAGGATCATTTAGGCGCAAAGATG
AAGAGCTCTCTCCCTATTCGGCCAAG
Found at i:9344965 original size:11 final size:13
Alignment explanation
Indices: 9344933--9344962 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
9344923 TGGCAAAAGA
9344933 TGAAAAGGTATGT
1 TGAAAAGGTATGT
9344946 TGAAAAGGTATG-
1 TGAAAAGGTATGT
9344958 TGAAA
1 TGAAA
9344963 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:9346966 original size:90 final size:91
Alignment explanation
Indices: 9346819--9346989 Score: 254
Period size: 90 Copynumber: 1.9 Consensus size: 91
9346809 CCTATGTGCC
* * *
9346819 TTGCATATGACCAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAAATGAAGAGCTCT
*
9346884 CTCCCTATTCGGCCAAGCCATGTGTT
66 CTCCCAATTCGGCCAAGCCATGTGTT
* * * * *
9346910 TTGCATATGAACAG-CTCCATGTGCCTTGCATGTGGTTTATTTAGGCGCCAAAATGAAGAGCTCT
1 TTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAAATGAAGAGCTCT
9346974 CTCCCAATTCGGCCAA
66 CTCCCAATTCGGCCAA
9346990 ACATTATTTA
Statistics
Matches: 71, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
90 58 0.82
91 13 0.18
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (91 bp):
TTGCATATGAACAGCCCCCATATGCCTTGCATGAGGATCATTTAGGCGCCAAAATGAAGAGCTCT
CTCCCAATTCGGCCAAGCCATGTGTT
Found at i:9354338 original size:12 final size:12
Alignment explanation
Indices: 9354321--9354348 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
9354311 CTTTATATCA
9354321 ACACATTCAGCT
1 ACACATTCAGCT
9354333 ACACATTCAGCT
1 ACACATTCAGCT
9354345 ACAC
1 ACAC
9354349 TTGGTGTCAC
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:0.36, C:0.36, G:0.07, T:0.21
Consensus pattern (12 bp):
ACACATTCAGCT
Found at i:9355710 original size:10 final size:10
Alignment explanation
Indices: 9355695--9355719 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
9355685 CCCAGGTTAG
9355695 AAAAAAAATC
1 AAAAAAAATC
9355705 AAAAAAAATC
1 AAAAAAAATC
9355715 AAAAA
1 AAAAA
9355720 GAGGGAGCAA
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:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:9356586 original size:21 final size:21
Alignment explanation
Indices: 9356562--9356601 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
9356552 GAAATTAGAG
9356562 TTGAAAA-AGACATTGAGAGCA
1 TTGAAAAGAGA-ATTGAGAGCA
9356583 TTGAAAAGAGAATTGAGAG
1 TTGAAAAGAGAATTGAGAG
9356602 TAAAGATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.20
Consensus pattern (21 bp):
TTGAAAAGAGAATTGAGAGCA
Found at i:9357793 original size:34 final size:34
Alignment explanation
Indices: 9357711--9357793 Score: 107
Period size: 34 Copynumber: 2.4 Consensus size: 34
9357701 GCATTTAAAT
9357711 CATCTAGTTCATTTAGGGAAGTACATCATTTATG
1 CATCTAGTTCATTTAGGGAAGTACATCATTTATG
* * *
9357745 CATTTAGATT-ATTTA-GTAAGCTACTTCATTTATG
1 CATCTAG-TTCATTTAGGGAAG-TACATCATTTATG
9357779 CATCTAGTTCATTTA
1 CATCTAGTTCATTTA
9357794 ATAAAGTTAG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
33 6 0.14
34 34 0.81
35 2 0.05
ACGTcount: A:0.29, C:0.14, G:0.13, T:0.43
Consensus pattern (34 bp):
CATCTAGTTCATTTAGGGAAGTACATCATTTATG
Found at i:9357914 original size:17 final size:17
Alignment explanation
Indices: 9357892--9357963 Score: 90
Period size: 17 Copynumber: 4.2 Consensus size: 17
9357882 ATTAAAGAGT
9357892 TAGTTTAATAAATGAAC
1 TAGTTTAATAAATGAAC
*
9357909 TAGTTTAATGAATGAAC
1 TAGTTTAATAAATGAAC
* *
9357926 TAGTTTAATTAATGAGC
1 TAGTTTAATAAATGAAC
* *
9357943 TAACTTTATTAAATGAAC
1 T-AGTTTAATAAATGAAC
9357961 TAG
1 TAG
9357964 ATGCATAAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
17 33 0.72
18 13 0.28
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.38
Consensus pattern (17 bp):
TAGTTTAATAAATGAAC
Found at i:9364717 original size:24 final size:23
Alignment explanation
Indices: 9364689--9364748 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
9364679 CCTTTTCTTT
*
9364689 CTTTCTTTTTCTTATTTTCGAGTG
1 CTTTCATTTTCTTATTTT-GAGTG
* *
9364713 CTTTCAATTTCTTCTTTTGAGTG
1 CTTTCATTTTCTTATTTTGAGTG
*
9364736 CTTTGATTTTCTT
1 CTTTCATTTTCTT
9364749 TGCTGGATTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 16 0.52
24 15 0.48
ACGTcount: A:0.10, C:0.17, G:0.12, T:0.62
Consensus pattern (23 bp):
CTTTCATTTTCTTATTTTGAGTG
Found at i:9365677 original size:90 final size:91
Alignment explanation
Indices: 9365523--9365704 Score: 258
Period size: 90 Copynumber: 2.0 Consensus size: 91
9365513 GGGAAATGAT
*
9365523 GCTTGGCCGAATAGGGAGAGAGCTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGAACAT-
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGAACATG
*
9365587 GGGGCTGTTCACATGCAAAACACATG
66 GGGGCTGGTCACATGCAAAACACATG
* * * * * *
9365613 GCTTGGCCGAATAGGGAGATAACTCTTGATCTTGGCGCCTAAATGATCCTCATGCAAGGCACATG
1 GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGAACATG
* **
9365678 GGGGCTGGTCATATGCAAGGCACATG
66 GGGGCTGGTCACATGCAAAACACATG
9365704 G
1 G
9365705 GTCTTCTAGG
Statistics
Matches: 80, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 57 0.71
91 23 0.29
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.21
Consensus pattern (91 bp):
GCTTGGCCGAATAGGGAGAGAACTCTTCATCTTGGCGCCTAAATAAACCACATGCAAGGAACATG
GGGGCTGGTCACATGCAAAACACATG
Found at i:9367220 original size:36 final size:36
Alignment explanation
Indices: 9367173--9367277 Score: 158
Period size: 36 Copynumber: 2.9 Consensus size: 36
9367163 GATACAATCT
*
9367173 GTCCATCACCATTATCACTCCTATATCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
9367209 GTCCATCACCATTATCACACCTATATCATCACCATA
1 GTCCATCACCATTATCACACCTATATCATCACCATA
* * * *
9367245 TTCCATTACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACACCTATATCATCACCA
9367278 ACTTATAAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.31, C:0.35, G:0.03, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACACCTATATCATCACCATA
Found at i:9367235 original size:11 final size:11
Alignment explanation
Indices: 9367176--9367260 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
9367166 ACAATCTGTC
9367176 CATCACCATTAT
1 CATCACCA-TAT
*
9367188 CACTC-CTATAT
1 CA-TCACCATAT
9367199 CATCACCATAGT
1 CATCACCATA-T
9367211 CCATCACCATTAT
1 -CATCACCA-TAT
9367224 CA-CACCTATAT
1 CATCACC-ATAT
9367235 CATCACCATATT
1 CATCACCATA-T
*
9367247 CCATTACCATAT
1 -CATCACCATAT
9367259 CA
1 CA
9367261 CGCCTATATT
Statistics
Matches: 61, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
10 2 0.03
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.33, C:0.35, G:0.01, T:0.31
Consensus pattern (11 bp):
CATCACCATAT
Found at i:9370451 original size:19 final size:20
Alignment explanation
Indices: 9370427--9370477 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
9370417 CGGCCAAGAG
* *
9370427 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATAAAAAAT
9370446 CATGTATTTTCATAAAAAAT
1 CATGTATTTTCATAAAAAAT
*
9370466 CGTGTATTTTCA
1 CATGTATTTTCA
9370478 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATAAAAAAT
Found at i:9371263 original size:30 final size:29
Alignment explanation
Indices: 9371206--9371263 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
9371196 GGAGTGCAAA
*
9371206 AAAAAAAAAGAGAAAAATCAGAAAAGAAG
1 AAAAAAAAAGAAAAAAATCAGAAAAGAAG
*
9371235 AAAAGAAAAGAAAAAGAATTCA-AAAAGAA
1 AAAAAAAAAGAAAAA-AA-TCAGAAAAGAA
9371264 AGCAAAGCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 13 0.52
30 9 0.36
31 3 0.12
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (29 bp):
AAAAAAAAAGAAAAAAATCAGAAAAGAAG
Found at i:9375998 original size:18 final size:18
Alignment explanation
Indices: 9375959--9376003 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
9375949 TAGATACAAT
* *
9375959 GAATGCATCTTCATGGAT
1 GAATGCATCTTCATAGAC
*
9375977 GAATGCATCTTCATAGCC
1 GAATGCATCTTCATAGAC
*
9375995 GAATTCATC
1 GAATGCATC
9376004 CTCTCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (18 bp):
GAATGCATCTTCATAGAC
Found at i:9376618 original size:16 final size:16
Alignment explanation
Indices: 9376597--9376629 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9376587 TTCTGCCACC
*
9376597 TATGTTGGAATGAAAA
1 TATGTTAGAATGAAAA
9376613 TATGTTAGAATGAAAA
1 TATGTTAGAATGAAAA
9376629 T
1 T
9376630 GAGCTAACTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (16 bp):
TATGTTAGAATGAAAA
Done.