Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009614.1 Hibiscus syriacus cultivar Beakdansim tig00117000_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: 2129691
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1031360 original size:14 final size:13
Alignment explanation
Indices: 1031334--1031367 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
1031324 TTATTTAACA
1031334 TTTTTTT-ATTTG
1 TTTTTTTAATTTG
1031346 TTTTATTTAATTTG
1 TTTT-TTTAATTTG
1031360 TTTTTTTA
1 TTTTTTTA
1031368 TTATTCTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 7 0.35
14 9 0.45
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (13 bp):
TTTTTTTAATTTG
Found at i:1031366 original size:29 final size:29
Alignment explanation
Indices: 1031334--1031404 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 29
1031324 TTATTTAACA
* *
1031334 TTTTTTTATTTGTTTTATTTAATTT-GTTT
1 TTTTTTTATTTATTTT-TTTAATTTCATTT
* *
1031363 TTTTATTATTCTATTTTTTTAGTTTCATTT
1 TTTTTTTATT-TATTTTTTTAATTTCATTT
*
1031393 TTTATTTATTTA
1 TTTTTTTATTTA
1031405 ATATTCATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 18 0.53
30 16 0.47
ACGTcount: A:0.17, C:0.03, G:0.04, T:0.76
Consensus pattern (29 bp):
TTTTTTTATTTATTTTTTTAATTTCATTT
Found at i:1033513 original size:11 final size:11
Alignment explanation
Indices: 1033497--1033559 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
1033487 AAAATTACAT
1033497 TATTAAAAATA
1 TATTAAAAATA
1033508 TATTAAAAATA
1 TATTAAAAATA
* ***
1033519 CATTATTGATA
1 TATTAAAAATA
1033530 -ATTATAAAAT-
1 TATTA-AAAATA
1033540 T-TTAAAAATA
1 TATTAAAAATA
1033550 TATTAAAAAT
1 TATTAAAAAT
1033560 TCTATAATAC
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:1033678 original size:7 final size:7
Alignment explanation
Indices: 1033666--1033716 Score: 57
Period size: 7 Copynumber: 7.3 Consensus size: 7
1033656 ATTTGTAATT
1033666 AACCCTA
1 AACCCTA
1033673 AACCCTA
1 AACCCTA
1033680 AACCCTA
1 AACCCTA
***
1033687 AATTATA
1 AACCCTA
1033694 AACCCTA
1 AACCCTA
**
1033701 ATTCCTA
1 AACCCTA
1033708 AACCCTA
1 AACCCTA
1033715 AA
1 AA
1033717 TCCGATTATG
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.22
Consensus pattern (7 bp):
AACCCTA
Found at i:1033685 original size:14 final size:14
Alignment explanation
Indices: 1033666--1033719 Score: 72
Period size: 14 Copynumber: 3.9 Consensus size: 14
1033656 ATTTGTAATT
*
1033666 AACCCTAAACCCTA
1 AACCCTAAATCCTA
**
1033680 AACCCTAAATTATA
1 AACCCTAAATCCTA
*
1033694 AACCCTAATTCCTA
1 AACCCTAAATCCTA
1033708 AACCCTAAATCC
1 AACCCTAAATCC
1033720 GATTATGTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (14 bp):
AACCCTAAATCCTA
Found at i:1035688 original size:22 final size:22
Alignment explanation
Indices: 1035663--1035704 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1035653 GAGCTTCAAA
*
1035663 CGAGCTAGAATCGAGCTCGAAT
1 CGAGCTACAATCGAGCTCGAAT
* *
1035685 CGAGCTTCATTCGAGCTCGA
1 CGAGCTACAATCGAGCTCGA
1035705 GTCTCAAGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (22 bp):
CGAGCTACAATCGAGCTCGAAT
Found at i:1035787 original size:31 final size:31
Alignment explanation
Indices: 1035751--1035833 Score: 166
Period size: 31 Copynumber: 2.7 Consensus size: 31
1035741 TTTCAAACCT
1035751 TTTCGAGTTCGAGTCGAGTTTCAATATTATC
1 TTTCGAGTTCGAGTCGAGTTTCAATATTATC
1035782 TTTCGAGTTCGAGTCGAGTTTCAATATTATC
1 TTTCGAGTTCGAGTCGAGTTTCAATATTATC
1035813 TTTCGAGTTCGAGTCGAGTTT
1 TTTCGAGTTCGAGTCGAGTTT
1035834 GAAAATTTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 52 1.00
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.42
Consensus pattern (31 bp):
TTTCGAGTTCGAGTCGAGTTTCAATATTATC
Found at i:1036368 original size:21 final size:21
Alignment explanation
Indices: 1036344--1036420 Score: 93
Period size: 21 Copynumber: 3.7 Consensus size: 21
1036334 TATCGCAAAT
1036344 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
1036365 TCGCATTGCGAT-TTTCTATT
1 TCGCGTTGCGATAGTTGAAAA
1036385 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
1036406 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
1036421 GTACAGTGTC
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 14 0.33
21 29 0.67
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1036433 original size:21 final size:21
Alignment explanation
Indices: 1036409--1036480 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
1036399 TTGAAAATCG
*
1036409 CGTTGCGATAGTGTACAGTGT
1 CGTTGCGATAGTCTACAGTGT
* * *
1036430 CGTTGCGAT--TTTCCA-TTT
1 CGTTGCGATAGTCTACAGTGT
1036448 CGCGTTGCGATAGTCTACAGTGT
1 --CGTTGCGATAGTCTACAGTGT
1036471 CGTTGCGATA
1 CGTTGCGATA
1036481 ATTTTCTCTA
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
18 2 0.05
19 4 0.10
20 9 0.22
21 19 0.47
22 4 0.10
23 2 0.05
ACGTcount: A:0.17, C:0.19, G:0.28, T:0.36
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTGT
Found at i:1039049 original size:20 final size:20
Alignment explanation
Indices: 1039024--1039061 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1039014 CATATATTAA
1039024 AGAATGCATCGATACACTAT
1 AGAATGCATCGATACACTAT
* *
1039044 AGAATGTATCGATGCACT
1 AGAATGCATCGATACACT
1039062 TCAAGGGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.26
Consensus pattern (20 bp):
AGAATGCATCGATACACTAT
Found at i:1039971 original size:32 final size:32
Alignment explanation
Indices: 1039930--1040022 Score: 116
Period size: 32 Copynumber: 2.9 Consensus size: 32
1039920 GAGTCGAGGT
1039930 TTACCTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACAGAA
* * * *
1039962 TTACCTATGTTTTTCGGGACATATGGACAGTA
1 TTACCTATGTTCTACGGAACATATGGACAGAA
* * *
1039994 -TACATATGTTCTAAGGAACATAAGGACAG
1 TTACCTATGTTCTACGGAACATATGGACAG
1040023 TTTAACTAGG
Statistics
Matches: 51, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 23 0.45
32 28 0.55
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.30
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATGGACAGAA
Found at i:1043551 original size:12 final size:12
Alignment explanation
Indices: 1043534--1043558 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1043524 TTATTTAAAG
1043534 ATAAACAAACTC
1 ATAAACAAACTC
1043546 ATAAACAAACTC
1 ATAAACAAACTC
1043558 A
1 A
1043559 CCAGAGGGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAACAAACTC
Found at i:1045519 original size:12 final size:12
Alignment explanation
Indices: 1045502--1045533 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1045492 AAGATTTTAT
1045502 TTTGAAATCAAG
1 TTTGAAATCAAG
1045514 TTTGAAATCAAG
1 TTTGAAATCAAG
1045526 TTTGAAAT
1 TTTGAAAT
1045534 TACTCTCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.38
Consensus pattern (12 bp):
TTTGAAATCAAG
Found at i:1047358 original size:23 final size:22
Alignment explanation
Indices: 1047325--1047380 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
1047315 ATCGATTCCC
* *
1047325 TCAAGGAGGGAATCAGTTCCCTT
1 TCAAGG-GGGAATCAATTCCCCT
1047348 TCAAAGGGGGAATCAATTCCCCT
1 TC-AAGGGGGAATCAATTCCCCT
1047371 TCAAGGGGGA
1 TCAAGGGGGA
1047381 TCGATTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 8 0.27
23 18 0.60
24 4 0.13
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (22 bp):
TCAAGGGGGAATCAATTCCCCT
Found at i:1047387 original size:21 final size:22
Alignment explanation
Indices: 1047315--1047387 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
1047305 CGTGGGAGGT
1047315 ATCGATT-CCC-TCAAGGAGGGA
1 ATCGATTCCCCTTCAAGG-GGGA
*
1047336 ATC-AGTTCCCTTTCAAAGGGGGA
1 ATCGA-TTCCCCTTC-AAGGGGGA
*
1047359 ATCAATTCCCCTTCAAGGGGG-
1 ATCGATTCCCCTTCAAGGGGGA
1047380 ATCGATTC
1 ATCGATTC
1047388 TATCTGCACT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 9 0.20
23 17 0.39
24 5 0.11
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (22 bp):
ATCGATTCCCCTTCAAGGGGGA
Found at i:1051504 original size:21 final size:24
Alignment explanation
Indices: 1051471--1051520 Score: 70
Period size: 21 Copynumber: 2.2 Consensus size: 24
1051461 AGTATATTAA
*
1051471 ATTATAATATAGATAAAT-AT-AT
1 ATTAAAATATAGATAAATAATCAT
1051493 ATTAAAAT-TAGATAAATAATCAT
1 ATTAAAATATAGATAAATAATCAT
1051516 ATTAA
1 ATTAA
1051521 TTTTTTTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 9 0.36
22 9 0.36
23 7 0.28
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTAAAATATAGATAAATAATCAT
Found at i:1051567 original size:15 final size:17
Alignment explanation
Indices: 1051547--1051579 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
1051537 TCTGATTTTT
1051547 TTAAATT-CAA-ATAGA
1 TTAAATTGCAAGATAGA
1051562 TTAAATTGCAAGATAGA
1 TTAAATTGCAAGATAGA
1051579 T
1 T
1051580 AAAAATACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 3 0.19
17 6 0.38
ACGTcount: A:0.48, C:0.06, G:0.12, T:0.33
Consensus pattern (17 bp):
TTAAATTGCAAGATAGA
Found at i:1051651 original size:9 final size:9
Alignment explanation
Indices: 1051615--1051653 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
1051605 AAACATACTA
1051615 ATTTTTTTGT
1 ATTTTTTT-T
*
1051625 AATTTTTTGT
1 -ATTTTTTTT
1051635 ATTTTTTTT
1 ATTTTTTTT
1051644 ATTTTTTTT
1 ATTTTTTTT
1051653 A
1 A
1051654 AATTCAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
9 18 0.69
10 1 0.04
11 7 0.27
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.79
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:1051652 original size:10 final size:10
Alignment explanation
Indices: 1051615--1051651 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
1051605 AAACATACTA
1051615 ATTTTTTTGT
1 ATTTTTTTGT
*
1051625 AATTTTTTGT
1 ATTTTTTTGT
1051635 ATTTTTTT-T
1 ATTTTTTTGT
1051644 ATTTTTTT
1 ATTTTTTT
1051652 TAAATTCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.14, C:0.00, G:0.05, T:0.81
Consensus pattern (10 bp):
ATTTTTTTGT
Found at i:1058389 original size:126 final size:126
Alignment explanation
Indices: 1058164--1058415 Score: 495
Period size: 126 Copynumber: 2.0 Consensus size: 126
1058154 ATGGTGTCTC
1058164 CGTCGACTACAGAAGCGGAATATAAGAGTTTAGCGGAAGTGGTTGCTGATGTAACATGGTTTGAA
1 CGTCGACTACAGAAGCGGAATATAAGAGTTTAGCGGAAGTGGTTGCTGATGTAACATGGTTTGAA
1058229 GCATTGCAAGGATATAAAGGTTGGTCTGCATGGGGTTCCGGTTGTGTGGAGTGACAACTCG
66 GCATTGCAAGGATATAAAGGTTGGTCTGCATGGGGTTCCGGTTGTGTGGAGTGACAACTCG
*
1058290 CGTCGACTACAGAAGCGGAATATAAGAGTTTAGCGGATGTGGTTGCTGATGTAACATGGTTTGAA
1 CGTCGACTACAGAAGCGGAATATAAGAGTTTAGCGGAAGTGGTTGCTGATGTAACATGGTTTGAA
1058355 GCATTGCAAGGATATAAAGGTTGGTCTGCATGGGGTTCCGGTTGTGTGGAGTGACAACTCG
66 GCATTGCAAGGATATAAAGGTTGGTCTGCATGGGGTTCCGGTTGTGTGGAGTGACAACTCG
1058416 AGTGCGATTG
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 125 1.00
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.27
Consensus pattern (126 bp):
CGTCGACTACAGAAGCGGAATATAAGAGTTTAGCGGAAGTGGTTGCTGATGTAACATGGTTTGAA
GCATTGCAAGGATATAAAGGTTGGTCTGCATGGGGTTCCGGTTGTGTGGAGTGACAACTCG
Found at i:1060249 original size:2 final size:2
Alignment explanation
Indices: 1060242--1060268 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1060232 ATCTTAGTCT
1060242 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1060269 TTGTTTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1062690 original size:8 final size:7
Alignment explanation
Indices: 1062666--1062707 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
1062656 TTTTCATACA
1062666 TGCA-TT
1 TGCATTT
1062672 TGCATTT
1 TGCATTT
1062679 TGCATCTT
1 TGCAT-TT
1062687 TGCATTT
1 TGCATTT
* *
1062694 TTCATTG
1 TGCATTT
1062701 TGCATTT
1 TGCATTT
1062708 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:1062690 original size:15 final size:14
Alignment explanation
Indices: 1062666--1062707 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
1062656 TTTTCATACA
1062666 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
1062679 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
1062694 TTCATTGTGCATTT
1 TGCATTTTGCATTT
1062708 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:1062795 original size:26 final size:26
Alignment explanation
Indices: 1062766--1062824 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
1062756 CATTCACATA
*
1062766 TTTACATTTGAATTTGCA-TTGCATTT
1 TTTACATTTGAATTTACATTTGCA-TT
* * *
1062792 TTTACGTTTGTATTTACATTTTCATT
1 TTTACATTTGAATTTACATTTGCATT
1062818 TTTACAT
1 TTTACAT
1062825 AATTACATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 23 0.85
27 4 0.15
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (26 bp):
TTTACATTTGAATTTACATTTGCATT
Found at i:1067397 original size:14 final size:14
Alignment explanation
Indices: 1067378--1067406 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1067368 TCAGATGAGT
1067378 TGTTATCAGAATCA
1 TGTTATCAGAATCA
1067392 TGTTATCAGAATCA
1 TGTTATCAGAATCA
1067406 T
1 T
1067407 CTTGTTATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (14 bp):
TGTTATCAGAATCA
Found at i:1069598 original size:22 final size:22
Alignment explanation
Indices: 1069546--1069663 Score: 170
Period size: 22 Copynumber: 5.5 Consensus size: 22
1069536 ATCTACATTC
1069546 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1069568 TT-AAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
1069589 TTCAAAGATGATATATTCTCTC
1 TTCAAAGATGATAGATTCTCTT
*
1069611 TTCAAAGATGATAAATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
1069633 TTTAAAGATGACAGA-T-TCTT
1 TTCAAAGATGATAGATTCTCTT
1069653 TTCAAAGATGA
1 TTCAAAGATGA
1069664 AAGCTTTATT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
20 14 0.16
21 22 0.25
22 51 0.59
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1070593 original size:113 final size:113
Alignment explanation
Indices: 1070394--1071142 Score: 1129
Period size: 113 Copynumber: 6.6 Consensus size: 113
1070384 TCATCTGTAG
* *
1070394 AGTTCATAATGAGAAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 AGTTCATAATGAG-AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
* *
1070459 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTTCCAGA-AGA
65 CAACCTTTTGCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAGA-A
* *
1070508 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
1070573 AACCTTTTGCTCGAATTCATCATTCAATGGATCAAC-TTTCCAGAGAA
66 AACCTTTTGCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAGAA
1070620 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
1070685 AA-CTTTTCGCTTGAATTCATTATTCGATGGATCAACATTGCCAG-GTCA
66 AACCTTTT-GCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAG-AA
* *
1070733 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
1070798 AACCTTTTGCTCGAATTCATCATTTGATGGATTAACTTTTCCAGAGAA
66 AACCTTTTGCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAGAA
* * *
1070846 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
1070911 AACCTTTTG-TCTGAATTCATCACTT-GATGGATTAACTTTTCCAGAGAA
66 AACCTTTTGCTC-GAATTCATCA-TTCGATGGATCAACTTTTCCAGAGAA
* * *
1070959 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAA-AAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
1071023 AACCTTTTGC-CTGAATTCATCACTT-GATGGATTAACTTTTCCAGAGAA
66 AACCTTTTGCTC-GAATTCATCA-TTCGATGGATCAACTTTTCCAGAGAA
* *
1071071 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1071136 AACCTTT
66 AACCTTT
1071143 GTTTGATGCT
Statistics
Matches: 594, Mismatches: 31, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
111 5 0.01
112 212 0.36
113 356 0.60
114 21 0.04
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAGAA
Found at i:1070802 original size:225 final size:224
Alignment explanation
Indices: 1070394--1071142 Score: 1177
Period size: 225 Copynumber: 3.3 Consensus size: 224
1070384 TCATCTGTAG
* * *
1070394 AGTTCATAATGAGAAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 AGTTCATAATGAG-AAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
*
1070459 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAG
65 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTTCCAGGA-AAGTTCATAATGAGAAG
1070524 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCGAAT
129 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCGAAT
* *
1070589 TCATCATTCAATGGATCAAC-TTTCCAGAGAA
194 TCATCATT-GATGGATTAACTTTTCCAGAGAA
*
1070620 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * *
1070685 AA-CTTTTCGCTTGAATTCATTATTCGATGGATCAACATTGCCAGGTCAAGTTCATAATGAGAAG
66 AACCTTTT-GCTTGAATTCATCATTCGATGGATCAACATTTCCAGG-AAAGTTCATAATGAGAAG
1070749 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCGAAT
129 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCGAAT
1070814 TCATCATTTGATGGATTAACTTTTCCAGAGAA
194 TCATCA-TTGATGGATTAACTTTTCCAGAGAA
* *
1070846 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *
1070911 AACCTTTTG-TCTGAATTCATCACTT-GATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAA
66 AACCTTTTGCT-TGAATTCATCA-TTCGATGGATCAACATTTCCAG-GAAAGTTCATAATGAGAA
* * ** *
1070974 GAACTCATATGAAGAAGGAAGAA-AAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC-CTGA
128 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTC-GA
1071037 ATTCATCACTTGATGGATTAACTTTTCCAGAGAA
192 ATTCATCA-TTGATGGATTAACTTTTCCAGAGAA
*
1071071 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1071136 AACCTTT
66 AACCTTT
1071143 GTTTGATGCT
Statistics
Matches: 489, Mismatches: 25, Indels: 19
0.92 0.05 0.04
Matches are distributed among these distances:
224 6 0.01
225 320 0.65
226 155 0.32
227 8 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (224 bp):
AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTTCCAGGAAAGTTCATAATGAGAAGAA
CTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCGAATTC
ATCATTGATGGATTAACTTTTCCAGAGAA
Found at i:1071011 original size:338 final size:338
Alignment explanation
Indices: 1070394--1071142 Score: 1152
Period size: 338 Copynumber: 2.2 Consensus size: 338
1070384 TCATCTGTAG
* * *
1070394 AGTTCATAATGAGAAAAAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTT
1 AGTTCATAATGAG-AAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
*
1070459 CAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAG
65 CAACCTTTTGCTCGAATTCATCATTCGATGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAG
* * *
1070524 AACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTGCTCGAAT
130 AACTCATATGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTCGAAT
*
1070589 TCATCATTCAATGGATCAACTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
195 TCATCATTCAATGGATCAACTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGA
* * *
1070654 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATTA-TTCGATGGAT
260 AGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTT-GCCTGAATTCATCACTT-GATGGAT
*
1070717 CAACATTGCCAG-GTCA
323 CAACATTGCCAGAG-AA
*
1070733 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
* * *
1070798 AACCTTTTGCTCGAATTCATCATTTGATGGATTAACTTTTCCAG-AGAAAGTTCATAATGAGAAG
66 AACCTTTTGCTCGAATTCATCATTCGATGGATCAACATTTCCAGAAG-AAGTTCATAATGAGAAG
* *
1070862 AACTCATATGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-TCTGAA
130 AACTCATATGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTC-GAA
* *
1070926 TTCATCACTT-GATGGATTAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAA
194 TTCATCA-TTCAATGGATCAAC-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAA
*
1070990 GGAAGAA-AAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGA
257 GGAAGAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGA
* * *
1071054 TTAACTTTTCCAGAGAA
322 TCAACATTGCCAGAGAA
*
1071071 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1071136 AACCTTT
66 AACCTTT
1071143 GTTTGATGCT
Statistics
Matches: 377, Mismatches: 26, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
337 4 0.01
338 302 0.80
339 71 0.19
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (338 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
AACCTTTTGCTCGAATTCATCATTCGATGGATCAACATTTCCAGAAGAAGTTCATAATGAGAAGA
ACTCATATGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACTTATTCAACCTTTTGCTCGAATT
CATCATTCAATGGATCAACTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATATGAAGAAGGAA
GAAGAAATTCATAATGAGAAGAACTTGTTCAACCTTTTGCCTGAATTCATCACTTGATGGATCAA
CATTGCCAGAGAA
Found at i:1074898 original size:38 final size:38
Alignment explanation
Indices: 1074825--1074900 Score: 91
Period size: 39 Copynumber: 2.0 Consensus size: 38
1074815 GAAAAATATT
* *
1074825 TTATATATTTTTGTTTAAAAAATTTAAATTCATAAAAA
1 TTATATATTTTTGTTTAAAAAATTGAAAATCATAAAAA
* **
1074863 TTATATAATTTTTTTTTTCAAAATTGAAAAT-ATAAAAA
1 TTATAT-ATTTTTGTTTAAAAAATTGAAAATCATAAAAA
1074901 AGTTTAATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
38 13 0.41
39 19 0.59
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (38 bp):
TTATATATTTTTGTTTAAAAAATTGAAAATCATAAAAA
Found at i:1077913 original size:21 final size:21
Alignment explanation
Indices: 1077876--1077942 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
1077866 AAATAATAAT
1077876 ATAAAAAATAT--TCATTTTAA
1 ATAAAAAATATAAT-ATTTTAA
*
1077896 ATAATAAAAT-TAATATTTTTA
1 ATAA-AAAATATAATATTTTAA
*
1077917 ATAAAAAATAATAATATTTTAG
1 ATAAAAAAT-ATAATATTTTAA
1077939 ATAA
1 ATAA
1077943 CATTATACTG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 10 0.26
21 15 0.38
22 14 0.36
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (21 bp):
ATAAAAAATATAATATTTTAA
Found at i:1077942 original size:22 final size:20
Alignment explanation
Indices: 1077889--1077942 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 20
1077879 AAAAATATTC
1077889 ATTTTAAATAATAAAATTAAT
1 ATTTT-AATAATAAAATTAAT
1077910 ATTTTTAATAA-AAAATAATAAT
1 A-TTTTAATAATAAAAT--TAAT
1077932 ATTTTAGATAA
1 ATTTTA-ATAA
1077943 CATTATACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.17
21 11 0.38
22 13 0.45
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATTTTAATAATAAAATTAAT
Found at i:1081601 original size:116 final size:114
Alignment explanation
Indices: 1081391--1081604 Score: 268
Period size: 116 Copynumber: 1.9 Consensus size: 114
1081381 AACCAATGTG
* * * * *
1081391 GAGATTATAAAATTTCCTTCTCTTTTCATTTTCGTGTGGTCAGGCCATCCCACTTCAAGCGCCTT
1 GAGATTATAAAATTTCCTTCCCTTTTCATTCTCATGTGGTCAGACCATCCCACTTCAAGCACCTT
*
1081456 CCTATAATTATTATATTAAAATATCTGTTTCTATATACTTAATCTGATT
66 CCTATAATTATTATATTAAAATATATGTTTCTATATACTTAATCTGATT
* *
1081505 GAGATTATAAAATTTCCTTCCCTTTAT-ATTCTCATATTTGGTCAGACCATCCTACTTCAAGCAC
1 GAGATTATAAAATTTCCTTCCCTTT-TCATTCTC--ATGTGGTCAGACCATCCCACTTCAAGCAC
* * ** * *
1081569 TTTGCTATGGTTATTATATTAGAATTTATGTTTCTA
63 CTTCCTATAATTATTATATTAAAATATATGTTTCTA
1081605 CAACATGCAG
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
114 29 0.35
115 1 0.01
116 53 0.64
ACGTcount: A:0.27, C:0.19, G:0.11, T:0.43
Consensus pattern (114 bp):
GAGATTATAAAATTTCCTTCCCTTTTCATTCTCATGTGGTCAGACCATCCCACTTCAAGCACCTT
CCTATAATTATTATATTAAAATATATGTTTCTATATACTTAATCTGATT
Found at i:1091053 original size:2 final size:2
Alignment explanation
Indices: 1091046--1091081 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1091036 GCAACAAGAC
1091046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1091082 TTGACAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1095377 original size:25 final size:25
Alignment explanation
Indices: 1095316--1095389 Score: 103
Period size: 26 Copynumber: 2.9 Consensus size: 25
1095306 TTTTAAATAA
* *
1095316 TTTTAATTATTATTTAATTAATTTT
1 TTTTAAATATTATTCAATTAATTTT
*
1095341 TTTAAAACTATTATTCAATTAATTTT
1 TTTTAAA-TATTATTCAATTAATTTT
*
1095367 TTTTAAATATTGTTCAATTAATT
1 TTTTAAATATTATTCAATTAATT
1095390 ATCAGGGCAC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
25 20 0.47
26 23 0.53
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (25 bp):
TTTTAAATATTATTCAATTAATTTT
Found at i:1096710 original size:17 final size:18
Alignment explanation
Indices: 1096688--1096728 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1096678 AATTGATTTT
*
1096688 TAATTCC-TGACAGATTC
1 TAATTCCTTCACAGATTC
1096705 TAATTCCTTCACAGATTC
1 TAATTCCTTCACAGATTC
1096723 TAATTC
1 TAATTC
1096729 ATTCGTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.39
Consensus pattern (18 bp):
TAATTCCTTCACAGATTC
Found at i:1096859 original size:6 final size:6
Alignment explanation
Indices: 1096850--1096879 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
1096840 ACATCACATT
1096850 CACACC CACACC CACACC CACACC CACACC
1 CACACC CACACC CACACC CACACC CACACC
1096880 TACAAGCATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (6 bp):
CACACC
Found at i:1097181 original size:26 final size:27
Alignment explanation
Indices: 1097134--1097185 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
1097124 TCTGATAATT
*
1097134 TTAAAATATATTTATTTTTTAAAAAAA
1 TTAAAATATATTTATTTATTAAAAAAA
1097161 TTAAAA-ATA-TTATTATATTAAAAAA
1 TTAAAATATATTTATT-TATTAAAAAA
1097186 CTCAGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 12 0.52
27 6 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAAAATATATTTATTTATTAAAAAAA
Found at i:1102023 original size:29 final size:29
Alignment explanation
Indices: 1101976--1102033 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
1101966 AGTACTTGTC
*
1101976 AAATTATATAATCACGTGAGCTTTATAGA
1 AAATTATATAACCACGTGAGCTTTATAGA
*
1102005 AAATTATATAACCATGTGAGCTTTATAGA
1 AAATTATATAACCACGTGAGCTTTATAGA
1102034 CCTATTCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.14, T:0.34
Consensus pattern (29 bp):
AAATTATATAACCACGTGAGCTTTATAGA
Found at i:1106164 original size:22 final size:23
Alignment explanation
Indices: 1106126--1106182 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
1106116 ATTAAATTTC
1106126 TAAAGGAACTTTTTTTTTCTGCT
1 TAAAGGAACTTTTTTTTTCTGCT
1106149 TAAAGGAACTTTTTTTTTCTGCT
1 TAAAGGAACTTTTTTTTTCTGCT
* *
1106172 TGAAGAAACTT
1 TAAAGGAACTT
1106183 GTTGAGTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.47
Consensus pattern (23 bp):
TAAAGGAACTTTTTTTTTCTGCT
Found at i:1118698 original size:2 final size:2
Alignment explanation
Indices: 1118693--1118731 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1118683 TTTTAAACTT
1118693 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1118732 TAACTTTGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1119647 original size:17 final size:18
Alignment explanation
Indices: 1119609--1119647 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1119599 TTCCTTTGTA
*
1119609 ATTTTTTATAAATAATTT
1 ATTTTTTATAAATAATTG
*
1119627 ATTTTTTA-AAATTATTG
1 ATTTTTTATAAATAATTG
1119644 ATTT
1 ATTT
1119648 ACTTTGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 11 0.58
18 8 0.42
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
ATTTTTTATAAATAATTG
Found at i:1134128 original size:29 final size:29
Alignment explanation
Indices: 1134095--1134164 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
1134085 AAATAAGTTC
*
1134095 ACATCTAAATTA-ATTTGATGTCATTGCTT
1 ACATC-AAATTAGATTTGATGTCATTACTT
* *
1134124 ACATCAATTTAGTTTTGATGTCATTACTT
1 ACATCAAATTAGATTTGATGTCATTACTT
*
1134153 ACATCAATTTAG
1 ACATCAAATTAG
1134165 TTAGGTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 5 0.14
29 32 0.86
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.44
Consensus pattern (29 bp):
ACATCAAATTAGATTTGATGTCATTACTT
Found at i:1134165 original size:29 final size:29
Alignment explanation
Indices: 1134108--1134166 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1134098 TCTAAATTAA
*
1134108 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
1134137 TTTGATGTCATTACTTACATCAATTTAGT
1 TTTGATGTCATTACTTACATCAATTTAGT
1134166 T
1 T
1134167 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.14, G:0.12, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTACTTACATCAATTTAGT
Found at i:1138604 original size:29 final size:29
Alignment explanation
Indices: 1138570--1138628 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1138560 CCTAAATTAA
1138570 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1138599 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
1138628 T
1 T
1138629 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:1140362 original size:36 final size:35
Alignment explanation
Indices: 1140282--1140456 Score: 262
Period size: 36 Copynumber: 4.9 Consensus size: 35
1140272 GAACAAGAAT
1140282 AACGGAAGGAAGCATCGCACTTCCGATTCAAGT-G
1 AACGGAAGGAAGCATCGCACTTCCGATTCAAGTCG
1140316 AACGGAAGGAAGCATCGACACTTCCGATTCAAGTCG
1 AACGGAAGGAAGCATCG-CACTTCCGATTCAAGTCG
1140352 AACGGAAGGAAGCATCGGCACTTCCGATTCAAGTCG
1 AACGGAAGGAAGCATC-GCACTTCCGATTCAAGTCG
* *
1140388 AACGGAAGAAAGCATCGGCACTTCCGATTCAAGTCT
1 AACGGAAGGAAGCATC-GCACTTCCGATTCAAGTCG
* * * *
1140424 AACGGAATGAGGCGTCGCACTTTCGATTCAAGT
1 AACGGAAGGAAGCATCGCACTTCCGATTCAAGT
1140457 GTTCATTTTT
Statistics
Matches: 131, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
34 17 0.13
35 32 0.24
36 81 0.62
37 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (35 bp):
AACGGAAGGAAGCATCGCACTTCCGATTCAAGTCG
Found at i:1146309 original size:24 final size:24
Alignment explanation
Indices: 1146282--1146333 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
1146272 CCGATGTGCC
1146282 TATTAAATTT-TTTATATAATAATA
1 TATTAAATTTCTTTATATAA-AATA
1146306 TATT---TTTCTTTATATAAAATA
1 TATTAAATTTCTTTATATAAAATA
1146327 -ATTAAAT
1 TATTAAAT
1146334 AAATTTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
20 3 0.12
21 7 0.29
22 9 0.38
23 1 0.04
24 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TATTAAATTTCTTTATATAAAATA
Found at i:1150857 original size:88 final size:88
Alignment explanation
Indices: 1150708--1150884 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
1150698 TTATATAAAT
1150708 AGATTTAATGTGTTATATTTTTATACTAATCAGAGTTGAGATTAGCTTTATAAATGATATCAATT
1 AGATTTAATGTGTTATATTTTTATACTAATCAGAGTTGAGATTAGCTTTATAAATGATATCAATT
1150773 AATTTGATATTTATAATCTAATA
66 AATTTGATATTTATAATCTAATA
1150796 AGATTTAATGTGTTATATTTTTATACTAATCAGAGTTGAGATTAGCTTTATAAATGATATCAATT
1 AGATTTAATGTGTTATATTTTTATACTAATCAGAGTTGAGATTAGCTTTATAAATGATATCAATT
1150861 AATTTGATATTTATAATCTAATA
66 AATTTGATATTTATAATCTAATA
1150884 A
1 A
1150885 CATCTAAAGA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (88 bp):
AGATTTAATGTGTTATATTTTTATACTAATCAGAGTTGAGATTAGCTTTATAAATGATATCAATT
AATTTGATATTTATAATCTAATA
Found at i:1151087 original size:27 final size:27
Alignment explanation
Indices: 1151033--1151094 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
1151023 TTAAAAATAT
* * *
1151033 ATAATACAAAATATATAAATAATTTTA
1 ATAATATAAAATATAAAAATAATATTA
1151060 ATAATATAAAATATAAAACAT-ATATTA
1 ATAATATAAAATATAAAA-ATAATATTA
1151087 A-AAT-TAAA
1 ATAATATAAA
1151095 TAAAGCGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 4 0.13
26 3 0.10
27 22 0.71
28 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (27 bp):
ATAATATAAAATATAAAAATAATATTA
Found at i:1151097 original size:34 final size:32
Alignment explanation
Indices: 1151019--1151097 Score: 79
Period size: 34 Copynumber: 2.4 Consensus size: 32
1151009 GACATCAAAG
* *
1151019 AAAATTAAA-AATATATAATACAAAATATATA
1 AAAATTAAATAATATAAAATAAAAAATATATA
* *
1151050 AATAATTTTAATAATATAAAATATAAAACATATATT
1 AA-AA-TTAAATAATATAAAATA-AAAA-ATATATA
1151086 AAAATTAAATAA
1 AAAATTAAATAA
1151098 AGCGATATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
31 2 0.05
32 2 0.05
33 4 0.11
34 17 0.45
35 5 0.13
36 8 0.21
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (32 bp):
AAAATTAAATAATATAAAATAAAAAATATATA
Found at i:1152500 original size:14 final size:14
Alignment explanation
Indices: 1152479--1152557 Score: 63
Period size: 16 Copynumber: 5.4 Consensus size: 14
1152469 TCCTCTTTTT
1152479 TTAT-TTATTTATA
1 TTATATTATTTATA
*
1152492 TTATATTATTTTTA
1 TTATATTATTTATA
*
1152506 GTATATATATCTTATA
1 TTATAT-TAT-TTATA
*
1152522 TTATA-TATATATA
1 TTATATTATTTATA
*
1152535 TATATATATATATATA
1 T-TATAT-TATTTATA
1152551 TATATAT
1 T-TATAT
1152558 GTATAGATGT
Statistics
Matches: 55, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
13 9 0.16
14 20 0.36
15 3 0.05
16 23 0.42
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (14 bp):
TTATATTATTTATA
Found at i:1152504 original size:27 final size:28
Alignment explanation
Indices: 1152441--1152533 Score: 75
Period size: 27 Copynumber: 3.2 Consensus size: 28
1152431 TATATTTTTA
1152441 ATTATATTTTTTTATTTATTTACTA-TAT
1 ATTATATTTTTTTATTTATTTA-TATTAT
** *
1152469 -TCCTCTTTTTTTATTTATTTATATTAT
1 ATTATATTTTTTTATTTATTTATATTAT
* *
1152496 ATTAT-TTTTAGTATATATATCTTATATTAT
1 ATTATATTTT--TTTATTTAT-TTATATTAT
1152526 ATATATAT
1 AT-TATAT
1152534 ATATATATAT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
26 2 0.04
27 25 0.49
28 2 0.04
29 7 0.14
30 11 0.22
31 3 0.06
32 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.01, T:0.65
Consensus pattern (28 bp):
ATTATATTTTTTTATTTATTTATATTAT
Found at i:1152514 original size:2 final size:2
Alignment explanation
Indices: 1152507--1152562 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
1152497 TTATTTTTAG
*
1152507 TA TA TA TA TC T- TA TA T- 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
*
1152547 TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA
1152563 GATGTATTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
1 2 0.04
2 47 0.96
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1152520 original size:20 final size:20
Alignment explanation
Indices: 1152479--1152562 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
1152469 TCCTCTTTTT
*
1152479 TTAT-TTATTTATAT-TATA
1 TTATATTATATATATATATA
* *
1152497 TTAT-TTTTAGTATATATATC
1 TTATATTATA-TATATATATA
1152517 TTATATTATATATATATATA
1 TTATATTATATATATATATA
1152537 -TATATATATATATATATATA
1 TTATAT-TATATATATATATA
1152557 TGTATA
1 T-TATA
1152563 GATGTATTAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
18 7 0.13
19 10 0.18
20 30 0.55
21 4 0.07
22 4 0.07
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (20 bp):
TTATATTATATATATATATA
Found at i:1152522 original size:30 final size:30
Alignment explanation
Indices: 1152487--1152562 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
1152477 TTTTATTTAT
* *
1152487 TTATATTATAT-TATTTTTAGTATATATATC
1 TTATATTATATATATATATA-TATATATATC
1152517 TTATATTATATATATATATATATATATAT-
1 TTATATTATATATATATATATATATATATC
* *
1152546 ATATA-TATATATGTATA
1 TTATATTATATATATATA
1152563 GATGTATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
28 11 0.27
29 4 0.10
30 20 0.49
31 6 0.15
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (30 bp):
TTATATTATATATATATATATATATATATC
Found at i:1152526 original size:16 final size:15
Alignment explanation
Indices: 1152484--1152557 Score: 82
Period size: 14 Copynumber: 5.1 Consensus size: 15
1152474 TTTTTTTATT
1152484 TATTTATATTATAT-
1 TATTTATATTATATA
* *
1152498 TATTTTTAGTATATA
1 TATTTATATTATATA
1152513 TATCTTATATTATATA
1 TAT-TTATATTATATA
*
1152529 TATATATA-TATATA
1 TATTTATATTATATA
*
1152543 TATATATA-TATATA
1 TATTTATATTATATA
1152557 T
1 T
1152558 GTATAGATGT
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
14 33 0.62
15 7 0.13
16 13 0.25
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (15 bp):
TATTTATATTATATA
Found at i:1152669 original size:34 final size:35
Alignment explanation
Indices: 1152590--1152708 Score: 108
Period size: 37 Copynumber: 3.5 Consensus size: 35
1152580 CCATTTGCTA
1152590 TATATATATTTTTCTTATATTATATTTTATACGTTTT
1 TATATAT-TTTTTCTTATATTATATTTTATA-GTTTT
*
1152627 TATATATTTTTTCTTAATATTCTATTTT-T-GTTTT
1 TATATATTTTTTCTT-ATATTATATTTTATAGTTTT
* * * *
1152661 TATTTA-TTTAT-ATATATTATATTTT-TACTTTAT
1 TATATATTTTTTCTTATATTATATTTTATAGTTT-T
1152694 TATAT-TTTTTT-TTAT
1 TATATATTTTTTCTTAT
1152709 TTTTTTTCTT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
31 12 0.17
32 4 0.06
33 16 0.23
34 10 0.14
36 9 0.13
37 18 0.26
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (35 bp):
TATATATTTTTTCTTATATTATATTTTATAGTTTT
Found at i:1155826 original size:15 final size:13
Alignment explanation
Indices: 1155803--1155855 Score: 63
Period size: 13 Copynumber: 4.0 Consensus size: 13
1155793 ACAAAAAGAG
1155803 AAAAAAGAGAAAA
1 AAAAAAGAGAAAA
1155816 AAAGTAAAGAGAAAA
1 AAA--AAAGAGAAAA
*
1155831 TAAAAAGAGAAAA
1 AAAAAAGAGAAAA
*
1155844 AACAAAG-GAAAA
1 AAAAAAGAGAAAA
1155856 TTGAAGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 5 0.14
13 18 0.51
15 12 0.34
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (13 bp):
AAAAAAGAGAAAA
Found at i:1158526 original size:110 final size:108
Alignment explanation
Indices: 1158320--1158586 Score: 341
Period size: 110 Copynumber: 2.5 Consensus size: 108
1158310 ACGAAGGGGC
* *
1158320 TTCCCAG-T-TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAG
1 TTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
* *
1158383 CTTAACTTCACAAAGAAGGGGCGACTGATTGTCAACAAATAACT
66 CTCAACTTCACAAAGAAGGGGCGACTGACTGTCAACAAATAA-T
* *
1158427 TT-CCAGTCTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAGACAACACA
1 TTCCCAGT-TC-TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACA
* ** *
1158491 AGCTCAACTTCATAGCGAAGGGGCGGCT-AGCTGTCAACAAATAAT
64 AGCTCAACTTCACAAAGAAGGGGCGACTGA-CTGTCAACAAATAAT
*
1158536 TTCCCAGTTC--CAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTCG
1 TTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTCG
1158587 GAACAATACT
Statistics
Matches: 140, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
105 1 0.01
106 40 0.29
107 2 0.01
108 1 0.01
109 6 0.04
110 90 0.64
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.23
Consensus pattern (108 bp):
TTCCCAGTTCTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAG
CTCAACTTCACAAAGAAGGGGCGACTGACTGTCAACAAATAAT
Found at i:1159978 original size:25 final size:25
Alignment explanation
Indices: 1159909--1160001 Score: 66
Period size: 25 Copynumber: 3.6 Consensus size: 25
1159899 GTCTCATATA
1159909 TATATATATAATTATATTTTTATTTATT
1 TATAT-TAT-ATTAT-TTTTTATTTATT
*
1159937 TACTA-TAT-TCCTCTTTTTTATTTATT
1 TA-TATTATAT--TATTTTTTATTTATT
* *
1159963 TATATTATATTA-TTTTTACTATATA
1 TATATTATATTATTTTTTA-TTTATT
*
1159988 TATCTTATATTATT
1 TATATTATATTATT
1160002 ATTATATATA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
24 6 0.11
25 19 0.36
26 18 0.34
27 6 0.11
28 2 0.04
29 2 0.04
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.63
Consensus pattern (25 bp):
TATATTATATTATTTTTTATTTATT
Found at i:1160092 original size:38 final size:36
Alignment explanation
Indices: 1160049--1160137 Score: 99
Period size: 38 Copynumber: 2.4 Consensus size: 36
1160039 TTGCTATGTA
*
1160049 TATATATTT-TTTTCTTAATATTATATTTTATACGTTTT
1 TATATATTTATATTCTTAATATTATATTTT-T--GTTTT
*
1160087 TATATATATATATATTCTTAATATTCTATTTTTGTTTT
1 TATATAT-T-TATATTCTTAATATTATATTTTTGTTTT
*
1160125 TATTTATTTATAT
1 TATATATTTATAT
1160138 ATATTATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
36 5 0.11
37 1 0.02
38 18 0.40
39 1 0.02
40 2 0.04
41 18 0.40
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.65
Consensus pattern (36 bp):
TATATATTTATATTCTTAATATTATATTTTTGTTTT
Found at i:1160138 original size:38 final size:40
Alignment explanation
Indices: 1160047--1160139 Score: 111
Period size: 41 Copynumber: 2.4 Consensus size: 40
1160037 ATTTGCTATG
* *
1160047 TATATATAT-TTTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATATATATTCTTAATATTATATTTTATA-GTTTT
*
1160087 TATATATATATATATTCTTAATATTCTATTTT-T-GTTTT
1 TATATATATATATATTCTTAATATTATATTTTATAGTTTT
* *
1160125 TATTTATTTATATAT
1 TATATATATATATAT
1160140 ATTATATTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 18 0.38
40 10 0.21
41 19 0.40
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (40 bp):
TATATATATATATATTCTTAATATTATATTTTATAGTTTT
Found at i:1160151 original size:21 final size:21
Alignment explanation
Indices: 1160127--1160197 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
1160117 TTTGTTTTTA
1160127 TTTATTTATATATATTATATT
1 TTTATTTATATATATTATATT
* * *
1160148 TTTACTTTATTTTTTTTATATT
1 TTTA-TTTATATATATTATATT
* *
1160170 TTT-CTTA-ATATCATGTATATC
1 TTTATTTATATAT-AT-TATATT
1160191 TTTATTT
1 TTTATTT
1160198 TTTACTTGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 7
0.70 0.17 0.13
Matches are distributed among these distances:
19 2 0.05
20 4 0.11
21 12 0.32
22 19 0.51
ACGTcount: A:0.25, C:0.06, G:0.01, T:0.68
Consensus pattern (21 bp):
TTTATTTATATATATTATATT
Found at i:1160379 original size:12 final size:11
Alignment explanation
Indices: 1160356--1160430 Score: 51
Period size: 12 Copynumber: 6.2 Consensus size: 11
1160346 CATTTTTTTG
1160356 TTTTTATTATTA
1 TTTTT-TTATTA
1160368 TTATTTTTATTA
1 TT-TTTTTATTA
*
1160380 TTTTTTTACGTA
1 TTTTTTTA-TTA
* *
1160392 TTTTGTTATTT
1 TTTTTTTATTA
*
1160403 TCCATTTTTTCTTA
1 T---TTTTTTATTA
1160417 TTTTATTTATTA
1 TTTT-TTTATTA
1160429 TT
1 TT
1160431 CTCACGTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
11 11 0.22
12 27 0.55
13 3 0.06
14 8 0.16
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (11 bp):
TTTTTTTATTA
Found at i:1167555 original size:18 final size:19
Alignment explanation
Indices: 1167518--1167555 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1167508 CACGGAATGT
*
1167518 AAGATTATCAGTGGGAATAA
1 AAGATTATCAG-GAGAATAA
1167538 AAGATTATCA-GAGAATAA
1 AAGATTATCAGGAGAATAA
1167556 TATTACTGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.24
Consensus pattern (19 bp):
AAGATTATCAGGAGAATAA
Found at i:1172646 original size:21 final size:21
Alignment explanation
Indices: 1172620--1172659 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1172610 CAGAACCACA
*
1172620 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1172641 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1172660 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1172694 original size:20 final size:21
Alignment explanation
Indices: 1172640--1172702 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1172630 GATTCCCCTG
1172640 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1172664 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1172684 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1172703 TGCACTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1176552 original size:22 final size:21
Alignment explanation
Indices: 1176510--1176549 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1176500 GAGTTTGTTT
*
1176510 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1176531 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1176550 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1186603 original size:20 final size:20
Alignment explanation
Indices: 1186578--1186638 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
1186568 TTTTAGTGCA
*
1186578 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
1186598 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
1186619 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
1186639 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:1204508 original size:2 final size:2
Alignment explanation
Indices: 1204501--1204540 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1204491 ATACCACATC
1204501 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1204541 GATACGAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1217742 original size:29 final size:29
Alignment explanation
Indices: 1217660--1217743 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
1217650 CGACATGACC
*
1217660 ATTTTTTACAAATCAATAACGTTAGTGAT
1 ATTTTTTACAAATCAATAACGTTGGTGAT
*
1217689 ATTTTTTACAAATCAATAACATTGGTGAT
1 ATTTTTTACAAATCAATAACGTTGGTGAT
*
1217718 ATTTTTTACAAATCGATAACGTTGGT
1 ATTTTTTACAAATCAATAACGTTGGT
1217744 AACTAGTTTA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (29 bp):
ATTTTTTACAAATCAATAACGTTGGTGAT
Found at i:1220528 original size:16 final size:16
Alignment explanation
Indices: 1220507--1220540 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1220497 AGATAATTTT
1220507 TTAAAA-AAAAATAGAA
1 TTAAAAGAAAAAT-GAA
1220523 TTAAAAGAAAAATGAA
1 TTAAAAGAAAAATGAA
1220539 TT
1 TT
1220541 TATTTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.09, T:0.24
Consensus pattern (16 bp):
TTAAAAGAAAAATGAA
Found at i:1223497 original size:21 final size:21
Alignment explanation
Indices: 1223467--1223519 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1223457 TTATAAGTAT
*
1223467 AGTATTGATACTCATTAATTG
1 AGTATCGATACTCATTAATTG
1223488 AGTATCGATACTCATTAATTG
1 AGTATCGATACTCATTAATTG
*
1223509 AATATCGATAC
1 AGTATCGATAC
1223520 CAGGGCAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (21 bp):
AGTATCGATACTCATTAATTG
Found at i:1225790 original size:23 final size:26
Alignment explanation
Indices: 1225762--1225810 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
1225752 GAAAATTAAA
*
1225762 TAAAAAC-ATTACAA-A-CTAAATAG
1 TAAAAACAATTAAAATAGCTAAATAG
1225785 TAAAAACAATTAAAATAGCTAAATAG
1 TAAAAACAATTAAAATAGCTAAATAG
1225811 AAACATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 6 0.27
25 1 0.05
26 8 0.36
ACGTcount: A:0.61, C:0.10, G:0.06, T:0.22
Consensus pattern (26 bp):
TAAAAACAATTAAAATAGCTAAATAG
Found at i:1225819 original size:22 final size:20
Alignment explanation
Indices: 1225753--1225820 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 20
1225743 TACTCAAGTG
* *
1225753 AAAATTAAATAAAAACATTA
1 AAAACTAAATAGAAACATTA
*
1225773 CAAACTAAATAGTAAAAACAATTA
1 AAAACTAAATAG---AAAC-ATTA
1225797 AAATAGCTAAATAGAAACATTA
1 AAA-A-CTAAATAGAAACATTA
1225819 AA
1 AA
1225821 TACAAACGTT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
20 9 0.24
22 6 0.16
23 8 0.21
24 6 0.16
25 1 0.03
26 8 0.21
ACGTcount: A:0.65, C:0.09, G:0.04, T:0.22
Consensus pattern (20 bp):
AAAACTAAATAGAAACATTA
Found at i:1226409 original size:21 final size:21
Alignment explanation
Indices: 1226380--1226419 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1226370 TTTGAACCGG
1226380 CTACAGTGCCATCTAAAACGA
1 CTACAGTGCCATCTAAAACGA
* *
1226401 CTACGGTGCCATCTGAAAC
1 CTACAGTGCCATCTAAAAC
1226420 AATTGCATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.30, G:0.17, T:0.20
Consensus pattern (21 bp):
CTACAGTGCCATCTAAAACGA
Found at i:1227936 original size:56 final size:56
Alignment explanation
Indices: 1227850--1227956 Score: 187
Period size: 56 Copynumber: 1.9 Consensus size: 56
1227840 TCAATGATAC
*
1227850 AGTGCCCTTTATATTTCGCTATGTAACTGAATTCAACCTCAACTAAATATGGTTAT
1 AGTGCCCTTCATATTTCGCTATGTAACTGAATTCAACCTCAACTAAATATGGTTAT
* *
1227906 AGTGCCCTTCATTTTTTGCTATGTAACTGAATTCAACCTCAACTAAATATG
1 AGTGCCCTTCATATTTCGCTATGTAACTGAATTCAACCTCAACTAAATATG
1227957 ATTAGACACG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 48 1.00
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (56 bp):
AGTGCCCTTCATATTTCGCTATGTAACTGAATTCAACCTCAACTAAATATGGTTAT
Found at i:1230962 original size:13 final size:13
Alignment explanation
Indices: 1230944--1230968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1230934 CCATTACTAT
1230944 TTCCATCACCATC
1 TTCCATCACCATC
1230957 TTCCATCACCAT
1 TTCCATCACCAT
1230969 TATCACGCCT
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:0.24, C:0.44, G:0.00, T:0.32
Consensus pattern (13 bp):
TTCCATCACCATC
Found at i:1230998 original size:36 final size:36
Alignment explanation
Indices: 1230947--1231061 Score: 196
Period size: 36 Copynumber: 3.2 Consensus size: 36
1230937 TTACTATTTC
*
1230947 CATCACCATCTTCCATCACCATTATCACGCCTATAT
1 CATCACCATATTCCATCACCATTATCACGCCTATAT
*
1230983 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCATATTCCATCACCATTATCACGCCTATAT
1231019 CATCACCATATTCCATCACCA-TATCACGCCTATAT
1 CATCACCATATTCCATCACCATTATCACGCCTATAT
*
1231054 TATCACCA
1 CATCACCA
1231062 ACTTCTAAAT
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
35 21 0.28
36 54 0.72
ACGTcount: A:0.30, C:0.37, G:0.03, T:0.29
Consensus pattern (36 bp):
CATCACCATATTCCATCACCATTATCACGCCTATAT
Found at i:1231001 original size:13 final size:11
Alignment explanation
Indices: 1230960--1231044 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
1230950 CACCATCTTC
1230960 CATCACCATTAT
1 CATCACCA-TAT
*
1230972 CA-CGCCTATAT
1 CATCACC-ATAT
1230983 CATCACCATAGT
1 CATCACCATA-T
1230995 CCATCACCATTAT
1 -CATCACCA-TAT
*
1231008 CA-CGCCTATAT
1 CATCACC-ATAT
1231019 CATCACCATATT
1 CATCACCATA-T
1231031 CCATCACCATAT
1 -CATCACCATAT
1231043 CA
1 CA
1231045 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:1235421 original size:13 final size:11
Alignment explanation
Indices: 1235380--1235464 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
1235370 TTACTATTTC
1235380 CATCACCATTAT
1 CATCACCA-TAT
*
1235392 CATGC-CTATAT
1 CAT-CACCATAT
1235403 CATCACCATAGT
1 CATCACCATA-T
1235415 CCATCACCATTAT
1 -CATCACCA-TAT
*
1235428 CA-CGCCTATAT
1 CATCACC-ATAT
1235439 CATCACCATATT
1 CATCACCATA-T
1235451 CCATCACCATAT
1 -CATCACCATAT
1235463 CA
1 CA
1235465 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
10 1 0.02
11 23 0.38
12 14 0.23
13 20 0.33
14 2 0.03
ACGTcount: A:0.32, C:0.35, G:0.04, T:0.29
Consensus pattern (11 bp):
CATCACCATAT
Found at i:1235425 original size:36 final size:36
Alignment explanation
Indices: 1235378--1235479 Score: 170
Period size: 36 Copynumber: 2.9 Consensus size: 36
1235368 CATTACTATT
*
1235378 TCCATCACCATTATCATGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1235414 TCCATCACCATTATCACGCCTATATCATCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
1235450 TCCATCACCA-TATCACGCCTATATTATCAC
1 TCCATCACCATTATCACGCCTATATCATCAC
1235480 TAACTTCTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
35 19 0.30
36 44 0.70
ACGTcount: A:0.30, C:0.35, G:0.04, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:1239199 original size:30 final size:30
Alignment explanation
Indices: 1239164--1239220 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1239154 TTATTTTGAC
1239164 TCTTAA-ATTTTAAATAAAATACTAATTTAT
1 TCTTAATA-TTTAAATAAAATACTAATTTAT
* *
1239194 TCTTAATATTTAGATAAAATATTAATT
1 TCTTAATATTTAAATAAAATACTAATT
1239221 AAATTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.96
31 1 0.04
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (30 bp):
TCTTAATATTTAAATAAAATACTAATTTAT
Found at i:1239239 original size:31 final size:30
Alignment explanation
Indices: 1239164--1239251 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 30
1239154 TTATTTTGAC
* * * *
1239164 TCTTAAATTTTAAATAAAATACTAATTTAT
1 TCTTAAAATTTAGATAAAATATTAATTAAT
*
1239194 TCTTAATATTTAGATAAAATATTAATTAAAT
1 TCTTAAAATTTAGATAAAATATTAATT-AAT
*
1239225 T-TATAAAATTTAGATAAAATATCAATT
1 TCT-TAAAATTTAGATAAAATATTAATT
1239252 TGACCAACTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
30 24 0.49
31 25 0.51
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (30 bp):
TCTTAAAATTTAGATAAAATATTAATTAAT
Found at i:1239244 original size:20 final size:20
Alignment explanation
Indices: 1239207--1239244 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1239197 TAATATTTAG
*
1239207 ATAAAATATTAATTAAATTT
1 ATAAAATATTAATAAAATTT
1239227 ATAAAAT-TTAGATAAAAT
1 ATAAAATATTA-ATAAAAT
1239245 ATCAATTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
ATAAAATATTAATAAAATTT
Found at i:1239438 original size:19 final size:19
Alignment explanation
Indices: 1239414--1239452 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1239404 AAAAAGGAAG
1239414 TGTACTAAAAATTTTAGGA
1 TGTACTAAAAATTTTAGGA
1239433 TGTACTAAAAATTTTAGGA
1 TGTACTAAAAATTTTAGGA
1239452 T
1 T
1239453 CCAACGATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (19 bp):
TGTACTAAAAATTTTAGGA
Found at i:1240336 original size:16 final size:16
Alignment explanation
Indices: 1240311--1240344 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1240301 AACAGCTCTC
1240311 TCTCTCTCTCTGCCTG
1 TCTCTCTCTCTGCCTG
* *
1240327 TCTCTGTCTCTGTCTG
1 TCTCTCTCTCTGCCTG
1240343 TC
1 TC
1240345 ACTGAGCTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.38, G:0.15, T:0.47
Consensus pattern (16 bp):
TCTCTCTCTCTGCCTG
Found at i:1247590 original size:240 final size:241
Alignment explanation
Indices: 1247167--1247649 Score: 959
Period size: 240 Copynumber: 2.0 Consensus size: 241
1247157 CATGCTAGTG
1247167 ATGTCAATCTCATTAGGCACGAATCCAGAACGAAGCATGAGGATCAAGTTACTAAAAGCTTTCAC
1 ATGTCAATCTCATTAGGCACGAATCCAGAACGAAGCATGAGGATCAAGTTACTAAAAGCTTTCAC
1247232 CTTTAAGCCCATTTTTTTTTTGAATGACCAACAATCATGGCATTACAAGACACTGTTCTTAGTAG
66 CTTTAAGCCCATTTTTTTTTTGAATGACCAACAATCATGGCATTACAAGACACTGTTCTTAGTAG
1247297 GCATTGTATGAAATAGCTCACTAGCTTTAGCCATTTCCCCTTCATCAATGTATGCCGTTATCATG
131 GCATTGTATGAAATAGCTCACTAGCTTTAGCCATTTCCCCTTCATCAATGTATGCCGTTATCATG
1247362 GCATTC-AAGCTGCTATGTCTTTGCTTACTGGCATCTGATCAAAAT
196 GCATTCAAAGCTGCTATGTCTTTGCTTACTGGCATCTGATCAAAAT
1247407 ATGTCAATCTCATTAGGCACGAATCCAGAACGAAGCATGAGGATCAAGTTACTAAAAGCTTTCAC
1 ATGTCAATCTCATTAGGCACGAATCCAGAACGAAGCATGAGGATCAAGTTACTAAAAGCTTTCAC
1247472 CTTTAAGCCCATTTTTTTTTTGAATGACCAACAATCATGGCATTACAAGACACTGTTCTTAGTAG
66 CTTTAAGCCCATTTTTTTTTTGAATGACCAACAATCATGGCATTACAAGACACTGTTCTTAGTAG
1247537 GCATTGTATGAAATAGCTCACTAGCTTTAGCCATTTCCCCTTCATCAATGTATGCCGTTATCATG
131 GCATTGTATGAAATAGCTCACTAGCTTTAGCCATTTCCCCTTCATCAATGTATGCCGTTATCATG
1247602 GCATTCAAAGCTGCTATGTCTTTGCTTACTGGCATCTGATCAAAAT
196 GCATTCAAAGCTGCTATGTCTTTGCTTACTGGCATCTGATCAAAAT
1247648 AT
1 AT
1247650 TCCCTAGCCT
Statistics
Matches: 242, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
240 201 0.83
241 41 0.17
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (241 bp):
ATGTCAATCTCATTAGGCACGAATCCAGAACGAAGCATGAGGATCAAGTTACTAAAAGCTTTCAC
CTTTAAGCCCATTTTTTTTTTGAATGACCAACAATCATGGCATTACAAGACACTGTTCTTAGTAG
GCATTGTATGAAATAGCTCACTAGCTTTAGCCATTTCCCCTTCATCAATGTATGCCGTTATCATG
GCATTCAAAGCTGCTATGTCTTTGCTTACTGGCATCTGATCAAAAT
Found at i:1270150 original size:3 final size:3
Alignment explanation
Indices: 1270142--1270179 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
1270132 ATAATTATAT
* *
1270142 TTA TTA TTA CTA TTA TTG TTA -TA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1270180 AATAATTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1274127 original size:22 final size:23
Alignment explanation
Indices: 1274092--1274143 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
1274082 GGCGCCATAT
1274092 AAAAA-TATTAAAAATG-A-TTA
1 AAAAATTATTAAAAATGAAGTTA
1274112 AAAAATTAGTTAAAAATGAAGTTA
1 AAAAATTA-TTAAAAATGAAGTTA
1274136 AAAAATTA
1 AAAAATTA
1274144 CCTTCCAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.18
21 2 0.07
22 9 0.32
23 1 0.04
24 11 0.39
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (23 bp):
AAAAATTATTAAAAATGAAGTTA
Found at i:1286802 original size:20 final size:21
Alignment explanation
Indices: 1286749--1286810 Score: 63
Period size: 20 Copynumber: 2.9 Consensus size: 21
1286739 ATTCCCCTGT
1286749 GGGGGGAATCGGTTCCCCTTCAAA
1 GGGGGG-ATCGGTT-CCC-TCAAA
* *
1286773 GGGTGAATCGGTTCCCTC-AA
1 GGGGGGATCGGTTCCCTCAAA
*
1286793 GGGGGGATCGATTCCCTC
1 GGGGGGATCGGTTCCCTC
1286811 TGCACCAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
20 17 0.52
21 2 0.06
22 3 0.09
23 7 0.21
24 4 0.12
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.23
Consensus pattern (21 bp):
GGGGGGATCGGTTCCCTCAAA
Found at i:1297219 original size:2 final size:2
Alignment explanation
Indices: 1297207--1297236 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1297197 TTTAAAATTA
*
1297207 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1297237 GATTTTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1301046 original size:17 final size:17
Alignment explanation
Indices: 1301024--1301067 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1301014 GAACTAATTT
1301024 TATTTTAAATATTTATA
1 TATTTTAAATATTTATA
*
1301041 TATTTTAAATATTTGTA
1 TATTTTAAATATTTATA
*
1301058 TTTTTTAAAT
1 TATTTTAAAT
1301068 GTTTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
TATTTTAAATATTTATA
Found at i:1305538 original size:17 final size:17
Alignment explanation
Indices: 1305502--1305576 Score: 51
Period size: 18 Copynumber: 4.1 Consensus size: 17
1305492 GGACGATTTC
*
1305502 ATTAAACGACATAGTTTT
1 ATTAAACGAC-TATTTTT
*
1305520 ATTAAATGACTATTTTT
1 ATTAAACGACTATTTTT
* *
1305537 ATTCGTTAAACGATGTAATTTT
1 A----TTAAACGA-CTATTTTT
*
1305559 ATTAAATGACTATTTTT
1 ATTAAACGACTATTTTT
1305576 A
1 A
1305577 AACCCCAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 11
0.70 0.13 0.17
Matches are distributed among these distances:
17 14 0.32
18 16 0.36
21 7 0.16
22 7 0.16
ACGTcount: A:0.36, C:0.08, G:0.09, T:0.47
Consensus pattern (17 bp):
ATTAAACGACTATTTTT
Found at i:1311238 original size:5 final size:5
Alignment explanation
Indices: 1311228--1311261 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
1311218 ATGCCCACTT
1311228 TTTTA TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
1311262 ATATTTTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTTA
Found at i:1311253 original size:9 final size:9
Alignment explanation
Indices: 1311229--1311259 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
1311219 TGCCCACTTT
1311229 TTTATTTTA
1 TTTATTTTA
1311238 TTTTATTTTA
1 -TTTATTTTA
1311248 TTTATTTTA
1 TTTATTTTA
1311257 TTT
1 TTT
1311260 TAATATTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTATTTTA
Found at i:1311253 original size:14 final size:15
Alignment explanation
Indices: 1311228--1311261 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
1311218 ATGCCCACTT
1311228 TTTTATTTTATTTTA
1 TTTTATTTTATTTTA
1311243 TTTTA-TTTATTTTA
1 TTTTATTTTATTTTA
1311257 TTTTA
1 TTTTA
1311262 ATATTTTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTATTTTATTTTA
Found at i:1316078 original size:34 final size:35
Alignment explanation
Indices: 1316033--1316113 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 35
1316023 ACCTATGAGA
* *
1316033 GAATGGGGATGGGATAAGTTTTATCCTCAAAGTTT
1 GAATGGGGATGGGATAAATTTTATCCTCAAAGTTC
* *
1316068 GAAT-GGGATGGGATAAATTTTATTCTTAAAGTTC
1 GAATGGGGATGGGATAAATTTTATCCTCAAAGTTC
1316102 GAATGGGGATGG
1 GAATGGGGATGG
1316114 AGACGGAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 30 0.73
35 11 0.27
ACGTcount: A:0.30, C:0.06, G:0.31, T:0.33
Consensus pattern (35 bp):
GAATGGGGATGGGATAAATTTTATCCTCAAAGTTC
Found at i:1318209 original size:23 final size:23
Alignment explanation
Indices: 1318183--1318229 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1318173 ATGTTTATAC
1318183 TCTTATATATGTAAGATAAGAGT
1 TCTTATATATGTAAGATAAGAGT
1318206 TCTTATATATGTAAGATAAGAGT
1 TCTTATATATGTAAGATAAGAGT
1318229 T
1 T
1318230 TAATATGTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (23 bp):
TCTTATATATGTAAGATAAGAGT
Found at i:1327123 original size:17 final size:18
Alignment explanation
Indices: 1327080--1327126 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1327070 TACGCTTTAG
1327080 GTTTATAAA-AAATTTTGGT
1 GTTTA-AAATAAATTTT-GT
1327099 GTTT-AAATAAATTTT-T
1 GTTTAAAATAAATTTTGT
1327115 GTTTAAAATAAA
1 GTTTAAAATAAA
1327127 GTGTTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.19
17 10 0.38
18 7 0.27
19 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
GTTTAAAATAAATTTTGT
Found at i:1327202 original size:15 final size:15
Alignment explanation
Indices: 1327182--1327211 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1327172 TAATATTTAG
1327182 ATTTTTAAAAAATAT
1 ATTTTTAAAAAATAT
*
1327197 ATTTTTAAATAATAT
1 ATTTTTAAAAAATAT
1327212 TTTATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTTTAAAAAATAT
Found at i:1328073 original size:61 final size:61
Alignment explanation
Indices: 1327998--1328120 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
1327988 CATAAGAATA
1327998 TCCATGGAATACGCCTAAAGCTTCTCGTTTGAATTTTGATGATGACCACAAACGTCCAGCG
1 TCCATGGAATACGCCTAAAGCTTCTCGTTTGAATTTTGATGATGACCACAAACGTCCAGCG
1328059 TCCATGGAATACGCCTAAAGCTTCTCGTTTGAATTTTGATGATGACCACAAACGTCCAGCG
1 TCCATGGAATACGCCTAAAGCTTCTCGTTTGAATTTTGATGATGACCACAAACGTCCAGCG
1328120 T
1 T
1328121 ATCGAGATCA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (61 bp):
TCCATGGAATACGCCTAAAGCTTCTCGTTTGAATTTTGATGATGACCACAAACGTCCAGCG
Found at i:1335113 original size:3 final size:3
Alignment explanation
Indices: 1335105--1335131 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1335095 GAAGTTATAA
1335105 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG
1335132 GCAAACCTCA
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:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1338198 original size:18 final size:18
Alignment explanation
Indices: 1338145--1338190 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1338135 GAGGGATTAT
1338145 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
1338163 CAGTGGTCCTTCGGGACA
1 CAGTGGTCCTTCGGGACA
*
1338181 TAGTGGTCCT
1 CAGTGGTCCT
1338191 ACAGGACAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.15, C:0.26, G:0.33, T:0.26
Consensus pattern (18 bp):
CAGTGGTCCTTCGGGACA
Found at i:1340087 original size:2 final size:2
Alignment explanation
Indices: 1340080--1340130 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1340070 TTAAAGGGTA
1340080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1340122 AT AT AT AT A
1 AT AT AT AT A
1340131 ATTCATGAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1340292 original size:3 final size:3
Alignment explanation
Indices: 1340284--1340311 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1340274 TAACCCACCC
1340284 CCT CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT CCT C
1340312 TCTTCCTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:1340405 original size:18 final size:18
Alignment explanation
Indices: 1340366--1340416 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
1340356 ACAAAAACTT
*
1340366 AAAAATCATAACCCCATT
1 AAAAATCATAACCCCATC
1340384 AAAAATCATAACCTCCA-C
1 AAAAATCATAACC-CCATC
*
1340402 -AAAATCATAATCCCA
1 AAAAATCATAACCCCA
1340417 AATAAAACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
16 3 0.10
17 11 0.37
18 13 0.43
19 3 0.10
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATCATAACCCCATC
Found at i:1342382 original size:91 final size:91
Alignment explanation
Indices: 1342262--1342460 Score: 330
Period size: 91 Copynumber: 2.2 Consensus size: 91
1342252 TCTATTAATA
* * *
1342262 ACTATTAATATTGAGTGATTATTTTATAATAAGCGATAATATTAATAAATGATTTGTGATTTTTT
1 ACTATTAATATTGAGTGATTATTTTATAATAAGCGACAATACTAATAAATGATTTGTGATTTTTA
1342327 AAATATTAATGATAAAAACGAACATT
66 AAATATTAATGATAAAAACGAACATT
1342353 ACTATTAATATTGAGTGATTATTTTATAATAAGCGACAATACTAATAAATGATTTGTGATTTTTA
1 ACTATTAATATTGAGTGATTATTTTATAATAAGCGACAATACTAATAAATGATTTGTGATTTTTA
*
1342418 AAATATTAATGATGAAAACGAACATT
66 AAATATTAATGATAAAAACGAACATT
*
1342444 A-TTTTAA-ATATGAGTGA
1 ACTATTAATAT-TGAGTGA
1342461 CCAGTTTACC
Statistics
Matches: 102, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
89 2 0.02
90 12 0.12
91 88 0.86
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (91 bp):
ACTATTAATATTGAGTGATTATTTTATAATAAGCGACAATACTAATAAATGATTTGTGATTTTTA
AAATATTAATGATAAAAACGAACATT
Found at i:1365461 original size:31 final size:31
Alignment explanation
Indices: 1365426--1365503 Score: 111
Period size: 31 Copynumber: 2.5 Consensus size: 31
1365416 ATAGATTCCG
* *
1365426 AAGAACCTAGGTAAACAATCCATATATCTCA
1 AAGAACATAGGTAAACAATCCATATATCCCA
* * *
1365457 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAATCCATATATCCCA
1365488 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
1365504 CCTCGACCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.45, C:0.21, G:0.15, T:0.19
Consensus pattern (31 bp):
AAGAACATAGGTAAACAATCCATATATCCCA
Found at i:1367403 original size:46 final size:46
Alignment explanation
Indices: 1367301--1367425 Score: 135
Period size: 46 Copynumber: 2.7 Consensus size: 46
1367291 ACCCGATTGT
* * * *
1367301 TTAGAAGGTTGGAATAGCATGGGGAATGTTAATTCTCAATCTACTGT
1 TTAGAAGGTTAGAA-AGCATGGGGAATGTTGATCCTCAATCTACTGC
* * * *
1367348 TTAAAAGGTTTGAAAGCATGGGGAATGTTGATCCTCACTCTGCTGC
1 TTAGAAGGTTAGAAAGCATGGGGAATGTTGATCCTCAATCTACTGC
* *
1367394 TTAGGAGGTTAGAGAGCACT-GGGAATGTTGAT
1 TTAGAAGGTTAGAAAGCA-TGGGGAATGTTGAT
1367426 GTTATAGAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 53 0.80
47 13 0.20
ACGTcount: A:0.28, C:0.12, G:0.29, T:0.31
Consensus pattern (46 bp):
TTAGAAGGTTAGAAAGCATGGGGAATGTTGATCCTCAATCTACTGC
Found at i:1375955 original size:35 final size:36
Alignment explanation
Indices: 1375902--1375976 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 36
1375892 AATATAATTT
1375902 TAAATATAACAAACTTACAATAA-GA-ATTAAATGG
1 TAAATATAACAAACTTACAATAACGATATTAAATGG
1375936 TAAATGATAATCAAA-TTACAATAACTGATATTAAATGG
1 TAAAT-ATAA-CAAACTTACAATAAC-GATATTAAATGG
1375974 TAA
1 TAA
1375977 TAAATAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
34 5 0.14
35 13 0.36
36 4 0.11
37 2 0.06
38 12 0.33
ACGTcount: A:0.53, C:0.08, G:0.09, T:0.29
Consensus pattern (36 bp):
TAAATATAACAAACTTACAATAACGATATTAAATGG
Found at i:1375987 original size:35 final size:35
Alignment explanation
Indices: 1375902--1375988 Score: 92
Period size: 35 Copynumber: 2.5 Consensus size: 35
1375892 AATATAATTT
* *
1375902 TAAAT-ATAACAAACTTACAATAAGAATTAAATGG
1 TAAATGATAATAAAATTACAATAAGAATTAAATGG
*
1375936 TAAATGATAATCAAATTACAATAACTGATATTAAATGG
1 TAAATGATAATAAAATTACAATAA--GA-ATTAAATGG
1375974 T-AAT-A-AATAAAATTA
1 TAAATGATAATAAAATTA
1375989 ACTGAAATAC
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.07, G:0.08, T:0.30
Consensus pattern (35 bp):
TAAATGATAATAAAATTACAATAAGAATTAAATGG
Found at i:1379479 original size:6 final size:6
Alignment explanation
Indices: 1379470--1379494 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1379460 TAAGGTTTAT
1379470 GTTTGA GTTTGA GTTTGA GTTTGA G
1 GTTTGA GTTTGA GTTTGA GTTTGA G
1379495 GCTTCAATCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GTTTGA
Found at i:1383022 original size:24 final size:24
Alignment explanation
Indices: 1382993--1383042 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
1382983 TTGATTGTAC
1382993 ATATGTCCCTTTCTTTTGAACTTG
1 ATATGTCCCTTTCTTTTGAACTTG
1383017 ATATGTCCCTTTCTTTTGAACTTG
1 ATATGTCCCTTTCTTTTGAACTTG
1383041 AT
1 AT
1383043 TGTATTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.50
Consensus pattern (24 bp):
ATATGTCCCTTTCTTTTGAACTTG
Found at i:1385458 original size:12 final size:12
Alignment explanation
Indices: 1385441--1385465 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1385431 ACAAAGCACC
1385441 ATTTGGTGCCTA
1 ATTTGGTGCCTA
1385453 ATTTGGTGCCTA
1 ATTTGGTGCCTA
1385465 A
1 A
1385466 ATTATTTGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:1388242 original size:20 final size:21
Alignment explanation
Indices: 1388205--1388244 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1388195 AAATTAAGTT
1388205 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1388226 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1388245 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:1388612 original size:64 final size:65
Alignment explanation
Indices: 1388461--1388621 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
1388451 GAATTAATTG
* * * ** *
1388461 AACATCGAATGCATTCCATGCACCGGTGCACACTCCATGCATCGATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
* **
1388526 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTCTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTT-TCA
1388589 A
65 A
1388590 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
1388622 CTTGGTGCAC
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 40 0.47
65 45 0.53
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCAA
Found at i:1388636 original size:64 final size:64
Alignment explanation
Indices: 1388412--1388641 Score: 225
Period size: 64 Copynumber: 3.6 Consensus size: 64
1388402 TATTCAAAGG
* * * *
1388412 CATGCACCGATGCATCAGTCCATGCATCGATGCATCGATGAAT-TAATT--GAACATCGAATGCA
1 CATGCATCGATGCA-CACTCCATGCATCGATGCATC-A-GAATAT-TTTCAAAACATCGAATGCA
*
1388474 TTC
62 TTT
* * *
1388477 CATGCACCGGTGCACACTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAAAACATCGAATGCATTT
* ** **
1388542 GATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTCTC-AAACATCGAATGCATTT
1 CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTT-TCAAAACATCGAATGCATTT
*** *
1388606 CATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 CATGCATCGATGCACACTCCATGCATCGATGCATCA
1388642 AGTGTTCCAA
Statistics
Matches: 139, Mismatches: 21, Indels: 11
0.81 0.12 0.06
Matches are distributed among these distances:
63 6 0.04
64 73 0.53
65 60 0.43
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (64 bp):
CATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAAAACATCGAATGCATTT
Found at i:1394411 original size:20 final size:21
Alignment explanation
Indices: 1394382--1394437 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
1394372 TTTGTGCTTC
*
1394382 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
1394402 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
1394424 ATGCATCGATGCAT
1 ATGCATCGATGCAT
1394438 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:1395722 original size:20 final size:21
Alignment explanation
Indices: 1395685--1395724 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1395675 AAATTAAGTT
1395685 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
1395706 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
1395725 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Done.