Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007807.1 Hibiscus syriacus cultivar Beakdansim tig00110126_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: 2195110
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 8 of 9
Found at i:1697465 original size:10 final size:10
Alignment explanation
Indices: 1697441--1697491 Score: 59
Period size: 10 Copynumber: 4.8 Consensus size: 10
1697431 CTATTTTTTT
1697441 CAAAAAAACACA
1 CAAAAAAA-A-A
1697453 CAAAAAAAAA
1 CAAAAAAAAA
1697463 CAAAAAAAAA
1 CAAAAAAAAA
1697473 GGC-AAAAAAAA
1 --CAAAAAAAAA
1697484 CAAAAAAA
1 CAAAAAAA
1697492 GCCAAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
9 1 0.03
10 17 0.47
11 9 0.25
12 9 0.25
ACGTcount: A:0.82, C:0.14, G:0.04, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:1697469 original size:22 final size:21
Alignment explanation
Indices: 1697441--1697491 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1697431 CTATTTTTTT
*
1697441 CAAAAAAACACACAAAAAAAAA
1 CAAAAAAAAACAC-AAAAAAAA
**
1697463 CAAAAAAAAAGGCAAAAAAAA
1 CAAAAAAAAACACAAAAAAAA
1697484 CAAAAAAA
1 CAAAAAAA
1697492 GCCAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.82, C:0.14, G:0.04, T:0.00
Consensus pattern (21 bp):
CAAAAAAAAACACAAAAAAAA
Found at i:1697479 original size:19 final size:19
Alignment explanation
Indices: 1697455--1697498 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
1697445 AAAACACACA
*
1697455 AAAAAAAACAAAAAAAAAGGC
1 AAAAAAAAC--AAAAAAAGCC
1697476 AAAAAAAACAAAAAAAGCC
1 AAAAAAAACAAAAAAAGCC
1697495 AAAA
1 AAAA
1697499 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.82, C:0.11, G:0.07, T:0.00
Consensus pattern (19 bp):
AAAAAAAACAAAAAAAGCC
Found at i:1705616 original size:20 final size:20
Alignment explanation
Indices: 1705591--1705642 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1705581 CGGCCAAGAG
* *
1705591 CATGTATCTTCATTAAAAAT
1 CATGTATTTTCATCAAAAAT
1705611 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
1705631 CATGTATTTTCA
1 CATGTATTTTCA
1705643 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:1709821 original size:20 final size:20
Alignment explanation
Indices: 1709796--1709847 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
1709786 CGGCCAAGAG
* *
1709796 CATGTATCTTCATTAAAAAT
1 CATGTATTTTCATCAAAAAT
1709816 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
1709836 CATGTATTTTCA
1 CATGTATTTTCA
1709848 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.06, T:0.42
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:1716042 original size:35 final size:36
Alignment explanation
Indices: 1715995--1716062 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 36
1715985 ATTTAGAAGT
*
1715995 TGGTGATAATATAGGCGTGAT-ATGGTGATGGAATA
1 TGGTGATAATATAGGCATGATAATGGTGATGGAATA
*
1716030 TGGTGATGATATAGGCATGATAATGGTGATGGA
1 TGGTGATAATATAGGCATGATAATGGTGATGGA
1716063 CAGATTGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 19 0.63
36 11 0.37
ACGTcount: A:0.31, C:0.03, G:0.35, T:0.31
Consensus pattern (36 bp):
TGGTGATAATATAGGCATGATAATGGTGATGGAATA
Found at i:1716439 original size:19 final size:20
Alignment explanation
Indices: 1716401--1716443 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
1716391 GAAACCCCTT
*
1716401 TGAAAACACATGATTTTTAA
1 TGAAAACACATGAATTTTAA
*
1716421 TGAAAATACAT-AATTTTAA
1 TGAAAACACATGAATTTTAA
1716440 TGAA
1 TGAA
1716444 GATAAATGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.49, C:0.07, G:0.09, T:0.35
Consensus pattern (20 bp):
TGAAAACACATGAATTTTAA
Found at i:1720572 original size:35 final size:37
Alignment explanation
Indices: 1720503--1720582 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
1720493 ATACTATTTC
*
1720503 CATCACCATAATCCATCTTCCATTATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
*
1720540 CATCACCATAGTCCATC-ACCA-TATCACGCCTATAT
1 CATCACCATAATCCATCTACCATTATCACGCCTATAT
1720575 CATCACCA
1 CATCACCA
1720583 AATTCTCAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 22 0.54
36 3 0.07
37 16 0.39
ACGTcount: A:0.31, C:0.38, G:0.04, T:0.28
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCACGCCTATAT
Found at i:1721000 original size:12 final size:12
Alignment explanation
Indices: 1720974--1721020 Score: 73
Period size: 12 Copynumber: 4.2 Consensus size: 12
1720964 TGGACTAGAG
1720974 GTAGCT-GGA-A
1 GTAGCTGGGAGA
1720984 GTAGCTGGGAGA
1 GTAGCTGGGAGA
1720996 GTAGCTGGGAGA
1 GTAGCTGGGAGA
1721008 GTAGCTGGG-GA
1 GTAGCTGGGAGA
1721019 GT
1 GT
1721021 TGAGAAGATG
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
10 6 0.17
11 7 0.20
12 22 0.63
ACGTcount: A:0.23, C:0.09, G:0.49, T:0.19
Consensus pattern (12 bp):
GTAGCTGGGAGA
Found at i:1725673 original size:19 final size:19
Alignment explanation
Indices: 1725649--1725697 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
1725639 TGACATGATT
1725649 TTTAATGAAAAAACAAGAC
1 TTTAATGAAAAAACAAGAC
1725668 TTTAATGAAAAAACAAGAC
1 TTTAATGAAAAAACAAGAC
1725687 TTTAATGAAAA
1 TTTAATGAAAA
1725698 TACATGCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.57, C:0.08, G:0.10, T:0.24
Consensus pattern (19 bp):
TTTAATGAAAAAACAAGAC
Found at i:1752906 original size:30 final size:30
Alignment explanation
Indices: 1752870--1752926 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
1752860 GTAACTCACC
1752870 ATTTGGAACAAAACAACACCCATGTGCATG
1 ATTTGGAACAAAACAACACCCATGTGCATG
*
1752900 ATTTGGAACAAAACAGCACCCATGTGC
1 ATTTGGAACAAAACAACACCCATGTGC
1752927 GTGCCAGCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.19
Consensus pattern (30 bp):
ATTTGGAACAAAACAACACCCATGTGCATG
Found at i:1753683 original size:25 final size:25
Alignment explanation
Indices: 1753630--1753687 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 25
1753620 ATTCATCTTG
*
1753630 AAAAAAAAAGAGAATTCCGAAAATT
1 AAAAAAAAACAGAATTCCGAAAATT
1753655 AAAAAAAAACA-AATTCCGAAAATT
1 AAAAAAAAACAGAATTCCGAAAATT
1753679 AAAAAAAAA
1 AAAAAAAAA
1753688 AAAGAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 22 0.69
25 10 0.31
ACGTcount: A:0.71, C:0.09, G:0.07, T:0.14
Consensus pattern (25 bp):
AAAAAAAAACAGAATTCCGAAAATT
Found at i:1759405 original size:30 final size:30
Alignment explanation
Indices: 1759369--1759425 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
1759359 GTAACTCACC
1759369 ATTTGGAACAAAACA-ACACCCATGTGCATG
1 ATTTGGAACAAAACAGA-ACCCATGTGCATG
1759399 ATTTGGAACAAAACAGAACCCATGTGC
1 ATTTGGAACAAAACAGAACCCATGTGC
1759426 GTGCCAGCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.40, C:0.23, G:0.18, T:0.19
Consensus pattern (30 bp):
ATTTGGAACAAAACAGAACCCATGTGCATG
Found at i:1761541 original size:39 final size:39
Alignment explanation
Indices: 1761487--1761564 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
1761477 GAACAAGCTT
1761487 CCTAGCCAAGTCCTTGTGAGCTCCTTAACATTATGTTCA
1 CCTAGCCAAGTCCTTGTGAGCTCCTTAACATTATGTTCA
1761526 CCTAGCCAAGTCCTTGTGAGCTCCTTAACATTATGTTCA
1 CCTAGCCAAGTCCTTGTGAGCTCCTTAACATTATGTTCA
1761565 GCTACATTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.33
Consensus pattern (39 bp):
CCTAGCCAAGTCCTTGTGAGCTCCTTAACATTATGTTCA
Found at i:1763234 original size:26 final size:28
Alignment explanation
Indices: 1763195--1763248 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
1763185 ATAAGGCTCC
1763195 CTAGAACACCCATGTG-CATGCCATATGA
1 CTAGAACACCCATGTGCCATG-CATATGA
1763223 CTAG-ACA-CCATGTGCCATGCATATGA
1 CTAGAACACCCATGTGCCATGCATATGA
1763249 TCTCATTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 14 0.56
27 7 0.28
28 4 0.16
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (28 bp):
CTAGAACACCCATGTGCCATGCATATGA
Found at i:1766183 original size:23 final size:24
Alignment explanation
Indices: 1766135--1766185 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
1766125 TCTTTCTTTC
1766135 TTTTTTTAATTTTCGGAATTTGTT
1 TTTTTTTAATTTTCGGAATTTGTT
1766159 TTTTTTTAATTTTCGGAATTT-TT
1 TTTTTTTAATTTTCGGAATTTGTT
1766182 TTTT
1 TTTT
1766186 CAGGATGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.16, C:0.04, G:0.10, T:0.71
Consensus pattern (24 bp):
TTTTTTTAATTTTCGGAATTTGTT
Found at i:1779570 original size:20 final size:21
Alignment explanation
Indices: 1779545--1779590 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1779535 TAATTTAATA
*
1779545 TAGGATGATTAATTATCTT-T
1 TAGGATCATTAATTATCTTAT
* *
1779565 TAGGATCATTTATTATTTTAT
1 TAGGATCATTAATTATCTTAT
1779586 TAGGA
1 TAGGA
1779591 ATTAAGGTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.30, C:0.04, G:0.15, T:0.50
Consensus pattern (21 bp):
TAGGATCATTAATTATCTTAT
Found at i:1780448 original size:15 final size:14
Alignment explanation
Indices: 1780428--1780489 Score: 72
Period size: 14 Copynumber: 4.2 Consensus size: 14
1780418 TCAAAAAAAC
1780428 AAAAAAAAA-CAAA
1 AAAAAAAAAGCAAA
1780441 AAACAAAAAAGGCAAA
1 AAA-AAAAAA-GCAAA
*
1780457 AAAAAAAAGGCAAA
1 AAAAAAAAAGCAAA
1780471 AAAAAAAAGAGCCAAA
1 AAAAAAAA-AG-CAAA
1780487 AAA
1 AAA
1780490 GCCAAAATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
13 3 0.07
14 19 0.45
15 6 0.14
16 14 0.33
ACGTcount: A:0.81, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAGCAAA
Found at i:1780450 original size:14 final size:13
Alignment explanation
Indices: 1780420--1780478 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 13
1780410 ATTTTTTTTC
1780420 AAAAAAACAAAAA
1 AAAAAAACAAAAA
*
1780433 AAAACAAA-AAACA
1 AAAA-AAACAAAAA
**
1780446 AAAAAGGCAAAAA
1 AAAAAAACAAAAA
*
1780459 AAAAAAGGCAAAAA
1 AAAAAA-ACAAAAA
1780473 AAAAAA
1 AAAAAA
1780479 GAGCCAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
12 1 0.03
13 21 0.55
14 16 0.42
ACGTcount: A:0.85, C:0.08, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:1780473 original size:16 final size:16
Alignment explanation
Indices: 1780421--1780489 Score: 70
Period size: 16 Copynumber: 4.4 Consensus size: 16
1780411 TTTTTTTTCA
**
1780421 AAAAAACAAAAAAAAAC
1 AAAAAA-AAAAAAAGGC
*
1780438 AAAAAACAAAAAAGGC
1 AAAAAAAAAAAAAGGC
1780454 --AAAAAAAAAAAGGC
1 AAAAAAAAAAAAAGGC
* *
1780468 AAAAAAAAAAAGAGCC
1 AAAAAAAAAAAAAGGC
1780484 AAAAAA
1 AAAAAA
1780490 GCCAAAATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
14 13 0.30
16 25 0.57
17 6 0.14
ACGTcount: A:0.81, C:0.10, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGGC
Found at i:1780479 original size:14 final size:14
Alignment explanation
Indices: 1780439--1780489 Score: 75
Period size: 14 Copynumber: 3.4 Consensus size: 14
1780429 AAAAAAAACA
1780439 AAAAACAAAAAAGGC
1 AAAAA-AAAAAAGGC
1780454 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
1780468 AAAAAAAAAAAGAGCC
1 AAAAAAAAAAAG-G-C
1780484 AAAAAA
1 AAAAAA
1780490 GCCAAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
14 21 0.62
15 6 0.18
16 7 0.21
ACGTcount: A:0.78, C:0.10, G:0.12, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:1787396 original size:28 final size:28
Alignment explanation
Indices: 1787364--1787445 Score: 155
Period size: 28 Copynumber: 2.9 Consensus size: 28
1787354 TGAATTAACT
1787364 AAACAAATGATGAACATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
1787392 AAACAAATGATGAACATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
*
1787420 AAATAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
1787446 TGAATGTGAG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:1790195 original size:19 final size:20
Alignment explanation
Indices: 1790152--1790205 Score: 83
Period size: 19 Copynumber: 2.7 Consensus size: 20
1790142 GAAACCCCTT
1790152 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGA-TTTTAAA
1790173 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
*
1790192 TGAAGATACATGAT
1 TGAAAATACATGAT
1790206 CTTGGCCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 15 0.47
20 4 0.12
21 13 0.41
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:1793495 original size:8 final size:8
Alignment explanation
Indices: 1793465--1793508 Score: 54
Period size: 8 Copynumber: 5.2 Consensus size: 8
1793455 TCTTTTTGAA
1793465 CTTCTCTTT
1 CTTCT-TTT
1793474 -TTCTTTT
1 CTTCTTTT
1793481 CTTTTCTTTT
1 C--TTCTTTT
1793491 CTTCTTTT
1 CTTCTTTT
1793499 CTTCTTTT
1 CTTCTTTT
1793507 CT
1 CT
1793509 GATTTTTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
7 3 0.09
8 21 0.66
10 8 0.25
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (8 bp):
CTTCTTTT
Found at i:1793803 original size:18 final size:18
Alignment explanation
Indices: 1793780--1793816 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1793770 AATAAAGGGT
1793780 AATAAT-ATAAGTAATGAA
1 AATAATAATAAG-AATGAA
1793798 AATAATAATAAGAATGAA
1 AATAATAATAAGAATGAA
1793816 A
1 A
1793817 TGAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.65, C:0.00, G:0.11, T:0.24
Consensus pattern (18 bp):
AATAATAATAAGAATGAA
Found at i:1794276 original size:19 final size:21
Alignment explanation
Indices: 1794233--1794284 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1794223 GAAACCCCTT
1794233 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
1794254 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
1794273 TGAAGATACATG
1 TGAAAATACATG
1794285 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:1797688 original size:24 final size:24
Alignment explanation
Indices: 1797642--1797688 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1797632 AGAAAATAAG
**
1797642 CACTCAAAAAGAAGAAATTGAAAA
1 CACTCAAAAAGAAGAAAAAGAAAA
1797666 CACTC-AAAAGAAGAAAAAAGAAA
1 CACTCAAAAAGAAG-AAAAAGAAA
1797689 GAAAAGTTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.66, C:0.13, G:0.13, T:0.09
Consensus pattern (24 bp):
CACTCAAAAAGAAGAAAAAGAAAA
Found at i:1799203 original size:16 final size:16
Alignment explanation
Indices: 1799179--1799210 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1799169 TAGTTAGCTC
1799179 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
*
1799195 ATTTTCATTCTAACAT
1 ATTTGCATTCTAACAT
1799211 TGGTGGAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:1806524 original size:20 final size:21
Alignment explanation
Indices: 1806487--1806525 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1806477 GATGGTCTTG
*
1806487 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
1806508 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
1806526 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:1815284 original size:24 final size:24
Alignment explanation
Indices: 1815230--1815284 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
1815220 GAAAAATTAG
*
1815230 AAAAG-AAGCACTCAAAAAGAAGA
1 AAAAGAAAACACTCAAAAAGAAGA
**
1815253 AATTGAAAACACTC-AAAAGAAGAA
1 AAAAGAAAACACTCAAAAAGAAG-A
1815277 AAAAGAAA
1 AAAAGAAA
1815285 GAAAAGTTGG
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.11, G:0.15, T:0.07
Consensus pattern (24 bp):
AAAAGAAAACACTCAAAAAGAAGA
Found at i:1818366 original size:28 final size:28
Alignment explanation
Indices: 1818334--1818387 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
1818324 TGAATTAACT
1818334 AAACAAATGATGAACATGCTGTTATGCA
1 AAACAAATGATGAACATGCTGTTATGCA
1818362 AAACAAATGATGAACATGCTGTTATG
1 AAACAAATGATGAACATGCTGTTATG
1818388 TGAATGTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.26
Consensus pattern (28 bp):
AAACAAATGATGAACATGCTGTTATGCA
Found at i:1824102 original size:10 final size:10
Alignment explanation
Indices: 1824087--1824112 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1824077 TCCAACTTTC
1824087 TTTCTTTCCT
1 TTTCTTTCCT
1824097 TTTCTTTCCT
1 TTTCTTTCCT
1824107 TTTCTT
1 TTTCTT
1824113 CTTTTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTCTTTCCT
Found at i:1845368 original size:22 final size:23
Alignment explanation
Indices: 1845339--1845382 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
1845329 GTTGTACGAG
1845339 TCTTTTTCTT-TT-CTTTTTTTT
1 TCTTTTTCTTGTTGCTTTTTTTT
1845360 TCTTCTTTCTTGTTGCTTTTTTT
1 TCTT-TTTCTTGTTGCTTTTTTT
1845383 ATTGTAGCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 6 0.30
23 2 0.10
24 8 0.40
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (23 bp):
TCTTTTTCTTGTTGCTTTTTTTT
Found at i:1855198 original size:19 final size:20
Alignment explanation
Indices: 1855174--1855224 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1855164 CGGCCAAGAG
* *
1855174 CATGTATCTTCAT-GAAAAT
1 CATGTATTTTCATCAAAAAT
1855193 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
1855213 CATGTATTTTCA
1 CATGTATTTTCA
1855225 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:1858581 original size:36 final size:36
Alignment explanation
Indices: 1858497--1858581 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
1858487 ATGGTGATGA
* *
1858497 AATGGTAATGGAATATGGTAATGATATAGGCGTGAT
1 AATGGTGATGGACTATGGTAATGATATAGGCGTGAT
*
1858533 AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGACTATGGTAATGATATAGGCGTGAT
1858569 AATGGTGATGGAC
1 AATGGTGATGGAC
1858582 AGATTGTATC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (36 bp):
AATGGTGATGGACTATGGTAATGATATAGGCGTGAT
Found at i:1862335 original size:23 final size:24
Alignment explanation
Indices: 1862292--1862340 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
1862282 AAAGGTTAAG
*
1862292 AAAGATGATAAGGTAATGAAAAGA
1 AAAGATGATAAGATAATGAAAAGA
*
1862316 AAAGATGA-AAGAATAA-GAAATGA
1 AAAGATGATAAG-ATAATGAAAAGA
1862339 AA
1 AA
1862341 TAGTAAGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.63, C:0.00, G:0.22, T:0.14
Consensus pattern (24 bp):
AAAGATGATAAGATAATGAAAAGA
Found at i:1863049 original size:36 final size:36
Alignment explanation
Indices: 1862965--1863049 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
1862955 ATGGTGATGA
* *
1862965 AATGGTAATGGAATATGGTAATGATATAGGCGTGAT
1 AATGGTGATGGACTATGGTAATGATATAGGCGTGAT
*
1863001 AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGACTATGGTAATGATATAGGCGTGAT
1863037 AATGGTGATGGAC
1 AATGGTGATGGAC
1863050 AGATTGTATC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.32, C:0.05, G:0.34, T:0.29
Consensus pattern (36 bp):
AATGGTGATGGACTATGGTAATGATATAGGCGTGAT
Found at i:1865045 original size:35 final size:36
Alignment explanation
Indices: 1864965--1865047 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
1864955 AGATACTATC
* *
1864965 TATTCATCACCACCTTCCATCACCATTTTCACGCCTA
1 TATT-ATCACCACATTCCATCACCATTATCACGCCTA
** * *
1865002 TAACATCACCATATTCCATTACCA-TATCACGCCTA
1 TATTATCACCACATTCCATCACCATTATCACGCCTA
1865037 TATTATCACCA
1 TATTATCACCA
1865048 ACTTATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 19 0.50
36 17 0.45
37 2 0.05
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (36 bp):
TATTATCACCACATTCCATCACCATTATCACGCCTA
Found at i:1866727 original size:36 final size:36
Alignment explanation
Indices: 1866680--1866764 Score: 143
Period size: 36 Copynumber: 2.4 Consensus size: 36
1866670 GATACAATCT
1866680 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
1866716 GTCCATCACCATTATCACGCCTATATCATTACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
1866752 TTCCATTACCATT
1 GTCCATCACCATT
1866765 TCATCACCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1872061 original size:12 final size:12
Alignment explanation
Indices: 1872044--1872069 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1872034 TATTTTTTTT
1872044 AAAAAAAAACAA
1 AAAAAAAAACAA
1872056 AAAAAAAAACAA
1 AAAAAAAAACAA
1872068 AA
1 AA
1872070 TAAATCCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:1872156 original size:16 final size:16
Alignment explanation
Indices: 1872105--1872160 Score: 71
Period size: 16 Copynumber: 3.6 Consensus size: 16
1872095 TTTTTTTAAA
**
1872105 AAAAAAAAAAAAAAAC
1 AAAAAAAAAAAAAGGC
*
1872121 AAAAAACAAAAAAGGC
1 AAAAAAAAAAAAAGGC
1872137 --AAAAAAAAAAAGGC
1 AAAAAAAAAAAAAGGC
1872151 AAAAAAAAAA
1 AAAAAAAAAA
1872161 GAGCCCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
14 13 0.38
16 21 0.62
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAAGGC
Found at i:1872161 original size:13 final size:14
Alignment explanation
Indices: 1872107--1872160 Score: 72
Period size: 14 Copynumber: 3.7 Consensus size: 14
1872097 TTTTTAAAAA
**
1872107 AAAAAAAAAAAAAC
1 AAAAAAAAAAAGGC
1872121 AAAAAACAAAAAAGGC
1 -AAAAA-AAAAAAGGC
1872137 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
1872151 AAAAAAAAAA
1 AAAAAAAAAA
1872161 GAGCCCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 19 0.53
15 10 0.28
16 7 0.19
ACGTcount: A:0.85, C:0.07, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:1872170 original size:30 final size:30
Alignment explanation
Indices: 1872107--1872173 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
1872097 TTTTTAAAAA
*
1872107 AAAAAAAAAAAAACAAAAAACAAAAAAGGC
1 AAAAAAAAAAAAACAAAAAACAAAAAAGCC
** *
1872137 AAAAAAAAAAAGGCAAAAAA-AAAAGAGCC
1 AAAAAAAAAAAAACAAAAAACAAAAAAGCC
*
1872166 CAAAAAAA
1 AAAAAAAA
1872174 GCCAAAATTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 14 0.44
30 18 0.56
ACGTcount: A:0.81, C:0.10, G:0.09, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAAAACAAAAAACAAAAAAGCC
Found at i:1872173 original size:14 final size:13
Alignment explanation
Indices: 1872123--1872161 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 13
1872113 AAAAAAACAA
1872123 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
1872137 AAAAAAAAAAAGGC
1 -AAAAAAAAAAGGC
1872151 AAAAAAAAAAG
1 AAAAAAAAAAG
1872162 AGCCCAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.46
14 9 0.38
15 4 0.17
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:1873667 original size:52 final size:53
Alignment explanation
Indices: 1873604--1873708 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 53
1873594 AGGAGATGCA
1873604 GTCCTTCTCAATA-GACTAACATAACCG-AAAAGAAGAGGTCACCGTGTCAAG
1 GTCCTTCTCAATAGGACTAACATAACCGAAAAAGAAGAGGTCACCGTGTCAAG
1873655 GTCCTTACTCAATAGGACTAACATAACCGAAAAAGAAGAGGTCACCGTGTCAAG
1 GTCCTT-CTCAATAGGACTAACATAACCGAAAAAGAAGAGGTCACCGTGTCAAG
1873709 ATTCATCGTC
Statistics
Matches: 51, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
51 6 0.12
52 7 0.14
53 14 0.27
54 24 0.47
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (53 bp):
GTCCTTCTCAATAGGACTAACATAACCGAAAAAGAAGAGGTCACCGTGTCAAG
Found at i:1878216 original size:32 final size:31
Alignment explanation
Indices: 1878168--1878227 Score: 111
Period size: 32 Copynumber: 1.9 Consensus size: 31
1878158 GATACAATCT
1878168 GTCCATCACATTATCACGCCTATATCATATA
1 GTCCATCACATTATCACGCCTATATCATATA
1878199 GTCCATCACCATTATCACGCCTATATCAT
1 GTCCATCA-CATTATCACGCCTATATCAT
1878228 TACCATATTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 8 0.29
32 20 0.71
ACGTcount: A:0.30, C:0.32, G:0.07, T:0.32
Consensus pattern (31 bp):
GTCCATCACATTATCACGCCTATATCATATA
Found at i:1888366 original size:35 final size:36
Alignment explanation
Indices: 1888286--1888368 Score: 96
Period size: 35 Copynumber: 2.3 Consensus size: 36
1888276 AGATACTATC
* *
1888286 TATTCATCACCACCTTCCATCACCATTTTCACGCCTA
1 TATT-ATCACCACATTCCATCACCATTATCACGCCTA
** * *
1888323 TAACATCACCATATTCCATTACCA-TATCACGCCTA
1 TATTATCACCACATTCCATCACCATTATCACGCCTA
1888358 TATTATCACCA
1 TATTATCACCA
1888369 ACTTATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
35 19 0.50
36 17 0.45
37 2 0.05
ACGTcount: A:0.30, C:0.36, G:0.02, T:0.31
Consensus pattern (36 bp):
TATTATCACCACATTCCATCACCATTATCACGCCTA
Found at i:1889389 original size:35 final size:37
Alignment explanation
Indices: 1889320--1889399 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
1889310 ATACTATTTC
*
1889320 CATCACCATAATCCATCTTCCATTATCAAGCCTATAT
1 CATCACCATAATCCATCTACCATTATCAAGCCTATAT
* *
1889357 CATCACCATAGTCCATC-ACCA-TATCATGCCTATAT
1 CATCACCATAATCCATCTACCATTATCAAGCCTATAT
1889392 CATCACCA
1 CATCACCA
1889400 AATTCTCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 3 0.08
37 16 0.40
ACGTcount: A:0.33, C:0.35, G:0.04, T:0.29
Consensus pattern (37 bp):
CATCACCATAATCCATCTACCATTATCAAGCCTATAT
Found at i:1893258 original size:23 final size:22
Alignment explanation
Indices: 1893228--1893270 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1893218 TTGGTGCTGG
1893228 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
1893251 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
1893271 AGAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:1895609 original size:15 final size:16
Alignment explanation
Indices: 1895589--1895618 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1895579 AAACTAGTGA
1895589 CCTCTTTTTC-TTTTG
1 CCTCTTTTTCGTTTTG
1895604 CCTCTTTTTCGTTTT
1 CCTCTTTTTCGTTTT
1895619 TTACTTTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.00, C:0.27, G:0.07, T:0.67
Consensus pattern (16 bp):
CCTCTTTTTCGTTTTG
Found at i:1897458 original size:21 final size:21
Alignment explanation
Indices: 1897434--1897479 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1897424 TTTTTTGAAA
*
1897434 TTTTGGCTTTTTTTTTTATTT
1 TTTTGGCCTTTTTTTTTATTT
*
1897455 TTTT-GCCTTTTTTTTTGTTT
1 TTTTGGCCTTTTTTTTTATTT
1897475 TTTTG
1 TTTTG
1897480 AAAAAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.02, C:0.07, G:0.11, T:0.80
Consensus pattern (21 bp):
TTTTGGCCTTTTTTTTTATTT
Found at i:1897837 original size:23 final size:22
Alignment explanation
Indices: 1897807--1897849 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1897797 TTGGTGCTGG
1897807 AAACAAGATAAAAAATAAGATTA
1 AAACAAGATAAAAAA-AAGATTA
*
1897830 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAAAAAAGAT
1897850 AGAGGAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.70, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAAAAAAGATTA
Found at i:1902265 original size:19 final size:21
Alignment explanation
Indices: 1902222--1902273 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1902212 GAAACCCCTT
1902222 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
1902243 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
1902262 TGAAGATACATG
1 TGAAAATACATG
1902274 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:1905604 original size:5 final size:5
Alignment explanation
Indices: 1905554--1905583 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1905544 TTTGAACTTC
1905554 TCTTT TACTTT TCTTT TCTTT TCTTT TCTT
1 TCTTT T-CTTT TCTTT TCTTT TCTTT TCTT
1905584 CTTTTCTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (5 bp):
TCTTT
Found at i:1906369 original size:19 final size:21
Alignment explanation
Indices: 1906326--1906377 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1906316 GAAACCCCTT
1906326 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
1906347 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
1906366 TGAAGATACATG
1 TGAAAATACATG
1906378 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:1908726 original size:11 final size:13
Alignment explanation
Indices: 1908694--1908723 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1908684 TGGCCAAAGA
1908694 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1908707 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1908719 TGAAA
1 TGAAA
1908724 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:1909969 original size:19 final size:20
Alignment explanation
Indices: 1909945--1909995 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1909935 CGGCCAAGAG
* *
1909945 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
1909964 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
1909984 CATGTATTTTCA
1 CATGTATTTTCA
1909996 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:1910722 original size:17 final size:16
Alignment explanation
Indices: 1910701--1910758 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 16
1910691 ATTGGAGTGC
1910701 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
1910717 ACAAAAGAAGAGAAAATTCAG
1 A-AAAAGAA-AGAAAA---AG
1910738 -AAAAG-AAGAAAAAG
1 AAAAAGAAAGAAAAAG
1910752 AAAAAGA
1 AAAAAGA
1910759 TTTCAAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
14 2 0.06
15 5 0.14
16 1 0.03
17 13 0.37
18 7 0.20
19 5 0.14
21 2 0.06
ACGTcount: A:0.74, C:0.03, G:0.19, T:0.03
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:1919149 original size:19 final size:20
Alignment explanation
Indices: 1919125--1919175 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
1919115 CGGCCAAGAG
* *
1919125 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
1919144 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
1919164 CATGTATTTTCA
1 CATGTATTTTCA
1919176 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:1921110 original size:21 final size:19
Alignment explanation
Indices: 1921086--1921137 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
1921076 GAAACCCCTT
1921086 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGA-TTTT-AA
*
1921107 TGAAAATACAAGATTTTAA
1 TGAAAATACATGATTTTAA
*
1921126 TGAAGATACATG
1 TGAAAATACATG
1921138 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (19 bp):
TGAAAATACATGATTTTAA
Found at i:1921129 original size:19 final size:21
Alignment explanation
Indices: 1921086--1921135 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1921076 GAAACCCCTT
*
1921086 TGAAAATACATGATTTTTAAA
1 TGAAAATACAAGATTTTTAAA
1921107 TGAAAATACAAGA-TTTT-AA
1 TGAAAATACAAGATTTTTAAA
*
1921126 TGAAGATACA
1 TGAAAATACA
1921136 TGCTCTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.32
Consensus pattern (21 bp):
TGAAAATACAAGATTTTTAAA
Found at i:1931275 original size:19 final size:21
Alignment explanation
Indices: 1931232--1931283 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
1931222 GAAACCCCTT
*
1931232 TGAAAATAAATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
1931253 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
1931272 TGAAGATACATG
1 TGAAAATACATG
1931284 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.45
20 4 0.14
21 12 0.41
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:1934519 original size:11 final size:11
Alignment explanation
Indices: 1934505--1934562 Score: 50
Period size: 11 Copynumber: 5.2 Consensus size: 11
1934495 TGGAGTGCAA
1934505 AAAAAAGAAAG
1 AAAAAAGAAAG
1934516 AAAAAAGACAA-
1 AAAAAAGA-AAG
*
1934527 AAAGAAG-AAG
1 AAAAAAGAAAG
1934537 AAAAGAAGAAAAG
1 AAAA-AAG-AAAG
1934550 AAAAGAA-AAAG
1 AAAA-AAGAAAG
1934561 AA
1 AA
1934563 TTCAAAAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 2 0.05
10 3 0.08
11 23 0.57
12 2 0.05
13 10 0.25
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:1934530 original size:19 final size:18
Alignment explanation
Indices: 1934505--1934559 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 18
1934495 TGGAGTGCAA
1934505 AAAAAAGAAAGAAAAAAG
1 AAAAAAGAAAGAAAAAAG
1934523 ACAAAAAG-AAGAAGAAAAG
1 A-AAAAAGAAAGAA-AAAAG
1934542 AAGAAAAGAAAAGAAAAA
1 AA-AAAAG-AAAGAAAAA
1934560 GAATTCAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 7 0.22
19 17 0.53
20 3 0.09
21 5 0.16
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAAG
Found at i:1941127 original size:21 final size:19
Alignment explanation
Indices: 1941089--1941135 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 19
1941079 GGGTAATAAT
1941089 ATAAGTAATGAAAATAAATA
1 ATAAG-AATGAAAATAAATA
1941109 ATAAGAATGAATGAATAAATA
1 ATAAGAATGAA--AATAAATA
*
1941130 AAAAGA
1 ATAAGA
1941136 TAGAGATGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 5 0.21
21 13 0.54
ACGTcount: A:0.66, C:0.00, G:0.13, T:0.21
Consensus pattern (19 bp):
ATAAGAATGAAAATAAATA
Found at i:1944493 original size:26 final size:26
Alignment explanation
Indices: 1944443--1944506 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 26
1944433 CTTGGCTTGC
1944443 TTTTCTCTTTT-TGAAATCTTTTTCT
1 TTTTCTCTTTTCTGAAATCTTTTTCT
1944468 TTTTCTTCTTTTCTG-AAT-TTTCTTCT
1 TTTTC-TCTTTTCTGAAATCTTT-TTCT
*
1944494 TTTTGTCTTTTCT
1 TTTTCTCTTTTCT
1944507 ATCGTTTTGC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 16 0.46
26 17 0.49
27 2 0.06
ACGTcount: A:0.08, C:0.17, G:0.05, T:0.70
Consensus pattern (26 bp):
TTTTCTCTTTTCTGAAATCTTTTTCT
Found at i:1945958 original size:16 final size:16
Alignment explanation
Indices: 1945937--1945968 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
1945927 TCTTCCACCA
1945937 ATGTTAGAATGAAAAT
1 ATGTTAGAATGAAAAT
*
1945953 ATGTTAGAATGCAAAT
1 ATGTTAGAATGAAAAT
1945969 GAGCTAACTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.19, T:0.31
Consensus pattern (16 bp):
ATGTTAGAATGAAAAT
Found at i:1957040 original size:36 final size:35
Alignment explanation
Indices: 1956989--1957099 Score: 143
Period size: 35 Copynumber: 3.2 Consensus size: 35
1956979 TAAGATACTA
1956989 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * *
1957024 CCTATAACATCACCATCTTCCATTACCATTGCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * *
1957059 CCTATATCATTACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
*
1957094 CTTATA
1 CCTATA
1957100 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:0.28, C:0.35, G:0.04, T:0.33
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:1957729 original size:16 final size:14
Alignment explanation
Indices: 1957703--1957760 Score: 62
Period size: 16 Copynumber: 3.8 Consensus size: 14
1957693 GAGTTGTAAG
*
1957703 TTATCTTCATTTTC
1 TTATTTTCATTTTC
1957717 TTACTATTTCATTTTC
1 TTA-T-TTTCATTTTC
1957733 TTATTCTTTCATTTTTC
1 TTA-T-TTTCA-TTTTC
1957750 TTATTTTCATT
1 TTATTTTCATT
1957761 ACTTTATCCT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 5 0.13
15 6 0.16
16 19 0.50
17 8 0.21
ACGTcount: A:0.16, C:0.17, G:0.00, T:0.67
Consensus pattern (14 bp):
TTATTTTCATTTTC
Found at i:1957750 original size:17 final size:16
Alignment explanation
Indices: 1957703--1957754 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
1957693 GAGTTGTAAG
1957703 TTATCTTCATTTTCTTA
1 TTAT-TTCATTTTCTTA
*
1957720 CTATTTCATTTTCTTA
1 TTATTTCATTTTCTTA
*
1957736 TTCTTTCATTTTTCTTA
1 TTATTTCA-TTTTCTTA
1957753 TT
1 TT
1957755 TTCATTACTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
16 18 0.58
17 13 0.42
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATTTCATTTTCTTA
Found at i:1961615 original size:35 final size:35
Alignment explanation
Indices: 1961514--1961615 Score: 132
Period size: 35 Copynumber: 2.9 Consensus size: 35
1961504 CCTAAACATC
*
1961514 ACCATCTTCCATCACCATTTTCACGCCTATAACAAT
1 ACCATCTTCCATCACCA-TTTCACGCCTATATCAAT
* * *
1961550 ACCATCTTCCATTACCATTACACGCCTATATCATT
1 ACCATCTTCCATCACCATTTCACGCCTATATCAAT
* * *
1961585 ACCATCTTCTATCACTATTTCACGCTTATAT
1 ACCATCTTCCATCACCATTTCACGCCTATAT
1961616 AACCACCAAT
Statistics
Matches: 57, Mismatches: 9, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
35 41 0.72
36 16 0.28
ACGTcount: A:0.28, C:0.33, G:0.03, T:0.35
Consensus pattern (35 bp):
ACCATCTTCCATCACCATTTCACGCCTATATCAAT
Found at i:1962253 original size:16 final size:16
Alignment explanation
Indices: 1962214--1962265 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
1962204 GAGTTGTAAG
1962214 TTATCTTCATTTTCTTA
1 TTAT-TTCATTTTCTTA
*
1962231 CTATTTCATTTTCTTA
1 TTATTTCATTTTCTTA
* *
1962247 TTCTTTCTTTTTTCTTA
1 TTATTTC-ATTTTCTTA
1962264 TT
1 TT
1962266 TTCATTACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
16 17 0.57
17 13 0.43
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTTCATTTTCTTA
Found at i:1964690 original size:19 final size:18
Alignment explanation
Indices: 1964665--1964712 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 18
1964655 AAAAAAAACA
1964665 AAAAAAAAACACAAAAAGGC
1 AAAAAAAAACA-AAAAA-GC
1964685 ACAAAAAAAACAAAAAAGC
1 A-AAAAAAAACAAAAAAGC
1964704 AAAAAAAAA
1 AAAAAAAAA
1964713 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.30
19 3 0.11
20 6 0.22
21 10 0.37
ACGTcount: A:0.81, C:0.12, G:0.06, T:0.00
Consensus pattern (18 bp):
AAAAAAAAACAAAAAAGC
Found at i:1964711 original size:10 final size:10
Alignment explanation
Indices: 1964653--1964701 Score: 53
Period size: 11 Copynumber: 4.7 Consensus size: 10
1964643 TCTATTTTTT
1964653 CAAAAAAAAA
1 CAAAAAAAAA
1964663 CAAAAAAAAAA
1 C-AAAAAAAAA
* **
1964674 CACAAAAAGG
1 CAAAAAAAAA
1964684 CACAAAAAAAA
1 CA-AAAAAAAA
1964695 CAAAAAA
1 CAAAAAA
1964702 GCAAAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
10 14 0.45
11 17 0.55
ACGTcount: A:0.82, C:0.14, G:0.04, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:1964719 original size:19 final size:18
Alignment explanation
Indices: 1964665--1964719 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 18
1964655 AAAAAAAACA
1964665 AAAAAAAAACACAAAAAGGC
1 AAAAAAAAAC-CAAAAA-GC
*
1964685 ACAAAAAAAACAAAAAAGC
1 A-AAAAAAAACCAAAAAGC
1964704 AAAAAAAAAGCCAAAA
1 AAAAAAAAA-CCAAAA
1964720 TTTCAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 8 0.26
19 8 0.26
20 6 0.19
21 9 0.29
ACGTcount: A:0.78, C:0.15, G:0.07, T:0.00
Consensus pattern (18 bp):
AAAAAAAAACCAAAAAGC
Found at i:1973763 original size:36 final size:35
Alignment explanation
Indices: 1973712--1973822 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
1973702 TAAGATACTA
1973712 CCTA-AACATCACCATCTTCCATCACCATTTTCACG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* * *
1973747 CCTATAACATCACCATCTTTCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * * *
1973782 CTTATATCATTACCATCTTCTATCACCATTTCATG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
1973817 CCTATA
1 CCTATA
1973823 TAACCACCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
35 42 0.67
36 21 0.33
ACGTcount: A:0.28, C:0.34, G:0.04, T:0.34
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Found at i:1976973 original size:13 final size:14
Alignment explanation
Indices: 1976957--1976989 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
1976947 AAAGAACAGT
*
1976957 GAAGAAGTAAAA-G
1 GAAGAAGCAAAAGG
1976970 GAAGAAGCAAAAGG
1 GAAGAAGCAAAAGG
1976984 GAAGAA
1 GAAGAA
1976990 TAAGATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.61, C:0.03, G:0.33, T:0.03
Consensus pattern (14 bp):
GAAGAAGCAAAAGG
Found at i:1978785 original size:11 final size:13
Alignment explanation
Indices: 1978753--1978782 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1978743 TGGCCAAAGA
1978753 TGAAAAGGTATGT
1 TGAAAAGGTATGT
1978766 TGAAAAGGTATG-
1 TGAAAAGGTATGT
1978778 TGAAA
1 TGAAA
1978783 GGTGTCTAGT
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:1980031 original size:28 final size:28
Alignment explanation
Indices: 1979998--1980053 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1979988 TCGTGGGGTT
* *
1979998 CATAACAGCATGTTCATCATTTGTTTTG
1 CATAACAGCATATTCATCATTAGTTTTG
*
1980026 CATAACAGCATATTTATCATTAGTTTTG
1 CATAACAGCATATTCATCATTAGTTTTG
1980054 TTAAATTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (28 bp):
CATAACAGCATATTCATCATTAGTTTTG
Found at i:1982087 original size:29 final size:29
Alignment explanation
Indices: 1982045--1982145 Score: 193
Period size: 29 Copynumber: 3.5 Consensus size: 29
1982035 GTGGTATTTT
1982045 GTAAATATTGTTAAAAAAATGTTAGTTTC
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
1982074 GTAAATATTGTTAAAAAAATGTTAGTTTC
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
*
1982103 GTAAATATTGTTAAAAAAATGATAGTTTC
1 GTAAATATTGTTAAAAAAATGTTAGTTTC
1982132 GTAAATATTGTTAA
1 GTAAATATTGTTAA
1982146 GATGTTAGTT
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.43, C:0.03, G:0.14, T:0.41
Consensus pattern (29 bp):
GTAAATATTGTTAAAAAAATGTTAGTTTC
Found at i:1982176 original size:55 final size:56
Alignment explanation
Indices: 1982041--1982166 Score: 191
Period size: 58 Copynumber: 2.2 Consensus size: 56
1982031 TATGGTGGTA
*
1982041 TTTTGTAAATATTGTTAAAAAAATGTTAGTTTCGTAAATATTGTTAAAAAAATGTTAG
1 TTTTGTAAATATTGTTAAAAAAATGATAGTTTCGTAAATATTGTT--AAAAATGTTAG
* *
1982099 TTTCGTAAATATTGTTAAAAAAATGATAGTTTCGTAAATATTGTT-AAGATGTTAG
1 TTTTGTAAATATTGTTAAAAAAATGATAGTTTCGTAAATATTGTTAAAAATGTTAG
*
1982154 TTTTATAAATATT
1 TTTTGTAAATATT
1982167 TTGAGAAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
55 20 0.32
58 43 0.68
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (56 bp):
TTTTGTAAATATTGTTAAAAAAATGATAGTTTCGTAAATATTGTTAAAAATGTTAG
Found at i:1982293 original size:80 final size:80
Alignment explanation
Indices: 1982174--1982418 Score: 339
Period size: 80 Copynumber: 3.0 Consensus size: 80
1982164 ATTTTGAGAA
*
1982174 AAAAAATGATATTTTGGTAATTATTTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTGA
1 AAAAAGTGATATTTTGG--A-TATTTC-AAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTGA
*
1982239 TATTTTGGTAATTATTTCG
62 TATTTTCGTAATTATTTCG
* * *
1982258 AAAAAGTGATATTTTGG-TATTTCAAAAAAGTGATATTTTTGTACTTATTTCGAAAAAGTGATAT
1 AAAAAGTGATATTTTGGATATTTC-AAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTGATAT
*
1982322 TTTTGTAATTATTTCG
65 TTTCGTAATTATTTCG
*
1982338 AAAAAGTGATATTTTGGTAATTATTTCAAAAAGTGATATTTTGGTAATTATTTCGAAAAAGGTGA
1 AAAAAGTGATATTTTGG--A-TATTTCAAAAAGTGATATTTTGGTAATTATTTC-AAAAAAGTGA
1982403 TATTTTCGTAATTATT
62 TATTTTCGTAATTATT
1982419 AAAAAAATGT
Statistics
Matches: 145, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
80 75 0.52
83 25 0.17
84 45 0.31
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.44
Consensus pattern (80 bp):
AAAAAGTGATATTTTGGATATTTCAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTGATATT
TTCGTAATTATTTCG
Found at i:1982306 original size:108 final size:107
Alignment explanation
Indices: 1982173--1982383 Score: 368
Period size: 108 Copynumber: 2.0 Consensus size: 107
1982163 TATTTTGAGA
1982173 AAAAAAATGATATTTTGGTAATTATTTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTG
1 AAAAAAATGATATTTTGGTAATTATTTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTG
1982238 ATATTTTGGTAATTATTTCGAAAAAGTGATATTTTGGTATTTC
66 ATATTTTGGTAATTATTTC-AAAAAGTGATATTTTGGTATTTC
* * * * *
1982281 AAAAAAGTGATATTTTTGTACTTATTTCGAAAAAGTGATATTTTTGTAATTATTTCGAAAAAGTG
1 AAAAAAATGATATTTTGGTAATTATTTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTG
1982346 ATATTTTGGTAATTATTTCAAAAAGTGATATTTTGGTA
66 ATATTTTGGTAATTATTTCAAAAAGTGATATTTTGGTA
1982384 ATTATTTCGA
Statistics
Matches: 98, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
107 19 0.19
108 79 0.81
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.43
Consensus pattern (107 bp):
AAAAAAATGATATTTTGGTAATTATTTCGAAAAAGTGATATTTTGGTAATTATTTCAAAAAAGTG
ATATTTTGGTAATTATTTCAAAAAGTGATATTTTGGTATTTC
Found at i:1982425 original size:28 final size:28
Alignment explanation
Indices: 1982174--1982418 Score: 383
Period size: 28 Copynumber: 8.9 Consensus size: 28
1982164 ATTTTGAGAA
*
1982174 AAAAAATGATATTTTGGTAATTATTTCG
1 AAAAAGTGATATTTTGGTAATTATTTCG
*
1982202 AAAAAGTGATATTTTGGTAATTATTTCA
1 AAAAAGTGATATTTTGGTAATTATTTCG
1982230 AAAAAGTGATATTTTGGTAATTATTTCG
1 AAAAAGTGATATTTTGGTAATTATTTCG
*
1982258 AAAAAGTGATATTTTGG----TATTTCA
1 AAAAAGTGATATTTTGGTAATTATTTCG
* *
1982282 AAAAAGTGATATTTTTGTACTTATTTCG
1 AAAAAGTGATATTTTGGTAATTATTTCG
*
1982310 AAAAAGTGATATTTTTGTAATTATTTCG
1 AAAAAGTGATATTTTGGTAATTATTTCG
1982338 AAAAAGTGATATTTTGGTAATTATTTC-
1 AAAAAGTGATATTTTGGTAATTATTTCG
1982365 AAAAAGTGATATTTTGGTAATTATTTCG
1 AAAAAGTGATATTTTGGTAATTATTTCG
*
1982393 AAAAAGGTGATATTTTCGTAATTATT
1 AAAAA-GTGATATTTTGGTAATTATT
1982419 AAAAAAATGT
Statistics
Matches: 202, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
24 22 0.11
27 27 0.13
28 134 0.66
29 19 0.09
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.44
Consensus pattern (28 bp):
AAAAAGTGATATTTTGGTAATTATTTCG
Found at i:1986477 original size:29 final size:28
Alignment explanation
Indices: 1986386--1986479 Score: 143
Period size: 28 Copynumber: 3.3 Consensus size: 28
1986376 GTGGTATTTT
1986386 GTAAATATTGTTAAAAAATGTTAGTTTC
1 GTAAATATTGTTAAAAAATGTTAGTTTC
*
1986414 GTAAATATTGTTAAAAAATGATAGTTTC
1 GTAAATATTGTTAAAAAATGTTAGTTTC
* *
1986442 GTAAATATTGTTAAGAAGATGTTAGTTTT
1 GTAAATATTGTTAA-AAAATGTTAGTTTC
*
1986471 ATAAATATT
1 GTAAATATT
1986480 TTGAGAAAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
28 41 0.68
29 19 0.32
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.43
Consensus pattern (28 bp):
GTAAATATTGTTAAAAAATGTTAGTTTC
Found at i:1986523 original size:28 final size:28
Alignment explanation
Indices: 1986485--1986785 Score: 407
Period size: 28 Copynumber: 10.8 Consensus size: 28
1986475 ATATTTTGAG
* *
1986485 AAAAAAATGATATTTTGATAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
1986513 AAAAAAGTGATATTTTTGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
1986541 GAAAAAGTGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
1986569 GAAAAAGTGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
1986597 AAAAAATTGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
1986625 GAAAAAGTGATATTTTGGT-A-T-TTT-
1 AAAAAAGTGATATTTTGGTAATTATTTC
*
1986649 GAAAAAGTGATATTTTGGTAATTATTTC
1 AAAAAAGTGATATTTTGGTAATTATTTC
1986677 AAAAAAAGTGATATTTTGGTAATTATTTC
1 -AAAAAAGTGATATTTTGGTAATTATTTC
1986706 AAAAAAAGGTGATATTTTGGTAATTATTTC
1 -AAAAAA-GTGATATTTTGGTAATTATTTC
*
1986736 AAAAAAATGTGATATTTTCGTAATTA-TT-
1 -AAAAAA-GTGATATTTTGGTAATTATTTC
* * *
1986764 AAAAAAATGTTATTTTCGTAAT
1 AAAAAAGTGATATTTTGGTAAT
1986786 AGTTGAATGT
Statistics
Matches: 253, Mismatches: 14, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
24 19 0.08
25 4 0.02
26 16 0.06
27 10 0.04
28 122 0.48
29 36 0.14
30 46 0.18
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.43
Consensus pattern (28 bp):
AAAAAAGTGATATTTTGGTAATTATTTC
Found at i:1987420 original size:77 final size:77
Alignment explanation
Indices: 1987293--1987448 Score: 312
Period size: 77 Copynumber: 2.0 Consensus size: 77
1987283 TGTTTAGAAT
1987293 ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
1 ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
1987358 GGCAGGTACTCG
66 GGCAGGTACTCG
1987370 ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
1 ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
1987435 GGCAGGTACTCG
66 GGCAGGTACTCG
1987447 AT
1 AT
1987449 AGATTTTCCG
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 79 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (77 bp):
ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
GGCAGGTACTCG
Found at i:1987559 original size:108 final size:108
Alignment explanation
Indices: 1987370--1987574 Score: 394
Period size: 108 Copynumber: 1.9 Consensus size: 108
1987360 CAGGTACTCG
1987370 ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
1 ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
1987435 GGCAGGTACTCGATAGA-TTTTCCGAAACTGATATGTTTAGAAT
66 GGCAGGTACTCGATAGATTTTTCCG-AACTGATATGTTTAGAAT
1987478 ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
1 ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
1987543 GGCAGGTACTCGATAGATTTTTCCGAACTGAT
66 GGCAGGTACTCGATAGATTTTTCCGAACTGAT
1987575 CCTGTTATCG
Statistics
Matches: 96, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
108 89 0.93
109 7 0.07
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (108 bp):
ATTATTCCAAATATAACCCTGTTCTGATATGACTTAGGTTCACATTCAGTCGAAGAGCCTAGTGA
GGCAGGTACTCGATAGATTTTTCCGAACTGATATGTTTAGAAT
Found at i:1996633 original size:19 final size:21
Alignment explanation
Indices: 1996590--1996641 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
1996580 GAAACCCCTT
1996590 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
1996611 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
1996630 TGAAGATACATG
1 TGAAAATACATG
1996642 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:2000618 original size:6 final size:6
Alignment explanation
Indices: 2000607--2000645 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
2000597 GTTGTAGGAG
*
2000607 TCTTTT TCTTTT TGTTTT TCTTCTT TCTTTT TCTCTTT T
1 TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT T
2000646 TTGTTGCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 19 0.66
7 10 0.34
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (6 bp):
TCTTTT
Found at i:2000626 original size:12 final size:12
Alignment explanation
Indices: 2000607--2000645 Score: 51
Period size: 13 Copynumber: 3.1 Consensus size: 12
2000597 GTTGTAGGAG
2000607 TCTTTTTCTTTT
1 TCTTTTTCTTTT
*
2000619 TGTTTTTCTTCTT
1 TCTTTTTCTT-TT
2000632 TCTTTTTCTCTTT
1 TCTTTTTCT-TTT
2000645 T
1 T
2000646 TTGTTGCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 9 0.39
13 13 0.57
14 1 0.04
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (12 bp):
TCTTTTTCTTTT
Found at i:2000884 original size:17 final size:15
Alignment explanation
Indices: 2000854--2000888 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 15
2000844 ATGAAAGAAA
2000854 AAAAGGAAATGATAAG
1 AAAAGGAAATGAT-AG
2000870 AAAAGGAAATGGATAG
1 AAAAGGAAAT-GATAG
2000886 AAA
1 AAA
2000889 TGTTATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.83
17 3 0.17
ACGTcount: A:0.63, C:0.00, G:0.26, T:0.11
Consensus pattern (15 bp):
AAAAGGAAATGATAG
Found at i:2002441 original size:30 final size:31
Alignment explanation
Indices: 2002389--2002448 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2002379 CTTAGCTTTA
**
2002389 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
2002419 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
2002449 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:2003381 original size:19 final size:20
Alignment explanation
Indices: 2003357--2003407 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
2003347 CGGCCAAGAG
* *
2003357 CATGTATCTTCATTAAA-AT
1 CATGTATTTTCATCAAATAT
2003376 CATGTATTTTCATCAAATAT
1 CATGTATTTTCATCAAATAT
2003396 CATGTATTTTCA
1 CATGTATTTTCA
2003408 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.45
Consensus pattern (20 bp):
CATGTATTTTCATCAAATAT
Found at i:2004160 original size:21 final size:21
Alignment explanation
Indices: 2004126--2004187 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
2004116 GGAGTGCAAA
*
2004126 AAGAAGAGAAAAAATCAGAAAAG
1 AAGAAAAGAAAAAA--AGAAAAG
2004149 AAGAAAAGAAAAAAAGAAACA-
1 AAGAAAAGAAAAAAAGAAA-AG
*
2004170 AAGAAAAGAAAAAGAGAA
1 AAGAAAAGAAAAAAAGAA
2004188 GTTCAAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
21 22 0.61
22 1 0.03
23 13 0.36
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.02
Consensus pattern (21 bp):
AAGAAAAGAAAAAAAGAAAAG
Found at i:2004163 original size:16 final size:16
Alignment explanation
Indices: 2004144--2004176 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2004134 AAAAAATCAG
2004144 AAAAGAAGA-AAAGAAA
1 AAAAGAA-ACAAAGAAA
2004160 AAAAGAAACAAAGAAA
1 AAAAGAAACAAAGAAA
2004176 A
1 A
2004177 GAAAAAGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 15 0.94
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (16 bp):
AAAAGAAACAAAGAAA
Found at i:2006557 original size:30 final size:31
Alignment explanation
Indices: 2006505--2006564 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
2006495 CTTAGCTTTA
**
2006505 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
2006535 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
2006565 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:2007488 original size:19 final size:20
Alignment explanation
Indices: 2007464--2007514 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
2007454 CGGCCAAGAG
* *
2007464 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
2007483 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
2007503 CATGTATTTTCA
1 CATGTATTTTCA
2007515 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:2014792 original size:11 final size:13
Alignment explanation
Indices: 2014760--2014789 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2014750 TGGCCAAAGA
2014760 TGAAAAGGTATGT
1 TGAAAAGGTATGT
2014773 TGAAAAGGTATG-
1 TGAAAAGGTATGT
2014785 TGAAA
1 TGAAA
2014790 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:2019365 original size:22 final size:23
Alignment explanation
Indices: 2019340--2019385 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2019330 TTGCAATTCC
2019340 TTAATC-T-TTTCTATATCTTGTT
1 TTAATCTTATTTCT-TATCTTGTT
2019362 TTAATCTTATTTCTTATCTTGTT
1 TTAATCTTATTTCTTATCTTGTT
2019385 T
1 T
2019386 CTAGCACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 11 0.50
24 5 0.23
ACGTcount: A:0.17, C:0.13, G:0.04, T:0.65
Consensus pattern (23 bp):
TTAATCTTATTTCTTATCTTGTT
Found at i:2024075 original size:22 final size:23
Alignment explanation
Indices: 2024050--2024095 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2024040 TTGCAATTCC
2024050 TTAATC-T-TTTCTTTATCTTGTT
1 TTAATCTTATTTC-TTATCTTGTT
2024072 TTAATCTTATTTCTTATCTTGTT
1 TTAATCTTATTTCTTATCTTGTT
2024095 T
1 T
2024096 CCAGCACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 12 0.55
24 4 0.18
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.67
Consensus pattern (23 bp):
TTAATCTTATTTCTTATCTTGTT
Found at i:2027358 original size:24 final size:21
Alignment explanation
Indices: 2027323--2027365 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
2027313 GGCTCATTCT
*
2027323 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
2027346 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
2027366 GTGAGCACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:2032199 original size:35 final size:34
Alignment explanation
Indices: 2032160--2032278 Score: 141
Period size: 35 Copynumber: 3.4 Consensus size: 34
2032150 TACAATATGT
* *
2032160 TCATCACCATCTTCTAACACCATTATCACG-CTATA
1 TCATCACCATATTC-ATCACCA-TATCACGCCTATA
*
2032195 TCATCACCATAGTCCATCACCATATCACGCCTATA
1 TCATCACCATA-TTCATCACCATATCACGCCTATA
* *
2032230 TAATCACCATAGTTCATCACCATATCACGCCTAAA
1 TCATCACCATA-TTCATCACCATATCACGCCTATA
*
2032265 TCATCACCAAATTC
1 TCATCACCATATTC
2032279 CATTTCCATT
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
34 10 0.14
35 62 0.84
36 2 0.03
ACGTcount: A:0.34, C:0.34, G:0.04, T:0.28
Consensus pattern (34 bp):
TCATCACCATATTCATCACCATATCACGCCTATA
Found at i:2033923 original size:16 final size:16
Alignment explanation
Indices: 2033902--2033943 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2033892 ATAAAAATAG
2033902 ATGAAATAATAAGAAA
1 ATGAAATAATAAGAAA
*
2033918 ATGAAATAGTAAGAAA
1 ATGAAATAATAAGAAA
*
2033934 GTGAAGATAA
1 ATGAA-ATAA
2033944 CTTATAACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 19 0.86
17 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.19, T:0.19
Consensus pattern (16 bp):
ATGAAATAATAAGAAA
Found at i:2034106 original size:27 final size:27
Alignment explanation
Indices: 2034054--2034111 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
2034044 TTTGAATGTA
2034054 CTTTGCAATTTTCTTCACTTTACTTTTT
1 CTTTGCAATTTTCTTCACTTTAC-TTTT
* *
2034082 CTTTG-AATTTTTCTTC-TTTTTCTTTT
1 CTTTGCAA-TTTTCTTCACTTTACTTTT
2034108 CTTT
1 CTTT
2034112 CTTTGGCACT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 8 0.30
27 6 0.22
28 13 0.48
ACGTcount: A:0.10, C:0.19, G:0.03, T:0.67
Consensus pattern (27 bp):
CTTTGCAATTTTCTTCACTTTACTTTT
Found at i:2038984 original size:50 final size:50
Alignment explanation
Indices: 2038887--2038984 Score: 110
Period size: 50 Copynumber: 2.0 Consensus size: 50
2038877 GTCTTAACTC
* ***
2038887 TAATTCCTAATAAAATAATTATAACTAAAATTAATGTTTTAACTCAACCT
1 TAATTCCTAATAAAATAATTATAACTAAAACTAATGTGAGAACTCAACCT
**
2038937 TAATTCCTAATAAAATAA-TA-AATCTAATCCTAATGTGAGAACATCAAC
1 TAATTCCTAATAAAATAATTATAA-CTAAAACTAATGTGAGAAC-TCAAC
2038985 GCCAGTAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
48 2 0.05
49 15 0.38
50 23 0.57
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.34
Consensus pattern (50 bp):
TAATTCCTAATAAAATAATTATAACTAAAACTAATGTGAGAACTCAACCT
Found at i:2046059 original size:36 final size:36
Alignment explanation
Indices: 2046019--2046159 Score: 203
Period size: 36 Copynumber: 3.9 Consensus size: 36
2046009 AACACCATCT
*
2046019 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
2046055 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
2046091 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
2046127 TCCACCACCATTATCACGTCC-ATATTATCACCA
1 TCCATCACCATTATCACG-CCTATATCATCACCA
2046160 ACTTATAAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
36 92 0.98
37 2 0.02
ACGTcount: A:0.28, C:0.37, G:0.05, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:2046577 original size:24 final size:24
Alignment explanation
Indices: 2046537--2046583 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
2046527 AAAGTGCTAC
2046537 AACAAAAAGCAACAAGAAAGAAGAA
1 AACAAAAAGCAACAAGAAA-AAGAA
2046562 AACAAAAGAG-AA-AAGAAAAAGA
1 AACAAAA-AGCAACAAGAAAAAGA
2046584 CTCCTACAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.74, C:0.09, G:0.17, T:0.00
Consensus pattern (24 bp):
AACAAAAAGCAACAAGAAAAAGAA
Found at i:2046830 original size:23 final size:24
Alignment explanation
Indices: 2046799--2046847 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
2046789 TTTCTTACTA
*
2046799 TTTCATTTC-TTATTCTT-TCATCT
1 TTTCATTTCATTA-CCTTATCATCT
*
2046822 TTTCTTTTCATTACCTTATCATCT
1 TTTCATTTCATTACCTTATCATCT
2046846 TT
1 TT
2046848 CTTAACCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.14, C:0.22, G:0.00, T:0.63
Consensus pattern (24 bp):
TTTCATTTCATTACCTTATCATCT
Found at i:2050626 original size:36 final size:36
Alignment explanation
Indices: 2050586--2050726 Score: 203
Period size: 36 Copynumber: 3.9 Consensus size: 36
2050576 AACACCATCT
*
2050586 TCCATCTCCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
*
2050622 TCCATCACCATTATCACGCCTTTATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* * *
2050658 TCCATCTCCATTATCACGCCTATATCGTCACCATAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAG
* *
2050694 TCCACCACCATTATCACGTCC-ATATTATCACCA
1 TCCATCACCATTATCACG-CCTATATCATCACCA
2050727 ACTTATAAAT
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
36 92 0.98
37 2 0.02
ACGTcount: A:0.28, C:0.37, G:0.05, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAG
Found at i:2051502 original size:17 final size:17
Alignment explanation
Indices: 2051480--2051518 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
2051470 CAGTATAGAA
2051480 GCAAGCAAATAAAGGTC
1 GCAAGCAAATAAAGGTC
2051497 GCAAGCAAATAAAGGTC
1 GCAAGCAAATAAAGGTC
2051514 GCAAG
1 GCAAG
2051519 AGAGTTACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.46, C:0.18, G:0.26, T:0.10
Consensus pattern (17 bp):
GCAAGCAAATAAAGGTC
Found at i:2056022 original size:22 final size:21
Alignment explanation
Indices: 2055996--2056036 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
2055986 GGCTACGAAA
2055996 TTGATGGTATTGATGGATGATG
1 TTGATGGTATTGAT-GATGATG
*
2056018 TTGATGGTTTTGATGATGA
1 TTGATGGTATTGATGATGA
2056037 AATGGAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
TTGATGGTATTGATGATGATG
Found at i:2064844 original size:20 final size:20
Alignment explanation
Indices: 2064816--2064863 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
2064806 CCTTGGTTTG
* *
2064816 ATTTCTCTTTTTTTTTAATTT
1 ATTT-TCTTCTTTTCTAATTT
*
2064837 ATTTTCTTCTTTTCTGATTT
1 ATTTTCTTCTTTTCTAATTT
*
2064857 TTTTTCT
1 ATTTTCT
2064864 AATTTTTGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.75
Consensus pattern (20 bp):
ATTTTCTTCTTTTCTAATTT
Found at i:2070778 original size:10 final size:10
Alignment explanation
Indices: 2070763--2070792 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
2070753 GATGTCAAAG
2070763 GTAGCTGAAT
1 GTAGCTGAAT
2070773 GTAGCTGAAT
1 GTAGCTGAAT
2070783 GTAGCTGAAT
1 GTAGCTGAAT
2070793 ATGCTGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.10, G:0.30, T:0.30
Consensus pattern (10 bp):
GTAGCTGAAT
Found at i:2071847 original size:23 final size:23
Alignment explanation
Indices: 2071819--2071863 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2071809 AAAATCAGCA
2071819 AAGAAAATAAAAGCACTCAAAAG
1 AAGAAAATAAAAGCACTCAAAAG
* *
2071842 AAGAAATTGAAAGCACTCAAAA
1 AAGAAAATAAAAGCACTCAAAA
2071864 AAAAAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.62, C:0.13, G:0.13, T:0.11
Consensus pattern (23 bp):
AAGAAAATAAAAGCACTCAAAAG
Found at i:2075841 original size:23 final size:24
Alignment explanation
Indices: 2075812--2075871 Score: 77
Period size: 23 Copynumber: 2.5 Consensus size: 24
2075802 AAAAATCAGC
2075812 AAAGAAAATAAAAGCACTC-AAAA
1 AAAGAAAATAAAAGCACTCAAAAA
* * *
2075835 GAAGAAATTGAAAGCACTCAAAAA
1 AAAGAAAATAAAAGCACTCAAAAA
2075859 AAAGAAAAATAAA
1 AAAG-AAAATAAA
2075872 GAAAGAAAAG
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
23 16 0.55
24 7 0.24
25 6 0.21
ACGTcount: A:0.68, C:0.10, G:0.12, T:0.10
Consensus pattern (24 bp):
AAAGAAAATAAAAGCACTCAAAAA
Found at i:2079827 original size:21 final size:22
Alignment explanation
Indices: 2079803--2079844 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2079793 AAAATCAGCA
2079803 AAGAAA-TAAAAGCACTCAAAG
1 AAGAAATTAAAAGCACTCAAAG
*
2079824 AAGAAATTGAAAGCACTCAAA
1 AAGAAATTAAAAGCACTCAAA
2079845 AAAAAAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.60, C:0.14, G:0.14, T:0.12
Consensus pattern (22 bp):
AAGAAATTAAAAGCACTCAAAG
Found at i:2089813 original size:24 final size:23
Alignment explanation
Indices: 2089786--2089838 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
2089776 TTTCTTTCTT
*
2089786 TTTCTTCTTTTCGAGTGCTTTCAG
1 TTTCTTCTTTT-GAATGCTTTCAG
* *
2089810 TTTCTTCTTTTGAATGCTTTTAT
1 TTTCTTCTTTTGAATGCTTTCAG
2089833 TTTCTT
1 TTTCTT
2089839 TGCTGATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.58
24 11 0.42
ACGTcount: A:0.09, C:0.17, G:0.11, T:0.62
Consensus pattern (23 bp):
TTTCTTCTTTTGAATGCTTTCAG
Found at i:2089836 original size:23 final size:24
Alignment explanation
Indices: 2089779--2089838 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
2089769 ACTTTTCTTT
* *
2089779 CTTTCTTTTTCTTCTTTTCGAGTG
1 CTTTCATTTTCTTCTTTTCGAATG
*
2089803 CTTTCAGTTTCTTCTTTT-GAATG
1 CTTTCATTTTCTTCTTTTCGAATG
*
2089826 CTTTTATTTTCTT
1 CTTTCATTTTCTT
2089839 TGCTGATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.08, C:0.18, G:0.10, T:0.63
Consensus pattern (24 bp):
CTTTCATTTTCTTCTTTTCGAATG
Found at i:2090804 original size:91 final size:91
Alignment explanation
Indices: 2090684--2090869 Score: 354
Period size: 91 Copynumber: 2.0 Consensus size: 91
2090674 GCCTAAATGG
2090684 AGTCACACGCCTAGCACATGGGTTGGCTGGTCACAAGGCATGCACATGGCTTCTCTTGGATGCTT
1 AGTCACACGCCTAGCACATGGGTTGGCTGGTCACAAGGCATGCACATGGCTTCTCTTGGATGCTT
2090749 GTGGTGCATCCTTATGCATAGGATGA
66 GTGGTGCATCCTTATGCATAGGATGA
* *
2090775 AGTCACACGCCTAGCACATGGGTTGGCTGGTCACAAGGCGTGCACATGGCTTTTCTTGGATGCTT
1 AGTCACACGCCTAGCACATGGGTTGGCTGGTCACAAGGCATGCACATGGCTTCTCTTGGATGCTT
2090840 GTGGTGCATCCTTATGCATAGGATGA
66 GTGGTGCATCCTTATGCATAGGATGA
2090866 AGTC
1 AGTC
2090870 CAAGCATGGG
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (91 bp):
AGTCACACGCCTAGCACATGGGTTGGCTGGTCACAAGGCATGCACATGGCTTCTCTTGGATGCTT
GTGGTGCATCCTTATGCATAGGATGA
Done.