Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008128.1 Hibiscus syriacus cultivar Beakdansim tig00110683_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: 4987688
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 20
Found at i:326563 original size:94 final size:96
Alignment explanation
Indices: 326397--326575 Score: 220
Period size: 94 Copynumber: 1.9 Consensus size: 96
326387 ATGAAGAAGG
* * **
326397 TATCGATACCATTGATTTACAGAATGCAGAAATGATATCGATACCGTAATAGAGTATTTGTACCA
1 TATCGATACCATGGATTTACAGAATGCAGAAATGATATCGATACCGTAAGAGAGTATCGGTACCA
* *
326462 TAGTATAGAAGTATCAGTACTAAGAGACATA
66 CAATATAGAAGTATCAGTACTAAGAGACATA
* * * * *
326493 TATCGATACCATGGA-TT-CATAATGTAGAAATGGTATCGATACTG-AAGGGGAGTATCGGTACC
1 TATCGATACCATGGATTTACAGAATGCAGAAATGATATCGATACCGTAA-GAGAGTATCGGTACC
*
326555 ACAATATAGAAGTATCGGTAC
65 ACAATATAGAAGTATCAGTAC
326576 CATAGTAGAA
Statistics
Matches: 70, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
93 2 0.03
94 52 0.74
95 2 0.03
96 14 0.20
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (96 bp):
TATCGATACCATGGATTTACAGAATGCAGAAATGATATCGATACCGTAAGAGAGTATCGGTACCA
CAATATAGAAGTATCAGTACTAAGAGACATA
Found at i:326591 original size:94 final size:96
Alignment explanation
Indices: 326383--326598 Score: 210
Period size: 94 Copynumber: 2.3 Consensus size: 96
326373 GTGGGTATGA
* *
326383 TACCAT-GAAGAAGGTATCGATACCATTGATTTACAGAATGCAGAAATGATATCGATACCGTAAT
1 TACCATAG-AGAAGGTATCGATACCATGGATTTACAGAATGCAGAAATGATATCGATACCGTAAG
** * *
326447 AGAGTATTTGTACCATAGTATAGAAGTATCAG
65 AGAGTATCGGTACCACAATATAGAAGTATCAG
* ** * * * *
326479 TACTA-AGAGACATATATCGATACCATGGA-TT-CATAATGTAGAAATGGTATCGATACTG-AAG
1 TACCATAGAGA-AGGTATCGATACCATGGATTTACAGAATGCAGAAATGATATCGATACCGTAA-
* *
326540 GGGAGTATCGGTACCACAATATAGAAGTATCGG
64 GAGAGTATCGGTACCACAATATAGAAGTATCAG
*
326573 TACCATAGTAGAA-GTATCGGTACCAT
1 TACCATAG-AGAAGGTATCGATACCAT
326599 AGTAGGGGTA
Statistics
Matches: 97, Mismatches: 18, Indels: 12
0.76 0.14 0.09
Matches are distributed among these distances:
93 2 0.02
94 64 0.66
95 8 0.08
96 23 0.24
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (96 bp):
TACCATAGAGAAGGTATCGATACCATGGATTTACAGAATGCAGAAATGATATCGATACCGTAAGA
GAGTATCGGTACCACAATATAGAAGTATCAG
Found at i:326611 original size:20 final size:20
Alignment explanation
Indices: 326543--326603 Score: 88
Period size: 20 Copynumber: 3.0 Consensus size: 20
326533 ACTGAAGGGG
326543 AGTATCGGTACCACAATA-TAGA
1 AGTATCGGTA-C-C-ATAGTAGA
326565 AGTATCGGTACCATAGTAGA
1 AGTATCGGTACCATAGTAGA
326585 AGTATCGGTACCATAGTAG
1 AGTATCGGTACCATAGTAG
326604 GGGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
19 3 0.08
20 24 0.63
21 1 0.03
22 10 0.26
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (20 bp):
AGTATCGGTACCATAGTAGA
Found at i:327024 original size:54 final size:54
Alignment explanation
Indices: 326939--327218 Score: 319
Period size: 54 Copynumber: 5.2 Consensus size: 54
326929 CTATATGTAC
* * * *
326939 TTTTGGAACTATATGTGCAATCTACGAAATTCATCATAAGTTGATGAATAACCG
1 TTTTGGCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAATAACCG
** * *
326993 TTTTGGCTTTATAAGTGCAACCCACGGAATTCATCACAAGTTGATGAATAACCG
1 TTTTGGCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAATAACCG
* *
327047 TTTTGGCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCA
1 TTTTGGCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAATAACCG
* * ** * * * *
327101 TTTTGGCACTATGTGTGCAACCTA-TTAACTCGTCATATGTTGATGAACAACCG
1 TTTTGGCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAATAACCG
* * * * * * *
327154 TTTAGGCACTATGTGTGCAACCCACAGAATTCATAATATGTTTATGAATGACCG
1 TTTTGGCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAATAACCG
*
327208 TATTGGCACTA
1 TTTTGGCACTA
327219 CGTTTGCATT
Statistics
Matches: 191, Mismatches: 34, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
53 45 0.24
54 146 0.76
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (54 bp):
TTTTGGCACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAATAACCG
Found at i:327177 original size:107 final size:108
Alignment explanation
Indices: 326946--327201 Score: 298
Period size: 107 Copynumber: 2.4 Consensus size: 108
326936 TACTTTTGGA
* * * * * **
326946 ACTATATGTGCAATCTACGAAATTCATCATAAGTTGATGAATAACCGTTTTGGCTTTATAAGTGC
1 ACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTATAAGTGC
* * *
327011 AACCCACGGAATTCATCACAAGTTGATGAATAACCGTTTTGGC
66 AACCCACGGAACTCATCACAAGTTGATGAACAACCGTTTAGGC
**
327054 ACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTATGTGTGC
1 ACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTATAAGTGC
* ** * * *
327119 AACCTA-TTAACTCGTCATATGTTGATGAACAACCGTTTAGGC
66 AACCCACGGAACTCATCACAAGTTGATGAACAACCGTTTAGGC
* * * * *
327161 ACTATGTGTGCAACCCACAGAATTCATAATATGTTTATGAA
1 ACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAA
327202 TGACCGTATT
Statistics
Matches: 125, Mismatches: 23, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
107 64 0.51
108 61 0.49
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (108 bp):
ACTATATGTGCAACCCACGGAATTCATCATAAGTTGATGAACAACCATTTTGGCACTATAAGTGC
AACCCACGGAACTCATCACAAGTTGATGAACAACCGTTTAGGC
Found at i:330016 original size:18 final size:18
Alignment explanation
Indices: 329970--330021 Score: 79
Period size: 17 Copynumber: 2.9 Consensus size: 18
329960 GGATTATCAA
*
329970 TGGTCCTTCGGGACATAG
1 TGGTCATTCGGGACATAG
329988 T-GTCATTCGGGACATAG
1 TGGTCATTCGGGACATAG
*
330005 TGGTCTTTCGGGACATA
1 TGGTCATTCGGGACATA
330022 TTTCAGTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 16 0.52
18 15 0.48
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (18 bp):
TGGTCATTCGGGACATAG
Found at i:340640 original size:16 final size:18
Alignment explanation
Indices: 340616--340650 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
340606 ATTTTTACGA
340616 TTATGGATTTTAA-ATGT
1 TTATGGATTTTAAGATGT
340633 TTAT-GATTTTAAGATGT
1 TTATGGATTTTAAGATGT
340650 T
1 T
340651 GATAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.29, C:0.00, G:0.17, T:0.54
Consensus pattern (18 bp):
TTATGGATTTTAAGATGT
Found at i:344779 original size:28 final size:28
Alignment explanation
Indices: 344708--344780 Score: 119
Period size: 28 Copynumber: 2.6 Consensus size: 28
344698 CATGCCATAC
*
344708 GTGGTCCTTCGAGACATATATGTTATAT
1 GTGGTCATTCGAGACATATATGTTATAT
* *
344736 GTGGTCATTTGGGACATATATGTTATAT
1 GTGGTCATTCGAGACATATATGTTATAT
344764 GTGGTCATTCGAGACAT
1 GTGGTCATTCGAGACAT
344781 TTACAAGGTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (28 bp):
GTGGTCATTCGAGACATATATGTTATAT
Found at i:347973 original size:2 final size:2
Alignment explanation
Indices: 347966--348008 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
347956 TAAAACGGGG
347966 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
348008 A
1 A
348009 AATGGAACAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:356164 original size:20 final size:20
Alignment explanation
Indices: 356139--356176 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
356129 TATATTTGGC
356139 TATGAATCTCGAATATGAGA
1 TATGAATCTCGAATATGAGA
* *
356159 TATGAATGTGGAATATGA
1 TATGAATCTCGAATATGA
356177 AACATGAATA
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:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (20 bp):
TATGAATCTCGAATATGAGA
Found at i:360519 original size:29 final size:29
Alignment explanation
Indices: 360487--360573 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
360477 AAATTTTGGC
360487 TAGTGACTAAAATATAAAATTTAAAAGTT
1 TAGTGACTAAAATATAAAATTTAAAAGTT
* * *
360516 TAGTGGCTAAAGTATAAACTTTAGAAAAGTT
1 TAGTGACTAAAATATAAAATTT--AAAAGTT
* * *
360547 CAGAGACTAAAA-ATATAATTTTAAAAG
1 TAGTGACTAAAATATA-AAATTTAAAAG
360574 CTATATATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
29 24 0.51
30 3 0.06
31 20 0.43
ACGTcount: A:0.49, C:0.06, G:0.14, T:0.31
Consensus pattern (29 bp):
TAGTGACTAAAATATAAAATTTAAAAGTT
Found at i:361489 original size:20 final size:22
Alignment explanation
Indices: 361466--361514 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
361456 GGAAATTGCA
*
361466 TGAATT-T-GATCATAGGAGGT
1 TGAATTATAGATCACAGGAGGT
361486 TGAATTCATAGATCACAGGAGGT
1 TGAATT-ATAGATCACAGGAGGT
361509 TGAATT
1 TGAATT
361515 CATACTTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 6 0.24
22 1 0.04
23 18 0.72
ACGTcount: A:0.33, C:0.08, G:0.27, T:0.33
Consensus pattern (22 bp):
TGAATTATAGATCACAGGAGGT
Found at i:361505 original size:23 final size:23
Alignment explanation
Indices: 361473--361518 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
361463 GCATGAATTT
*
361473 GATCATAGGAGGTTGAATTCATA
1 GATCACAGGAGGTTGAATTCATA
361496 GATCACAGGAGGTTGAATTCATA
1 GATCACAGGAGGTTGAATTCATA
361519 CTTGAAATTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.11, G:0.26, T:0.28
Consensus pattern (23 bp):
GATCACAGGAGGTTGAATTCATA
Found at i:363014 original size:53 final size:54
Alignment explanation
Indices: 362950--363066 Score: 173
Period size: 54 Copynumber: 2.2 Consensus size: 54
362940 ATTGCACCTA
* * *
362950 AGTGCCAAAATGGCAATTCA-TAAACTCATTATGAATTCCATGGATGAACACAT
1 AGTGCCGAAATGGCAATTCACAAAACTCATTATGAATACCATGGATGAACACAT
* * *
363003 AGTGCCGAAATGGTAATTCACAAAACTCATTATGAATACCATGGGTGCACACAT
1 AGTGCCGAAATGGCAATTCACAAAACTCATTATGAATACCATGGATGAACACAT
363057 AGTGCCGAAA
1 AGTGCCGAAA
363067 GTACACATAG
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 18 0.32
54 39 0.68
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (54 bp):
AGTGCCGAAATGGCAATTCACAAAACTCATTATGAATACCATGGATGAACACAT
Found at i:373088 original size:14 final size:14
Alignment explanation
Indices: 373069--373104 Score: 63
Period size: 14 Copynumber: 2.5 Consensus size: 14
373059 TATTCTCTTC
373069 TCTTCATTTATTCT
1 TCTTCATTTATTCT
373083 TCTTCATTTATTCT
1 TCTTCATTTATTCT
373097 TCCTTCAT
1 T-CTTCAT
373105 CTTCTCTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (14 bp):
TCTTCATTTATTCT
Found at i:375808 original size:22 final size:23
Alignment explanation
Indices: 375772--375827 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
375762 CAAGAACTAC
375772 TCCTTTCTT-GAAAAATATTTTTC-
1 TCCTTTCTTAG-AAAATA-TTTTCG
375795 TCC-TTCTTAGAAAATATTTTCG
1 TCCTTTCTTAGAAAATATTTTCG
375817 TCCTTTCTTAG
1 TCCTTTCTTAG
375828 TTTTTCGGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.17
22 14 0.47
23 11 0.37
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (23 bp):
TCCTTTCTTAGAAAATATTTTCG
Found at i:379241 original size:40 final size:42
Alignment explanation
Indices: 379179--379274 Score: 124
Period size: 40 Copynumber: 2.3 Consensus size: 42
379169 GTATATATAT
* * * * *
379179 ATATAAGATATAATATATAGTTTTTTATAATATTTT-AAAAA
1 ATATAATATATAATATATAGTTTATGAAAACATTTTGAAAAA
*
379220 ATAT-ATATATAATATATAGTTTATGAAAACATTTTGAAAAT
1 ATATAATATATAATATATAGTTTATGAAAACATTTTGAAAAA
379261 ATATAATATATAAT
1 ATATAATATATAAT
379275 TTTAAAACAC
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
40 26 0.55
41 12 0.26
42 9 0.19
ACGTcount: A:0.50, C:0.01, G:0.05, T:0.44
Consensus pattern (42 bp):
ATATAATATATAATATATAGTTTATGAAAACATTTTGAAAAA
Found at i:379320 original size:20 final size:21
Alignment explanation
Indices: 379292--379339 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
379282 CACTTTCATG
379292 TATTATTATTTATTTTCTTTT-
1 TATT-TTATTTATTTTCTTTTC
379313 TATTTTATTTATTTTCTTTTC
1 TATTTTATTTATTTTCTTTTC
379334 TATTTT
1 TATTTT
379340 GGTCTAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (21 bp):
TATTTTATTTATTTTCTTTTC
Found at i:380352 original size:47 final size:47
Alignment explanation
Indices: 380283--380382 Score: 164
Period size: 47 Copynumber: 2.1 Consensus size: 47
380273 AGGATCCGCG
* * * *
380283 TGTTTTCACGTGGGTTAGGTCTATTTGCGGCATTGGTCCTCCGATTA
1 TGTTTTCACGTGAGCTAGGTCTATTTGCGGCATTAGTCCTCCAATTA
380330 TGTTTTCACGTGAGCTAGGTCTATTTGCGGCATTAGTCCTCCAATTA
1 TGTTTTCACGTGAGCTAGGTCTATTTGCGGCATTAGTCCTCCAATTA
380377 TGTTTT
1 TGTTTT
380383 TAATTATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (47 bp):
TGTTTTCACGTGAGCTAGGTCTATTTGCGGCATTAGTCCTCCAATTA
Found at i:380550 original size:12 final size:12
Alignment explanation
Indices: 380533--380558 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
380523 TTTCCTTTTA
380533 TTATTTTTTATT
1 TTATTTTTTATT
380545 TTATTTTTTATT
1 TTATTTTTTATT
380557 TT
1 TT
380559 TATTCACTTT
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:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTATTTTTTATT
Found at i:392713 original size:45 final size:47
Alignment explanation
Indices: 392617--392733 Score: 150
Period size: 45 Copynumber: 2.5 Consensus size: 47
392607 CCCGGGTTTT
* * * * *
392617 TTTTGTATATATATATATATAAGATATAATATATAGTTTTTTATAATA
1 TTTTGAATATATATATATAT-ATATATAATATATAGTTTTTGAAAACA
392665 TTTTGAATATATATATATATATATAT-A-ATATAGTTTTTGAAAACA
1 TTTTGAATATATATATATATATATATAATATATAGTTTTTGAAAACA
*
392710 TTTTGAAAATATATATA-ATATATA
1 TTTTGAATATATATATATATATATA
392734 ATTTTAAAAC
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
44 7 0.11
45 31 0.49
46 1 0.02
47 5 0.08
48 19 0.30
ACGTcount: A:0.44, C:0.01, G:0.06, T:0.49
Consensus pattern (47 bp):
TTTTGAATATATATATATATATATATAATATATAGTTTTTGAAAACA
Found at i:392764 original size:15 final size:15
Alignment explanation
Indices: 392746--392786 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
392736 TTTAAAACAT
392746 TTTAATTTATTATTA
1 TTTAATTTATTATTA
392761 TTT-ATTATATTATTA
1 TTTAATT-TATTATTA
*
392776 TTTATTTTATT
1 TTTAATTTATT
392787 TTTTTTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 18 0.78
16 2 0.09
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTAATTTATTATTA
Found at i:393981 original size:9 final size:9
Alignment explanation
Indices: 393944--394000 Score: 53
Period size: 9 Copynumber: 6.0 Consensus size: 9
393934 TTTATCCAAC
393944 ATTTTTATTT
1 ATTTTTA-TT
393954 ATTATTTGATT
1 ATT-TTT-ATT
**
393965 CCTTTTATT
1 ATTTTTATT
393974 ATTTTTATT
1 ATTTTTATT
393983 -TTATTTATT
1 ATT-TTTATT
393992 ATTTTTATT
1 ATTTTTATT
394001 CACTTTACTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 2 0.05
9 22 0.56
10 8 0.21
11 6 0.15
12 1 0.03
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (9 bp):
ATTTTTATT
Found at i:393988 original size:11 final size:12
Alignment explanation
Indices: 393946--393996 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
393936 TATCCAACAT
393946 TTTTATTTATTA
1 TTTTATTTATTA
* **
393958 TTTGATTCCTT-
1 TTTTATTTATTA
393969 TTATTATTT-TTA
1 TT-TTATTTATTA
393981 TTTTATTTATTA
1 TTTTATTTATTA
393993 TTTT
1 TTTT
393997 TATTCACTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
11 10 0.32
12 21 0.68
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTATTTATTA
Found at i:393991 original size:18 final size:18
Alignment explanation
Indices: 393946--394000 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
393936 TATCCAACAT
*
393946 TTTTATTTATTA-TTTGA
1 TTTTATTTATTATTTTTA
*
393963 TTCCT-TTTATTATTTTTA
1 TT-TTATTTATTATTTTTA
393981 TTTTATTTATTATTTTTA
1 TTTTATTTATTATTTTTA
393999 TT
1 TT
394001 CACTTTACTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 10 0.31
18 22 0.69
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.75
Consensus pattern (18 bp):
TTTTATTTATTATTTTTA
Found at i:394007 original size:18 final size:18
Alignment explanation
Indices: 393951--394007 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
393941 AACATTTTTA
*
393951 TTTATTA-TTTGATTC-C
1 TTTATTATTTTTATTCAC
*
393967 TTTTATTATTTTTATTTTA-
1 -TTTATTATTTTTA-TTCAC
393986 TTTATTATTTTTATTCAC
1 TTTATTATTTTTATTCAC
394004 TTTA
1 TTTA
394008 CTTTCTTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 10 0.30
18 21 0.64
19 2 0.06
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (18 bp):
TTTATTATTTTTATTCAC
Found at i:394895 original size:24 final size:24
Alignment explanation
Indices: 394841--394896 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
394831 ACAAGCGTGT
*
394841 ATATGTGAAAACTACAAACATTGG
1 ATATGTTAAAACTACAAACATTGG
394865 ATATGTTAAAACTACAAACATTGG
1 ATATGTTAAAACTACAAACATTGG
394889 ATATGTTA
1 ATATGTTA
394897 TTCTATGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.30
Consensus pattern (24 bp):
ATATGTTAAAACTACAAACATTGG
Found at i:398224 original size:21 final size:21
Alignment explanation
Indices: 398188--398241 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
398178 TTTACACTTG
*
398188 ATGCAGCGAT-CACCTTGTGT
1 ATGCATCGATGCACCTTGTGT
398208 ATGCATCGATGCACCTTGTGT
1 ATGCATCGATGCACCTTGTGT
398229 ATGCATCGATGCA
1 ATGCATCGATGCA
398242 TTGACGCTCC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 9 0.28
21 23 0.72
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (21 bp):
ATGCATCGATGCACCTTGTGT
Found at i:401588 original size:23 final size:22
Alignment explanation
Indices: 401513--401589 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
401503 ACACCTACCA
401513 GTGCATCGATG-CATCCTTGAAT
1 GTGCATCGATGACA-CCTTGAAT
* *
401535 GTGCATCGAT-ACACCATGAAG
1 GTGCATCGATGACACCTTGAAT
* * *
401556 GTACACCGATGGACGCCTTGAAT
1 GTGCATCGAT-GACACCTTGAAT
401579 GTGCATCGATG
1 GTGCATCGATG
401590 CACAAGGTCA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
21 14 0.33
22 13 0.30
23 16 0.37
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (22 bp):
GTGCATCGATGACACCTTGAAT
Found at i:403547 original size:28 final size:28
Alignment explanation
Indices: 403515--403571 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
403505 GGATGATTAA
* *
403515 ATTTGATGGTTTTTGGATGTTTGAACTT
1 ATTTGATGCTTTATGGATGTTTGAACTT
* *
403543 ATTTGTTGCTTTATGGATTTTTGAACTT
1 ATTTGATGCTTTATGGATGTTTGAACTT
403571 A
1 A
403572 ATATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.19, C:0.05, G:0.21, T:0.54
Consensus pattern (28 bp):
ATTTGATGCTTTATGGATGTTTGAACTT
Found at i:410132 original size:11 final size:11
Alignment explanation
Indices: 410096--410143 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
410086 AAATTTTGGC
410096 TTTTGTTTTTAT
1 TTTTGTTTTT-T
*
410108 TTTT-TTTGCCTT
1 TTTTGTTT--TTT
410120 TTTTGTTTTTT
1 TTTTGTTTTTT
410131 TTTTGTTTTTT
1 TTTTGTTTTTT
410142 TT
1 TT
410144 AAAATAGCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
11 18 0.58
12 9 0.29
13 4 0.13
ACGTcount: A:0.02, C:0.04, G:0.08, T:0.85
Consensus pattern (11 bp):
TTTTGTTTTTT
Found at i:412599 original size:2 final size:2
Alignment explanation
Indices: 412592--412621 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
412582 TAAAACGGGG
412592 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
412622 TATTTAGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:413963 original size:27 final size:29
Alignment explanation
Indices: 413887--413965 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 29
413877 TTACAATTTG
* *
413887 TATATTATAAATTTGATTTTTATGTTAAT
1 TATATTATAAATTTTATTTATATGTTAAT
* *
413916 TCATATTCATAAA-TTTCTTTATAT-TT-CT
1 T-ATATT-ATAAATTTTATTTATATGTTAAT
413944 TATATTATAAATTTTATTTATA
1 TATATTATAAATTTTATTTATA
413966 ATCACTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
26 5 0.12
27 14 0.33
28 2 0.05
29 3 0.07
30 13 0.31
31 5 0.12
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (29 bp):
TATATTATAAATTTTATTTATATGTTAAT
Found at i:414709 original size:20 final size:20
Alignment explanation
Indices: 414684--414737 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
414674 AACCCTTACA
**
414684 AATATCAAGTAGAAGCAAAC
1 AATATCAAACAGAAGCAAAC
414704 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAAGCAAAC
*
414724 AATATAAAACAGAA
1 AATATCAAACAGAA
414738 TCAAGCTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.61, C:0.15, G:0.11, T:0.13
Consensus pattern (20 bp):
AATATCAAACAGAAGCAAAC
Found at i:417116 original size:31 final size:31
Alignment explanation
Indices: 417084--417605 Score: 710
Period size: 31 Copynumber: 16.9 Consensus size: 31
417074 AAACTAATAT
* *
417084 ATCATTTATATCAACAACAATAAACCAGTAT
1 ATCATTTACATCAACAACAATAAACCAGTAC
* * *
417115 ATAATTTACATCAACAGCAATAAACCAGTAT
1 ATCATTTACATCAACAACAATAAACCAGTAC
** * *
417146 ATCATTTACATCAACAGTAATAAATCAGTAT
1 ATCATTTACATCAACAACAATAAACCAGTAC
* *
417177 ATCATTTACATCAACAGCAATAAACCAGTAT
1 ATCATTTACATCAACAACAATAAACCAGTAC
*
417208 ATCATTTACATCAACAACAATAAACCAATAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
* *
417239 ATAATTTACATCAA-AAGTAATAAACCAGTAC
1 ATCATTTACATCAACAA-CAATAAACCAGTAC
* *
417270 ATCATTTATATCAACAGCAATAAACCAGTAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
*
417301 ATCATTTACATCAACATCAATAAACCAGTAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
* *
417332 ATCATTTACATCAACAATAATAAATCAGTAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
* *
417363 ATCATTTACATCAACAGCAATAAACCAATAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
*
417394 ATCATTTACATCAACAGCAATAAACCAGTAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
*
417425 ATCATTTACATCTAA-AGA-AATAAACCCGTAC
1 ATCATTTACATC-AACA-ACAATAAACCAGTAC
*
417456 ATCATTTACATCAACAGCAATAAACCAGTAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
417487 ATCATTTACATCAACAACAATAAACCAGTAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
* *
417518 ATCATTTACATCAATAACAACAAACCAGTAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
* *
417549 ATCA-TTACATCAACAATAATAAATCAGTAC
1 ATCATTTACATCAACAACAATAAACCAGTAC
* **
417579 ATCATTTATATCAACAGTAATAAACCA
1 ATCATTTACATCAACAACAATAAACCA
417606 ATATATATAT
Statistics
Matches: 442, Mismatches: 42, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
30 30 0.07
31 409 0.93
32 3 0.01
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.26
Consensus pattern (31 bp):
ATCATTTACATCAACAACAATAAACCAGTAC
Found at i:417702 original size:63 final size:63
Alignment explanation
Indices: 417627--417854 Score: 332
Period size: 63 Copynumber: 3.6 Consensus size: 63
417617 TATATATTGG
*
417627 TTTATTGTTGTTGATGTACATGATATACTGTCAGAAGCATTTAATGTAAACTAACCCTAGTTT
1 TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCCTAGTTT
*
417690 TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGCATTTCATGTAAACTAACCCTAGTTT
1 TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCCTAGTTT
* * * *
417753 TTTATTGATGTTTATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCATGGTTT
1 TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCCTAGTTT
* *** * *
417816 TTTTTTCAAG-GGAATGTAAATGATATACTGTCCGAAGCA
1 TTTATTGTTGTTG-ATGTAAATGATATACTGTCAGAAGCA
417855 ATTGATTTAA
Statistics
Matches: 151, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
63 151 1.00
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (63 bp):
TTTATTGTTGTTGATGTAAATGATATACTGTCAGAAGCATTTAATGTAAACTAACCCTAGTTT
Found at i:420907 original size:21 final size:20
Alignment explanation
Indices: 420868--420905 Score: 55
Period size: 17 Copynumber: 2.0 Consensus size: 20
420858 ATTTAAATTT
420868 AATTTAGTAATTATAAATAA
1 AATTTAGTAATTATAAATAA
420888 AATTTA-TAA-TAT-AATAA
1 AATTTAGTAATTATAAATAA
420905 A
1 A
420906 TATAAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 3 0.17
20 6 0.33
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (20 bp):
AATTTAGTAATTATAAATAA
Found at i:421916 original size:39 final size:38
Alignment explanation
Indices: 421873--421971 Score: 144
Period size: 39 Copynumber: 2.6 Consensus size: 38
421863 AACGGATCAT
**
421873 TAAAATGAAACAAAAACTAAAGTTTCTAACGACATGTAC
1 TAAAATGAAACAAAAACTAAAAATT-TAACGACATGTAC
*
421912 TAAAATAAAACAAAAACTAAAAAATTTAACGACATGTAC
1 TAAAATGAAACAAAAACT-AAAAATTTAACGACATGTAC
*
421951 TAAAATGAAACAAAGACTAAA
1 TAAAATGAAACAAAAACTAAA
421972 CTTTGGGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
38 3 0.06
39 46 0.85
40 5 0.09
ACGTcount: A:0.59, C:0.13, G:0.08, T:0.20
Consensus pattern (38 bp):
TAAAATGAAACAAAAACTAAAAATTTAACGACATGTAC
Found at i:423584 original size:5 final size:5
Alignment explanation
Indices: 423574--423652 Score: 110
Period size: 5 Copynumber: 16.4 Consensus size: 5
423564 CGATAATCTC
* *
423574 TTTCT TTTCT TTTCT TTTAT TTTCT TTTC- -TTCT TTCCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
*
423622 TTTCT TTCCT TTTCT TTTCT TTTC- TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TT
423653 CTACTTACAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
3 3 0.05
4 4 0.06
5 58 0.89
ACGTcount: A:0.01, C:0.22, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTCT
Found at i:424331 original size:26 final size:26
Alignment explanation
Indices: 424295--424378 Score: 141
Period size: 26 Copynumber: 3.2 Consensus size: 26
424285 TTTCGGTGGA
**
424295 TTAATTCCACCTTTCGGTGGATTTGT
1 TTAATTCCACCTTTCTATGGATTTGT
424321 TTAATTCCACCTTTCTATGGATTTGT
1 TTAATTCCACCTTTCTATGGATTTGT
*
424347 TTAATTCCACCTTTCTATGGTTTTGT
1 TTAATTCCACCTTTCTATGGATTTGT
424373 TTAATT
1 TTAATT
424379 TTCAACAATC
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 55 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (26 bp):
TTAATTCCACCTTTCTATGGATTTGT
Found at i:430335 original size:13 final size:13
Alignment explanation
Indices: 430298--430337 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
430288 TCGATATTGA
430298 AAAATAAATA-TT
1 AAAATAAATATTT
*
430310 AAAATAATTTATTT
1 AAAATAA-ATATTT
430324 AAAATAAATATTT
1 AAAATAAATATTT
430337 A
1 A
430338 TTTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:431746 original size:3 final size:3
Alignment explanation
Indices: 431738--431791 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
431728 GGCCTGGTTG
* *
431738 TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
431784 TAA TAA TA
1 TAA TAA TA
431792 TAAATAAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 2 0.05
3 36 0.82
4 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:431755 original size:12 final size:11
Alignment explanation
Indices: 431738--431794 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
431728 GGCCTGGTTG
431738 TAATAATAATA
1 TAATAATAATA
431749 TTAATAATAA-A
1 -TAATAATAATA
431760 -AATATATAATA
1 TAATA-ATAATA
431771 -AATAAT-ATAA
1 TAATAATAAT-A
431781 TAATAATAATA
1 TAATAATAATA
431792 TAA
1 TAA
431795 ATAAAACCGG
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
9 6 0.15
10 7 0.17
11 16 0.40
12 11 0.28
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAATAATA
Found at i:431798 original size:12 final size:14
Alignment explanation
Indices: 431738--431794 Score: 80
Period size: 14 Copynumber: 4.0 Consensus size: 14
431728 GGCCTGGTTG
431738 TAATAATAATATTAA
1 TAATAATAATA-TAA
*
431753 TAATAAAAATAT-A
1 TAATAATAATATAA
431766 TAATAAATAATATAA
1 TAAT-AATAATATAA
431781 TAATAATAATATAA
1 TAATAATAATATAA
431795 ATAAAACCGG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
13 5 0.13
14 18 0.47
15 15 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:432236 original size:112 final size:113
Alignment explanation
Indices: 432024--432432 Score: 580
Period size: 113 Copynumber: 3.7 Consensus size: 113
432014 CAGAGTTATG
* * *
432024 CAAAAGGCTGAACAAACTCTTCTCATTGTGAACTTCTTCTT-CTTCA--A-ATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCATCAGATGAGTTCTTCTCA
* * * * * * * *
432085 TTATGAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAG
66 TTATGAACTTTCTCTGGCAATGTTAATCCATTAATTGATGAATTTAAA
* * * *
432133 CAAAAGGTTGAACAAATTCTTCTCATTATGAATTTTTTCTT-CTTCAT-ATGACGAGTTCTTCTT
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCATCA-GATGAGTTCTTCTC
*
432196 ATTATGAACTGTAC-CTGGCAATGTTAATCCATTAATTGATGAATTTAAA
65 ATTATGAACT-TTCTCTGGCAATGTTAATCCATTAATTGATGAATTTAAA
*
432245 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCATCAGATGAGTTCTTCTCA
432310 TTATGAACTTTCTCTGGCAATGTTAATCCATTAATTGATGAATTTAAA
66 TTATGAACTTTCTCTGGCAATGTTAATCCATTAATTGATGAATTTAAA
* *
432358 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTA
1 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCATCAGATGAGTTCTTCTCA
432423 TTATGAACTT
66 TTATGAACTT
432433 CTTCTTCCTT
Statistics
Matches: 270, Mismatches: 23, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
109 41 0.15
110 1 0.00
112 89 0.33
113 138 0.51
114 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (113 bp):
CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCATCAGATGAGTTCTTCTCA
TTATGAACTTTCTCTGGCAATGTTAATCCATTAATTGATGAATTTAAA
Found at i:432364 original size:225 final size:222
Alignment explanation
Indices: 432024--432431 Score: 613
Period size: 225 Copynumber: 1.8 Consensus size: 222
432014 CAGAGTTATG
*
432024 CAAAAGGCTGAACAAACTCTTCTCATTGTGAACTTCTTCTTCTTCAAATGAGTTCTTCTCATTAT
1 CAAAAGGCTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAAATGAGTTCTTCTCATTAT
* * * *
432089 GAACTTTCTCTGGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAATTCTT
66 GAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTT
* *
432154 CTCATTATGAATTTTTTCTT-CTTCAT-ATGACGAGTTCTTCTTATTATGAACTGTACCTGGCAA
131 CTCATTATGAACTTCTTCTTCCTTCATCA-GACGAGTTCTTCTTATTATGAACTGTACCTGGCAA
432217 TGTTAATCCATTAATTGATGAATTTAAA
195 TGTTAATCCATTAATTGATGAATTTAAA
* * *
432245 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 CAAAAGGCTGAACAAACTCTTCTCATTATGAA---CTTCTT-CTTCTTCAAATGAGTTCTTCTCA
* * * *
432310 TTATGAACTTTCTCTGGCAATGTTAATCCATTAATTGATGAATTTAAACAAAAGGTTGAACAAAT
62 TTATGAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAAT
* *
432375 TCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACT
127 TCTTCTCATTATGAACTTCTTCTTCCTTCATCAGACGAGTTCTTCTTATTATGAACT
432432 TCTTCTTCCT
Statistics
Matches: 165, Mismatches: 16, Indels: 7
0.88 0.09 0.04
Matches are distributed among these distances:
221 29 0.18
224 6 0.04
225 101 0.61
226 28 0.17
227 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (222 bp):
CAAAAGGCTGAACAAACTCTTCTCATTATGAACTTCTTCTTCTTCAAATGAGTTCTTCTCATTAT
GAACTTTCTCTGGAAAAGTTAATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTT
CTCATTATGAACTTCTTCTTCCTTCATCAGACGAGTTCTTCTTATTATGAACTGTACCTGGCAAT
GTTAATCCATTAATTGATGAATTTAAA
Found at i:432417 original size:20 final size:20
Alignment explanation
Indices: 432394--432459 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
432384 TATGAACTTC
432394 TTCTTCCTTCTTCAGATGAG
1 TTCTTCCTTCTTCAGATGAG
* **
432414 TTCTT-CTTATT-ATGAACT-TC
1 TTCTTCCTTCTTCA-G-A-TGAG
432434 TTCTTCCTTCTTCAGATGAG
1 TTCTTCCTTCTTCAGATGAG
432454 TTCTTC
1 TTCTTC
432460 TCATTATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 1 0.03
19 7 0.21
20 18 0.53
21 7 0.21
22 1 0.03
ACGTcount: A:0.15, C:0.24, G:0.11, T:0.50
Consensus pattern (20 bp):
TTCTTCCTTCTTCAGATGAG
Found at i:432418 original size:40 final size:40
Alignment explanation
Indices: 432374--432626 Score: 198
Period size: 40 Copynumber: 6.5 Consensus size: 40
432364 GTTGAACAAA
432374 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
*
432414 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
**** *
432454 TTCTTCTCATTATGAAC-T-TTC-T-CTTGAAAAGCTGA-
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * * * * * *** ****** * ** *
432489 TCCATC-AAGTGATGGATTTGAAC-AAAAGGTTGA-ACAAA
1 TTCTTCTCA-TTATGAACTTCTTCTTCCTTCTTCAGATGAG
*
432527 TTCTTCTCATTATGAACTTCTTCTTCCTTTTTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCC-TTCTTCAGATGAG
432568 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
432608 TTCTTCTCATTATGAACTT
1 TTCTTCTCATTATGAACTT
432627 TCTCTGGAAA
Statistics
Matches: 159, Mismatches: 45, Indels: 18
0.72 0.20 0.08
Matches are distributed among these distances:
34 1 0.01
35 9 0.06
36 9 0.06
37 3 0.02
38 17 0.11
39 2 0.01
40 89 0.56
41 29 0.18
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (40 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:432434 original size:153 final size:153
Alignment explanation
Indices: 432261--432739 Score: 787
Period size: 153 Copynumber: 3.1 Consensus size: 153
432251 GTTGAACAAA
432261 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
432326 GCAATGTTAATCCATTAATTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GAAAAGCTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
432391 TTCTTCTTCCTTCTTCAGATGAG
131 TTCTTCTTCCTTCTTCAGATGAG
* *
432414 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
432479 GAAAAGCTGATCCATCAAGTGATGGATTTGAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 GAAAAGCTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
432544 TTCTTCTTCCTTTTTTCAGATGAG
131 TTCTTCTTCC-TTCTTCAGATGAG
432568 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
** * **
432633 GAAAAGCTGATCCATCAAGTGATGAATTTAGGCAAAAGGTTAAACATGTTCTTCTCATTATGAAC
66 GAAAAGCTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
*
432698 TTCTTCTTCCTTCTTCAGAGGAG
131 TTCTTCTTCCTTCTTCAGATGAG
*
432721 TTCTTCTTATTATGAACTT
1 TTCTTCTCATTATGAACTT
432740 TCTCTGGAAA
Statistics
Matches: 302, Mismatches: 23, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
153 159 0.53
154 143 0.47
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.42
Consensus pattern (153 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAG
Found at i:433794 original size:83 final size:83
Alignment explanation
Indices: 433565--433917 Score: 553
Period size: 83 Copynumber: 4.2 Consensus size: 83
433555 CTTATTTCTA
* * *
433565 CTATGAGCAAATTCATCTTTTAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
* *
433630 TAACATTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * *
433648 TTATTGGGTACATTCATCTTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCA
1 CTA-TGAGCACATTCATCTTT-CAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCA
433713 AAGAACACTTCCAGAAGATG
64 AAGAACACTTCCAGAAGATG
* *
433733 CTATGAGCACATTCATCTTTCAGATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
433798 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
433816 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTGCCAAACCAGATTAGATAACTCAAA
1 CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
433881 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
433899 CTATTGGGCACATTCATCT
1 CTA-TGAGCACATTCATCT
433918 GTTCCAGTTA
Statistics
Matches: 247, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
83 144 0.58
84 43 0.17
85 60 0.24
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.29
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTTCAAATTCAATGATTGGTTCTACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:435072 original size:8 final size:8
Alignment explanation
Indices: 435059--435138 Score: 106
Period size: 8 Copynumber: 9.5 Consensus size: 8
435049 TTGACCCACC
435059 TTTTTCTT
1 TTTTTCTT
435067 TTTTTCTTT
1 TTTTTC-TT
435076 TTTTTCTT
1 TTTTTCTT
435084 TTTTCTCTTT
1 TTTT-TC-TT
*
435094 TTTTTCTC
1 TTTTTCTT
435102 TTTTTCTT
1 TTTTTCTT
*
435110 TTTCTCTT
1 TTTTTCTT
435118 TTCTTTCTT
1 TT-TTTCTT
435127 TTTTTCTT
1 TTTTTCTT
435135 TTTT
1 TTTT
435139 CTTCAAGCAT
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
8 39 0.61
9 19 0.30
10 6 0.09
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTCTT
Found at i:435087 original size:25 final size:25
Alignment explanation
Indices: 435059--435138 Score: 101
Period size: 26 Copynumber: 3.2 Consensus size: 25
435049 TTGACCCACC
435059 TTTTTCTTTTTTTCTTTTTTTTCTT
1 TTTTTCTTTTTTTCTTTTTTTTCTT
*
435084 TTTTCTCTTTTTTT-TCTCTTTTTCTT
1 TTTT-TCTTTTTTTCT-TTTTTTTCTT
*
435110 TTTCTCTTTTCTTTC-TTTTTTTCTT
1 TTTTTCTTTT-TTTCTTTTTTTTCTT
435135 TTTT
1 TTTT
435139 CTTCAAGCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
25 23 0.49
26 24 0.51
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (25 bp):
TTTTTCTTTTTTTCTTTTTTTTCTT
Found at i:435106 original size:43 final size:42
Alignment explanation
Indices: 435058--435138 Score: 135
Period size: 43 Copynumber: 1.9 Consensus size: 42
435048 CTTGACCCAC
* *
435058 CTTTTTCTTTTTTTCTTTTTTTTCTTTTTTCTCTTTTTTTTCT
1 CTTTTTCTTTTTCTCTTTTCTTTCTTTTTT-TCTTTTTTTTCT
435101 CTTTTTCTTTTTCTCTTTTCTTTCTTTTTTTCTTTTTT
1 CTTTTTCTTTTTCTCTTTTCTTTCTTTTTTTCTTTTTT
435139 CTTCAAGCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
42 8 0.22
43 28 0.78
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (42 bp):
CTTTTTCTTTTTCTCTTTTCTTTCTTTTTTTCTTTTTTTTCT
Found at i:445274 original size:12 final size:12
Alignment explanation
Indices: 445257--445281 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
445247 TCTATTATTA
445257 AAAATTCAAAAT
1 AAAATTCAAAAT
445269 AAAATTCAAAAT
1 AAAATTCAAAAT
445281 A
1 A
445282 TATTTAATTT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATTCAAAAT
Found at i:445525 original size:13 final size:13
Alignment explanation
Indices: 445488--445527 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
445478 TCGATATTGA
445488 AAAATAAATA-TT
1 AAAATAAATATTT
*
445500 AAAATAATTTATTT
1 AAAATAA-ATATTT
445514 AAAATAAATATTT
1 AAAATAAATATTT
445527 A
1 A
445528 TTTTATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 7 0.29
13 8 0.33
14 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATAAATATTT
Found at i:446404 original size:14 final size:16
Alignment explanation
Indices: 446385--446416 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
446375 AGCTCCTTTC
446385 TTCTTTCT-TTTT-TT
1 TTCTTTCTGTTTTGTT
446399 TTCTTTCTGTTTTGTT
1 TTCTTTCTGTTTTGTT
446415 TT
1 TT
446417 TTGCTAGTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 4 0.25
16 4 0.25
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.81
Consensus pattern (16 bp):
TTCTTTCTGTTTTGTT
Found at i:446922 original size:3 final size:3
Alignment explanation
Indices: 446914--446970 Score: 71
Period size: 3 Copynumber: 18.7 Consensus size: 3
446904 GGCCTGGTTG
* *
446914 TAA TAA TAA TAT TAA TAA TAA AAA TATA TAA TAAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA T-AA TAA TAA TAA TAA
446960 TAA TAA TAA TA
1 TAA TAA TAA TA
446971 TAAATAAAAC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 2 0.04
3 39 0.83
4 6 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:446931 original size:9 final size:9
Alignment explanation
Indices: 446917--446977 Score: 52
Period size: 9 Copynumber: 6.7 Consensus size: 9
446907 CTGGTTGTAA
446917 TAATAATAT
1 TAATAATAT
*
446926 TAATAATAA
1 TAATAATAT
*
446935 AAATATATAAT
1 TAATA-AT-AT
*
446946 AAATAATA-
1 TAATAATAT
*
446954 TAATAATAA
1 TAATAATAT
446963 TAATAATAT
1 TAATAATAT
*
446972 AAATAA
1 TAATAA
446978 AACCGGGAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
8 7 0.16
9 26 0.60
10 4 0.09
11 6 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TAATAATAT
Found at i:446976 original size:12 final size:12
Alignment explanation
Indices: 446915--446977 Score: 53
Period size: 12 Copynumber: 5.4 Consensus size: 12
446905 GCCTGGTTGT
*
446915 AATAATAATATT
1 AATAATAATATA
*
446927 AATAATAAAAATA
1 AATAAT-AATATA
*
446940 TATAATAA-AT-
1 AATAATAATATA
446950 AAT-ATAATA-A
1 AATAATAATATA
446960 TAATAATAATATA
1 -AATAATAATATA
446973 AATAA
1 AATAA
446978 AACCGGGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
9 4 0.10
10 3 0.07
11 5 0.12
12 19 0.46
13 10 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AATAATAATATA
Found at i:449596 original size:17 final size:17
Alignment explanation
Indices: 449563--449596 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
449553 CCTTCTATTT
* *
449563 TTATTTTATTTTTAAAA
1 TTATTTTATATTAAAAA
449580 TTATTTTATATTAAAAA
1 TTATTTTATATTAAAAA
449597 ATAATTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTTTATATTAAAAA
Found at i:450204 original size:24 final size:26
Alignment explanation
Indices: 450177--450225 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
450167 TATTTTTAGT
*
450177 CACTCATGTTTA-AT-TATATATATA
1 CACTCATGTGTATATATATATATATA
*
450201 CACTTATGTGTATATATATATATAT
1 CACTCATGTGTATATATATATATAT
450226 TTGTGTACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.48
25 2 0.10
26 9 0.43
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (26 bp):
CACTCATGTGTATATATATATATATA
Found at i:450263 original size:4 final size:4
Alignment explanation
Indices: 450249--451343 Score: 1740
Period size: 4 Copynumber: 276.0 Consensus size: 4
450239 TCACATGTAT
* * *
450249 ATAC TTAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ACAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
450297 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
450345 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * * * *
450393 ATAC ATAT ACAC ATAT ATAC ATAT ACAC ATAC ATAC ATAT ACAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
450441 ATGC ATAT ACAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAT ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
450489 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
450537 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
450585 ATAC ATAC ATAC ATAC ATAC --AC ATAC -TAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
450630 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
450678 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * ** * * *
450726 ATAC ATAC ATAC ATAC AGAC ATGC ATGC ATGC ATGT ATGC ATGC ATGC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
450774 ATGC ATGC ATAC ATGC ATAC ATGC ATAC ATGC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
450822 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
450870 ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
450918 ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* * * * *
450966 ATAC ATAC GTAC GTAC ATAC ATAC ATAT ATAC ATAT AT-C GTAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
451013 ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAT ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
451061 ATAC ATAC -TAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC --AC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
451106 ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT-- ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
451152 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
451200 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
451248 ATAC ATAC ATAC ATAC ATAC ATAC ATAC TTAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
*
451296 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
451344 TTATATATAT
Statistics
Matches: 1016, Mismatches: 66, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
2 6 0.01
3 7 0.01
4 1003 0.99
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:451371 original size:15 final size:15
Alignment explanation
Indices: 451353--451404 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
451343 CTTATATATA
451353 TATATATTTTATACT
1 TATATATTTTATACT
*
451368 TATATATTATATACT
1 TATATATTTTATACT
451383 TA-ATACTTTTATA-T
1 TATATA-TTTTATACT
451397 ATATATAT
1 -TATATAT
451405 ATATATAAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
14 4 0.12
15 25 0.78
16 3 0.09
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (15 bp):
TATATATTTTATACT
Found at i:458560 original size:55 final size:55
Alignment explanation
Indices: 458455--458901 Score: 556
Period size: 55 Copynumber: 8.1 Consensus size: 55
458445 ATGAACAATT
* * *
458455 AGTGCCTATACGG-GAATTCATCAACTCATGATGAATTTCGTGGATTTGCACAC-A
1 AGTGCCTGTACGGTG-ATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
* * * * * *
458509 AGGAGCTTGTATGGCGATTCATCAACTTATGATGAATTCCGTGAATATGCACACGA
1 A-GTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
* * * *
458565 AGTGCCTGTACGGTGATTCATCAAGTTATGATGAATTCCGTTAATATGCACACGA
1 AGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
* *
458620 AGTGCCTGTACAGTGATTCATCAACTTATGATGAATTTCGTGAATATGCACACGA
1 AGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
*
458675 AGTGCATGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
1 AGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
* * * * * *
458730 AGTGCTTGTACGATGATTCATAAACTCATGATGAATTACTTAAATATGCACACGA
1 AGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
* ** * * *
458785 AGTGCCCGTAAAGTGATTCATCAACTTAAGATGAATTTCGTGAATATGCACATGA
1 AGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
* * * * *
458840 AGTGCATGTATGGTGATTCATCAACTCATGATGAACTCCGTAAATATGCACACGA
1 AGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
*
458895 GGTGCCT
1 AGTGCCT
458902 ATAGTACACA
Statistics
Matches: 339, Mismatches: 51, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
54 1 0.00
55 335 0.99
56 3 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (55 bp):
AGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATATGCACACGA
Found at i:458727 original size:165 final size:165
Alignment explanation
Indices: 458470--458901 Score: 634
Period size: 165 Copynumber: 2.6 Consensus size: 165
458460 CTATACGGGA
* * * * * *
458470 ATTCATCAACTCATGATGAATTTCGTGGATTTGCACAC-AAGGAGCTTGTATGGCGATTCATCAA
1 ATTCATCAACTTATGATGAATTTCGTGAATATGCACACGAA-GTGCATGTATGGTGATTCATCAA
* * * * *
458534 CTTATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGGTGATTCATCAAGTTATGATGA
65 CTCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGATGATTCATAAACTCATGATGA
* * *
458599 ATTCCGTT-AATATGCACACGAAGTGCCTGTACAGTG
130 ATTAC-TTAAATATGCACACGAAGTGCCCGTAAAGTG
*
458635 ATTCATCAACTTATGATGAATTTCGTGAATATGCACACGAAGTGCATGTACGGTGATTCATCAAC
1 ATTCATCAACTTATGATGAATTTCGTGAATATGCACACGAAGTGCATGTATGGTGATTCATCAAC
* *
458700 TCATGATGAATTTCGTGAATATGCACACGAAGTGCTTGTACGATGATTCATAAACTCATGATGAA
66 TCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGATGATTCATAAACTCATGATGAA
458765 TTACTTAAATATGCACACGAAGTGCCCGTAAAGTG
131 TTACTTAAATATGCACACGAAGTGCCCGTAAAGTG
* *
458800 ATTCATCAACTTAAGATGAATTTCGTGAATATGCACATGAAGTGCATGTATGGTGATTCATCAAC
1 ATTCATCAACTTATGATGAATTTCGTGAATATGCACACGAAGTGCATGTATGGTGATTCATCAAC
* * *
458865 TCATGATGAACTCCGTAAATATGCACACGAGGTGCCT
66 TCATGATGAATTCCGTGAATATGCACACGAAGTGCCT
458902 ATAGTACACA
Statistics
Matches: 240, Mismatches: 25, Indels: 4
0.89 0.09 0.01
Matches are distributed among these distances:
164 2 0.01
165 236 0.98
166 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.30
Consensus pattern (165 bp):
ATTCATCAACTTATGATGAATTTCGTGAATATGCACACGAAGTGCATGTATGGTGATTCATCAAC
TCATGATGAATTCCGTGAATATGCACACGAAGTGCCTGTACGATGATTCATAAACTCATGATGAA
TTACTTAAATATGCACACGAAGTGCCCGTAAAGTG
Found at i:459465 original size:20 final size:19
Alignment explanation
Indices: 459436--459499 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
459426 ATACCCCTGA
459436 TCAT-GGTATCGATACTACC
1 TCATCGGTATCGATACTA-C
*
459455 TCATCGGTATCGATACTAAT
1 TCATCGGTATCGATACT-AC
* *
459475 TGAATCAGTATCGATACTAC
1 T-CATCGGTATCGATACTAC
459495 TCATC
1 TCATC
459500 CAATTTATCT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 7 0.19
20 15 0.41
21 15 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (19 bp):
TCATCGGTATCGATACTAC
Found at i:477172 original size:55 final size:55
Alignment explanation
Indices: 477106--477254 Score: 226
Period size: 55 Copynumber: 2.7 Consensus size: 55
477096 ATCATGCTCA
* * *
477106 TACGGTGATTCATCAACTTATGATGAATTTCGTGAATATGCACATGAAGTGCATG
1 TACGGTGATTCATCAACTTATGATGAATTCCGTGAATATGCAAACGAAGTGCATG
* *
477161 TACGGTGATTCATCAACTTATGATGAATTCCGTGGATATGCAAACGAAGTGCCTG
1 TACGGTGATTCATCAACTTATGATGAATTCCGTGAATATGCAAACGAAGTGCATG
* * *
477216 TACGGTGATTCATCAACTGACGATGAATTCCATGAATAT
1 TACGGTGATTCATCAACTTATGATGAATTCCGTGAATAT
477255 TAGAGCTGGG
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 85 1.00
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (55 bp):
TACGGTGATTCATCAACTTATGATGAATTCCGTGAATATGCAAACGAAGTGCATG
Found at i:477609 original size:42 final size:42
Alignment explanation
Indices: 477561--477678 Score: 202
Period size: 42 Copynumber: 2.8 Consensus size: 42
477551 AAGTAAATAA
* *
477561 ATAACACCATTAAGTCTCAATAAGTCTAAAATAAATAACACC
1 ATAACACTAATAAGTCTCAATAAGTCTAAAATAAATAACACC
*
477603 ATAACACTAATAAATCTCAATAAGTCTAAAATAAATAACACC
1 ATAACACTAATAAGTCTCAATAAGTCTAAAATAAATAACACC
477645 ATAACACTAATAAGTCTCAATAAGTCT-AAATAAA
1 ATAACACTAATAAGTCTCAATAAGTCTAAAATAAA
477679 ATCAACATCA
Statistics
Matches: 72, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 7 0.10
42 65 0.90
ACGTcount: A:0.53, C:0.19, G:0.04, T:0.25
Consensus pattern (42 bp):
ATAACACTAATAAGTCTCAATAAGTCTAAAATAAATAACACC
Found at i:477616 original size:21 final size:21
Alignment explanation
Indices: 477590--477657 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
477580 ATAAGTCTAA
477590 AATAAATAACACCATAACACT
1 AATAAATAACACCATAACACT
* * **
477611 AATAAAT--CTCAATAAGTCT
1 AATAAATAACACCATAACACT
477630 AAAATAAATAACACCATAACACT
1 --AATAAATAACACCATAACACT
477653 AATAA
1 AATAA
477658 GTCTCAATAA
Statistics
Matches: 35, Mismatches: 8, Indels: 8
0.69 0.16 0.16
Matches are distributed among these distances:
19 8 0.23
21 19 0.54
23 8 0.23
ACGTcount: A:0.57, C:0.19, G:0.01, T:0.22
Consensus pattern (21 bp):
AATAAATAACACCATAACACT
Found at i:480152 original size:56 final size:53
Alignment explanation
Indices: 480085--480202 Score: 155
Period size: 56 Copynumber: 2.2 Consensus size: 53
480075 ATCAATATAA
* *
480085 AAAAAATCAAGAATAAACACAAGCACTATAAGCATAACAATTAACAAACAAAGAAC
1 AAAAACTCAAGAACAAACACAAGCACTATAAGCATAACAATT---AAACAAAGAAC
* * * *
480141 AAAAACTCAAGAACACACACAAGTATTATAAGCATAATAATTAAACAAAGAAC
1 AAAAACTCAAGAACAAACACAAGCACTATAAGCATAACAATTAAACAAAGAAC
480194 AAAAACTCA
1 AAAAACTCA
480203 CTACATGGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
53 20 0.36
56 36 0.64
ACGTcount: A:0.61, C:0.18, G:0.07, T:0.14
Consensus pattern (53 bp):
AAAAACTCAAGAACAAACACAAGCACTATAAGCATAACAATTAAACAAAGAAC
Found at i:481078 original size:55 final size:55
Alignment explanation
Indices: 480986--481227 Score: 340
Period size: 55 Copynumber: 4.4 Consensus size: 55
480976 CCTCTAGTGT
* * *
480986 ATATGCAAACGAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGA
1 ATATGCACACGAAGTGCATGTACGGTGATTCATCAACTCATGATGAATTCCGTGA
* * * *
481041 ATATTCACACGAAGTGCTTGTACGGTGATTCATCAACTCATGATGAATTCCATAA
1 ATATGCACACGAAGTGCATGTACGGTGATTCATCAACTCATGATGAATTCCGTGA
* * * * *
481096 ATATGCACACGAAGTTCATGCATGGTTATTCATCAACTTATGATGAATTCCGTGA
1 ATATGCACACGAAGTGCATGTACGGTGATTCATCAACTCATGATGAATTCCGTGA
* * *
481151 ATATGCACACAAAGTGCATGTACTGTGATTCATCAACTCATGATGAATTTCGTGA
1 ATATGCACACGAAGTGCATGTACGGTGATTCATCAACTCATGATGAATTCCGTGA
*
481206 ATATGCACACGAAGTGCCTGTA
1 ATATGCACACGAAGTGCATGTA
481228 GTACACATAG
Statistics
Matches: 162, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
55 162 1.00
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.30
Consensus pattern (55 bp):
ATATGCACACGAAGTGCATGTACGGTGATTCATCAACTCATGATGAATTCCGTGA
Found at i:481651 original size:18 final size:17
Alignment explanation
Indices: 481621--481654 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
481611 TACTACCCTA
481621 CTATGGTACTGATACCC
1 CTATGGTACTGATACCC
*
481638 CTATCGGTATTGATACC
1 CTAT-GGTACTGATACC
481655 AAAATTAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (17 bp):
CTATGGTACTGATACCC
Found at i:484676 original size:21 final size:20
Alignment explanation
Indices: 484659--484698 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
484649 TCTTAATGAT
484659 GAACTA-TGGCTTTGTAATA
1 GAACTACTGGCTTTGTAATA
*
484678 GAGCTACTTGGCTTTGTAATA
1 GAACTAC-TGGCTTTGTAATA
484699 AAGTACATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.38
Consensus pattern (20 bp):
GAACTACTGGCTTTGTAATA
Found at i:484771 original size:21 final size:20
Alignment explanation
Indices: 484746--484784 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
484736 TATCAAGGTC
*
484746 TTTGTTGAAGCCATGAAATCT
1 TTTGTCGAAGCCAT-AAATCT
*
484767 TTTGTCGAGGCCATAAAT
1 TTTGTCGAAGCCATAAAT
484785 TTCTGCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (20 bp):
TTTGTCGAAGCCATAAATCT
Found at i:500163 original size:11 final size:11
Alignment explanation
Indices: 500147--500181 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
500137 ATATATATAT
500147 ATACATGCATC
1 ATACATGCATC
*
500158 ATACATACATC
1 ATACATGCATC
*
500169 ATGCATGCATC
1 ATACATGCATC
500180 AT
1 AT
500182 TGATCATACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.37, C:0.26, G:0.09, T:0.29
Consensus pattern (11 bp):
ATACATGCATC
Found at i:500231 original size:13 final size:15
Alignment explanation
Indices: 500199--500295 Score: 57
Period size: 15 Copynumber: 6.9 Consensus size: 15
500189 ACATAATTAC
500199 ATATATACTTATAAT
1 ATATATACTTATAAT
*
500214 ATATATACTTAT-GT
1 ATATATACTTATAAT
*
500228 -TATATAGTT-T-AT
1 ATATATACTTATAAT
*
500240 ATA-GT--TTATATAT
1 ATATATACTTATA-AT
500253 ATATATA-TTATAAT
1 ATATATACTTATAAT
* *
500267 TTATATACTTTATAGT
1 ATATATAC-TTATAAT
* *
500283 TTATATGCTTATA
1 ATATATACTTATA
500296 CTTTATAGTT
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
10 2 0.03
11 1 0.02
12 3 0.05
13 15 0.23
14 10 0.15
15 22 0.33
16 13 0.20
ACGTcount: A:0.38, C:0.04, G:0.05, T:0.53
Consensus pattern (15 bp):
ATATATACTTATAAT
Found at i:500239 original size:9 final size:9
Alignment explanation
Indices: 500227--500319 Score: 58
Period size: 9 Copynumber: 10.7 Consensus size: 9
500217 TATACTTATG
500227 TTATATAGT
1 TTATATAGT
500236 TTATATAGT
1 TTATATAGT
500245 TTATATA-T
1 TTATATAGT
*
500253 ATATATA--
1 TTATATAGT
500260 TTATA-A-T
1 TTATATAGT
*
500267 TTATATA-C
1 TTATATAGT
500275 TT-TATAGT
1 TTATATAGT
500283 TTATAT-GCT
1 TTATATAG-T
500292 TATACTTTATAGT
1 T-TA---TATAGT
*
500305 TTATATATT
1 TTATATAGT
500314 TTATAT
1 TTATAT
500320 TTTATATGTA
Statistics
Matches: 69, Mismatches: 5, Indels: 20
0.73 0.05 0.21
Matches are distributed among these distances:
6 1 0.01
7 13 0.19
8 13 0.19
9 32 0.46
10 2 0.03
12 2 0.03
13 5 0.07
14 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (9 bp):
TTATATAGT
Found at i:500240 original size:22 final size:23
Alignment explanation
Indices: 500215--500319 Score: 78
Period size: 22 Copynumber: 4.7 Consensus size: 23
500205 ACTTATAATA
*
500215 TATATACTTATGT-TATATAGTT
1 TATATACTTATATATATATAGTT
*
500237 TATATAGTTTATATATATATA-TAT
1 TATATA-CTTATATATATATAGT-T
* *
500261 TATA-ATTTATATACTTTATAGTT
1 TATATACTTATATA-TATATAGTT
*
500284 TATATGCTTATACT-T-TATAGTT
1 TATATACTTATA-TATATATAGTT
*
500306 TATATA-TTTTATAT
1 TATATACTTATATAT
500320 TTTATATGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
20 1 0.01
21 5 0.07
22 26 0.38
23 18 0.26
24 17 0.25
25 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (23 bp):
TATATACTTATATATATATAGTT
Found at i:500270 original size:31 final size:30
Alignment explanation
Indices: 500230--500320 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 30
500220 ACTTATGTTA
*
500230 TATAGTTTATATAGTTTATATATATATATAT
1 TATAATTTATATAGTTTATATAT-TATATAT
* *
500261 TATAATTTATATACTTTATAGT-TTATATGCT
1 TATAATTTATATAGTTTATA-TATTATAT-AT
* *
500292 TAT-ACTT-TATAGTTTATATATTTTATAT
1 TATAATTTATATAGTTTATATATTATATAT
500320 T
1 T
500321 TTATATGTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
28 3 0.06
29 15 0.30
30 8 0.16
31 23 0.46
32 1 0.02
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (30 bp):
TATAATTTATATAGTTTATATATTATATAT
Found at i:500273 original size:16 final size:16
Alignment explanation
Indices: 500230--500302 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 16
500220 ACTTATGTTA
* *
500230 TATAGTTTATATAGTT
1 TATAATTTATATACTT
*
500246 TAT-ATATATATA-TAT
1 TATAATTTATATACT-T
500261 TATAATTTATATACTT
1 TATAATTTATATACTT
* *
500277 TATAGTTTATATGC-T
1 TATAATTTATATACTT
*
500292 TATACTTTATA
1 TATAATTTATA
500303 GTTTATATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
14 1 0.02
15 22 0.46
16 24 0.50
17 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.05, T:0.55
Consensus pattern (16 bp):
TATAATTTATATACTT
Found at i:500281 original size:38 final size:38
Alignment explanation
Indices: 500239--500331 Score: 109
Period size: 38 Copynumber: 2.4 Consensus size: 38
500229 ATATAGTTTA
500239 TATAGTTTATATATATATA-TATTATAATTTATATACTT
1 TATAGTTTATATATATATACT-TTATAATTTATATACTT
* * *
500277 TATAGTTTATATGCT-TATACTTTATAGTTTATATATTT
1 TATAGTTTATAT-ATATATACTTTATAATTTATATACTT
* *
500315 TATATTTTATATGTATA
1 TATAGTTTATATATATA
500332 CACACTTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
37 1 0.02
38 44 0.94
39 2 0.04
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.57
Consensus pattern (38 bp):
TATAGTTTATATATATATACTTTATAATTTATATACTT
Found at i:500567 original size:16 final size:16
Alignment explanation
Indices: 500537--500567 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
500527 TATTAAGTAT
500537 AGTGTATACTTATATA
1 AGTGTATACTTATATA
*
500553 AGTGTATATTTATAT
1 AGTGTATACTTATAT
500568 TGTATGCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.48
Consensus pattern (16 bp):
AGTGTATACTTATATA
Found at i:500741 original size:12 final size:12
Alignment explanation
Indices: 500724--500767 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
500714 CTCTAAAAAA
500724 AGTATAATGTAC
1 AGTATAATGTAC
500736 AGTATAATGTAC
1 AGTATAATGTAC
500748 AGTATAATGTAC
1 AGTATAATGTAC
*
500760 ATTATAAT
1 AGTATAAT
500768 ATATATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (12 bp):
AGTATAATGTAC
Found at i:501805 original size:17 final size:17
Alignment explanation
Indices: 501785--501822 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
501775 ATAACTTCAA
*
501785 TTAAAAAATAATGTTGG
1 TTAAAAAATAATGTTGC
*
501802 TTAAAAAATATTGTTGC
1 TTAAAAAATAATGTTGC
501819 TTAA
1 TTAA
501823 CTTGATTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.39
Consensus pattern (17 bp):
TTAAAAAATAATGTTGC
Found at i:502214 original size:67 final size:67
Alignment explanation
Indices: 502064--502255 Score: 222
Period size: 67 Copynumber: 2.8 Consensus size: 67
502054 TTAGACATTG
* * * * * * *
502064 CTCGACTTGTGCTTGTTAAAAAAATTGTTGCTTGACTTGACTCATTACTTGTTAAGCTCATTAAA
1 CTCGACTAGTGCTCGTTAAAAAAA-T-TT-ATTG-CTCGACTCATTGCTCGTTAAACTCATTAAA
502129 ATTTTA
62 ATTTTA
* * * *
502135 CTCGACTCGTGCTCGTTAAAAAAATTTATTGCTCGATTCGTTGCTCGTTAAACTCGTTAAAATTT
1 CTCGACTAGTGCTCGTTAAAAAAATTTATTGCTCGACTCATTGCTCGTTAAACTCATTAAAATTT
502200 TA
66 TA
* * *
502202 CTCGACTAGTGCTCGTTAAGAAAATTTATTGCTTGACTCATTGCTCATTAAACT
1 CTCGACTAGTGCTCGTTAAAAAAATTTATTGCTCGACTCATTGCTCGTTAAACT
502256 AGTTGCTCGC
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
67 77 0.73
68 3 0.03
69 2 0.02
70 1 0.01
71 22 0.21
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.40
Consensus pattern (67 bp):
CTCGACTAGTGCTCGTTAAAAAAATTTATTGCTCGACTCATTGCTCGTTAAACTCATTAAAATTT
TA
Found at i:509577 original size:42 final size:43
Alignment explanation
Indices: 509496--509806 Score: 162
Period size: 43 Copynumber: 7.3 Consensus size: 43
509486 TTAAAATATA
* **
509496 AAAG-TAAAAAGT-ATGATTGAAAAAATTAG-GGACCCCAATTAT
1 AAAGATAAAAAGTGA-GATTAAAAAAATTAGAGG-CATCAATTAT
* * * *
509538 AAAGATAAAACGTGACATTAAAAAAA-TAGGGGCATCAATTTT
1 AAAGATAAAAAGTGAGATTAAAAAAATTAGAGGCATCAATTAT
* *
509580 AAAGGTAAAAAGTAAGATTGAAAAAAATTAGAGGCATCAATTAT
1 AAAGATAAAAAGTGAGATT-AAAAAAATTAGAGGCATCAATTAT
* * *
509624 AAA-AGTAAAAAATGAGATT-AAAAAA--AGCAGGAACTTAATTAT
1 AAAGA-TAAAAAGTGAGATTAAAAAAATTAG-AGGCA-TCAATTAT
* * * * * * **
509666 AAAGGTACAAGGTGTGATTGAAAAACTTAGAATCATCAATTAT
1 AAAGATAAAAAGTGAGATTAAAAAAATTAGAGGCATCAATTAT
* * * *
509709 AAATG-TAAAAAAATGGGATTGAAAAAATTA-AGGGTC-TCCATTAT
1 AAA-GAT-AAAAAGTGAGATTAAAAAAATTAGA-GG-CATCAATTAT
* * * *
509753 AAAGATAAAAAAT-AGGAATACAAAAATTAG-GGACAACAATTAT
1 AAAGATAAAAAGTGA-GATTAAAAAAATTAGAGG-CATCAATTAT
*
509796 AAGGATAAAAA
1 AAAGATAAAAA
509807 ACTAAAATTA
Statistics
Matches: 206, Mismatches: 43, Indels: 39
0.72 0.15 0.14
Matches are distributed among these distances:
40 2 0.01
41 4 0.02
42 58 0.28
43 77 0.37
44 62 0.30
45 3 0.01
ACGTcount: A:0.53, C:0.07, G:0.17, T:0.23
Consensus pattern (43 bp):
AAAGATAAAAAGTGAGATTAAAAAAATTAGAGGCATCAATTAT
Found at i:509669 original size:86 final size:85
Alignment explanation
Indices: 509492--509735 Score: 233
Period size: 86 Copynumber: 2.8 Consensus size: 85
509482 GGGCTTAAAA
* ** ** *
509492 TATAAAAGTAAAAAGTATGATTGAAAAAATTAG-GGACCCCAATTAT-AAAGATAAAACGTGACA
1 TATAAAGGTAAAAAGTATGATTGAAAAAATTAGAGG-CATCAATTATAAAAG-TAAAAAATGAGA
* **
509555 TTAAAAAAATAGGGGCATCAAT
64 TTAAAAAAACAGGAACATCAAT
* *
509577 TTTAAAGGTAAAAAGTAAGATTGAAAAAAATTAGAGGCATCAATTATAAAAGTAAAAAATGAGAT
1 TATAAAGGTAAAAAGTATGATTG-AAAAAATTAGAGGCATCAATTATAAAAGTAAAAAATGAGAT
*
509642 TAAAAAAAGCAGGAAC-TTAAT
65 TAAAAAAA-CAGGAACATCAAT
* * * * ** * *
509663 TATAAAGGTACAAGGTGTGATTGAAAAACTTAGAATCATCAATTATAAATGTAAAAAAATGGGAT
1 TATAAAGGTAAAAAGTATGATTGAAAAAATTAGAGGCATCAATTATAAAAGT-AAAAAATGAGAT
*
509728 TGAAAAAA
65 TAAAAAAA
509736 TTAAGGGTCT
Statistics
Matches: 131, Mismatches: 23, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
85 45 0.34
86 76 0.58
87 10 0.08
ACGTcount: A:0.53, C:0.07, G:0.17, T:0.24
Consensus pattern (85 bp):
TATAAAGGTAAAAAGTATGATTGAAAAAATTAGAGGCATCAATTATAAAAGTAAAAAATGAGATT
AAAAAAACAGGAACATCAAT
Found at i:512406 original size:24 final size:24
Alignment explanation
Indices: 512324--512408 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
512314 TATATCAAAA
* * *
512324 ATCAAAACATAATTCAGGTCAAGT
1 ATCATAACAGAATCCAGGTCAAGT
* *
512348 ATTA-AATCAGAATCCAGATCAAGT
1 ATCATAA-CAGAATCCAGGTCAAGT
* *
512372 ATCCAT-TCAGAATCCAGGTCAGGT
1 AT-CATAACAGAATCCAGGTCAAGT
512396 ATCATAACAGAAT
1 ATCATAACAGAAT
512409 TCATGTTGAA
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
23 5 0.10
24 42 0.88
25 1 0.02
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.25
Consensus pattern (24 bp):
ATCATAACAGAATCCAGGTCAAGT
Found at i:514913 original size:3 final size:3
Alignment explanation
Indices: 514905--514967 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
514895 TCATTTCGTT
* ** **
514905 TTA TTA TTA ATA TTA TTA TTA TTA TTA AAA TTA AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
514953 TATA TTA TTA TTA TT
1 T-TA TTA TTA TTA TT
514968 TAATAAAAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
3 46 0.94
4 3 0.06
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:516762 original size:18 final size:17
Alignment explanation
Indices: 516738--516781 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
516728 CCATTTTCTA
516738 ATATATTTTAAATAA-AT
1 ATATATTTTAAA-AATAT
*
516755 ATTATATTATAAAAATAT
1 A-TATATTTTAAAAATAT
516773 ATATATTTT
1 ATATATTTT
516782 TTTACATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATATTTTAAAAATAT
Found at i:516812 original size:18 final size:17
Alignment explanation
Indices: 516738--516830 Score: 75
Period size: 16 Copynumber: 5.6 Consensus size: 17
516728 CCATTTTCTA
*
516738 ATATATTTTAAATAAAT
1 ATATATTTTAAATATAT
* *
516755 ATTATATTATAAAAATAT
1 A-TATATTTTAAATATAT
** *
516773 ATATATTTT-TTTACAT
1 ATATATTTTAAATATAT
*
516789 AAATATTTTAAAT-TAT
1 ATATATTTTAAATATAT
* *
516805 ATATATATTATATATAT
1 ATATATTTTAAATATAT
516822 AT-TATTTTA
1 ATATATTTTA
516831 GTTTACTTTA
Statistics
Matches: 57, Mismatches: 16, Indels: 7
0.71 0.20 0.09
Matches are distributed among these distances:
16 29 0.51
17 14 0.25
18 14 0.25
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATTTTAAATATAT
Found at i:516816 original size:11 final size:11
Alignment explanation
Indices: 516800--516826 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
516790 AATATTTTAA
516800 ATTATATATAT
1 ATTATATATAT
516811 ATTATATATAT
1 ATTATATATAT
516822 ATTAT
1 ATTAT
516827 TTTAGTTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
ATTATATATAT
Found at i:516936 original size:23 final size:24
Alignment explanation
Indices: 516900--516951 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
516890 CATTTTCTGA
516900 TATTTTTAAAATAAATATTTTAAT
1 TATTTTTAAAATAAATATTTTAAT
* * *
516924 TATTTTT-AGATAAATGTTTTTAT
1 TATTTTTAAAATAAATATTTTAAT
516947 TATTT
1 TATTT
516952 ATTTATATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 18 0.72
24 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (24 bp):
TATTTTTAAAATAAATATTTTAAT
Found at i:517526 original size:7 final size:7
Alignment explanation
Indices: 517516--517561 Score: 83
Period size: 7 Copynumber: 6.4 Consensus size: 7
517506 AATTCATATA
517516 TTTAATT
1 TTTAATT
517523 TTTAATT
1 TTTAATT
517530 TTTAATTT
1 TTTAA-TT
517538 TTTAATT
1 TTTAATT
517545 TTTAATT
1 TTTAATT
517552 TTTAATT
1 TTTAATT
517559 TTT
1 TTT
517562 TTAAAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 31 0.82
8 7 0.18
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTAATT
Found at i:517542 original size:22 final size:22
Alignment explanation
Indices: 517516--517562 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
517506 AATTCATATA
517516 TTTAATTTTTAATTTTTAATTT
1 TTTAATTTTTAATTTTTAATTT
517538 TTTAATTTTTAATTTTTAATTT
1 TTTAATTTTTAATTTTTAATTT
517560 TTT
1 TTT
517563 TAAAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (22 bp):
TTTAATTTTTAATTTTTAATTT
Found at i:517601 original size:18 final size:19
Alignment explanation
Indices: 517573--517625 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
517563 TAAAAAATTT
517573 ATATATTTATTATTTCA-TA
1 ATAT-TTTATTATTTCATTA
*
517592 ATATTTTATTATTTTATTA
1 ATATTTTATTATTTCATTA
*
517611 ATTTTTTATTTATTT
1 ATATTTTA-TTATTT
517626 TTCAAGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 11 0.37
19 13 0.43
20 6 0.20
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
ATATTTTATTATTTCATTA
Found at i:517612 original size:19 final size:18
Alignment explanation
Indices: 517570--517626 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
517560 TTTTAAAAAA
517570 TTTAT-ATA-TTTATTAT
1 TTTATAATATTTTATTAT
*
517586 TTCATAATATTTTATTAT
1 TTTATAATATTTTATTAT
*
517604 TTTATTAATTTTTTATTTAT
1 TTTA-TAATATTTTA-TTAT
517624 TTT
1 TTT
517627 TCAAGTATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 11 0.32
19 9 0.26
20 7 0.21
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTATAATATTTTATTAT
Found at i:519691 original size:15 final size:14
Alignment explanation
Indices: 519667--519709 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
519657 TTTTCATACA
519667 TACA-TTTGCATTT
1 TACATTTTGCATTT
519680 TACATCTTTGCATTT
1 TACAT-TTTGCATTT
* *
519695 TTCATTTTTCATTT
1 TACATTTTGCATTT
519709 T
1 T
519710 TGCATTTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
13 4 0.15
14 9 0.35
15 13 0.50
ACGTcount: A:0.19, C:0.16, G:0.05, T:0.60
Consensus pattern (14 bp):
TACATTTTGCATTT
Found at i:519701 original size:22 final size:22
Alignment explanation
Indices: 519675--519716 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
519665 CATACATTTG
519675 CATTTTACATCTTTGCATTTTT
1 CATTTTACATCTTTGCATTTTT
* *
519697 CATTTTTCATTTTTGCATTT
1 CATTTTACATCTTTGCATTT
519717 ATACTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.62
Consensus pattern (22 bp):
CATTTTACATCTTTGCATTTTT
Found at i:519833 original size:20 final size:20
Alignment explanation
Indices: 519774--519839 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
519764 TACATTCACA
*
519774 TATTTACATTTGCAT-TTTG
1 TATTTACATTTTCATGTTTG
* *
519793 CATATTTACATTTTTACGTTTG
1 --TATTTACATTTTCATGTTTG
519815 TATTTACATTTTCATGTTTG
1 TATTTACATTTTCATGTTTG
*
519835 CATTT
1 TATTT
519840 GCATATTTGC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 22 0.58
21 12 0.32
22 4 0.11
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (20 bp):
TATTTACATTTTCATGTTTG
Found at i:522198 original size:1 final size:1
Alignment explanation
Indices: 522192--522277 Score: 91
Period size: 1 Copynumber: 86.0 Consensus size: 1
522182 AAGAAAGAAG
* * * * * ** *
522192 AAAAAAAAGAAAAAGAAAGAAACAAAAAAAAAAAAAAAAACAAAAAAAAAGGAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
522257 AGAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAA
522278 GGAAATTGAA
Statistics
Matches: 69, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.90, C:0.02, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:522251 original size:43 final size:39
Alignment explanation
Indices: 522192--522277 Score: 127
Period size: 41 Copynumber: 2.1 Consensus size: 39
522182 AAGAAAGAAG
522192 AAAAAAAAGAAAAAGAAAGAAACAAAAAAAAAAAAAAAAACA
1 AAAAAAAAGAAAAAGAAA-AAA-AAAAAAAAAAAAAAAAA-A
*
522234 AAAAAAAAGGAAAAAGAAAAAAAAGAAAAAAAAAAAAAAA
1 AAAAAAAA-GAAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
522274 AAAA
1 AAAA
522278 GGAAATTGAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
40 5 0.12
41 16 0.38
42 11 0.26
43 10 0.24
ACGTcount: A:0.90, C:0.02, G:0.08, T:0.00
Consensus pattern (39 bp):
AAAAAAAAGAAAAAGAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:522264 original size:44 final size:42
Alignment explanation
Indices: 522192--522275 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 42
522182 AAGAAAGAAG
*
522192 AAAAAAAAGAAAAAGAAAGAAACAAAAAAAAAAAAAAAAACA
1 AAAAAAAAGAAAAAGAAAAAAACAAAAAAAAAAAAAAAAACA
*
522234 AAAAAAAAGGAAAAAGAAAAAAAAGAAAAAAAAAAAAAAAAA
1 AAAAAAAA-GAAAAAG-AAAAAAACAAAAAAAAAAAAAAAAA
522276 AAGGAAATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
42 8 0.21
43 7 0.18
44 23 0.61
ACGTcount: A:0.89, C:0.02, G:0.08, T:0.00
Consensus pattern (42 bp):
AAAAAAAAGAAAAAGAAAAAAACAAAAAAAAAAAAAAAAACA
Found at i:526955 original size:22 final size:22
Alignment explanation
Indices: 526922--527006 Score: 125
Period size: 22 Copynumber: 3.9 Consensus size: 22
526912 ACATCTACAT
526922 TTTTCAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
* * *
526944 TCTTCAACGATGATATATTCTC
1 TTTTCAAAGATGATAGATTCTC
*
526966 TTTTTAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
*
526988 TTTTCAAAGATGAAAGATT
1 TTTTCAAAGATGATAGATT
527007 TATGGGATCT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (22 bp):
TTTTCAAAGATGATAGATTCTC
Found at i:527775 original size:76 final size:76
Alignment explanation
Indices: 527680--528617 Score: 1657
Period size: 76 Copynumber: 12.3 Consensus size: 76
527670 TTACCACATT
*
527680 TGTAAGTCCTACAGTGCATGATGTTACCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
527745 TTAGGGTCATC
66 TTAGGGTCATC
*
527756 TGTAAGTCCTACAGTGCATGATGTTT-CAAAAAGCCTTCGGGAACTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
527820 TTAGGGTCATC
66 TTAGGGTCATC
527831 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCAAAGC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCAAAGC
527896 CTTAGGGTCATC
65 CTTAGGGTCATC
* * *
527908 TGTAAGTACTACAGTGCATGAAGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
527973 TTAGGGTCATC
66 TTAGGGTCATC
*
527984 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCTTTCGGGAGCTTTTTTGATGTTTTCAAAGC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCAAAGC
*
528049 CTTAGGGCCATC
65 CTTAGGGTCATC
*
528061 TGTAATTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
* *
528126 TTAGGATCATA
66 TTAGGGTCATC
528137 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
528202 TTAGGGTCATC
66 TTAGGGTCATC
*
528213 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
*
528278 TTAGGGTCACC
66 TTAGGGTCATC
* *
528289 TGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
528354 TTAGGGTCATC
66 TTAGGGTCATC
528365 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
528430 TTAGGGTCATC
66 TTAGGGTCATC
528441 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAAAGCC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
528505 TTAGGGTCATC
66 TTAGGGTCATC
*
528516 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACC
1 TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
*
528581 TTATGGTCATAC
66 TTAGGGTCAT-C
* * *
528593 -GTAAGCCCTTCAGTGCATGTTGTTT
1 TGTAAGTCCTACAGTGCATGATGTTT
528618 TTAACATTTC
Statistics
Matches: 825, Mismatches: 32, Indels: 10
0.95 0.04 0.01
Matches are distributed among these distances:
75 149 0.18
76 529 0.64
77 147 0.18
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (76 bp):
TGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCC
TTAGGGTCATC
Found at i:528769 original size:3 final size:3
Alignment explanation
Indices: 528761--528840 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
528751 TCATTTCGTT
** **
528761 TTA TTA TTA TTA TTA TTA AAA TTA AAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
528809 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
528841 TAATAAAAAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:530834 original size:22 final size:24
Alignment explanation
Indices: 530784--530834 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
530774 CATTTTTTGA
530784 TATTTTTAAAATAAATATTTTAAT
1 TATTTTTAAAATAAATATTTTAAT
* *
530808 TATTTTT-AGATAAATGTTTT-AT
1 TATTTTTAAAATAAATATTTTAAT
530830 TATTT
1 TATTT
530835 ATTTATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
23 11 0.44
24 7 0.28
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (24 bp):
TATTTTTAAAATAAATATTTTAAT
Found at i:535634 original size:20 final size:20
Alignment explanation
Indices: 535611--535655 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
535601 TTAACTTTTT
*
535611 CTTTTCTCTTTCATCCTTAA
1 CTTTTCTATTTCATCCTTAA
**
535631 CTTTTCTATTTCATTTTTAA
1 CTTTTCTATTTCATCCTTAA
535651 CTTTT
1 CTTTT
535656 ACTTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (20 bp):
CTTTTCTATTTCATCCTTAA
Found at i:537724 original size:23 final size:23
Alignment explanation
Indices: 537697--537744 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
537687 TGGTGGTTGG
537697 TTAATG-GATATTTAGACTTTATT
1 TTAATGAGATATTTA-ACTTTATT
* *
537720 TTAATGATATATTTAAGTTTATT
1 TTAATGAGATATTTAACTTTATT
537743 TT
1 TT
537745 GGTTCTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (23 bp):
TTAATGAGATATTTAACTTTATT
Found at i:538986 original size:25 final size:25
Alignment explanation
Indices: 538931--538992 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
538921 ATAAGTCTAG
*
538931 ATTCAATATTTTGATACATGATCACA
1 ATTC-ATATTATGATACATGATCACA
* *
538957 TTTCATATTATGATACATGA-CATGA
1 ATTCATATTATGATACATGATCA-CA
538982 ATTCATATTAT
1 ATTCATATTAT
538993 ATGCATTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
24 2 0.06
25 26 0.84
26 3 0.10
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCACA
Found at i:539089 original size:30 final size:31
Alignment explanation
Indices: 539033--539096 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
539023 GTTATATGAG
* *
539033 CTATGTGATAAAGGTATGGAAAATGATATGT
1 CTATGAGAAAAAGGTATGGAAAATGATATGT
539064 CTATGAGAAAAAGGTATGG-AAATGATATGT
1 CTATGAGAAAAAGGTATGGAAAATGATATGT
539094 CTA
1 CTA
539097 CGTGATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 14 0.45
31 17 0.55
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.30
Consensus pattern (31 bp):
CTATGAGAAAAAGGTATGGAAAATGATATGT
Found at i:539969 original size:21 final size:22
Alignment explanation
Indices: 539934--539980 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
539924 TACGGAAGTA
539934 CTGTAGCAGGGGAATCGGTACC
1 CTGTAGCAGGGGAATCGGTACC
*
539956 CTGTAGCA-GGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGGTACC
539977 CTGT
1 CTGT
539981 TTGCAATCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.23
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGGTACC
Found at i:542839 original size:149 final size:155
Alignment explanation
Indices: 542510--542869 Score: 448
Period size: 149 Copynumber: 2.3 Consensus size: 155
542500 TTATTTCTTT
* * * *
542510 AATTCCTCCTTTATTTTAAGTTCATTTTTTTACCAAATTTGAACCACATGCTCCTAAACCATATT
1 AATTCATCATTTATTTTAAGTTCATTTTTTTATCAAATTTGAACCACATGCTCCTAAACCATATG
*
542575 AGAACATATGTATACTTTCAATTCTTCTTTTTGATAACAAATTTTTTATTTTTCAATTTAGTCTT
66 AGAACATATGTATACTTTCAATTCCTCTTTTTGATAAC--A-TTTTTATTTTTCAATTTAGTCTT
* *
542640 TAAAATTTTCATAATCTCTTATTTCTTC
128 TAAAATTTTCATAATCTCTTAGTCCTTC
* * *
542668 AATTCGTCATTTATTTTAAGTTCATTTTTTTATCAAATTTGAGCCACATGCTTCTAAA-C-TA-G
1 AATTCATCATTTATTTTAAGTTCATTTTTTTATCAAATTTGAACCACATGCTCCTAAACCATATG
* * * *
542730 AGTAGA-ATGTGTACTTTCAGTTCCTCTTTTTGAT-AC-TTTTT-TTTTTCAATTTAGTCATTT-
66 AGAACATATGTATACTTTCAATTCCTCTTTTTGATAACATTTTTATTTTTCAATTTAGTC-TTTA
* *
542790 AATTTTTCATTATCTCCTTAGTCCTTC
130 AAATTTTCATAATCT-CTTAGTCCTTC
* * *
542817 CATTTATCATTTATTTTAAGTTCATTTTTTTATCAAATTTAAACCACATGCTC
1 AATTCATCATTTATTTTAAGTTCATTTTTTTATCAAATTTGAACCACATGCTC
542870 ATATATCACA
Statistics
Matches: 179, Mismatches: 21, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
148 28 0.16
149 64 0.36
153 2 0.01
154 25 0.14
155 4 0.02
156 2 0.01
157 1 0.01
158 53 0.30
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.49
Consensus pattern (155 bp):
AATTCATCATTTATTTTAAGTTCATTTTTTTATCAAATTTGAACCACATGCTCCTAAACCATATG
AGAACATATGTATACTTTCAATTCCTCTTTTTGATAACATTTTTATTTTTCAATTTAGTCTTTAA
AATTTTCATAATCTCTTAGTCCTTC
Found at i:543171 original size:2 final size:2
Alignment explanation
Indices: 543121--543162 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
543111 ATATGAAATA
543121 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
543163 GGTTATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:545665 original size:28 final size:27
Alignment explanation
Indices: 545641--545708 Score: 73
Period size: 29 Copynumber: 2.4 Consensus size: 27
545631 AATAAATGTT
545641 GGAAATTAAAGGACTAAAATAAAATACA
1 GGAAATTAAAGGACTAAAAT-AAATACA
* * *
545669 GGAAATTAAAGGAACAGAAAATAAAAACT
1 GGAAATTAAAGG-AC-TAAAATAAATACA
*
545698 GAAAATTAAAG
1 GGAAATTAAAG
545709 CGATGGAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.35
29 17 0.50
30 5 0.15
ACGTcount: A:0.62, C:0.06, G:0.16, T:0.16
Consensus pattern (27 bp):
GGAAATTAAAGGACTAAAATAAATACA
Found at i:546202 original size:33 final size:33
Alignment explanation
Indices: 545895--546187 Score: 482
Period size: 33 Copynumber: 8.9 Consensus size: 33
545885 TGAGTTAGGT
* *
545895 TGAACAA-ATAAATAAAACGTTAGTAAGTTAGTA
1 TGAACAATA-AAATAAAATGTTAGTATGTTAGTA
* * *
545928 TAAAGAATAAAATAAAATGTTAGTCTGTTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
* *
545961 CGAACAATAAAATAAAATGTTAATATGTTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
*
545994 TGAACAATGAAA-AAAATGTTAGTATGTTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
*
546026 TGAACAATGAAATAAAATGTTAGTATGTTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
546059 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
546092 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
546125 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
1 TGAACAATAAAATAAAATGTTAGTATGTTAGTA
546158 TGAACAATAAAATAAAATGTTAGTATGTTA
1 TGAACAATAAAATAAAATGTTAGTATGTTA
546188 TTAGTCAAAT
Statistics
Matches: 244, Mismatches: 14, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
32 31 0.13
33 212 0.87
34 1 0.00
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (33 bp):
TGAACAATAAAATAAAATGTTAGTATGTTAGTA
Found at i:546992 original size:13 final size:13
Alignment explanation
Indices: 546928--546992 Score: 78
Period size: 13 Copynumber: 5.0 Consensus size: 13
546918 GTCATAAATC
*
546928 TATGACGCACATT
1 TATGACGCGCATT
546941 TATGACAG-GCATT
1 TATGAC-GCGCATT
*
546954 TATGACACGCATT
1 TATGACGCGCATT
*
546967 TATGACGCACATT
1 TATGACGCGCATT
*
546980 TATGACGTGCATT
1 TATGACGCGCATT
546993 GAGCATCATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
13 43 0.98
14 1 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:551815 original size:4 final size:4
Alignment explanation
Indices: 551806--551834 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
551796 GATGGGAATT
551806 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
551835 TAGTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:553389 original size:3 final size:3
Alignment explanation
Indices: 553381--553430 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
553371 TGTGAAAATA
* * *
553381 AAT AAT AAT AAT AAT AAT -AT AAT GAT ATT AAT AAT ATT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
553426 AAT AA
1 AAT AA
553431 AAAATAAAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:553412 original size:14 final size:14
Alignment explanation
Indices: 553377--553430 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
553367 GGCATGTGAA
553377 AATA-AATAATAAT
1 AATATAATAATAAT
553390 AATAATAAT-ATAAT
1 AAT-ATAATAATAAT
* *
553404 GATATTAATAATATT
1 AATA-TAATAATAAT
553419 AATA-AATAATAA
1 AATATAATAATAA
553431 AAAATAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 11 0.33
14 12 0.36
15 10 0.30
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (14 bp):
AATATAATAATAAT
Done.