Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008747.1 Hibiscus syriacus cultivar Beakdansim tig00111837_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: 12616935
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 51
Found at i:3481061 original size:32 final size:29
Alignment explanation
Indices: 3481003--3481061 Score: 73
Period size: 32 Copynumber: 1.9 Consensus size: 29
3480993 TGCAACAAAG
*
3481003 ATAAGAAAGGAAATAAGATTAGTAATGGA
1 ATAAGAAAGGAAATAAGATAAGTAATGGA
*
3481032 ATAAGAAATGGATAATTAAGATAATTAATG
1 ATAAGAAA-GGA-AA-TAAGATAAGTAATG
3481062 AAATGAAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.32
30 3 0.12
31 2 0.08
32 12 0.48
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.25
Consensus pattern (29 bp):
ATAAGAAAGGAAATAAGATAAGTAATGGA
Found at i:3487503 original size:3 final size:3
Alignment explanation
Indices: 3487495--3487528 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3487485 ACCTTAAAAC
3487495 AAT AAT AAT AAT AA- ATAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A
3487529 TTAAAAATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 27 0.93
4 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3487516 original size:12 final size:13
Alignment explanation
Indices: 3487495--3487533 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
3487485 ACCTTAAAAC
3487495 AATAATAATAATA
1 AATAATAATAATA
3487508 AAT-ATAATAAT-
1 AATAATAATAATA
*
3487519 AATAATAATATTA
1 AATAATAATAATA
3487532 AA
1 AA
3487534 AATGTCGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
11 3 0.13
12 15 0.65
13 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:3490317 original size:24 final size:24
Alignment explanation
Indices: 3490285--3490330 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3490275 TTAATGCTCT
* *
3490285 TGAATGTGTTCATTTATATGTTCA
1 TGAACGTGTTCATTTACATGTTCA
3490309 TGAACGTGTTCATTTACATGTT
1 TGAACGTGTTCATTTACATGTT
3490331 TGTTTAGCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.24, C:0.11, G:0.17, T:0.48
Consensus pattern (24 bp):
TGAACGTGTTCATTTACATGTTCA
Found at i:3492331 original size:3 final size:3
Alignment explanation
Indices: 3492323--3492362 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
3492313 GTAACCTTAA
3492323 AAT AAT AAT AAT AAT AAT AA- ATAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A
3492363 TTATTAAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 1 0.03
3 33 0.94
4 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3492811 original size:22 final size:22
Alignment explanation
Indices: 3492785--3492838 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
3492775 TTCACGAACA
3492785 TGTTTGTTTAGCGTTCATTTAG
1 TGTTTGTTTAGCGTTCATTTAG
* **
3492807 TGTTTATTTAGCGTTGTTTTAG
1 TGTTTGTTTAGCGTTCATTTAG
3492829 TGTTTGTTTA
1 TGTTTGTTTA
3492839 TCATACGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.13, C:0.06, G:0.22, T:0.59
Consensus pattern (22 bp):
TGTTTGTTTAGCGTTCATTTAG
Found at i:3497421 original size:22 final size:22
Alignment explanation
Indices: 3497380--3497422 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3497370 ATTTTCAACC
*
3497380 ATTTGTAAGTCATGTAATTACA
1 ATTTGTAACTCATGTAATTACA
* *
3497402 ATTTGTAACTCTTGTGATTAC
1 ATTTGTAACTCATGTAATTAC
3497423 TCTGGCACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (22 bp):
ATTTGTAACTCATGTAATTACA
Found at i:3500259 original size:85 final size:85
Alignment explanation
Indices: 3500159--3500451 Score: 424
Period size: 85 Copynumber: 3.4 Consensus size: 85
3500149 CACAGTGTTT
* * * *
3500159 GTTGACATATAGCCCTTCTCGCCTAGAGCTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGT
1 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGT
*
3500224 AATCAAACTCGAAGGTCTTG
66 AATCGAACTCGAAGGTCTTG
* * * ** ** **
3500244 GTTGACAGATAGCCCTTATCTCCTTGAGTTATATTGTAAATAGGATAAACCTTTGAGCTGAATGT
1 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGT
*
3500309 AATCGAACTCGAAGGTCTTT
66 AATCGAACTCGAAGGTCTTG
* *
3500329 GATGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAGTGT
1 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGT
3500394 AATCGAACTCGAAGGTCTTG
66 AATCGAACTCGAAGGTCTTG
*
3500414 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGTTGTA
1 GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTA
3500452 CTGGGTTGGG
Statistics
Matches: 181, Mismatches: 27, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
85 181 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.34
Consensus pattern (85 bp):
GTTGACAGATAACCCTTCTCGCCTTGAGTTATGCTGTAAATTTGATATGCCTTTGAGCTGAATGT
AATCGAACTCGAAGGTCTTG
Found at i:3500722 original size:121 final size:121
Alignment explanation
Indices: 3500506--3500849 Score: 501
Period size: 121 Copynumber: 2.8 Consensus size: 121
3500496 CGATCCATTA
* * * *
3500506 GGCACGATATCCTTCATCGTGAAGTTGAAATCATGGATGACT-CTTTCGTTGTGAAGTTCAGCTT
1 GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTT-GTTGTGAAGTTGAGCTT
* * * * *
3500570 TGAATTGGATATCGTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGCTTCTTGTG
65 TGAATTGGATATCCTTCATCATGAAGTTGAAATCCAAGGATTGAATTGCTGCTTGTG
* * *
3500627 GTCACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGGCTCCTTTGTCGTGAAGTTGAGCTTT
1 GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTTGTTGTGAAGTTGAGCTTT
* * *
3500692 GAATTGGATATCCTTCGTCCTAAAGTTGAAATCCAAGGATTGAATTGCTGCTTGTG
66 GAATTGGATATCCTTCATCATGAAGTTGAAATCCAAGGATTGAATTGCTGCTTGTG
* * * *
3500748 GGCACGATATCCTTCGTCGTGAAGTGGAAGTCGTGGATGGCTCATTCGTTGTGAAGTTGAGCTTT
1 GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTTGTTGTGAAGTTGAGCTTT
3500813 GAATTGGATATCCTTCATCATGAAGTTGAAATCCAAG
66 GAATTGGATATCCTTCATCATGAAGTTGAAATCCAAG
3500850 CTTGTGTAAG
Statistics
Matches: 198, Mismatches: 24, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
121 194 0.98
122 4 0.02
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (121 bp):
GGCACGATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCTCCTTTGTTGTGAAGTTGAGCTTT
GAATTGGATATCCTTCATCATGAAGTTGAAATCCAAGGATTGAATTGCTGCTTGTG
Found at i:3500947 original size:64 final size:64
Alignment explanation
Indices: 3500872--3501235 Score: 557
Period size: 64 Copynumber: 5.7 Consensus size: 64
3500862 ACATTGTTTC
* *
3500872 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
*** *
3500936 GAGTCCAATATCCTTTTATGTGAAGTTGAAATTGACTCTGAATGAAACTGGAGAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * *
3501000 AAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGTAATTGGAAAGTCGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
3501064 GAGTCCAACATCCTTCGCTGTGAAGATGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
** * * *
3501128 GAGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTAAATGAAACTGGATAGTTGTTTATT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* *
3501192 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATG
3501236 CTGCAAAAAT
Statistics
Matches: 272, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 272 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:3501085 original size:192 final size:192
Alignment explanation
Indices: 3500872--3501235 Score: 613
Period size: 192 Copynumber: 1.9 Consensus size: 192
3500862 ACATTGTTTC
* *
3500872 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAG
1 GAGTCCAACATCCTTCGCTGTGAAGATGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAG
* * *
3500937 AGTCCAATATCCTT-TTATGTGAAGTTGAAATTGACTCTGAATGAAACTGGAGAGTTGTTTGTTA
66 AGTCCAATATCCTTCAT-TGTGAAGTTGAAATTGACTCTAAATGAAACTGGAGAGTTGTTTATTA
*
3501001 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGTAATTGGAAAGTCGTTTGTT
130 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGTAATTGGAAAGTCGTTTGTT
* *
3501064 GAGTCCAACATCCTTCGCTGTGAAGATGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTTG
1 GAGTCCAACATCCTTCGCTGTGAAGATGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAG
* *
3501129 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTAAATGAAACTGGATAGTTGTTTATTGA
66 AGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAGAGTTGTTTATTAA
*
3501194 GTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTAAATG
131 GTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATG
3501236 CTGCAAAAAT
Statistics
Matches: 160, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
192 159 0.99
193 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (192 bp):
GAGTCCAACATCCTTCGCTGTGAAGATGAAATTGACTCTGAATGAAACTGAAAAGTTGTTTGTAG
AGTCCAATATCCTTCATTGTGAAGTTGAAATTGACTCTAAATGAAACTGGAGAGTTGTTTATTAA
GTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAATGTAATTGGAAAGTCGTTTGTT
Found at i:3502595 original size:13 final size:13
Alignment explanation
Indices: 3502566--3502619 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
3502556 TATTCCTTTG
*
3502566 TTTTTGTTTCTCT
1 TTTTTATTTCTCT
3502579 TTTTTATTT-TCT
1 TTTTTATTTCTCT
*
3502591 ATTTT-TTTC-CT
1 TTTTTATTTCTCT
*
3502602 TTTTTCCTTTCTCT
1 TTTTT-ATTTCTCT
3502616 TTTT
1 TTTT
3502620 GTTCTGATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 9 0.26
12 7 0.21
13 12 0.35
14 6 0.18
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTTATTTCTCT
Found at i:3502612 original size:23 final size:23
Alignment explanation
Indices: 3502540--3502624 Score: 66
Period size: 23 Copynumber: 3.6 Consensus size: 23
3502530 GCATCTTTTC
* *
3502540 TTCTTTTTTCTTCAC-TTATTCCT
1 TTCTTTTTT-TTCTCTTTTTTCCT
* **
3502563 TTGTTTTTGTTTCTCTTTTTTATT
1 TTCTTTTT-TTTCTCTTTTTTCCT
3502587 TTCTATTTTTTTC-CTTTTTTCCT
1 TTCT-TTTTTTTCTCTTTTTTCCT
3502610 TTCTCTTTTTGTTCT
1 TTCT-TTTTT-TTCT
3502625 GATTGAATCT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
23 28 0.58
24 16 0.33
25 4 0.08
ACGTcount: A:0.05, C:0.19, G:0.04, T:0.73
Consensus pattern (23 bp):
TTCTTTTTTTTCTCTTTTTTCCT
Found at i:3504560 original size:21 final size:20
Alignment explanation
Indices: 3504528--3504573 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
3504518 TGAATGATGC
*
3504528 AAAT-GATAAAAATAAAATG
1 AAATAGATAAAAATAAAAGG
*
3504547 AAATAGATCAAAAATGAAAGG
1 AAATAGAT-AAAAATAAAAGG
3504568 AAATAG
1 AAATAG
3504574 TTAGTGAGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 3 0.13
21 16 0.70
ACGTcount: A:0.65, C:0.02, G:0.15, T:0.17
Consensus pattern (20 bp):
AAATAGATAAAAATAAAAGG
Found at i:3507330 original size:83 final size:83
Alignment explanation
Indices: 3507175--3507337 Score: 222
Period size: 83 Copynumber: 2.0 Consensus size: 83
3507165 TGTATATATG
* * *
3507175 TTTAATATTTTAAATTTAAAAGATATTATTATCTATTCAAATTTATATATTAAAATATATCTTGT
1 TTTAATATTTTAAATTTAAAAGACATTATTATCTATTCAAATTTATATATTAAAAGATATCTTGA
** *
3507240 TGGAGTAAATCTCTCAGA
66 TAAAGTAAAACTCTCAGA
* *
3507258 TTTAATATTTTAAATTTAAAAGACATTATTATCCT-TTTAAATTTATATGTTAAAAGATAT-TTA
1 TTTAATATTTTAAATTTAAAAGACATTATTAT-CTATTCAAATTTATATATTAAAAGATATCTT-
3507321 GATAAAGTAAAACTCTC
64 GATAAAGTAAAACTCTC
3507338 TCGGAATTCC
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
82 2 0.03
83 66 0.94
84 2 0.03
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.45
Consensus pattern (83 bp):
TTTAATATTTTAAATTTAAAAGACATTATTATCTATTCAAATTTATATATTAAAAGATATCTTGA
TAAAGTAAAACTCTCAGA
Found at i:3511953 original size:16 final size:17
Alignment explanation
Indices: 3511922--3511954 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3511912 AGATCACCAA
3511922 AAAATTTATCATTTTAAT
1 AAAATTTA-CATTTTAAT
3511940 AAAATTTA-ATTTTAA
1 AAAATTTACATTTTAA
3511955 AAATTATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
18 8 0.53
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
AAAATTTACATTTTAAT
Found at i:3514215 original size:17 final size:17
Alignment explanation
Indices: 3514188--3514235 Score: 55
Period size: 18 Copynumber: 2.9 Consensus size: 17
3514178 TTGGACCCGT
3514188 AAAAT-AAGATAAAATA
1 AAAATAAAGATAAAATA
*
3514204 AAAATAAAGATACAAATG
1 AAAATAAAGATA-AAATA
*
3514222 AAACTAAA-ATAAAA
1 AAAATAAAGATAAAA
3514236 GCAGAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.29
17 9 0.32
18 11 0.39
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (17 bp):
AAAATAAAGATAAAATA
Found at i:3514327 original size:2 final size:2
Alignment explanation
Indices: 3514287--3514311 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3514277 AAAATTAAAT
3514287 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3514312 TCAAAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3515521 original size:6 final size:7
Alignment explanation
Indices: 3515500--3515526 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
3515490 GATTCAATCC
3515500 TTTATTT
1 TTTATTT
3515507 TTTATTT
1 TTTATTT
3515514 TTTATTT
1 TTTATTT
3515521 TTTATT
1 TTTATT
3515527 ACATATCTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTATTT
Found at i:3515916 original size:31 final size:31
Alignment explanation
Indices: 3515880--3515939 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
3515870 AACTTAAAAG
*
3515880 AGTTTTGCAATACT-GAGATTTAAATAATTTT
1 AGTTTTACAATACTGGA-ATTTAAATAATTTT
3515911 AGTTTTACAATACTGGAATTTAAATAATT
1 AGTTTTACAATACTGGAATTTAAATAATT
3515940 CATACAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 25 0.93
32 2 0.07
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.43
Consensus pattern (31 bp):
AGTTTTACAATACTGGAATTTAAATAATTTT
Found at i:3516292 original size:23 final size:22
Alignment explanation
Indices: 3516266--3516327 Score: 65
Period size: 25 Copynumber: 2.7 Consensus size: 22
3516256 GTAATACTTT
3516266 TAATTTTTTTAAATATATATTCA
1 TAATTTTTTTAAATATATA-TCA
*
3516289 TAATTTATTTTTATAAT-TATATGA
1 TAA-TT-TTTTTA-AATATATATCA
3516313 T-ATTTTTTTAAATAT
1 TAATTTTTTTAAATAT
3516328 GCAATCAATG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
20 3 0.09
21 7 0.21
22 2 0.06
23 4 0.12
24 5 0.15
25 10 0.29
26 3 0.09
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TAATTTTTTTAAATATATATCA
Found at i:3516466 original size:19 final size:19
Alignment explanation
Indices: 3516444--3516496 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 19
3516434 TATTTAAACG
3516444 TAAATCAAAATAATTAA-AA
1 TAAAT-AAAATAATTAATAA
3516463 TAAATATAAA-ATATTAATAA
1 TAAATA-AAATA-ATTAATAA
*
3516483 TATATAAAATAATT
1 TAAATAAAATAATT
3516497 TATATGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 2 0.07
19 19 0.66
20 8 0.28
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
TAAATAAAATAATTAATAA
Found at i:3516508 original size:19 final size:18
Alignment explanation
Indices: 3516461--3516511 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
3516451 AAATAATTAA
3516461 AATAA-ATATAAAATATT
1 AATAATATATAAAATATT
3516478 AATAATATATAAAATAATT
1 AATAATATATAAAAT-ATT
*
3516497 TAT-ATGATATAAAAT
1 AATAAT-ATATAAAAT
3516512 TAGATATCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 5 0.17
18 11 0.37
19 14 0.47
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATAATATATAAAATATT
Found at i:3516544 original size:64 final size:59
Alignment explanation
Indices: 3516461--3516666 Score: 157
Period size: 64 Copynumber: 3.2 Consensus size: 59
3516451 AAATAATTAA
* *
3516461 AATA-AATA-TAAAATATTAATAATATA-TAAAATAATTTATATGATATAAAATTAGATATCTAT
1 AATATAATATTAAAAAATTAATAATATATTAAAA-AA-TTA-AT-AT-TAAAATTA-ATATATAT
* *
3516523 AATATAATATTAAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTAATATATAT
1 AATATAATATTAAAAAATT-A-A--TAATATATTAAAAAATTAATATTAAAATTAATATATAT
* * *
3516586 AATATAATATTAAAAAAATTAATATTTAATTTATTTAAAAATTAATATTAAAATTAAAATCAAAT
1 AATATAATATT-AAAAAATT-A-A--TAATATATTAAAAAATTAATATTAAAATT--AAT-ATAT
3516651 AT
58 AT
*
3516653 AATATAAAATTAAA
1 AATATAATATTAAA
3516667 TATAAAACCT
Statistics
Matches: 127, Mismatches: 6, Indels: 18
0.84 0.04 0.12
Matches are distributed among these distances:
62 4 0.03
63 22 0.17
64 59 0.46
65 3 0.02
66 9 0.07
67 18 0.14
68 8 0.06
69 4 0.03
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (59 bp):
AATATAATATTAAAAAATTAATAATATATTAAAAAATTAATATTAAAATTAATATATAT
Found at i:3516668 original size:12 final size:12
Alignment explanation
Indices: 3516623--3516673 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
3516613 AATTTATTTA
3516623 AAAATT-AATATT
1 AAAATTAAATA-T
3516635 AAAATTAAA-AT
1 AAAATTAAATAT
*
3516646 CAAA-TATAATAT
1 AAAATTA-AATAT
3516658 AAAATTAAATAT
1 AAAATTAAATAT
3516670 AAAA
1 AAAA
3516674 CCTATTTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 2 0.06
11 6 0.18
12 21 0.64
13 4 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAAATAT
Found at i:3516960 original size:18 final size:19
Alignment explanation
Indices: 3516926--3516963 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3516916 CAATTTTATT
3516926 TTATTCATTTACATATTTA
1 TTATTCATTTACATATTTA
*
3516945 TTATTCA-TTACTTATTTA
1 TTATTCATTTACATATTTA
3516963 T
1 T
3516964 GTTTATTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTCATTTACATATTTA
Found at i:3523119 original size:199 final size:199
Alignment explanation
Indices: 3522795--3523339 Score: 556
Period size: 199 Copynumber: 2.7 Consensus size: 199
3522785 ACACAACTTA
* * * * *
3522795 AATTAAGAAGAGCTATCTG-CAGACCAAAGCTTTCAAGTTCGATACCACTCAACTCGAGAGGACG
1 AATTAAGAAGAGTTATCTGTC-GACCAAAGCTTTCAAGTTTGATTCCACTCAACTCGAGAGCAAG
* * * * * ** * * *
3522859 TTGATCACATGCTAGTAATGAGGAACTATCTTCATATCTAAATTTAAATA-AGGTTTTTAAGCCA
65 TTGATCGCATGGTAGCAATAAGGAACTACCTTCCGATCAAAATTCAAACACAGGTTTTTAAGCCA
* * * * *
3522923 AGAAGAAAACCCACGTT-GACTGTAATTTAGCT-ACAA-GAAAC-CACTTT-CTAGCCATATTTT
130 AGAAGAAAACCCACGTTGGA-TGGAATTCAG-TAACAATG--ACGCA-TTTCCTAACCAGACTTT
3522983 AACATAGCTT
190 AACATAGCTT
*
3522993 ATATTGAGAAGAGTTATCTGTCGACCAAAGCTTTCAAGTTTGATTCCACTCAACTC-AGAGCAAG
1 A-ATTAAGAAGAGTTATCTGTCGACCAAAGCTTTCAAGTTTGATTCCACTCAACTCGAGAGCAAG
* *
3523057 TTGATCGCATGGTAGCAATAAGGAACTACCTTCCGATAAAAATTCAAACACAGGTATTTAAGCCA
65 TTGATCGCATGGTAGCAATAAGGAACTACCTTCCGATCAAAATTCAAACACAGGTTTTTAAGCCA
* * * * * *
3523122 AGAAGAAGA-CCATGTTGGATGGGATTCAGTAACAATGACGTATTTCCTAACTAGACTTTGACAT
130 AGAAGAAAACCCACGTTGGATGGAATTCAGTAACAATGACGCATTTCCTAACCAGACTTTAACAT
3523186 AGCTT
195 AGCTT
* * * *
3523191 AACTCAAAAAGAGCTT-TCTCTCGACCAAAGCTTTCAAGTTTGATTCCACTCAATTCGAGAGCAC
1 AA-TTAAGAAGAG-TTATCTGTCGACCAAAGCTTTCAAGTTTGATTCCACTCAACTCGAGAGCA-
* * *
3523255 A-TTGACCGCATGGTAGCAATAAGGAACTACATTCCGGTCAAAATTCAAAC-CGAGGTTTTTAAG
63 AGTTGATCGCATGGTAGCAATAAGGAACTACCTTCCGATCAAAATTCAAACAC-AGGTTTTTAAG
* * *
3523318 CTAAGAAGAAAACTCATGTTGG
127 CCAAGAAGAAAACCCACGTTGG
3523340 TTGTGATTTG
Statistics
Matches: 291, Mismatches: 42, Indels: 26
0.81 0.12 0.07
Matches are distributed among these distances:
197 7 0.02
198 129 0.44
199 145 0.50
200 10 0.03
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (199 bp):
AATTAAGAAGAGTTATCTGTCGACCAAAGCTTTCAAGTTTGATTCCACTCAACTCGAGAGCAAGT
TGATCGCATGGTAGCAATAAGGAACTACCTTCCGATCAAAATTCAAACACAGGTTTTTAAGCCAA
GAAGAAAACCCACGTTGGATGGAATTCAGTAACAATGACGCATTTCCTAACCAGACTTTAACATA
GCTT
Found at i:3526382 original size:18 final size:17
Alignment explanation
Indices: 3526359--3526399 Score: 66
Period size: 16 Copynumber: 2.4 Consensus size: 17
3526349 TCTTGAACCC
3526359 CTTTTATTTTTTTCTCTT
1 CTTTTA-TTTTTTCTCTT
3526377 CTTTTA-TTTTTCTCTT
1 CTTTTATTTTTTCTCTT
3526393 CTTTTAT
1 CTTTTAT
3526400 ATCTAAAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 16 0.73
18 6 0.27
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (17 bp):
CTTTTATTTTTTCTCTT
Found at i:3527828 original size:18 final size:18
Alignment explanation
Indices: 3527805--3527840 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3527795 AATGCTGCAG
3527805 CCAACATAGCTAAAGCAT
1 CCAACATAGCTAAAGCAT
3527823 CCAACATAGCTAAAGCAT
1 CCAACATAGCTAAAGCAT
3527841 TCTACACCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.11, T:0.17
Consensus pattern (18 bp):
CCAACATAGCTAAAGCAT
Found at i:3531367 original size:20 final size:20
Alignment explanation
Indices: 3531342--3531382 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3531332 TTTTTGAAAT
3531342 CAAGTTTTGAAATTACTCCC
1 CAAGTTTTGAAATTACTCCC
3531362 CAAGTTTTGAAATTACTCCC
1 CAAGTTTTGAAATTACTCCC
3531382 C
1 C
3531383 CTTACTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (20 bp):
CAAGTTTTGAAATTACTCCC
Found at i:3533662 original size:21 final size:21
Alignment explanation
Indices: 3533636--3533716 Score: 78
Period size: 21 Copynumber: 3.8 Consensus size: 21
3533626 CAGAACCCCA
3533636 GGGGGGAATCGGTTCCCCTGT
1 GGGGGGAATCGGTTCCCCTGT
*
3533657 GGGGGGAATCGGTTCCCAT-T
1 GGGGGGAATCGGTTCCCCTGT
*
3533677 CAAAGGGGGAATCGGTTCCCTCTG-
1 ---GGGGGGAATCGGTTCCC-CTGT
*
3533701 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGGTTCCC
3533717 TCTGCACCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 11
0.76 0.08 0.17
Matches are distributed among these distances:
20 10 0.20
21 23 0.46
23 16 0.32
24 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.40, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGGTTCCCCTGT
Found at i:3533710 original size:20 final size:20
Alignment explanation
Indices: 3533636--3533720 Score: 89
Period size: 20 Copynumber: 4.0 Consensus size: 20
3533626 CAGAACCCCA
*
3533636 GGGGGGAATCGGTTCCCCTGT
1 GGGGGGAATCGGTT-CCCTCT
*
3533657 GGGGGGAATCGGTTCCCATTCAA
1 GGGGGGAATCGGTTCCC--TC-T
*
3533680 AGGGGGAATCGGTTCCCTCT
1 GGGGGGAATCGGTTCCCTCT
* *
3533700 GGGGGGGATCGATTCCCTCT
1 GGGGGGAATCGGTTCCCTCT
3533720 G
1 G
3533721 CACCAAAATG
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
20 21 0.39
21 16 0.30
22 1 0.02
23 16 0.30
ACGTcount: A:0.14, C:0.24, G:0.39, T:0.24
Consensus pattern (20 bp):
GGGGGGAATCGGTTCCCTCT
Found at i:3549116 original size:19 final size:21
Alignment explanation
Indices: 3549073--3549128 Score: 82
Period size: 19 Copynumber: 2.8 Consensus size: 21
3549063 GAAACCCCTT
3549073 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
3549094 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
3549113 TGAAGATACATG-CTTT
1 TGAAAATACATGACTTT
3549129 GATTCGGCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 16 0.48
20 4 0.12
21 13 0.39
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:3552463 original size:19 final size:18
Alignment explanation
Indices: 3552439--3552485 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 18
3552429 CTTTTTCTTT
3552439 TCTTCTTTTCTGAT-TTTTC
1 TCTTCTTTT-TG-TCTTTTC
3552458 TCTTCTTTTTGTCTTTTC
1 TCTTCTTTTTGTCTTTTC
3552476 T-TTCTTTTTG
1 TCTTCTTTTTG
3552486 CACTCCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.37
18 8 0.30
19 9 0.33
ACGTcount: A:0.02, C:0.19, G:0.06, T:0.72
Consensus pattern (18 bp):
TCTTCTTTTTGTCTTTTC
Found at i:3553236 original size:19 final size:21
Alignment explanation
Indices: 3553193--3553248 Score: 82
Period size: 19 Copynumber: 2.8 Consensus size: 21
3553183 GAAACCCCTT
3553193 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
3553214 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
3553233 TGAAGATACATG-CTTT
1 TGAAAATACATGACTTT
3553249 GATTCGGCCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 16 0.48
20 4 0.12
21 13 0.39
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:3562291 original size:3 final size:3
Alignment explanation
Indices: 3562285--3562372 Score: 176
Period size: 3 Copynumber: 29.3 Consensus size: 3
3562275 ACATTACAAC
3562285 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3562333 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
3562373 TTTACATCAA
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3566384 original size:3 final size:3
Alignment explanation
Indices: 3566376--3566402 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3566366 AAAATGCAAC
3566376 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
3566403 TTTACCATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3571455 original size:5 final size:5
Alignment explanation
Indices: 3571445--3571523 Score: 59
Period size: 6 Copynumber: 14.0 Consensus size: 5
3571435 TTTCTACCTG
* *
3571445 TAAAA TAAAA TAAAC TAAAAA TTAAAA TTAAAA TGAAAA TAAAGA TAAAGG
1 TAAAA TAAAA TAAAA T-AAAA -TAAAA -TAAAA T-AAAA TAAA-A TAAA-A
3571496 TAAAGA TACAAA TGAAAA TAAAA TAAAA
1 TAAA-A TA-AAA T-AAAA TAAAA TAAAA
3571524 CCATAAATAT
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
5 23 0.36
6 37 0.58
7 4 0.06
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:3571628 original size:17 final size:18
Alignment explanation
Indices: 3571606--3571647 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
3571596 TATATATATA
3571606 TATATATGTTTT-AAAAC
1 TATATATGTTTTCAAAAC
3571623 TATATATGTTTTCAAAAC
1 TATATATGTTTTCAAAAC
3571641 TATATAT
1 TATATAT
3571648 TATATATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (18 bp):
TATATATGTTTTCAAAAC
Found at i:3571629 original size:2 final size:2
Alignment explanation
Indices: 3571570--3571612 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
3571560 CTTTCAAAAT
3571570 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3571612 T
1 T
3571613 GTTTTAAAAC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3571676 original size:17 final size:17
Alignment explanation
Indices: 3571656--3571688 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3571646 ATTATATATT
3571656 TTTTAAGAA-CATATACA
1 TTTTAA-AATCATATACA
3571673 TTTTAAAATCATATAC
1 TTTTAAAATCATATAC
3571689 GTTTCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.39
Consensus pattern (17 bp):
TTTTAAAATCATATACA
Found at i:3572657 original size:17 final size:18
Alignment explanation
Indices: 3572633--3572679 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
3572623 AATTAAGAAA
3572633 GAAGAAAA-AAAGAACAT
1 GAAGAAAATAAAGAACAT
*
3572650 GGAGAAAATATAAAGAACAT
1 GAAG-AAA-ATAAAGAACAT
3572670 GAAGAAAATA
1 GAAGAAAATA
3572680 CAAAGAAGAG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
17 3 0.12
18 6 0.24
19 4 0.16
20 12 0.48
ACGTcount: A:0.66, C:0.04, G:0.19, T:0.11
Consensus pattern (18 bp):
GAAGAAAATAAAGAACAT
Found at i:3572664 original size:20 final size:20
Alignment explanation
Indices: 3572641--3572686 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
3572631 AAGAAGAAAA
* *
3572641 AAAGAACATGGAGAAAATAT
1 AAAGAACATGAAGAAAATAC
3572661 AAAGAACATGAAGAAAATAC
1 AAAGAACATGAAGAAAATAC
3572681 AAAGAA
1 AAAGAA
3572687 GAGGATCGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.65, C:0.07, G:0.17, T:0.11
Consensus pattern (20 bp):
AAAGAACATGAAGAAAATAC
Found at i:3574095 original size:41 final size:41
Alignment explanation
Indices: 3574048--3574249 Score: 147
Period size: 41 Copynumber: 4.9 Consensus size: 41
3574038 TTGATTGTTG
*
3574048 CCATGATTGAATTGAATCGAATGGTGAATTATTGCATGCTA
1 CCATGATTGAATTGAATCGAATGGTGAATTATTACATGCTA
* * * * * * * ** *
3574089 CTATGATCGAA-TCAATTTGAATGATGAACTATTATATAATG
1 CCATGATTGAATTGAA-TCGAATGGTGAATTATTACATGCTA
* *
3574130 CCAAGATTGAATTGAATCGAATGGTGAATTACTACATGCTA
1 CCATGATTGAATTGAATCGAATGGTGAATTATTACATGCTA
* * * * * * * * *
3574171 CCATGATCGAA-TCAAGTTGAATGATAAACTATTATATGTTG
1 CCATGATTGAATTGAA-TCGAATGGTGAATTATTACATGCTA
* * *
3574212 CCGTGATTGAATTGAATCAAATGGTGAATTATTGCATG
1 CCATGATTGAATTGAATCGAATGGTGAATTATTACATG
3574250 GTTCCAAGAT
Statistics
Matches: 113, Mismatches: 44, Indels: 8
0.68 0.27 0.05
Matches are distributed among these distances:
40 6 0.05
41 101 0.89
42 6 0.05
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.34
Consensus pattern (41 bp):
CCATGATTGAATTGAATCGAATGGTGAATTATTACATGCTA
Found at i:3574141 original size:82 final size:82
Alignment explanation
Indices: 3574046--3574249 Score: 318
Period size: 82 Copynumber: 2.5 Consensus size: 82
3574036 TATTGATTGT
* *
3574046 TGCCATGATTGAATTGAATCGAATGGTGAATTATTGCATGCTACTATGATCGAATCAATTTGAAT
1 TGCCATGATTGAATTGAATCGAATGGTGAATTATTGCATGCTACCATGATCGAATCAAGTTGAAT
*
3574111 GATGAACTATTATATAA
66 GATAAACTATTATATAA
* * *
3574128 TGCCAAGATTGAATTGAATCGAATGGTGAATTACTACATGCTACCATGATCGAATCAAGTTGAAT
1 TGCCATGATTGAATTGAATCGAATGGTGAATTATTGCATGCTACCATGATCGAATCAAGTTGAAT
**
3574193 GATAAACTATTATATGT
66 GATAAACTATTATATAA
* *
3574210 TGCCGTGATTGAATTGAATCAAATGGTGAATTATTGCATG
1 TGCCATGATTGAATTGAATCGAATGGTGAATTATTGCATG
3574250 GTTCCAAGAT
Statistics
Matches: 109, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 109 1.00
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (82 bp):
TGCCATGATTGAATTGAATCGAATGGTGAATTATTGCATGCTACCATGATCGAATCAAGTTGAAT
GATAAACTATTATATAA
Found at i:3575443 original size:84 final size:84
Alignment explanation
Indices: 3575342--3575511 Score: 295
Period size: 84 Copynumber: 2.0 Consensus size: 84
3575332 TAGTGTATAT
* *
3575342 ATCGTTAATGGATCTTTTGGAATGTATATAGTTTACTAGTATGTCATTTGGTATAATCCATTAAG
1 ATCGTTAATGGATCTTTTGGAATGTATATAGCTTACTAGTAAGTCATTTGGTATAATCCATTAAG
3575407 GGTCTATTTTATAATGTAA
66 GGTCTATTTTATAATGTAA
*
3575426 ATCGTTAATGGCTCTTTTGGAATGTATATAGCTTACTAGTAAGTCATTTGGTATAATCCATTAAG
1 ATCGTTAATGGATCTTTTGGAATGTATATAGCTTACTAGTAAGTCATTTGGTATAATCCATTAAG
* *
3575491 GGTCTCTTTTGTAATGTAA
66 GGTCTATTTTATAATGTAA
3575510 AT
1 AT
3575512 ATATAAGTTG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 81 1.00
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.43
Consensus pattern (84 bp):
ATCGTTAATGGATCTTTTGGAATGTATATAGCTTACTAGTAAGTCATTTGGTATAATCCATTAAG
GGTCTATTTTATAATGTAA
Found at i:3576939 original size:29 final size:31
Alignment explanation
Indices: 3576906--3576977 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 31
3576896 CAAATTTTGG
*
3576906 TTAGTGACCAAAATATAAA-TT-TGGAAAGT
1 TTAGTGACCAAAATATAAACTTGGGGAAAGT
* **
3576935 TTAGTGGCCAATGTATAAACTTGGGGAAAGT
1 TTAGTGACCAAAATATAAACTTGGGGAAAGT
3576966 TTAG-GTACCAAA
1 TTAGTG-ACCAAA
3576978 GTGAGAATTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 16 0.47
30 3 0.09
31 15 0.44
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (31 bp):
TTAGTGACCAAAATATAAACTTGGGGAAAGT
Found at i:3593898 original size:26 final size:26
Alignment explanation
Indices: 3593861--3593915 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
3593851 CCCAACACAA
*
3593861 TTCCTTCTATCCACATAAAGTGACAT
1 TTCCTTCCATCCACATAAAGTGACAT
* *
3593887 TTCCTTCCATCCCCATAAAGTGATAT
1 TTCCTTCCATCCACATAAAGTGACAT
3593913 TTC
1 TTC
3593916 TCACAGTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.29, G:0.07, T:0.36
Consensus pattern (26 bp):
TTCCTTCCATCCACATAAAGTGACAT
Found at i:3609072 original size:2 final size:2
Alignment explanation
Indices: 3609065--3609131 Score: 127
Period size: 2 Copynumber: 34.0 Consensus size: 2
3609055 TGTGGACTCG
3609065 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
3609107 AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3609132 TCGAGTTAGT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 63 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3616638 original size:17 final size:16
Alignment explanation
Indices: 3616599--3616630 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
3616589 TAACAACCCT
3616599 CCACTTTA--GCCATC
1 CCACTTTATTGCCATC
3616613 CCACTTTATTGCCATC
1 CCACTTTATTGCCATC
3616629 CC
1 CC
3616631 GCCTTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
16 8 0.50
ACGTcount: A:0.19, C:0.44, G:0.06, T:0.31
Consensus pattern (16 bp):
CCACTTTATTGCCATC
Found at i:3622369 original size:29 final size:30
Alignment explanation
Indices: 3622334--3622393 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
3622324 TGAATAATCA
*
3622334 TTTTTACTAA-TTTGA-TTCTTTTTGTCTTG
1 TTTTTACTAACTTT-ATTTCATTTTGTCTTG
3622363 TTTTTACTAACTTTATTTCATTTTGTCTTG
1 TTTTTACTAACTTTATTTCATTTTGTCTTG
3622393 T
1 T
3622394 ATTATGCTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.15, C:0.12, G:0.08, T:0.65
Consensus pattern (30 bp):
TTTTTACTAACTTTATTTCATTTTGTCTTG
Found at i:3623777 original size:9 final size:9
Alignment explanation
Indices: 3623765--3623791 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
3623755 AGAAATAAAG
3623765 GAAATAATT
1 GAAATAATT
3623774 GAAATAATT
1 GAAATAATT
3623783 GAAATAATT
1 GAAATAATT
3623792 CTATCGTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.11, T:0.33
Consensus pattern (9 bp):
GAAATAATT
Found at i:3623777 original size:18 final size:18
Alignment explanation
Indices: 3623756--3623791 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3623746 GGAAGAAGAA
3623756 GAAATAAAGGAAATAATT
1 GAAATAAAGGAAATAATT
**
3623774 GAAATAATTGAAATAATT
1 GAAATAAAGGAAATAATT
3623792 CTATCGTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.14, T:0.28
Consensus pattern (18 bp):
GAAATAAAGGAAATAATT
Found at i:3624190 original size:20 final size:20
Alignment explanation
Indices: 3624167--3624213 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
3624157 AGATATAACA
*
3624167 AAAAAACATAGAA-AAGAGAG
1 AAAAAA-ATAAAAGAAGAGAG
3624187 AAAAAAATAAAAGAAGAGAG
1 AAAAAAATAAAAGAAGAGAG
3624207 AAAAAAA
1 AAAAAAA
3624214 AAGCAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (20 bp):
AAAAAAATAAAAGAAGAGAG
Found at i:3624191 original size:22 final size:22
Alignment explanation
Indices: 3624166--3624233 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
3624156 GAGATATAAC
*
3624166 AAAAAAACATAGAAAAGAGAGA
1 AAAAAAACAAAGAAAAGAGAGA
*
3624188 AAAAAATA-AAAGAAGAGAGA-A
1 AAAAAA-ACAAAGAAAAGAGAGA
*
3624209 AAAAAAAGCAAAAAAAAGAGAGA
1 AAAAAAA-CAAAGAAAAGAGAGA
3624232 AA
1 AA
3624234 GAAATAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 1 0.03
21 7 0.18
22 26 0.68
23 4 0.11
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (22 bp):
AAAAAAACAAAGAAAAGAGAGA
Found at i:3624229 original size:44 final size:46
Alignment explanation
Indices: 3624149--3624242 Score: 129
Period size: 44 Copynumber: 2.1 Consensus size: 46
3624139 ACAAAGAGAA
* * *
3624149 AAAAGAAGAGATATAACAAAAAAACATAGAAAAGAGAGAAAAAAAT
1 AAAAGAAGAGAGATAACAAAAAAACAAAAAAAAGAGAGAAAAAAAT
* *
3624195 AAAAGAAGAGAGA-AA-AAAAAAGCAAAAAAAAGAGAGAAAGAAAT
1 AAAAGAAGAGAGATAACAAAAAAACAAAAAAAAGAGAGAAAAAAAT
3624239 AAAA
1 AAAA
3624243 TGGAAAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 29 0.67
45 2 0.05
46 12 0.28
ACGTcount: A:0.74, C:0.03, G:0.17, T:0.05
Consensus pattern (46 bp):
AAAAGAAGAGAGATAACAAAAAAACAAAAAAAAGAGAGAAAAAAAT
Found at i:3627293 original size:35 final size:36
Alignment explanation
Indices: 3627247--3627316 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 36
3627237 CTGTAAAGTC
*
3627247 TATTTCAAGAAACTATTTT-GTCTTTCCTAGGATAA
1 TATTTCAAGAAACTATTTTAGTCATTCCTAGGATAA
* * *
3627282 TATTTCTAGAAATTTTTTTGAGTCATTCCTAGGAT
1 TATTTCAAGAAACTATTTT-AGTCATTCCTAGGAT
3627317 CGTTTTCTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 16 0.55
37 13 0.45
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.46
Consensus pattern (36 bp):
TATTTCAAGAAACTATTTTAGTCATTCCTAGGATAA
Found at i:3628308 original size:159 final size:159
Alignment explanation
Indices: 3627982--3628340 Score: 398
Period size: 159 Copynumber: 2.3 Consensus size: 159
3627972 ATTTCCAATA
* * *
3627982 AAGAAGTTCATAAGGAGAAGAAC-TGTTCAAACACTTTGCTCATCCACCGCATATGGAGTTGGAG
1 AAGAAGTTCATAATGAGAAGAACTTGTTC-AAC-CTTAGCTCATCCACCACATATGGAGTTGGAG
* * * * * * ** *
3628046 CATCATCATTACTTTATTCAATTTCATCATAGAAGGATGTAGATCAAAATTTTTAGTAGAGAGTT
64 CAGCATCATTACTTTATCCAATTCCATCATAAAAAGAGGTAGATCAAAATTTCCAGCAGAGAGTT
* * *
3628111 CTTAATGAGAAGAACTCATCTGATGAGGGAG
129 CATAATGAGAAGAACTCATCCGATGAGAGAG
* * * * *
3628142 ACGAAGTTCATAATGAGAAAAACTTGTTCAACCTTAGCTCATCCATCACATTTGGAGTTGGATCA
1 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATCCACCACATATGGAGTTGGAGCA
* * * * * *
3628207 GCATCATTGCTTTGTCCGATTCCATCATAAAAAGAGGTGGATCAACATTTCCAGCGGAGAGTTCA
66 GCATCATTACTTTATCCAATTCCATCATAAAAAGAGGTAGATCAAAATTTCCAGCAGAGAGTTCA
*
3628272 TAATGAGAATAACT-ATTCCGATGAGAGAG
131 TAATGAGAAGAACTCA-TCCGATGAGAGAG
* * * *
3628301 AATAAGTTTATAATGAGAAGAACTTGTTAAACTTTAGCTC
1 AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTC
3628341 GTTTCCATCA
Statistics
Matches: 164, Mismatches: 33, Indels: 5
0.81 0.16 0.02
Matches are distributed among these distances:
158 1 0.01
159 135 0.82
160 23 0.14
161 5 0.03
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (159 bp):
AAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGCTCATCCACCACATATGGAGTTGGAGCA
GCATCATTACTTTATCCAATTCCATCATAAAAAGAGGTAGATCAAAATTTCCAGCAGAGAGTTCA
TAATGAGAAGAACTCATCCGATGAGAGAG
Found at i:3628706 original size:116 final size:117
Alignment explanation
Indices: 3628456--3628768 Score: 411
Period size: 116 Copynumber: 2.7 Consensus size: 117
3628446 GTGGATTGAC
* * *
3628456 ATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCTGACGA--G-GTAGAAGTTCATAATGAG
1 ATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAG
* * * * * * *
3628518 AAGAACATGTTCAACCTTGGTTTAATTCTATCACATAATGAGTTGGATCAAT
66 AAGAACTTGTTCAACCTTGGTTCAATTCCATCACAGAAGGAGTAGGACCAAT
* *
3628570 ATTTCTAGTGAAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAG
1 ATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAG
* * * *
3628635 ACGAA-TTGTTCAACCTTGGTTCGATTCCATCATAGAAGGA-TGAGGACCAGT
66 AAGAACTTGTTCAACCTTGGTTCAATTCCATCACAGAAGGAGT-AGGACCAAT
* *
3628686 ATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATAAGGCAGAAGAAGTTCATAATGAG
1 ATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAG
*
3628751 AAGAATTTGTTCAACCTT
66 AAGAACTTGTTCAACCTT
3628769 AGCTCAAACC
Statistics
Matches: 173, Mismatches: 21, Indels: 7
0.86 0.10 0.03
Matches are distributed among these distances:
114 39 0.23
115 1 0.01
116 100 0.58
117 33 0.19
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (117 bp):
ATTTCCAGTGGAGAGTTCATAATGAGAATAACTCATCCGATGAGGGAGAAGAAGTTCATAATGAG
AAGAACTTGTTCAACCTTGGTTCAATTCCATCACAGAAGGAGTAGGACCAAT
Found at i:3628837 original size:42 final size:42
Alignment explanation
Indices: 3628791--3628923 Score: 128
Period size: 42 Copynumber: 3.2 Consensus size: 42
3628781 TCAAATAAAA
* * ** *
3628791 AGTTGGATCAATATCATGATTTTGCTCGTCCATCACATAAGG
1 AGTTGGATCAACATCATCATTTCACTCATCCATCACATAAGG
* *
3628833 AGTTGGATCAGCATTATCATTTCACTCATCCATCACATAAGG
1 AGTTGGATCAACATCATCATTTCACTCATCCATCACATAAGG
* * * ** *
3628875 AGTTGAATCAGCATCA-C-CTTGGCTCA-CCATCTCATAAGG
1 AGTTGGATCAACATCATCATTTCACTCATCCATCACATAAGG
3628914 AGTTGGATCA
1 AGTTGGATCA
3628924 TAATCACCTT
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
39 21 0.27
40 6 0.08
41 1 0.01
42 49 0.64
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (42 bp):
AGTTGGATCAACATCATCATTTCACTCATCCATCACATAAGG
Found at i:3628916 original size:39 final size:40
Alignment explanation
Indices: 3628814--3628935 Score: 138
Period size: 39 Copynumber: 3.0 Consensus size: 40
3628804 TCATGATTTT
* * * *
3628814 GCTCGTCCATCACATAAGGAGTTGGATCAGCATTATCATTTC
1 GCTCATCCATCACATAAGGAGTTGGATCAGCATCA-C-CTTG
* *
3628856 ACTCATCCATCACATAAGGAGTTGAATCAGCATCACCTTG
1 GCTCATCCATCACATAAGGAGTTGGATCAGCATCACCTTG
* **
3628896 GCTCA-CCATCTCATAAGGAGTTGGATCATAATCACCTTG
1 GCTCATCCATCACATAAGGAGTTGGATCAGCATCACCTTG
3628935 G
1 G
3628936 GTGAACCATC
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
39 31 0.45
40 6 0.09
41 1 0.01
42 31 0.45
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (40 bp):
GCTCATCCATCACATAAGGAGTTGGATCAGCATCACCTTG
Found at i:3628953 original size:39 final size:39
Alignment explanation
Indices: 3628862--3628956 Score: 111
Period size: 39 Copynumber: 2.4 Consensus size: 39
3628852 TTTCACTCAT
* *
3628862 CCATCACATAAGGAGTTGAATCAGCATCACCTTGGCTCA
1 CCATCACATAAGGAGTTGAATCAGAATCACCTTGGCTAA
* * * *
3628901 CCATCTCATAAGGAGTTGGATCATAATCACCTTGGGTGAA
1 CCATCACATAAGGAGTTGAATCAGAATCACCTTGGCT-AA
*
3628941 CCATCGCA-AAGGAGTT
1 CCATCACATAAGGAGTT
3628957 TGGTCAACAT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
39 40 0.83
40 8 0.17
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (39 bp):
CCATCACATAAGGAGTTGAATCAGAATCACCTTGGCTAA
Found at i:3631379 original size:183 final size:183
Alignment explanation
Indices: 3630993--3631379 Score: 636
Period size: 183 Copynumber: 2.1 Consensus size: 183
3630983 ATTAAATTTT
*
3630993 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAATCATTTAAAACCCAATTAATAA
1 AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
* **
3631058 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTATATAATTTTTT
66 TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATATATAAAATTTT
* *
3631123 TATTTTATAATTATATATTATTTAAATTATTTGTAAACTGTTTTTTAATTAAA
131 TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
*
3631176 AAATATTAAATATATTATATATAACATATGGGCT-AAGCCCAAACCATTTAAAACCTAATTAATA
1 AAATATTAAATATATTATATATAACATATGGGCTCAA-CCCAAACCATTTAAAACCCAATTAATA
*
3631240 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAAATATCTAAAATT
65 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATT-AAAAAAATATATAAAATT
3631305 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACT-TTTTTTGAATTAAA
129 TTTATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTT-AATTAAA
* *
3631360 AAATATTTAAT-TTTTATATA
1 AAATATTAAATATATTATATA
3631380 AATTAGAAAA
Statistics
Matches: 191, Mismatches: 10, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
182 2 0.01
183 119 0.62
184 70 0.37
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (183 bp):
AAATATTAAATATATTATATATAACATATGGGCTCAACCCAAACCATTTAAAACCCAATTAATAA
TTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAAATATATAAAATTTT
TATTTTATAATTATATATTATTTAAATTAATTATAAACTGTTTTTTAATTAAA
Found at i:3631520 original size:15 final size:15
Alignment explanation
Indices: 3631500--3631528 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3631490 AAAAAAAGTT
3631500 TGGTTAATTCGGTTA
1 TGGTTAATTCGGTTA
3631515 TGGTTAATTCGGTT
1 TGGTTAATTCGGTT
3631529 CGGCCGGCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.07, G:0.28, T:0.48
Consensus pattern (15 bp):
TGGTTAATTCGGTTA
Found at i:3633613 original size:24 final size:24
Alignment explanation
Indices: 3633584--3633638 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
3633574 ATATTAGGGT
3633584 TTCTCCCTAACCCTACCACGTGGG
1 TTCTCCCTAACCCTACCACGTGGG
3633608 TTCTCCCTAACCCTACCACGTGGG
1 TTCTCCCTAACCCTACCACGTGGG
3633632 TTCTCCC
1 TTCTCCC
3633639 AAATAGACCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.15, C:0.44, G:0.15, T:0.27
Consensus pattern (24 bp):
TTCTCCCTAACCCTACCACGTGGG
Found at i:3633750 original size:44 final size:44
Alignment explanation
Indices: 3633687--3633776 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 44
3633677 TATGTTTGAC
* * *
3633687 TTTTTAATGATTTAGGTCTTGTGTTGGGTTAGGGTTATTTGTTTT
1 TTTTTAATGATTTA-GTCTTGTGTTAGGTTAGAGTTATTTGGTTT
3633732 TTTTTAAATGATTT-GTCTTGTGTTAGGTTAGAGTTATTTGGTTT
1 TTTTT-AATGATTTAGTCTTGTGTTAGGTTAGAGTTATTTGGTTT
3633776 T
1 T
3633777 ATAATGATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
44 28 0.68
45 5 0.12
46 8 0.20
ACGTcount: A:0.16, C:0.02, G:0.24, T:0.58
Consensus pattern (44 bp):
TTTTTAATGATTTAGTCTTGTGTTAGGTTAGAGTTATTTGGTTT
Found at i:3638999 original size:19 final size:19
Alignment explanation
Indices: 3638975--3639012 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
3638965 TCGAGGGGGA
3638975 GAATACTTGAGCATAGAGT
1 GAATACTTGAGCATAGAGT
3638994 GAATACTTGAGCATAGAGT
1 GAATACTTGAGCATAGAGT
3639013 TTGATAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (19 bp):
GAATACTTGAGCATAGAGT
Found at i:3641208 original size:36 final size:36
Alignment explanation
Indices: 3641167--3641287 Score: 97
Period size: 35 Copynumber: 3.3 Consensus size: 36
3641157 AAGGGAATTG
3641167 TCTCAAGTGAGACAAAATCTAT-TTTTAAG-AAAACAA
1 TCTCAAGTGAGACAAAAT-T-TGTTTTAAGAAAAACAA
* * *
3641203 TCTCAAATGAGACGAAATTTGTTTTAAGAAAAAAATAA
1 TCTCAAGTGAGACAAAATTTGTTTTAAG--AAAAACAA
* * *
3641241 TCTCAAGTGAGAC--GATTTTTTCTTAAGAAAAATAA
1 TCTCAAGTGAGACAAAATTTGTT-TTAAGAAAAACAA
* *
3641276 TCTTAAGCGAGA
1 TCTCAAGTGAGA
3641288 TAATTCTTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
34 1 0.01
35 26 0.36
36 22 0.31
37 5 0.07
38 18 0.25
ACGTcount: A:0.45, C:0.12, G:0.14, T:0.30
Consensus pattern (36 bp):
TCTCAAGTGAGACAAAATTTGTTTTAAGAAAAACAA
Found at i:3641252 original size:38 final size:37
Alignment explanation
Indices: 3641167--3641272 Score: 112
Period size: 38 Copynumber: 2.9 Consensus size: 37
3641157 AAGGGAATTG
*
3641167 TCTCAAGTGAGACAAAATCTATTTTTAAG---AAAACAA
1 TCTCAAGTGAGACGAAAT-T-TTTTTAAGAAAAAAACAA
* *
3641203 TCTCAAATGAGACGAAATTTGTTTTAAGAAAAAAATAA
1 TCTCAAGTGAGACGAAATTT-TTTTAAGAAAAAAACAA
*
3641241 TCTCAAGTGAGACG-ATTTTTTCTTAAGAAAAA
1 TCTCAAGTGAGACGAAATTTTT-TTAAGAAAAA
3641273 TAATCTTAAG
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
34 1 0.02
35 8 0.13
36 18 0.30
37 14 0.23
38 19 0.32
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (37 bp):
TCTCAAGTGAGACGAAATTTTTTTAAGAAAAAAACAA
Found at i:3646073 original size:217 final size:219
Alignment explanation
Indices: 3645698--3646118 Score: 812
Period size: 217 Copynumber: 1.9 Consensus size: 219
3645688 TATTTACTCA
3645698 AACATGCTTTTATTAAATAACAATCATACCCAGACATGCTTTCTACCTGACATACTTTATCTTAA
1 AACATGCTTTTATTAAATAACAATCATACCCAGACATGCTTTCTACCTGACATACTTTATCTTAA
3645763 GATATTAATCGTAACTGCATGGTATCTAGTTTGCATGCTTTCATCCAGAAAGAAACTTATTCTAT
66 GATATTAATCGTAACTGCATGGTATCTAGTTTGCATGCTTTCATCCAGAAAGAAACTTATTCTAT
3645828 GAATTTAAAGAAAAATGTAAAGGTTCAGAGTCGTTCCTCCTTTGTGTACTAGTTATT-CGGTA-C
131 GAATTTAAAGAAAAATGTAAAGGTTCAGAGTCGTTCCTCCTTTGTGTACTAGTTATTCCGGTACC
3645891 TATCGATGATACAGGTTTGGTATG
196 TATCGATGATACAGGTTTGGTATG
3645915 AACATGCTTTTATTAAATAACAATCATACCCAGACATGCTTTTCTA-CTGACATACTTTATCTTA
1 AACATGCTTTTATTAAATAACAATCATACCCAGACATGC-TTTCTACCTGACATACTTTATCTTA
3645979 AGATATTAATCGTAACTGCATGGTATCTAGTTTGCATGCTTTCATCCAGAAAGAAACTTATTCTA
65 AGATATTAATCGTAACTGCATGGTATCTAGTTTGCATGCTTTCATCCAGAAAGAAACTTATTCTA
3646044 TGAATTTAAAGAAAAATGTAAAGGTTCAGAGTCGTTCCTCCTTTGTGTACTAGTTATTCCGGTAC
130 TGAATTTAAAGAAAAATGTAAAGGTTCAGAGTCGTTCCTCCTTTGTGTACTAGTTATTCCGGTAC
3646109 CTATCGATGA
195 CTATCGATGA
3646119 ATACGATCAT
Statistics
Matches: 201, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
217 180 0.90
218 11 0.05
219 10 0.05
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (219 bp):
AACATGCTTTTATTAAATAACAATCATACCCAGACATGCTTTCTACCTGACATACTTTATCTTAA
GATATTAATCGTAACTGCATGGTATCTAGTTTGCATGCTTTCATCCAGAAAGAAACTTATTCTAT
GAATTTAAAGAAAAATGTAAAGGTTCAGAGTCGTTCCTCCTTTGTGTACTAGTTATTCCGGTACC
TATCGATGATACAGGTTTGGTATG
Found at i:3660765 original size:11 final size:11
Alignment explanation
Indices: 3660749--3660779 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
3660739 CAATCAAGAG
3660749 TTCAAATCGAA
1 TTCAAATCGAA
3660760 TTCAAATCGAA
1 TTCAAATCGAA
3660771 TTCAAATCG
1 TTCAAATCG
3660780 TACAAGTGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (11 bp):
TTCAAATCGAA
Found at i:3669582 original size:17 final size:17
Alignment explanation
Indices: 3669560--3669592 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3669550 AGTACCATAG
3669560 TATAGTAGTATCGATAA
1 TATAGTAGTATCGATAA
3669577 TATAGTAGTATCGATA
1 TATAGTAGTATCGATA
3669593 CCGAGGAGCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (17 bp):
TATAGTAGTATCGATAA
Found at i:3669994 original size:55 final size:55
Alignment explanation
Indices: 3669934--3670358 Score: 555
Period size: 55 Copynumber: 7.7 Consensus size: 55
3669924 GAGTGTGCAA
* * * *
3669934 AAACTTAAGAAATTCATACTGAGTGTATTAATTTCCATATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
* ** * *
3669989 AAACTTAAGAAATTCATACTATGTGGATGAATTTTTGTATGGACACTTTAGGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
* *
3670044 AAACTTAAGAAATTTATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
* * *
3670099 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGACACTTTATTTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
*
3670154 AAACTTAAGAAATTCATACTATGTGGATGAATTTCCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
* * * * *
3670209 AAACTTAATAAATTCATACTAAATGGATGAATTTCTGTATTGGCACTTTATGTCT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
* * *** * * *
3670264 AAACTTAAGGAATTCATACTGAGTGGATGAATTTATATATGGCCACTATATGTTT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
* * *
3670319 AAAAC-TAGGAAATTCATACTAAGTGTATAAATTTCCGTAT
1 -AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTAT
3670359 TGGTAGTGGG
Statistics
Matches: 324, Mismatches: 45, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
55 320 0.99
56 4 0.01
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.37
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTCCGTATGGGCACTTTATGTGT
Found at i:3673147 original size:29 final size:30
Alignment explanation
Indices: 3673077--3673136 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
3673067 CAATTTAAGG
3673077 CAAAATGGTTTTTGGACTTGAATTAAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTAAATTTA
* *
3673108 CAAAATGTTTTTGGGCTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTAAATTTA
3673137 TTCAAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 10 0.37
30 11 0.41
31 6 0.22
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTAAATTTA
Found at i:3673242 original size:21 final size:21
Alignment explanation
Indices: 3673216--3673334 Score: 129
Period size: 21 Copynumber: 5.7 Consensus size: 21
3673206 AGGGTGTCAA
*
3673216 AGTGCATCCATGCACCCCTAC
1 AGTGCATCCATGCACCCCTGC
3673237 AGTGCATCCATGCA-CCCTGC
1 AGTGCATCCATGCACCCCTGC
*
3673257 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTGC
*
3673278 AGTGCATCCATGCA--TCTGCAC
1 AGTGCATCCATGCACCCCTG--C
* * *
3673299 TAGTGAATCAATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
3673320 AGTGCATCCATGCAC
1 AGTGCATCCATGCAC
3673335 TCAAACACCG
Statistics
Matches: 84, Mismatches: 8, Indels: 12
0.81 0.08 0.12
Matches are distributed among these distances:
19 3 0.04
20 31 0.37
21 36 0.43
22 12 0.14
23 2 0.02
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:3673281 original size:41 final size:42
Alignment explanation
Indices: 3673216--3673334 Score: 145
Period size: 41 Copynumber: 2.8 Consensus size: 42
3673206 AGGGTGTCAA
*
3673216 AGTGCATCCATGCACCCCTACAGTGCATCCATGCACCCTG-C-
1 AGTGCATCCATGCA-CCCTGCAGTGCATCCATGCACCCTGACT
*
3673257 AGTGCATCCATGCATCCCTGCAGTGCATCCATGCA-TCTGCACT
1 AGTGCATCCATGCA-CCCTGCAGTGCATCCATGCACCCTG-ACT
* * *
3673300 AGTGAATCAATGCACCATGCAGTGCATCCATGCAC
1 AGTGCATCCATGCACCCTGCAGTGCATCCATGCAC
3673335 TCAAACACCG
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
40 3 0.04
41 33 0.49
42 20 0.29
43 12 0.18
ACGTcount: A:0.24, C:0.35, G:0.18, T:0.22
Consensus pattern (42 bp):
AGTGCATCCATGCACCCTGCAGTGCATCCATGCACCCTGACT
Found at i:3673323 original size:63 final size:62
Alignment explanation
Indices: 3673216--3673333 Score: 166
Period size: 63 Copynumber: 1.9 Consensus size: 62
3673206 AGGGTGTCAA
* * *
3673216 AGTGCATCCATGCACCCCTACAGTGCATCCATGCACCCTGCAGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCACCCCTACAGTGAATCAATGCACCATGCAGTGCATCCATGCATCCCTGC
**
3673278 AGTGCATCCATGCATCTGC-ACTAGTGAATCAATGCACCATGCAGTGCATCCATGCA
1 AGTGCATCCATGCA-CCCCTAC-AGTGAATCAATGCACCATGCAGTGCATCCATGCA
3673334 CTCAAACACC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
62 16 0.33
63 33 0.67
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.22
Consensus pattern (62 bp):
AGTGCATCCATGCACCCCTACAGTGAATCAATGCACCATGCAGTGCATCCATGCATCCCTGC
Found at i:3686023 original size:55 final size:55
Alignment explanation
Indices: 3685950--3686319 Score: 566
Period size: 55 Copynumber: 6.7 Consensus size: 55
3685940 AAGTGTGCAA
*
3685950 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTTTATATGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTTTATGTGT
* * *
3686005 AAAGTTAGGAAATTCATACTAAGTGGAAGAATTTTTGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTTTATGTGT
*
3686060 AAAGTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTTTATGTGT
* * *
3686115 AAACTTAAGAAATTCACACTATGTGGATGAATTTCTGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTTTATGTGT
*
3686170 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTTTATGTGT
* *
3686225 AAACTTAACG-AATTCATACTAAGTGGATGAATTTCTGTATGGGCACTATATGT-T
1 AAACTTAA-GAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTTTATGTGT
* * *
3686279 CAAAAC-TAAGAAATTCATACTAAGTGTATAAATTTTCGTAT
1 --AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTAT
3686320 TTGTAGTGGG
Statistics
Matches: 290, Mismatches: 21, Indels: 8
0.91 0.07 0.03
Matches are distributed among these distances:
54 2 0.01
55 283 0.98
56 5 0.02
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTTTGTATGGGCACTTTATGTGT
Found at i:3692403 original size:22 final size:19
Alignment explanation
Indices: 3692353--3692405 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
3692343 GCAAAAATGT
*
3692353 TATCGATACCATAATAGGG
1 TATCGATACCATAATAGAG
* *
3692372 TATTGGTACCATAGTATAGTAG
1 TATCGATACCATA--ATAG-AG
3692394 TATCGATACCAT
1 TATCGATACCAT
3692406 GGTAGGGGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 11 0.42
21 4 0.15
22 11 0.42
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (19 bp):
TATCGATACCATAATAGAG
Found at i:3692832 original size:55 final size:55
Alignment explanation
Indices: 3692751--3693504 Score: 1086
Period size: 55 Copynumber: 13.7 Consensus size: 55
3692741 AAGTGTGTTA
* * *
3692751 AAACTTAAGAAATTCATACTACGTGGATGAATTTTTGTATGGTCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
*
3692806 AAACTTAAGAAATTCATACTAAGTGGACGAATTTTCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
*
3692861 AAACTTAAGAAATTCATATTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
**
3692916 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGATACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
* **
3692971 AAACTTAAGAAAATCATACTGTGTGGATGAATTTTCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
* * *
3693026 AAACTTAAGAAATTCATACTAAGTAGAAGAATTTTCGTATAGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
* * *
3693081 AAACTTAAAAAATTCATAATAAGTGGATGAATTTTCATATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
* *
3693136 AAACTTAAGAAATTCATATTATGTGGATGAATTTTCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
*
3693191 AAACTTAAGAAATTCATATTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
* **
3693246 AAACTTAAGAAATTCATACTATA-TGGAT-AATTTCCGTATGGATACTTTATGTGT
1 AAACTTAAGAAATTCATACTA-AGTGGATGAATTTTCGTATGGGCACTTTATGTGT
* ** * *
3693300 AAACTTAAGAGAA-TCATAGTTTGTGGATGAATTTCCGTATGGGCACTTTATGCGT
1 AAACTTAAGA-AATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
** *
3693355 AAACTTAAGAAATTCATAGGAAGTGGAAGAATTTTCGTATGGGCACTTTATGTGT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
* * * *
3693410 AAACTTAAGGAATTCATACTAATTGGATGAA-TTTCTGTATGGGCACTATATGTGCA
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTC-GTATGGGCACTTTATGTG-T
* * * * *
3693466 AAAC-TAGGAAATTCATACAAAGTGTATAAATTTACGTAT
1 AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTAT
3693505 TGGTAATGGG
Statistics
Matches: 630, Mismatches: 61, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
54 50 0.08
55 572 0.91
56 8 0.01
ACGTcount: A:0.34, C:0.10, G:0.19, T:0.36
Consensus pattern (55 bp):
AAACTTAAGAAATTCATACTAAGTGGATGAATTTTCGTATGGGCACTTTATGTGT
Found at i:3704589 original size:40 final size:40
Alignment explanation
Indices: 3704545--3704653 Score: 173
Period size: 40 Copynumber: 2.7 Consensus size: 40
3704535 GAACACTAAA
* *
3704545 TGTATATGGTGGGCACGACCTTATGTGTAATGCATTTTGG
1 TGTATATGGTGGGCACGACCTTATGTGTAATGCACTTCGG
* *
3704585 TGTATATGGTGGGCACGACTTTATGTGTAATGCGCTTCGG
1 TGTATATGGTGGGCACGACCTTATGTGTAATGCACTTCGG
*
3704625 TGTATATGGTGGGCACGTCCTTATGTGTA
1 TGTATATGGTGGGCACGACCTTATGTGTA
3704654 GCATTACGGT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.18, C:0.14, G:0.31, T:0.37
Consensus pattern (40 bp):
TGTATATGGTGGGCACGACCTTATGTGTAATGCACTTCGG
Found at i:3705482 original size:21 final size:21
Alignment explanation
Indices: 3705458--3705509 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
3705448 TCAAGGAGCT
*
3705458 TTGCTTCATAATCAATGTACC
1 TTGCTTCATAATCAATGCACC
* *
3705479 TTGCTTCATAGTCAATGCGCC
1 TTGCTTCATAATCAATGCACC
*
3705500 TTACTTCATA
1 TTGCTTCATA
3705510 GCCATAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.38
Consensus pattern (21 bp):
TTGCTTCATAATCAATGCACC
Found at i:3710378 original size:81 final size:80
Alignment explanation
Indices: 3710238--3710489 Score: 364
Period size: 81 Copynumber: 3.1 Consensus size: 80
3710228 ATTGATATTA
* *
3710238 TGAGTAAAAGATTAAATGTCTAACTGTGCATTTGGCAGAAAAGTGACC-ATCATGCTAGTTAGAT
1 TGAGGAAAAGATTAAATG-CTAACTGTGCATTTGGCAGAAAGGTG-CCAATCATGCTAGTTAGAT
3710302 GAAAGGTTAAATGCCTT
64 GAAAGGTTAAATGCCTT
3710319 TGAGGAAAAGATTAAATGCATAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATG
1 TGAGGAAAAGATTAAATGC-TAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATG
3710384 AAAGGTTAAATGCCTT
65 AAAGGTTAAATGCCTT
* * * * * *
3710400 TG-GGTAAAAGATTAAATACCTAACTATTCATTTGCCAGAAAGGTGCCAATAATGCAAGTTAGAT
1 TGAGG-AAAAGATTAAAT-GCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGAT
3710464 GAAAGGTTAAATGCCTT
64 GAAAGGTTAAATGCCTT
3710481 TAGAGGAAA
1 T-GAGGAAA
3710490 TAATACATGT
Statistics
Matches: 157, Mismatches: 8, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
80 5 0.03
81 145 0.92
82 5 0.03
83 2 0.01
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (80 bp):
TGAGGAAAAGATTAAATGCTAACTGTGCATTTGGCAGAAAGGTGCCAATCATGCTAGTTAGATGA
AAGGTTAAATGCCTT
Found at i:3717073 original size:22 final size:22
Alignment explanation
Indices: 3717045--3717096 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
3717035 ATCATGCTAG
*
3717045 TTAAATGCCTTTTGGTAAAAGA
1 TTAAATGCCTTTGGGTAAAAGA
3717067 TTAAATGCCTTTGGGTAAAAGA
1 TTAAATGCCTTTGGGTAAAAGA
3717089 TTAAATGC
1 TTAAATGC
3717097 TTAACTATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (22 bp):
TTAAATGCCTTTGGGTAAAAGA
Found at i:3720432 original size:63 final size:64
Alignment explanation
Indices: 3720354--3720492 Score: 212
Period size: 64 Copynumber: 2.2 Consensus size: 64
3720344 CACTAACCAT
* *
3720354 ATCGAATGCATTTTATGCATCGATGCAC-TACCATGCATCGATGCACTCA-GGTT-TTATGAAAA
1 ATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCATGCTTGTT-T-AAAA
3720416 C
64 C
*
3720417 ATCGAATGCATTTTATGCATCGATTCACAGACCATGCATCGATGCACTCATGCTTGTTTAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCATGCTTGTTTAAAAC
3720481 ATCGAATGCATT
1 ATCGAATGCATT
3720493 GATGCACTCA
Statistics
Matches: 70, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
63 27 0.39
64 37 0.53
65 4 0.06
66 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (64 bp):
ATCGAATGCATTTTATGCATCGATGCACAGACCATGCATCGATGCACTCATGCTTGTTTAAAAC
Found at i:3726289 original size:21 final size:21
Alignment explanation
Indices: 3726263--3726310 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3726253 TTGTGCATAA
3726263 TGCATCGATACAATATGAAAG
1 TGCATCGATACAATATGAAAG
* *
3726284 TGCATCGATGCACTATGAAAG
1 TGCATCGATACAATATGAAAG
3726305 TGCATC
1 TGCATC
3726311 AATGCATCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (21 bp):
TGCATCGATACAATATGAAAG
Found at i:3726315 original size:21 final size:21
Alignment explanation
Indices: 3726276--3726316 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3726266 ATCGATACAA
*
3726276 TATGAAAGTGCATCGATGCAC
1 TATGAAAGTGCATCAATGCAC
3726297 TATGAAAGTGCATCAATGCA
1 TATGAAAGTGCATCAATGCA
3726317 TCCCTTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (21 bp):
TATGAAAGTGCATCAATGCAC
Found at i:3729133 original size:64 final size:64
Alignment explanation
Indices: 3729054--3729176 Score: 196
Period size: 64 Copynumber: 1.9 Consensus size: 64
3729044 AATCCATTTT
*
3729054 ATGCATCGATGCACTCAGG-TT-TTATGAAAACATCTAATGCATTTTATGCATCGATGCACAGAC
1 ATGCATCGATGCACTCAGGCTTGTT-T-AAAACATCAAATGCATTTTATGCATCGATGCACAGAC
3729117 C
64 C
*
3729118 ATGCATCGATGCACTCAGGCTTGTTTAAAACATCAAATGCATTTTATGCATTGATGCAC
1 ATGCATCGATGCACTCAGGCTTGTTTAAAACATCAAATGCATTTTATGCATCGATGCAC
3729177 TCTTAGTGCA
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
64 50 0.91
65 3 0.05
66 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (64 bp):
ATGCATCGATGCACTCAGGCTTGTTTAAAACATCAAATGCATTTTATGCATCGATGCACAGACC
Found at i:3729822 original size:14 final size:14
Alignment explanation
Indices: 3729803--3729830 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3729793 GAATTACTTT
3729803 CAATTTTCTGCAAA
1 CAATTTTCTGCAAA
3729817 CAATTTTCTGCAAA
1 CAATTTTCTGCAAA
3729831 AGCTTCCACC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
CAATTTTCTGCAAA
Found at i:3730677 original size:2 final size:2
Alignment explanation
Indices: 3730670--3730696 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3730660 AACATTATGA
3730670 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
3730697 GTAAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3739302 original size:21 final size:21
Alignment explanation
Indices: 3739278--3739344 Score: 100
Period size: 21 Copynumber: 3.2 Consensus size: 21
3739268 TTTCAAAGAC
*
3739278 ACTTACCAATG-TAATTTATCT
1 ACTTACCAA-GATAATTCATCT
*
3739299 ACTTACCAAGATAGTTCATCT
1 ACTTACCAAGATAATTCATCT
3739320 ACTTACCAAGATAATTCATCT
1 ACTTACCAAGATAATTCATCT
3739341 ACTT
1 ACTT
3739345 CCACTTCTTC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.37
Consensus pattern (21 bp):
ACTTACCAAGATAATTCATCT
Found at i:3742129 original size:14 final size:14
Alignment explanation
Indices: 3742084--3742132 Score: 80
Period size: 14 Copynumber: 3.5 Consensus size: 14
3742074 AAAAGGTTAG
3742084 CGGTTAGTAATTAA
1 CGGTTAGTAATTAA
*
3742098 CAGTTAGTAATTAA
1 CGGTTAGTAATTAA
*
3742112 CGGTTAGTAATTAG
1 CGGTTAGTAATTAA
3742126 CGGTTAG
1 CGGTTAG
3742133 AAAGGTTAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.33, C:0.08, G:0.24, T:0.35
Consensus pattern (14 bp):
CGGTTAGTAATTAA
Found at i:3742164 original size:16 final size:16
Alignment explanation
Indices: 3742122--3742164 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
3742112 CGGTTAGTAA
*
3742122 TTAGCGGTTAGAAAGG
1 TTAGCGGTTAGAAAAG
**
3742138 TTAGCTATTAGAAAAG
1 TTAGCGGTTAGAAAAG
3742154 TTAGCGGTTAG
1 TTAGCGGTTAG
3742165 TGGTTAGTAG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.30, T:0.30
Consensus pattern (16 bp):
TTAGCGGTTAGAAAAG
Found at i:3746838 original size:10 final size:9
Alignment explanation
Indices: 3746786--3746846 Score: 59
Period size: 9 Copynumber: 6.3 Consensus size: 9
3746776 CTCCTTTCAG
3746786 TTTTCTTTT
1 TTTTCTTTT
* *
3746795 TTTTCCTTC
1 TTTTCTTTT
*
3746804 TTTTATTTAT
1 TTTTCTTT-T
3746814 TTTTCTCTCTT
1 TTTTCT-T-TT
3746825 TTTTCTTTT
1 TTTTCTTTT
3746834 CTTTTCTTTT
1 -TTTTCTTTT
3746844 TTT
1 TTT
3746847 AGCTGTAATT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 18 0.43
10 15 0.36
11 8 0.19
12 1 0.02
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:3746838 original size:21 final size:21
Alignment explanation
Indices: 3746786--3746840 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
3746776 CTCCTTTCAG
3746786 TTTTCTTTTTTTTC-CTTCTT
1 TTTTCTTTTTTTTCTCTTCTT
* *
3746806 TTAT-TTATTTTTCTC-TCTT
1 TTTTCTTTTTTTTCTCTTCTT
3746825 TTTTCTTTTCTTTTCT
1 TTTTCTTTT-TTTTCT
3746841 TTTTTTAGCT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
19 15 0.54
20 7 0.25
21 6 0.21
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTTTTTTTTCTCTTCTT
Found at i:3746845 original size:19 final size:18
Alignment explanation
Indices: 3746786--3746846 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 18
3746776 CTCCTTTCAG
* *
3746786 TTTTCTTTTTTTTCCTTC
1 TTTTCTTTTTTTTCTTTT
*
3746804 TTTTATTTATTTTTCTCTCTT
1 TTTTCTTT-TTTTTCT-T-TT
3746825 TTTTCTTTTCTTTTCTTTT
1 TTTTCTTTT-TTTTCTTTT
3746844 TTT
1 TTT
3746847 AGCTGTAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
18 7 0.20
19 11 0.31
20 3 0.09
21 14 0.40
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTCTTTTTTTTCTTTT
Found at i:3753356 original size:17 final size:17
Alignment explanation
Indices: 3753334--3753368 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3753324 AATGCTAAAA
3753334 GGAAAGAAAACAAACAT
1 GGAAAGAAAACAAACAT
*
3753351 GGAAAGAAAATAAACAT
1 GGAAAGAAAACAAACAT
3753368 G
1 G
3753369 AAGGAGAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.63, C:0.09, G:0.20, T:0.09
Consensus pattern (17 bp):
GGAAAGAAAACAAACAT
Found at i:3756805 original size:16 final size:16
Alignment explanation
Indices: 3756751--3756803 Score: 97
Period size: 16 Copynumber: 3.3 Consensus size: 16
3756741 CTGTCGAACG
3756751 GTTCACTGAACGTTCA
1 GTTCACTGAACGTTCA
3756767 GTTCACTGAACGTTCA
1 GTTCACTGAACGTTCA
*
3756783 GTTCATTGAACGTTCA
1 GTTCACTGAACGTTCA
3756799 GTTCA
1 GTTCA
3756804 TTTACAAGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.34
Consensus pattern (16 bp):
GTTCACTGAACGTTCA
Found at i:3765306 original size:19 final size:21
Alignment explanation
Indices: 3765282--3765324 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
3765272 TGTTATTTGT
3765282 ATATAAATT-T-TATTAAAAA
1 ATATAAATTATATATTAAAAA
3765301 ATATAAATTATAATATTAAAAA
1 ATATAAATTAT-ATATTAAAAA
3765323 AT
1 AT
3765325 TATATTAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 9 0.43
20 1 0.05
22 11 0.52
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATATAAATTATATATTAAAAA
Found at i:3765683 original size:51 final size:50
Alignment explanation
Indices: 3765543--3765686 Score: 180
Period size: 51 Copynumber: 2.8 Consensus size: 50
3765533 TTTATACGAC
* *
3765543 AAAAAAATGTAGCACTTAACACATACTTATACTGATGCAAGTGAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTATAC-GGTGTAAGTGAATAAAAT
* * *
3765594 AAAAAAATGTATCACTTAACACATACTTAGACCAGTGTAAGTGAATAAAAT
1 AAAAAAATGTAGCACTTAACACATACTTATA-CGGTGTAAGTGAATAAAAT
* * * *
3765645 AGAAAAATGTAGCACTTAGCATATATTTATATCGGTGTAAGT
1 AAAAAAATGTAGCACTTAACACATACTTATA-CGGTGTAAGT
3765687 ATGCACATCG
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
51 78 0.99
52 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (50 bp):
AAAAAAATGTAGCACTTAACACATACTTATACGGTGTAAGTGAATAAAAT
Found at i:3766171 original size:19 final size:19
Alignment explanation
Indices: 3766139--3766178 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3766129 AAGTTATTTG
**
3766139 TATATATATTTTATAAAAA
1 TATATATAAATTATAAAAA
*
3766158 TATATATAAATTATAATAA
1 TATATATAAATTATAAAAA
3766177 TA
1 TA
3766179 GAAAATTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATATATAAATTATAAAAA
Found at i:3766232 original size:62 final size:63
Alignment explanation
Indices: 3766111--3766235 Score: 146
Period size: 62 Copynumber: 2.0 Consensus size: 63
3766101 CCCTTAATCC
* * * * * *
3766111 TAATAAAAAATATATATTAAGTTATTTGTATATATATTTTATAAAAATATATATAAATTATAA
1 TAATAAAAAATATATATTAAGTTATTTGTATAAAAATATAATAAAAAGAAATATAAATTATAA
* * *
3766174 TAATAGAAAAT-TATATTAAGTTATTTGTGTAAAAATATAATAAATTAGAAATAT-AATTATAA
1 TAATAAAAAATATATATTAAGTTATTTGTATAAAAATATAATAAA-AAGAAATATAAATTATAA
3766236 ATTTAATTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
62 36 0.69
63 16 0.31
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (63 bp):
TAATAAAAAATATATATTAAGTTATTTGTATAAAAATATAATAAAAAGAAATATAAATTATAA
Found at i:3766486 original size:12 final size:12
Alignment explanation
Indices: 3766469--3766493 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3766459 AAGAGATATA
3766469 GATAGAATTGAT
1 GATAGAATTGAT
3766481 GATAGAATTGAT
1 GATAGAATTGAT
3766493 G
1 G
3766494 CATCGAGAAT
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:0.40, C:0.00, G:0.28, T:0.32
Consensus pattern (12 bp):
GATAGAATTGAT
Found at i:3768027 original size:71 final size:72
Alignment explanation
Indices: 3767945--3768526 Score: 334
Period size: 71 Copynumber: 8.2 Consensus size: 72
3767935 CTATTAACAA
* * *
3767945 GGTGTCCTCCATGATTGAGGCTCAGGGTTAAGTTTAGTC-TCTTCCATGGCTGAGGGTTCACCTA
1 GGTGTCCTCCATGACTGAGGCTCAGGGTTAAGTTTAGACTTCCTCCATGGCTGAGGGTTCACCTA
3768009 CTAATGG
66 CTAATGG
* * * * **** *
3768016 GGTGTCCTCCATGACTGAGGCTCGGGGTTGCA-TTCA-ACTTCCTCTAAAATTGAGGGTTCATCT
1 GGTGTCCTCCATGACTGAGGCTCAGGGTT-AAGTTTAGACTTCCTCCATGGCTGAGGGTTCACCT
*
3768079 ACTAATAG
65 ACTAATGG
* * * * * * * *
3768087 GGTATCTTCCATGA-TCAAGGCTCCA-GGTTGCA-TTTAG-TTTTCTCCATGGTTGATGGTTCAC
1 GGTGTCCTCCATGACT-GAGGCT-CAGGGTT-AAGTTTAGACTTCCTCCATGGCTGAGGGTTCAC
*
3768148 CTACTAATGA
63 CTACTAATGG
* * *** * ** * **
3768158 GGTGTCCTTCATGACCGAGGCTTTCGGTT--GTGTTCGACTTCCTCCATGAATGAAGGTTCGTCT
1 GGTGTCCTCCATGACTGAGGCTCAGGGTTAAGT-TTAGACTTCCTCCATGGCTGAGGGTTCACCT
3768221 ACTAATGG
65 ACTAATGG
* * * * * *
3768229 AGTGTCCTCCATGGCTAAGGCTCAGGGTCACA-TTT-GACTTCCTCCATAGCTGAGGGTTCACCA
1 GGTGTCCTCCATGACTGAGGCTCAGGGTTA-AGTTTAGACTTCCTCCATGGCTGAGGGTTCACCT
***
3768292 ACTAACAA
65 ACTAATGG
* * * * **
3768300 GGTGTCCTCCATGACTGAAGCTCTA-GGTTACG-TTAGACTTTCTCCATGGTTGAGGGTTCGTCT
1 GGTGTCCTCCATGACTGAGGCTC-AGGGTTAAGTTTAGACTTCCTCCATGGCTGAGGGTTCACCT
**
3768363 ACTAACAG
65 ACTAATGG
* * *** * * **
3768371 GGTGTCATCCATGACTGAGG-TCCGGAGTCGTGTTTA-TCTTCCTCCATGGCTAACTGTTCACCT
1 GGTGTCCTCCATGACTGAGGCTCAGG-GTTAAGTTTAGACTTCCTCCATGGCTGAGGGTTCACCT
*
3768434 ACTAATGA
65 ACTAATGG
* * * * * * *
3768442 GGTGTCCTCCATGACTGAGGCTTAGGGTTGCA-TTCA-AATTCCTCCATGGCTGAGGATTTATCT
1 GGTGTCCTCCATGACTGAGGCTCAGGGTT-AAGTTTAGACTTCCTCCATGGCTGAGGGTTCACCT
*
3768505 ACCAATGG
65 ACTAATGG
* *
3768513 GGTTTTCTCCATGA
1 GGTGTCCTCCATGA
3768527 TTAGGGCTCG
Statistics
Matches: 378, Mismatches: 112, Indels: 42
0.71 0.21 0.08
Matches are distributed among these distances:
69 1 0.00
70 10 0.03
71 355 0.94
72 11 0.03
73 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.32
Consensus pattern (72 bp):
GGTGTCCTCCATGACTGAGGCTCAGGGTTAAGTTTAGACTTCCTCCATGGCTGAGGGTTCACCTA
CTAATGG
Found at i:3768147 original size:142 final size:142
Alignment explanation
Indices: 3767977--3768749 Score: 582
Period size: 142 Copynumber: 5.4 Consensus size: 142
3767967 CAGGGTTAAG
* * * *
3767977 TTTAGTCTCTTCCATGGCTGAGGGTTCACCTACTAATGGGGTGTCCTCCATGACTGAGGCTCGGG
1 TTTAGTTTCCTCCATGGCTGAGGGTTCACCTACTAATGAGGTGTCCTCCATGACTGAGGCTCTGG
* * *** * *
3768042 GTTGCATTCAACTTCCTCTAAAATTGAGGGTTCATCTACTAATAGGGTATCTTCCATGA-TCAAG
66 GTTGCGTTCAACTTCCTCCATGGTTGAGGGTTCGTCTACTAATAGGGTGTCTTCCATGACT-AAG
*
3768106 GCTCCAGGTTGCA
130 GCTCCAGGTCGCA
* * * * * * *
3768119 TTTAGTTTTCTCCATGGTTGATGGTTCACCTACTAATGAGGTGTCCTTCATGACCGAGGCTTTCG
1 TTTAGTTTCCTCCATGGCTGAGGGTTCACCTACTAATGAGGTGTCCTCCATGACTGAGGCTCTGG
* * ** * * *
3768184 GTTGTGTTCGACTTCCTCCATGAATGAAGGTTCGTCTACTAAT-GGAGTGTCCTCCATGGCTAAG
66 GTTGCGTTCAACTTCCTCCATGGTTGAGGGTTCGTCTACTAATAGG-GTGTCTTCCATGACTAAG
*
3768248 GCT-CAGGGTCACA
130 GCTCCA-GGTCGCA
* * * ** * *
3768261 TTT-GACTTCCTCCATAGCTGAGGGTTCACCAACTAACAAGGTGTCCTCCATGACTGAAGCTCTA
1 TTTAG-TTTCCTCCATGGCTGAGGGTTCACCTACTAATGAGGTGTCCTCCATGACTGAGGCTCTG
* * * * *
3768325 GGTTACGTT-AGACTTTCTCCATGGTTGAGGGTTCGTCTACTAACAGGGTGTCATCCATGACTGA
65 GGTTGCGTTCA-ACTTCCTCCATGGTTGAGGGTTCGTCTACTAATAGGGTGTCTTCCATGACTAA
* **
3768389 GG-TCCGGAGTCGTG
129 GGCTCCAG-GTCGCA
* **
3768403 TTTA-TCTTCCTCCATGGCTAACTGTTCACCTACTAATGAGGTGTCCTCCATGACTGAGGCT-TA
1 TTTAGT-TTCCTCCATGGCTGAGGGTTCACCTACTAATGAGGTGTCCTCCATGACTGAGGCTCT-
* * * * ** * * * *
3768466 GGGTTGCATTCAAATTCCTCCATGGCTGAGGATTTATCTACCAATGGGGT-TTTCTCCATGATTA
64 GGGTTGCGTTCAACTTCCTCCATGGTTGAGGGTTCGTCTACTAATAGGGTGTCT-TCCATGACTA
* * * *
3768530 GGGCTCGAGGTTGTA
128 AGGCTCCAGGTCGCA
* * * * * * ** * * *
3768545 TTCAGTTTCCTCCATGGTTAACGGTTCACTTACTAAT-AGGGTTTCCTATATTACTAATGCTCTG
1 TTTAGTTTCCTCCATGGCTGAGGGTTCACCTACTAATGA-GGTGTCCTCCATGACTGAGGCTCTG
* * * * ** * * *
3768609 TGTTGCGTTCAAATTCCTCTATGGTTGAGGGTTTGTCTACTAACGGGGTTTCTGCTATGACTAAG
65 GGTTGCGTTCAACTTCCTCCATGGTTGAGGGTTCGTCTACTAATAGGGTGTCTTCCATGACTAAG
*
3768674 GCT-CGGAGTCGCA
130 GCTCCAG-GTCGCA
* * * *
3768687 -TTAGGTTTCCTCCATGGATGAGGGTTCACCTACTAATAAGTTGTCATCCATGA-TCGAGGCTCT
1 TTTA-GTTTCCTCCATGGCTGAGGGTTCACCTACTAATGAGGTGTCCTCCATGACT-GAGGCTCT
3768750 AACTTTTAAA
Statistics
Matches: 486, Mismatches: 123, Indels: 44
0.74 0.19 0.07
Matches are distributed among these distances:
141 14 0.03
142 460 0.95
143 12 0.02
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (142 bp):
TTTAGTTTCCTCCATGGCTGAGGGTTCACCTACTAATGAGGTGTCCTCCATGACTGAGGCTCTGG
GTTGCGTTCAACTTCCTCCATGGTTGAGGGTTCGTCTACTAATAGGGTGTCTTCCATGACTAAGG
CTCCAGGTCGCA
Found at i:3769221 original size:36 final size:36
Alignment explanation
Indices: 3769100--3769533 Score: 271
Period size: 36 Copynumber: 12.2 Consensus size: 36
3769090 TGCTTTCAAA
* * * *
3769100 AAGACTA-ACTTGATTTCTAGGGAAACGATCTAAATG
1 AAGACTAGA-TTGGTTTCTAGGGAAACAATCTTAAGG
* * * * *
3769136 AAGACT-G-TGTTGTCTCTAGGGCAATAATATTAA-G
1 AAGACTAGAT-TGGTTTCTAGGGAAACAATCTTAAGG
* * *
3769170 AAGATTATG-TTGGTTTCTAGGGAAACAATCTTTACG
1 AAGACTA-GATTGGTTTCTAGGGAAACAATCTTAAGG
* * * *
3769206 AAGGCTAGATTGGTTTCTAGGAAAATAGTCTTAAGG
1 AAGACTAGATTGGTTTCTAGGGAAACAATCTTAAGG
* * * * *
3769242 AAGATTATG-TTGGTTTCTAAGAAAACAATCGTAAGT
1 AAGACTA-GATTGGTTTCTAGGGAAACAATCTTAAGG
* * *
3769278 AAGTCTAGATTGGGTTCTAGGGAAACAATCCTAAGG
1 AAGACTAGATTGGTTTCTAGGGAAACAATCTTAAGG
* * * *
3769314 AAGATTATG-TTGGTTTCTAGGGGAGCAGTCTTAAGG
1 AAGACTA-GATTGGTTTCTAGGGAAACAATCTTAAGG
* * ** *
3769350 AAGGCTAGATTTGTTTCTATAGAAACAATCTTAAAG
1 AAGACTAGATTGGTTTCTAGGGAAACAATCTTAAGG
* * * * * *
3769386 AATACTATATTAGTTTTTAGAGAAACAGTCTT-A--
1 AAGACTAGATTGGTTTCTAGGGAAACAATCTTAAGG
* * *
3769419 AAGACAAGGTTGGTTTCTAGGGAAACATTCTTAAGG
1 AAGACTAGATTGGTTTCTAGGGAAACAATCTTAAGG
* * * *
3769455 AAGATTATG-TTGGTTTCTAAGG-AACAATCTTACGA
1 AAGACTA-GATTGGTTTCTAGGGAAACAATCTTAAGG
* * * * *
3769490 AAGACTAGGTTGGTTACAAGTGAAACAATCTTAATG
1 AAGACTAGATTGGTTTCTAGGGAAACAATCTTAAGG
3769526 AAGACTAG
1 AAGACTAG
3769534 GGAAATGGTT
Statistics
Matches: 301, Mismatches: 81, Indels: 32
0.73 0.20 0.08
Matches are distributed among these distances:
33 24 0.08
34 9 0.03
35 63 0.21
36 202 0.67
37 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (36 bp):
AAGACTAGATTGGTTTCTAGGGAAACAATCTTAAGG
Found at i:3770413 original size:166 final size:167
Alignment explanation
Indices: 3770139--3770472 Score: 652
Period size: 166 Copynumber: 2.0 Consensus size: 167
3770129 TGCCTCGACA
3770139 TGAACTGAGTCCTTAATGATGCTTCCTAATAGTTATTTTTCCTATTTTATCAAATCATTGTCGTT
1 TGAACTGAGTCCTTAATGATGCTTCCTAATAGTTATTTTTCCTATTTTATCAAATCATTGTCGTT
3770204 TAAGTGCAAAAATATCTTTCTAGAATATATTTTACTTGTATCAATCTCGTTAACAAACATCAAGT
66 TAAGTGCAAAAATATCTTTCTAGAATATATTTTACTTGTATCAATCTCGTTAACAAACATCAAGT
*
3770269 TCTCCACTTGGTCATCTAC-ATGACACCATGGCATTT
131 TCTCAACTTGGTCATCTACAATGACACCATGGCATTT
3770305 TGAACTGAGTCCTTAATGATGCTTCCTAATAGTTATTTTTCCTATTTTATCAAATCATTGTCGTT
1 TGAACTGAGTCCTTAATGATGCTTCCTAATAGTTATTTTTCCTATTTTATCAAATCATTGTCGTT
3770370 TAAGTGCAAAAATATCTTTCTAGAATATATTTTACTTGTATCAATCTCGTTAACAAACATCAAGT
66 TAAGTGCAAAAATATCTTTCTAGAATATATTTTACTTGTATCAATCTCGTTAACAAACATCAAGT
3770435 TCTCAACTTGGTCATCTACAATGACACCATGGCATTT
131 TCTCAACTTGGTCATCTACAATGACACCATGGCATTT
3770472 T
1 T
3770473 TCTTTCACTC
Statistics
Matches: 166, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
166 148 0.89
167 18 0.11
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (167 bp):
TGAACTGAGTCCTTAATGATGCTTCCTAATAGTTATTTTTCCTATTTTATCAAATCATTGTCGTT
TAAGTGCAAAAATATCTTTCTAGAATATATTTTACTTGTATCAATCTCGTTAACAAACATCAAGT
TCTCAACTTGGTCATCTACAATGACACCATGGCATTT
Found at i:3771543 original size:25 final size:25
Alignment explanation
Indices: 3771515--3771564 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3771505 ATGTGCTTGC
3771515 TTTGATTTGTTATCTT-TTTTTTCTT
1 TTTG-TTTGTTATCTTCTTTTTTCTT
* *
3771540 TTTGTTTTTTTTCTTCTTTTTTCTT
1 TTTGTTTGTTATCTTCTTTTTTCTT
3771565 CAGGGGATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.04, C:0.10, G:0.06, T:0.80
Consensus pattern (25 bp):
TTTGTTTGTTATCTTCTTTTTTCTT
Found at i:3779513 original size:5 final size:5
Alignment explanation
Indices: 3779505--3779570 Score: 55
Period size: 5 Copynumber: 13.4 Consensus size: 5
3779495 TAGAAGGTAA
* * * *
3779505 TATAT TATAT TATAT TATAT TATAC TAAAT TA-A- TATTT TAGTAT TTTAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
* *
3779554 TAAAT TATTT TATAT TA
1 TATAT TATAT TATAT TA
3779571 ATTTTTTGGC
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 41 0.87
6 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:3781636 original size:20 final size:20
Alignment explanation
Indices: 3781598--3781656 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
3781588 AATGCCCCCC
** *
3781598 TTTCCCCTTTTTTTGGTGAA
1 TTTCCCCTTTTGCTCGTGAA
3781618 TTTCCCCTTTTGCTCGTGAA
1 TTTCCCCTTTTGCTCGTGAA
*
3781638 --CCCCACTTTTGCTCGTGAA
1 TTTCCC-CTTTTGCTCGTGAA
3781657 CCCCCTGTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 3 0.09
19 14 0.41
20 17 0.50
ACGTcount: A:0.12, C:0.29, G:0.15, T:0.44
Consensus pattern (20 bp):
TTTCCCCTTTTGCTCGTGAA
Found at i:3781646 original size:19 final size:19
Alignment explanation
Indices: 3781624--3781660 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
3781614 TGAATTTCCC
3781624 CTTTTGCTCGTGAACCCCA
1 CTTTTGCTCGTGAACCCCA
3781643 CTTTTGCTCGTGAACCCC
1 CTTTTGCTCGTGAACCCC
3781661 CTGTCCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.14, C:0.38, G:0.16, T:0.32
Consensus pattern (19 bp):
CTTTTGCTCGTGAACCCCA
Found at i:3782794 original size:16 final size:17
Alignment explanation
Indices: 3782773--3782806 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3782763 ACATTATTAT
3782773 TAATAAT-AAAATAATA
1 TAATAATAAAAATAATA
3782789 TAATAATAAAAATAATA
1 TAATAATAAAAATAATA
3782806 T
1 T
3782807 CCCGGACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAATAATAAAAATAATA
Found at i:3791501 original size:22 final size:22
Alignment explanation
Indices: 3791471--3791559 Score: 142
Period size: 22 Copynumber: 4.0 Consensus size: 22
3791461 GGCATGTGAA
* *
3791471 ATATATCCCGAACGACCTATGT
1 ATATGTCCCGAAGGACCTATGT
*
3791493 ATATGTCCCGAAGGACCTGTGT
1 ATATGTCCCGAAGGACCTATGT
*
3791515 ATATGTCCCGAAGGACCTGTGT
1 ATATGTCCCGAAGGACCTATGT
3791537 ATATGTCCCGAAGGACCTATGT
1 ATATGTCCCGAAGGACCTATGT
3791559 A
1 A
3791560 AACCTCGACT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (22 bp):
ATATGTCCCGAAGGACCTATGT
Found at i:3798531 original size:22 final size:22
Alignment explanation
Indices: 3798503--3798570 Score: 91
Period size: 22 Copynumber: 3.1 Consensus size: 22
3798493 GCATATGAAA
* *
3798503 TATATGTCCCGAATGACCTATT
1 TATATGTCCCGAAGGACCTATG
* *
3798525 TATATGTTCCGAAGGACCTGTG
1 TATATGTCCCGAAGGACCTATG
*
3798547 TATATGTCCAGAAGGACCTATG
1 TATATGTCCCGAAGGACCTATG
3798569 TA
1 TA
3798571 ACCCTCGACT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (22 bp):
TATATGTCCCGAAGGACCTATG
Found at i:3802106 original size:23 final size:23
Alignment explanation
Indices: 3802069--3802137 Score: 79
Period size: 22 Copynumber: 3.0 Consensus size: 23
3802059 ATATATTTAA
*
3802069 TATTTATGTTTTATGGCATATTTT
1 TATTTAT-TTTTATGACATATTTT
*
3802093 TATTTATTTTTATGACAT-GTTT
1 TATTTATTTTTATGACATATTTT
* *
3802115 TATTTGTCTTT-TGACATATTTT
1 TATTTATTTTTATGACATATTTT
3802137 T
1 T
3802138 GGTCTTCTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 6 0.15
22 16 0.41
23 10 0.26
24 7 0.18
ACGTcount: A:0.20, C:0.06, G:0.10, T:0.64
Consensus pattern (23 bp):
TATTTATTTTTATGACATATTTT
Found at i:3802710 original size:19 final size:19
Alignment explanation
Indices: 3802675--3802714 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3802665 TCATCTATTA
3802675 ATTTGAAAATATATTATAT
1 ATTTGAAAATATATTATAT
*
3802694 ATTTGCAAAA-ATCTTATAT
1 ATTTG-AAAATATATTATAT
3802713 AT
1 AT
3802715 CCAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTGAAAATATATTATAT
Found at i:3804979 original size:41 final size:41
Alignment explanation
Indices: 3804926--3805017 Score: 105
Period size: 41 Copynumber: 2.3 Consensus size: 41
3804916 TTTTAGCGGT
* * **
3804926 TTTTTTAT-CAAACGCCGCAAAAGTCTCTTACTTTAGTGCC
1 TTTTGTATACAAACGCCGCAAAAGACTCAGACTTTAGTGCC
* * *
3804966 TTTTGTATACAAACGCCGCTACAGACTCAGACTTTAGTGGC
1 TTTTGTATACAAACGCCGCAAAAGACTCAGACTTTAGTGCC
*
3805007 GTTTGTATACA
1 TTTTGTATACA
3805018 TACACCGCTA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 7 0.16
41 36 0.84
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (41 bp):
TTTTGTATACAAACGCCGCAAAAGACTCAGACTTTAGTGCC
Found at i:3805044 original size:41 final size:41
Alignment explanation
Indices: 3804958--3805070 Score: 118
Period size: 41 Copynumber: 2.8 Consensus size: 41
3804948 GTCTCTTACT
* * * * * *
3804958 TTAGTGCCTTTTGTATACAAACGCCGCTACAGACTCAGACT
1 TTAGTGGCATTTGTATACAAACGCCGCTATAAACCCAGACG
* * * *
3804999 TTAGTGGCGTTTGTATACATACACCGCTATAAACCCATACG
1 TTAGTGGCATTTGTATACAAACGCCGCTATAAACCCAGACG
* *
3805040 TTAGTGGCATTTATAAACAAACGCCGCTATA
1 TTAGTGGCATTTGTATACAAACGCCGCTATA
3805071 TACTTGAACT
Statistics
Matches: 58, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (41 bp):
TTAGTGGCATTTGTATACAAACGCCGCTATAAACCCAGACG
Found at i:3805718 original size:22 final size:21
Alignment explanation
Indices: 3805680--3805720 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
3805670 TATTCACTTA
*
3805680 TACTTTTGTTTGTCATTTCAT
1 TACTTTTGTTTGCCATTTCAT
*
3805701 TACTTTTTTCTTGCCATTTC
1 TACTTTTGT-TTGCCATTTC
3805721 GTGTCACATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.12, C:0.20, G:0.07, T:0.61
Consensus pattern (21 bp):
TACTTTTGTTTGCCATTTCAT
Found at i:3811011 original size:22 final size:21
Alignment explanation
Indices: 3810978--3811018 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3810968 CAAATATATA
*
3810978 TATTTATAATATTTTTGTTGG
1 TATTTATAATATTGTTGTTGG
3810999 TATTTACTAATATTGTTGTT
1 TATTTA-TAATATTGTTGTT
3811019 TGTTTATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.24, C:0.02, G:0.12, T:0.61
Consensus pattern (21 bp):
TATTTATAATATTGTTGTTGG
Done.