Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009343.1 Hibiscus syriacus cultivar Beakdansim tig00113123_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: 2141224
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 11
Found at i:1594382 original size:62 final size:61
Alignment explanation
Indices: 1594316--1594431 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 61
1594306 ATGAAGGTAT
* * *
1594316 GCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGATGTTTATTATTAATGGGG
1 GCATCGATGCAATACTTATGCATCGATGCACT-AAATGCATTCGATGTTT-TTATTAATGGGG
* *
1594378 GCATCGATGCAATCCTTATGCATCGATGCACTAATTGCATTCGATGTTTTTATT
1 GCATCGATGCAATACTTATGCATCGATGCACTAAATGCATTCGATGTTTTTATT
1594432 TTAAAAGAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
61 5 0.10
62 42 0.88
63 1 0.02
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (61 bp):
GCATCGATGCAATACTTATGCATCGATGCACTAAATGCATTCGATGTTTTTATTAATGGGG
Found at i:1597499 original size:79 final size:78
Alignment explanation
Indices: 1597368--1597525 Score: 291
Period size: 79 Copynumber: 2.0 Consensus size: 78
1597358 ATGTCCAAAG
1597368 GAATGTCACTTCATTCAACCAAATTCACATTTAGAAAATTTAGCATAAAACTTGTCTCGTAAAAT
1 GAATGTCACTTCATTCAACCAAATTCACATTTAGAAAATTTAGCATAAAACTTGTCTCGTAAAAT
1597433 CAGTAAAACAATCT
66 CAGTAAAAC-ATCT
1597447 GAATGTCACTTCATTCAACCAAAATTCACATTTAG-AAATTTAGCATAAAACTTGTCTCGTAAAA
1 GAATGTCACTTCATTCAACC-AAATTCACATTTAGAAAATTTAGCATAAAACTTGTCTCGTAAAA
1597511 TCAGTAAAACATCT
65 TCAGTAAAACATCT
1597525 G
1 G
1597526 TAAGTATGAA
Statistics
Matches: 78, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
78 5 0.06
79 59 0.76
80 14 0.18
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.30
Consensus pattern (78 bp):
GAATGTCACTTCATTCAACCAAATTCACATTTAGAAAATTTAGCATAAAACTTGTCTCGTAAAAT
CAGTAAAACATCT
Found at i:1602538 original size:60 final size:59
Alignment explanation
Indices: 1602474--1602642 Score: 225
Period size: 60 Copynumber: 2.9 Consensus size: 59
1602464 GCGAATATGA
*
1602474 AAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACG-GTATCCGT
* *** * *
1602534 AAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTATATCGCAAC-GTATCCGT
1 AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGGTATCCGT
**
1602592 AAATCGCAACGATAATACATAAAATCGCAACGCGTAT-CGTAAATCGCAACG
1 AAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTAAATCGCAACG
1602643 CGATTTAAAG
Statistics
Matches: 92, Mismatches: 15, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
58 34 0.37
59 15 0.16
60 43 0.47
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (59 bp):
AAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTAAATCGCAACGGTATCCGT
Found at i:1602549 original size:20 final size:20
Alignment explanation
Indices: 1602455--1602644 Score: 192
Period size: 20 Copynumber: 9.6 Consensus size: 20
1602445 GATTTTCCAT
* ** *
1602455 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1602475 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1602495 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1602515 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1602535 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1602555 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1602575 TATCGCAA--CGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
1602593 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
1602614 AATCGCAACGCGTAT-CGTA
1 AATCGCAACGCGTATCCGTA
1602633 AATCGCAACGCG
1 AATCGCAACGCG
1602645 ATTTAAAGCC
Statistics
Matches: 142, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
18 17 0.12
19 15 0.11
20 94 0.66
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1603052 original size:34 final size:34
Alignment explanation
Indices: 1603012--1603081 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
1603002 TTCACTTAGA
*
1603012 TTTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1603046 TTTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1603080 TT
1 TT
1603082 CAAGTTAGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.10, C:0.21, G:0.19, T:0.50
Consensus pattern (34 bp):
TTTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1603221 original size:14 final size:14
Alignment explanation
Indices: 1603202--1603255 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
1603192 AGAATGACTG
1603202 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
1603216 TCGCAACGCGAAATGAAA
1 TCGCAA--CGAGA-G-AA
1603234 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1603248 TCGCAACG
1 TCGCAACG
1603256 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 8 0.24
17 1 0.03
18 8 0.24
ACGTcount: A:0.41, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:1603237 original size:18 final size:16
Alignment explanation
Indices: 1603212--1603260 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1603202 TCGCAACGAG
1603212 AGAATCGCAACGCGAA
1 AGAATCGCAACGCGAA
*
1603228 ATGAAATCGCAA--CGAG
1 A-G-AATCGCAACGCGAA
1603244 AGAATCGCAACGCGAA
1 AGAATCGCAACGCGAA
1603260 A
1 A
1603261 CCAAAATCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
15 1 0.04
16 9 0.33
17 1 0.04
18 8 0.30
ACGTcount: A:0.45, C:0.22, G:0.24, T:0.08
Consensus pattern (16 bp):
AGAATCGCAACGCGAA
Found at i:1603289 original size:19 final size:19
Alignment explanation
Indices: 1603267--1603338 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
1603257 GAAACCAAAA
*
1603267 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1603286 TCGCGTTGTGCGATTTTCATT
1 TCGCG-T-TGCGATTTTCATT
* *
1603307 TCGCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
1603326 TCGCGTTGCGATT
1 TCGCGTTGCGATT
1603339 CTCTCGTTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
19 28 0.58
20 2 0.04
21 18 0.38
ACGTcount: A:0.11, C:0.22, G:0.24, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1603297 original size:21 final size:21
Alignment explanation
Indices: 1603273--1603333 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
1603263 AAAATCGCAT
1603273 TGCGATTTTCATTTCGCGTTG
1 TGCGATTTTCATTTCGCGTTG
1603294 TGCGATTTTCATTTCGCG-T-
1 TGCGATTTTCATTTCGCGTTG
* *
1603313 TGCGATTGTCATCTCGCGTTG
1 TGCGATTTTCATTTCGCGTTG
1603334 CGATTCTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.44
20 2 0.06
21 18 0.50
ACGTcount: A:0.10, C:0.21, G:0.25, T:0.44
Consensus pattern (21 bp):
TGCGATTTTCATTTCGCGTTG
Found at i:1608656 original size:16 final size:17
Alignment explanation
Indices: 1608627--1608665 Score: 62
Period size: 16 Copynumber: 2.4 Consensus size: 17
1608617 TTAAATAATT
1608627 TTTTATATTTTTATTAA
1 TTTTATATTTTTATTAA
1608644 TTTTATA-TTTTATTAA
1 TTTTATATTTTTATTAA
*
1608660 TATTAT
1 TTTTAT
1608666 TTTCACCCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTTTATATTTTTATTAA
Found at i:1608773 original size:293 final size:298
Alignment explanation
Indices: 1608410--1609007 Score: 1017
Period size: 291 Copynumber: 2.0 Consensus size: 298
1608400 CTAAAATGAA
1608410 ATAAA-AACTAAATCTCAAGTATGATTTTGATTTTTTAAAGGTTTAGATATCAGAATAGACTAAA
1 ATAAATAACTAAATCTCAAGTATGATTTTGATTTTTTAAAGGTTTAGATATCAGAATAGAC-AAA
1608474 TGATAGTTTAGATATTAAACTCGTTTACTC-TT-TAATTTTATCCTGAAAAATATACAATTTTTT
65 TGATAGTTTAG--A-TAAACTCGTTTACTCTTTATAATTTTATCCTGAAAAATATACAA--TTTT
1608537 TATTTCACA-TATTAATTTTCA-TTTCCCATTATCCTCGAATGGTCGGAGGTGGCCTCCCTCTTA
125 TATTTCACATTA-TAATTTTCATTTTCCCATTATCCTCGAATGGTCGGAGGTGGCCTCCCTCTTA
1608600 AAAAATTT-AA-T-T-ATATATTAAATAATTTTTTATATTTTTATTAATTTTATA-TTTTATTAA
189 AAAAATTTAAATTATAATATATTAAATAATTTTTTATATTTTTATTAATTTTATATTTTTATTAA
1608660 TA-T-TATTTTCACCCCTTAAAATTTTATAAATTATTCA-ATAAC
254 TATTATATTTTCACCCCTTAAAATTTTATAAATTATTCATATAAC
1608702 ATAAATAACTAAATCTCAAGTATGATTTTGATTTTTTTAAAGGTTTAGATATCAGAATAGA-AAA
1 ATAAATAACTAAATCTCAAGTATGATTTTGA-TTTTTTAAAGGTTTAGATATCAGAATAGACAAA
1608766 TTGATAGTTTAGATAAACTCGTTTACTCTTTATAATTTTATCCTGAAAAATATACAATTTTTATT
65 -TGATAGTTTAGATAAACTCGTTTACTCTTTATAATTTTATCCTGAAAAATATACAATTTTTATT
1608831 TCACATTATAATTTTCATTTTCCCATTATCCTCGAATGGTCGGAGGTGGCCTCCCTCTTAAAAAA
129 TCACATTATAATTTTCATTTTCCCATTATCCTCGAATGGTCGGAGGTGGCCTCCCTCTTAAAAAA
1608896 TTTAAATTATAATATATTAAATAATTTTTTATATTTTTATTAATTTTATATTTTTATTAATATTA
194 TTTAAATTATAATATATTAAATAATTTTTTATATTTTTATTAATTTTATATTTTTATTAATATTA
1608961 TATTTTCACCCCTTAAAATTTTATAAATTATTCATATAAC
259 TATTTTCACCCCTTAAAATTTTATAAATTATTCATATAAC
1609001 ATAAATA
1 ATAAATA
1609008 TATATATATA
Statistics
Matches: 291, Mismatches: 0, Indels: 23
0.93 0.00 0.07
Matches are distributed among these distances:
290 37 0.13
291 55 0.19
292 35 0.12
293 37 0.13
294 30 0.10
295 39 0.13
296 11 0.04
297 1 0.00
298 34 0.12
299 12 0.04
ACGTcount: A:0.36, C:0.12, G:0.07, T:0.45
Consensus pattern (298 bp):
ATAAATAACTAAATCTCAAGTATGATTTTGATTTTTTAAAGGTTTAGATATCAGAATAGACAAAT
GATAGTTTAGATAAACTCGTTTACTCTTTATAATTTTATCCTGAAAAATATACAATTTTTATTTC
ACATTATAATTTTCATTTTCCCATTATCCTCGAATGGTCGGAGGTGGCCTCCCTCTTAAAAAATT
TAAATTATAATATATTAAATAATTTTTTATATTTTTATTAATTTTATATTTTTATTAATATTATA
TTTTCACCCCTTAAAATTTTATAAATTATTCATATAAC
Found at i:1608942 original size:17 final size:17
Alignment explanation
Indices: 1608922--1608966 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
1608912 TTAAATAATT
1608922 TTTTATATTTTTATTAA
1 TTTTATATTTTTATTAA
1608939 TTTTATATTTTTATTAA
1 TTTTATATTTTTATTAA
*
1608956 TATTATATTTT
1 TTTTATATTTT
1608967 CACCCCTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATATTTTTATTAA
Found at i:1609012 original size:2 final size:2
Alignment explanation
Indices: 1609005--1609034 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1608995 TATAACATAA
1609005 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
1609035 CTCCACCTTG
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:1610715 original size:9 final size:9
Alignment explanation
Indices: 1610703--1610735 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1610693 AATATTTTGC
1610703 ATTTAATTT
1 ATTTAATTT
*
1610712 ATTTAA-GT
1 ATTTAATTT
1610720 ATTTAATTT
1 ATTTAATTT
1610729 ATTTAAT
1 ATTTAAT
1610736 ATTTTACTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (9 bp):
ATTTAATTT
Found at i:1610741 original size:17 final size:17
Alignment explanation
Indices: 1610703--1610739 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
1610693 AATATTTTGC
1610703 ATTTAATTTATTTAAGT
1 ATTTAATTTATTTAAGT
1610720 ATTTAATTTATTTAA-T
1 ATTTAATTTATTTAAGT
1610736 ATTT
1 ATTT
1610740 TACTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
ATTTAATTTATTTAAGT
Found at i:1617288 original size:20 final size:20
Alignment explanation
Indices: 1617263--1617315 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
1617253 ATTTTTCTCC
1617263 TAGTTCAGCAGATCTTCCCA
1 TAGTTCAGCAGATCTTCCCA
1617283 TAGTTCAGCAGATCTTCCCA
1 TAGTTCAGCAGATCTTCCCA
*
1617303 -ATGCTCAGCAGAT
1 TA-GTTCAGCAGAT
1617316 ATAGCTACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.28
Consensus pattern (20 bp):
TAGTTCAGCAGATCTTCCCA
Found at i:1630670 original size:14 final size:14
Alignment explanation
Indices: 1630651--1630680 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1630641 AAGAACTTGG
1630651 AGTCAACAATGATC
1 AGTCAACAATGATC
1630665 AGTCAACAATGATC
1 AGTCAACAATGATC
1630679 AG
1 AG
1630681 CCGACAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (14 bp):
AGTCAACAATGATC
Found at i:1630687 original size:14 final size:14
Alignment explanation
Indices: 1630654--1630687 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1630644 AACTTGGAGT
*
1630654 CAACAATGATCAGT
1 CAACAATGATCAGC
1630668 CAACAATGATCAGC
1 CAACAATGATCAGC
*
1630682 CGACAA
1 CAACAA
1630688 AGGTTTACAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.26, G:0.15, T:0.15
Consensus pattern (14 bp):
CAACAATGATCAGC
Found at i:1638034 original size:22 final size:23
Alignment explanation
Indices: 1637982--1638039 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
1637972 AAATTATAAA
1637982 ATTATATT-TTGAAGATTTATATT
1 ATTATATTATT-AAGATTTATATT
*
1638005 ATTCTATTATTAA-ATTTA-ATT
1 ATTATATTATTAAGATTTATATT
1638026 ATTTATATTATTAA
1 A-TTATATTATTAA
1638040 TTGTTATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 4 0.13
22 16 0.52
23 9 0.29
24 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (23 bp):
ATTATATTATTAAGATTTATATT
Found at i:1638142 original size:29 final size:31
Alignment explanation
Indices: 1638106--1638174 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
1638096 TAGATTTTAG
* *
1638106 AAAATATTAATTT-A-TCTTTAATATTAGAT
1 AAAATATTAATTTAACTCATAAATATTAGAT
* *
1638135 AAAATATTATTTTAACTCATAAATTTTAGAT
1 AAAATATTAATTTAACTCATAAATATTAGAT
1638166 AAAATATTA
1 AAAATATTA
1638175 TTTTGATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 12 0.35
30 1 0.03
31 21 0.62
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (31 bp):
AAAATATTAATTTAACTCATAAATATTAGAT
Found at i:1639488 original size:29 final size:28
Alignment explanation
Indices: 1639396--1639505 Score: 114
Period size: 28 Copynumber: 3.9 Consensus size: 28
1639386 ATAATCCCAT
*
1639396 AATCAGGACGGGGACTAAGCCCGTGTAG
1 AATCAGGACGGGGACTAAGCCCATGTAG
* **
1639424 AATCAAGACGGGGACTAAGCCCATACAG
1 AATCAGGACGGGGACTAAGCCCATGTAG
* *
1639452 ATTTAGGACGGGGA-TATAGTCCCATGTAG
1 AATCAGGACGGGGACTA-AG-CCCATGTAG
** *
1639481 AATCAGGACATGGATTAAGCCCATG
1 AATCAGGACGGGGACTAAGCCCATG
1639506 CAAAATTATG
Statistics
Matches: 66, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
27 2 0.03
28 43 0.65
29 19 0.29
30 2 0.03
ACGTcount: A:0.33, C:0.20, G:0.29, T:0.18
Consensus pattern (28 bp):
AATCAGGACGGGGACTAAGCCCATGTAG
Found at i:1644048 original size:30 final size:30
Alignment explanation
Indices: 1644014--1644088 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
1644004 AAATGGATTT
* * *
1644014 AGTTTAGTGATCAAATTATAAGATTTTG-AA
1 AGTTTAGTGACCAAAGTATAA-ACTTTGAAA
*
1644044 AGTTTGGTGACCAAAGTATAAACTTTGAAA
1 AGTTTAGTGACCAAAGTATAAACTTTGAAA
*
1644074 AGTTTAGGGACCAAA
1 AGTTTAGTGACCAAA
1644089 ATGTAATTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 5 0.13
30 33 0.87
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (30 bp):
AGTTTAGTGACCAAAGTATAAACTTTGAAA
Found at i:1644277 original size:106 final size:106
Alignment explanation
Indices: 1644092--1644313 Score: 417
Period size: 106 Copynumber: 2.1 Consensus size: 106
1644082 GACCAAAATG
* *
1644092 TAATTTTAAAAAAGTTACAAATTGGTCACGAAAATAAGAAAATAAAAATATTATTTTAACATTTT
1 TAATTTGAACAAAGTTACAAATTGGTCACGAAAATAAGAAAATAAAAATATTATTTTAACATTTT
1644157 TAAAATGTTGGAAAATAATATTTAATGGTTTAATTCATGTT
66 TAAAATGTTGGAAAATAATATTTAATGGTTTAATTCATGTT
*
1644198 TAATTTGAACAAAGTTACAAATTGGTCACGAAAATAAGAAAATAAAAATATTATTTTCACATTTT
1 TAATTTGAACAAAGTTACAAATTGGTCACGAAAATAAGAAAATAAAAATATTATTTTAACATTTT
1644263 TAAAATGTTGGAAAATAATATTTAATGGTTTAATTCATGTT
66 TAAAATGTTGGAAAATAATATTTAATGGTTTAATTCATGTT
1644304 TAATTTGAAC
1 TAATTTGAAC
1644314 CGTTAGATTA
Statistics
Matches: 113, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 113 1.00
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (106 bp):
TAATTTGAACAAAGTTACAAATTGGTCACGAAAATAAGAAAATAAAAATATTATTTTAACATTTT
TAAAATGTTGGAAAATAATATTTAATGGTTTAATTCATGTT
Found at i:1645168 original size:30 final size:30
Alignment explanation
Indices: 1645122--1645195 Score: 103
Period size: 30 Copynumber: 2.5 Consensus size: 30
1645112 TCTACAAGCC
* * *
1645122 TTGGAAAAATTTGGGGACCATTTTATAATT
1 TTGGAAAAATTAGGGGACCAATTCATAATT
* *
1645152 TTTGAAAAGTTAGGGGACCAATTCATAATT
1 TTGGAAAAATTAGGGGACCAATTCATAATT
1645182 TTGGAAAAATTAGG
1 TTGGAAAAATTAGG
1645196 AACGATTGTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.36, C:0.07, G:0.22, T:0.35
Consensus pattern (30 bp):
TTGGAAAAATTAGGGGACCAATTCATAATT
Found at i:1646355 original size:33 final size:33
Alignment explanation
Indices: 1646310--1646374 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1646300 TATGGAAAGG
* *
1646310 GATCTATGAGATCATACAATAATGTTACACAAC
1 GATCTATAAGATCATACAAGAATGTTACACAAC
*
1646343 GATCTATAAGATCATACAAGAATGTTATACAA
1 GATCTATAAGATCATACAAGAATGTTACACAA
1646375 GATACATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
GATCTATAAGATCATACAAGAATGTTACACAAC
Found at i:1646579 original size:17 final size:17
Alignment explanation
Indices: 1646557--1646619 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
1646547 AGATGACATT
1646557 CTTCGGGATGATAGGTC
1 CTTCGGGATGATAGGTC
**
1646574 CTTCGGGACATAGATGACATC
1 CTTCGGG--AT-GAT-AGGTC
*
1646595 CTTCAGGATGATAGGTC
1 CTTCGGGATGATAGGTC
1646612 CTTCGGGA
1 CTTCGGGA
1646620 CACAATGACA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
17 17 0.47
18 3 0.08
19 4 0.11
20 3 0.08
21 9 0.25
ACGTcount: A:0.22, C:0.21, G:0.30, T:0.27
Consensus pattern (17 bp):
CTTCGGGATGATAGGTC
Found at i:1646582 original size:38 final size:38
Alignment explanation
Indices: 1646526--1646639 Score: 185
Period size: 38 Copynumber: 3.0 Consensus size: 38
1646516 TTTGGGACAT
* *
1646526 ATGATAGGTCCTTTGGGACACAGATGACATTCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
* *
1646564 ATGATAGGTCCTTCGGGACATAGATGACATCCTTCAGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1646602 ATGATAGGTCCTTCGGGACACA-ATGACATCCTTCGGG
1 ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
1646639 A
1 A
1646640 CATTTATATG
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
37 15 0.21
38 55 0.79
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (38 bp):
ATGATAGGTCCTTCGGGACACAGATGACATCCTTCGGG
Found at i:1648905 original size:17 final size:18
Alignment explanation
Indices: 1648871--1648911 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
1648861 TTTTAAATAA
1648871 ATATTTATTCTAATAATT
1 ATATTTATTCTAATAATT
*
1648889 ATATTTA-TCTTATAATT
1 ATATTTATTCTAATAATT
*
1648906 TTATTT
1 ATATTT
1648912 GTGCTCTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTATTCTAATAATT
Found at i:1648950 original size:2 final size:2
Alignment explanation
Indices: 1648945--1648976 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1648935 ACAATATTAA
1648945 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
1648977 TCTTGAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1650810 original size:524 final size:524
Alignment explanation
Indices: 1649553--1651103 Score: 2660
Period size: 524 Copynumber: 3.0 Consensus size: 524
1649543 CGATAATCCT
* *
1649553 TTATCTTTGATTTAGAAGTTCGTTCGATCTTTCGTTGTAAGGTAA-TTTTTTAATATATAATATT
1 TTATCTTTGATTCAGAAGTTCGTTTGATCTTTCGTTGTAAGGTAATTTTTTTAATATATAATATT
1649617 TTTTATAATTATATATGATTATTTG-AAAAAATATTATAGTAATTATTTTCAATTAATTTTTGTG
66 TTTTATAATTATATATGATTATTTGAAAAAAATATTATAGTAATTATTTTCAATTAATTTTTGTG
1649681 GTTGTAAAATTAGAAAGCGAGAGCATACGTCGAAA-ATTTTTTGTCGATACGGTAATAATATAAA
131 GTTGTAAAATTAGAAAGCGAGAGCATACGTCGAAATA-TTTTTGTCGATACGGTAATAATATAAA
*
1649745 ATTATATTATTTAAATTATTTACGTTTATGTTTAAGAATGAAGCGAATTTCAGCTATTGTTTATT
195 ATTATATTATTTAAATTATTTACGTTTATGTGTAAGAATGAAGCGAATTTCAGCTATTGTTTATT
*
1649810 ATGATGGAGAAATTCAGGAAGATGAAACCGACGTTGTTTTCATATTAAATCATTATGTTAAAATA
260 ATGATGGAGAAATTCAGGAAGATGAAACCGACGTTGTTTTCATATCAAATCATTATGTTAAAATA
*
1649875 TCCTTCAAGAGAAACATAACTCTTGAGGAGGTGATAATGAAGATTTCAATGAAGGTTCATGTTAG
325 TCCTTCAAGAGAAACATAACTCTTGAGGAGGTGATAATGAAGATTTCAAGGAAGGTTCATGTTAG
* *
1649940 AGGTACTAGAAGAAAGACGTCGCTTCAGTACAGATTTTAACATAATGATTTAA--GAAAAAAAAA
390 AGGTATTAGAAGAAAGACGTCGCTTCAGTACATATTTTAACATAATGATTTAAGGGAAAAAAAAA
* *
1650003 AATACTAAAAAAATAATGCAAAGGGTGTTAGATCGGGAATATTATTTCAAAGGGTGTCTGGCACG
455 AATACTAAAAAAATAATACAAAGGGTGTTAGATCGGGAATATTATTTCAAAGGGTGTCTGACACG
1650068 TACTC
520 TACTC
* *
1650073 TTATCTTTGATTCAAAAGTTCGTTTCATCTTTCGTTGTAAGGTAATTTTTTTAATATATAAT-TT
1 TTATCTTTGATTCAGAAGTTCGTTTGATCTTTCGTTGTAAGGTAATTTTTTTAATATATAATATT
1650137 TTTTATAATTATATATGATTATTTGAAAAAAAAATATTATAGTAATTATTTTCAATTAATTTTTG
66 TTTTATAATTATATATGATTATTTG--AAAAAAATATTATAGTAATTATTTTCAATTAATTTTTG
*
1650202 TGGTTGTAAAATTAGAAAGCGAGAGCATACGTCAAAATATTTTTGTCGATACGGTAATAATATAA
129 TGGTTGTAAAATTAGAAAGCGAGAGCATACGTCGAAATATTTTTGTCGATACGGTAATAATATAA
1650267 AATTATATTATTTAAATTATTTACGTTTATGTGTAAGAATGAAGCGAATTTCAGCTATTGTTTAT
194 AATTATATTATTTAAATTATTTACGTTTATGTGTAAGAATGAAGCGAATTTCAGCTATTGTTTAT
* *
1650332 TATGATAGAGAAATTCAGGAAGATGAAA-CAACGTTGTTTTCATATCAAATCATTATGTTAAAAT
259 TATGATGGAGAAATTCAGGAAGATGAAACCGACGTTGTTTTCATATCAAATCATTATGTTAAAAT
* * *
1650396 ATCTTTCAAGAGAAACATAACTCTTGAGGAGGTGATAATCAAGATTTCAAGGAATGTTCATGTTA
324 ATCCTTCAAGAGAAACATAACTCTTGAGGAGGTGATAATGAAGATTTCAAGGAAGGTTCATGTTA
* * ** *
1650461 GAGGTATTAGAATAAAGACGTCGATTCAGTACATATTTTAACATAATGATTTAAGGGGGAAAATA
389 GAGGTATTAGAAGAAAGACGTCGCTTCAGTACATATTTTAACATAATGATTTAAGGGAAAAAAAA
*
1650526 AAATACTAAAAAAAATAATATAAAGGGTGTTAGATCGGGAATATTATTTCAAAGGGTGTCTGACA
454 AAATACT-AAAAAAATAATACAAAGGGTGTTAGATCGGGAATATTATTTCAAAGGGTGTCTGACA
1650591 CGTACTC
518 CGTACTC
1650598 TTATCTTTGATTCAGAAGTTCGTTTGATCTTTCGTTGTAAGGTAATTTTTTTAATATATAATATT
1 TTATCTTTGATTCAGAAGTTCGTTTGATCTTTCGTTGTAAGGTAATTTTTTTAATATATAATATT
1650663 TTTTATAATTATATATGATTATTTGAAAAAAATATTATAGTAATTATTTTCAATTAATTTTTGTG
66 TTTTATAATTATATATGATTATTTGAAAAAAATATTATAGTAATTATTTTCAATTAATTTTTGTG
1650728 GTTGTAAAATTAGAAAGCGAGAGCATACGTCGAAATATTTTTGTCGATACGGTAATAATATAAAA
131 GTTGTAAAATTAGAAAGCGAGAGCATACGTCGAAATATTTTTGTCGATACGGTAATAATATAAAA
1650793 TTATATTATTTAAATTATTTACGTTTATGTGTAAGAATGAAGCGAATTTCAGCTATTGTTT-TTA
196 TTATATTATTTAAATTATTTACGTTTATGTGTAAGAATGAAGCGAATTTCAGCTATTGTTTATTA
* *
1650857 TGATGGAGAAATTCAGGAAGATGAAACCGGCGTTGTTTTCGTATCAAATCATTATGTTAAAATAT
261 TGATGGAGAAATTCAGGAAGATGAAACCGACGTTGTTTTCATATCAAATCATTATGTTAAAATAT
*
1650922 CCTTCAAGAAAAACATAACTCTTGAGGAGGTGATAATGAAGATTTCAAGGAAGGTTCATGTTAGA
326 CCTTCAAGAGAAACATAACTCTTGAGGAGGTGATAATGAAGATTTCAAGGAAGGTTCATGTTAGA
1650987 GGTATTAGAAGAAAGACGTCGCTTCAGTACATATTTTAACATAATGATTTAA-GG----AAAAAA
391 GGTATTAGAAGAAAGACGTCGCTTCAGTACATATTTTAACATAATGATTTAAGGGAAAAAAAAAA
* *
1651047 AT--T----AAATAATACAAAGGGTGTTA-ATCAGGAATATTATTTCAAA-TG-GTCTGACACGT
456 ATACTAAAAAAATAATACAAAGGGTGTTAGATCGGGAATATTATTTCAAAGGGTGTCTGACACGT
1651103 A
521 A
1651104 AATATTTAAG
Statistics
Matches: 981, Mismatches: 40, Indels: 31
0.93 0.04 0.03
Matches are distributed among these distances:
509 12 0.01
510 1 0.00
511 19 0.02
512 19 0.02
517 1 0.00
519 7 0.01
520 68 0.07
521 16 0.02
522 145 0.15
523 220 0.22
524 325 0.33
525 121 0.12
526 27 0.03
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (524 bp):
TTATCTTTGATTCAGAAGTTCGTTTGATCTTTCGTTGTAAGGTAATTTTTTTAATATATAATATT
TTTTATAATTATATATGATTATTTGAAAAAAATATTATAGTAATTATTTTCAATTAATTTTTGTG
GTTGTAAAATTAGAAAGCGAGAGCATACGTCGAAATATTTTTGTCGATACGGTAATAATATAAAA
TTATATTATTTAAATTATTTACGTTTATGTGTAAGAATGAAGCGAATTTCAGCTATTGTTTATTA
TGATGGAGAAATTCAGGAAGATGAAACCGACGTTGTTTTCATATCAAATCATTATGTTAAAATAT
CCTTCAAGAGAAACATAACTCTTGAGGAGGTGATAATGAAGATTTCAAGGAAGGTTCATGTTAGA
GGTATTAGAAGAAAGACGTCGCTTCAGTACATATTTTAACATAATGATTTAAGGGAAAAAAAAAA
ATACTAAAAAAATAATACAAAGGGTGTTAGATCGGGAATATTATTTCAAAGGGTGTCTGACACGT
ACTC
Found at i:1662353 original size:23 final size:23
Alignment explanation
Indices: 1662327--1662390 Score: 87
Period size: 23 Copynumber: 2.8 Consensus size: 23
1662317 CAGCTCATAT
1662327 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCTAAGTGCCACGTAG
*
1662350 AATTACACC-AGAGTGCCACGTAG
1 AATTGCACCTA-AGTGCCACGTAG
1662373 AATTGCACCGT-AGTGCCA
1 AATTGCACC-TAAGTGCCA
1662391 TATAATAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 1 0.03
23 35 0.97
ACGTcount: A:0.31, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
AATTGCACCTAAGTGCCACGTAG
Found at i:1662532 original size:103 final size:103
Alignment explanation
Indices: 1662406--1662623 Score: 409
Period size: 103 Copynumber: 2.1 Consensus size: 103
1662396 TAATGTCCAT
*
1662406 AAGGATCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
1662471 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
1662509 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1662574 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
*
1662612 AAAGACCACATA
1 AAGGACCACATA
1662624 GACCCTCTAC
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1669415 original size:103 final size:103
Alignment explanation
Indices: 1669245--1669456 Score: 388
Period size: 103 Copynumber: 2.1 Consensus size: 103
1669235 CCATAAGGAT
* *
1669245 CACATATCATTCCTTAAGAATTATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTC
1 CACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTC
1669310 ACACATGTTCCAAAGAATACATATATGTCCCGAAAGAC
66 ACACATGTTCCAAAGAATACATATATGTCCCGAAAGAC
1669348 CACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTC
1 CACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTC
* *
1669413 ACACATGTTCCAAAGAATATATATATGTCCCGAAGGAC
66 ACACATGTTCCAAAGAATACATATATGTCCCGAAAGAC
1669451 CACATA
1 CACATA
1669457 GACCCTCTAC
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (103 bp):
CACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACCTC
ACACATGTTCCAAAGAATACATATATGTCCCGAAAGAC
Found at i:1670859 original size:32 final size:31
Alignment explanation
Indices: 1670823--1670909 Score: 106
Period size: 32 Copynumber: 2.7 Consensus size: 31
1670813 GTTCTACAGA
1670823 ACATATGGACATAATTACCTATGTCTTTCTG-G
1 ACATATGGACA-AATTACCTATGTCTTT-TGAG
* *
1670855 ACATATGGAGAGAATTACTTATGTCTTTTGAG
1 ACATATGGACA-AATTACCTATGTCTTTTGAG
1670887 ACATATGGACAACA-TACCTATGT
1 ACATATGGACAA-ATTACCTATGT
1670910 TCTAAGGAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
31 11 0.23
32 37 0.77
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (31 bp):
ACATATGGACAAATTACCTATGTCTTTTGAG
Found at i:1671804 original size:21 final size:21
Alignment explanation
Indices: 1671780--1671829 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1671770 ATAGCAGTAC
1671780 TGTAGCAGGGTATCGATTCCA
1 TGTAGCAGGGTATCGATTCCA
* *
1671801 TGTAGCAGGGTATCGGTTCCC
1 TGTAGCAGGGTATCGATTCCA
1671822 TGTTAGCA
1 TG-TAGCA
1671830 ATCTGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (21 bp):
TGTAGCAGGGTATCGATTCCA
Found at i:1676165 original size:220 final size:224
Alignment explanation
Indices: 1675776--1676225 Score: 865
Period size: 220 Copynumber: 2.0 Consensus size: 224
1675766 GAGGGAGCTA
1675776 TTCC-ACTACTTGAACCAGATAACTGTCTGAATGGTTGGGCATGTCCCACCCGGGGATAACTTCA
1 TTCCGACTACTTGAACCAGATAACTGTCTGAATGGTTGGGCATGTCCCACCCGGGGATAACTTCA
1675840 TGGTAAGGGGTCCGGAGTACTTTTCAAACAAGGTTAAAATTCCCGGTGGTAAGTATCTACTCAAG
66 TGGTAAGGGGTCCGGAGTACTTTTCAAACAAGGTTAAAATTCCCGGTGGTAAGTATCTACTCAAG
1675905 TCTCTTGGTTTTGACTGGATGAGAACTTCCACAAAACTCGGTGACCCCTTGAGCCATCGT-AAAA
131 TCTCTTGGTTTTGACTGGATGAGAACTTCCACAAAACTCGGTGACCCCTTGAGCCATCGTAAAAA
1675969 CCATGTTAGAAAGGCTGTTGACGAAGCCT
196 CCATGTTAGAAAGGCTGTTGACGAAGCCT
1675998 TTCCGACTACTTGAACCAGATAACTGTCTGAATGG-TGGGCATGTCCCA-CCGGGGATAACTTCA
1 TTCCGACTACTTGAACCAGATAACTGTCTGAATGGTTGGGCATGTCCCACCCGGGGATAACTTCA
1676061 TGGTAAGGGGTCCGGAGTAC-TTTCAAACAAGGTTAAAATTCCCGGTGGTAAGTATCTACTCAAG
66 TGGTAAGGGGTCCGGAGTACTTTTCAAACAAGGTTAAAATTCCCGGTGGTAAGTATCTACTCAAG
1676125 TCTCTTGGTTTTGACTGGATGAGAACTTCCACAAAACTCGGTGACCCCTTGAGCCATCGTAAAAA
131 TCTCTTGGTTTTGACTGGATGAGAACTTCCACAAAACTCGGTGACCCCTTGAGCCATCGTAAAAA
1676190 CCATGTTAGAAAGGCTGTTGACGAAGCCT
196 CCATGTTAGAAAGGCTGTTGACGAAGCCT
1676219 TTCCGAC
1 TTCCGAC
1676226 CAGCGATAAG
Statistics
Matches: 226, Mismatches: 0, Indels: 5
0.98 0.00 0.02
Matches are distributed among these distances:
220 104 0.46
221 75 0.33
222 17 0.08
223 30 0.13
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.27
Consensus pattern (224 bp):
TTCCGACTACTTGAACCAGATAACTGTCTGAATGGTTGGGCATGTCCCACCCGGGGATAACTTCA
TGGTAAGGGGTCCGGAGTACTTTTCAAACAAGGTTAAAATTCCCGGTGGTAAGTATCTACTCAAG
TCTCTTGGTTTTGACTGGATGAGAACTTCCACAAAACTCGGTGACCCCTTGAGCCATCGTAAAAA
CCATGTTAGAAAGGCTGTTGACGAAGCCT
Found at i:1677922 original size:18 final size:18
Alignment explanation
Indices: 1677899--1677934 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1677889 TATAAAATTA
1677899 AAATTTGTAACTTTATGC
1 AAATTTGTAACTTTATGC
1677917 AAATTTGTAACTTTATGC
1 AAATTTGTAACTTTATGC
1677935 TTCTTCTCTG
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:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (18 bp):
AAATTTGTAACTTTATGC
Found at i:1682435 original size:20 final size:20
Alignment explanation
Indices: 1682412--1682502 Score: 128
Period size: 20 Copynumber: 4.5 Consensus size: 20
1682402 CACAGTTTTC
* *
1682412 AAAATCGTAGTGTGAATAGT
1 AAAATCGCAATGTGAATAGT
*
1682432 AAAAATTGCAATGTGAATAGT
1 -AAAATCGCAATGTGAATAGT
* *
1682453 AAAATTGCAACGTGAATAGT
1 AAAATCGCAATGTGAATAGT
1682473 AAAATCGCAATGTGAATAGT
1 AAAATCGCAATGTGAATAGT
1682493 AAAATCGCAA
1 AAAATCGCAA
1682503 CGCGAATTTA
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
20 47 0.73
21 17 0.27
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (20 bp):
AAAATCGCAATGTGAATAGT
Found at i:1682488 original size:40 final size:40
Alignment explanation
Indices: 1682423--1682522 Score: 139
Period size: 40 Copynumber: 2.5 Consensus size: 40
1682413 AAATCGTAGT
* *
1682423 GTGAATAGTAAAAATTGCAATGTGAATAGTAAAATTGCAAC
1 GTGAATAGT-AAAATCGCAATGTGAATAGTAAAATCGCAAC
1682464 GTGAATAGTAAAATCGCAATGTGAATAGTAAAATCGCAAC
1 GTGAATAGTAAAATCGCAATGTGAATAGTAAAATCGCAAC
* *
1682504 GCGAAT-TTAGAAATCGCAA
1 GTGAATAGTA-AAATCGCAA
1682523 AATCGCGTTG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
39 2 0.04
40 43 0.80
41 9 0.17
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (40 bp):
GTGAATAGTAAAATCGCAATGTGAATAGTAAAATCGCAAC
Found at i:1682509 original size:20 final size:20
Alignment explanation
Indices: 1682423--1682522 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
1682413 AAATCGTAGT
* *
1682423 GTGAATAGTAAAAATTGCAAT
1 GTGAATAGT-AAAATCGCAAC
*
1682444 GTGAATAGTAAAATTGCAAC
1 GTGAATAGTAAAATCGCAAC
*
1682464 GTGAATAGTAAAATCGCAAT
1 GTGAATAGTAAAATCGCAAC
1682484 GTGAATAGTAAAATCGCAAC
1 GTGAATAGTAAAATCGCAAC
* *
1682504 GCGAAT-TTAGAAATCGCAA
1 GTGAATAGTA-AAATCGCAA
1682523 AATCGCGTTG
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
19 2 0.03
20 61 0.85
21 9 0.12
ACGTcount: A:0.45, C:0.11, G:0.20, T:0.24
Consensus pattern (20 bp):
GTGAATAGTAAAATCGCAAC
Found at i:1682746 original size:39 final size:38
Alignment explanation
Indices: 1682686--1682765 Score: 151
Period size: 39 Copynumber: 2.1 Consensus size: 38
1682676 GATTTTTTCA
1682686 AATTTCAAACTTAACTAATTGAATTTAGAATAATTTGT
1 AATTTCAAACTTAACTAATTGAATTTAGAATAATTTGT
1682724 AATTTCAAACTTTAACTAATTGAATTTAGAATAATTTGT
1 AATTTCAAAC-TTAACTAATTGAATTTAGAATAATTTGT
1682763 AAT
1 AAT
1682766 AAAGATTGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
38 10 0.24
39 31 0.76
ACGTcount: A:0.42, C:0.07, G:0.07, T:0.42
Consensus pattern (38 bp):
AATTTCAAACTTAACTAATTGAATTTAGAATAATTTGT
Found at i:1682979 original size:21 final size:20
Alignment explanation
Indices: 1682912--1682993 Score: 121
Period size: 20 Copynumber: 4.1 Consensus size: 20
1682902 GATTCATTGT
* *
1682912 GATTTTACTATTTACGTT-G
1 GATTTTACTATTCACGTTAC
1682931 GATTTTACTATTCACGTTAC
1 GATTTTACTATTCACGTTAC
*
1682951 GATTTTACTATTCATGTTAC
1 GATTTTACTATTCACGTTAC
1682971 GATTTTTACTATTCACGTTAC
1 GA-TTTTACTATTCACGTTAC
1682992 GA
1 GA
1682994 ATTTGACTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
19 17 0.30
20 21 0.37
21 19 0.33
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (20 bp):
GATTTTACTATTCACGTTAC
Found at i:1682985 original size:41 final size:39
Alignment explanation
Indices: 1682912--1683002 Score: 119
Period size: 41 Copynumber: 2.3 Consensus size: 39
1682902 GATTCATTGT
* *
1682912 GATTTTACTATTTACGTTGGATTTTACTATTCACGTTAC
1 GATTTTACTATTCACGTTCGATTTTACTATTCACGTTAC
*
1682951 GATTTTACTATTCATGTTACGATTTTTACTATTCACGTTAC
1 GATTTTACTATTCACGTT-CGA-TTTTACTATTCACGTTAC
*
1682992 GAATTTGACTA
1 G-ATTTTACTA
1683003 ACGCGTTGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
39 16 0.36
40 2 0.04
41 19 0.42
42 8 0.18
ACGTcount: A:0.25, C:0.15, G:0.12, T:0.47
Consensus pattern (39 bp):
GATTTTACTATTCACGTTCGATTTTACTATTCACGTTAC
Found at i:1683002 original size:21 final size:21
Alignment explanation
Indices: 1682913--1683002 Score: 114
Period size: 21 Copynumber: 4.4 Consensus size: 21
1682903 ATTCATTGTG
* *
1682913 ATTTTACTATTTACGTT--GG
1 ATTTTACTATTCACGTTACGA
1682932 ATTTTACTATTCACGTTACG-
1 ATTTTACTATTCACGTTACGA
*
1682952 ATTTTACTATTCATGTTACGA
1 ATTTTACTATTCACGTTACGA
*
1682973 TTTTTACTATTCACGTTACGA
1 ATTTTACTATTCACGTTACGA
*
1682994 ATTTGACTA
1 ATTTTACTA
1683003 ACGCGTTGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.26
20 19 0.31
21 27 0.44
ACGTcount: A:0.26, C:0.16, G:0.11, T:0.48
Consensus pattern (21 bp):
ATTTTACTATTCACGTTACGA
Found at i:1683032 original size:20 final size:20
Alignment explanation
Indices: 1683009--1683047 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1682999 ACTAACGCGT
* *
1683009 TGTGAATTTGACTTTTGTGA
1 TGTGAATTTAACTTCTGTGA
1683029 TGTGAATTTAACTTCTGTG
1 TGTGAATTTAACTTCTGTG
1683048 TTGCGATTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.49
Consensus pattern (20 bp):
TGTGAATTTAACTTCTGTGA
Found at i:1683803 original size:20 final size:20
Alignment explanation
Indices: 1683778--1683828 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
1683768 TGTTGCGAAA
*
1683778 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCAGT
1683798 TCGCGTTGCGA-TTTCCAGT
1 TCGCGTTGCGATTTTCCAGT
1683817 TCGCGTTGCGAT
1 TCGCGTTGCGAT
1683829 AGTTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.10, C:0.25, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCAGT
Found at i:1684497 original size:6 final size:6
Alignment explanation
Indices: 1684476--1684512 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1684466 TCTCGTCTCG
*
1684476 GGTCG- GGTCG- GGTCGT GGTCGT GGTTGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1684513 AATACGTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.00, C:0.14, G:0.54, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1684636 original size:21 final size:22
Alignment explanation
Indices: 1684611--1684663 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
1684601 AATTTAGAAA
1684611 ATCGCAACGACAA-TGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
1684632 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
1684654 ATCGCAACGA
1 ATCGCAACGA
1684664 ATTTGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:1684742 original size:21 final size:21
Alignment explanation
Indices: 1684713--1684868 Score: 129
Period size: 21 Copynumber: 7.6 Consensus size: 21
1684703 GAAATGGAAA
1684713 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
* ** ** *
1684734 ATAGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
1684754 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
1684775 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
1684795 ATCACAACGCGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
** ** *
1684816 ATCGCAACGCGAAATGGAA-A
1 ATCGCAACGCGATTTTCAACT
*
1684836 ATCGCAACGTGATTTTCAACT
1 ATCGCAACGCGATTTTCAACT
1684857 ATCGCAACGCGA
1 ATCGCAACGCGA
1684869 AATGGAAAAT
Statistics
Matches: 96, Mismatches: 36, Indels: 6
0.70 0.26 0.04
Matches are distributed among these distances:
20 42 0.44
21 54 0.56
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.21
Consensus pattern (21 bp):
ATCGCAACGCGATTTTCAACT
Found at i:1684743 original size:41 final size:41
Alignment explanation
Indices: 1684690--1684888 Score: 371
Period size: 41 Copynumber: 4.9 Consensus size: 41
1684680 GACATTGTAG
1684690 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1684731 ACTATAGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1684772 ACTATCGCAACGCGAAATGGAAAATCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
1684813 ACTATCGCAACGCGAAATGGAAAATCGCAACGTGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1684854 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA
1684889 ATTTGCGATA
Statistics
Matches: 152, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 152 1.00
ACGTcount: A:0.38, C:0.24, G:0.20, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:1685767 original size:31 final size:31
Alignment explanation
Indices: 1685701--1685768 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
1685691 CAGTGATCGT
** *
1685701 ATCTTAATTAAATAAATCCAAAAGTAACTAC
1 ATCTTAATTAAATAAAAACAAAAGTAACTAA
*
1685732 ATCTTAATTAAATAAAAACGAAAGTAAGC-AA
1 ATCTTAATTAAATAAAAACAAAAGTAA-CTAA
1685763 ATCTTA
1 ATCTTA
1685769 TTTTCCTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.53, C:0.13, G:0.06, T:0.28
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTAACTAA
Found at i:1686309 original size:22 final size:22
Alignment explanation
Indices: 1686258--1686316 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
1686248 ACGCGATTCT
1686258 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * * * *
1686280 AAAT-TCGCGTTGTGATTTTTC
1 GACTATCGCATTGCGATTTTCC
*
1686301 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
1686317 ATATGTAAAT
Statistics
Matches: 26, Mismatches: 10, Indels: 2
0.68 0.26 0.05
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:1686359 original size:40 final size:40
Alignment explanation
Indices: 1686301--1686396 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 40
1686291 GTGATTTTTC
*
1686301 GACTATCGCAATGCGAATATGTAAATCGCAATGCGAGTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
* * *
1686341 GGCTATCGCAACGTGAATATGTAAATCGCAATGCGATTAT
1 GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
* *
1686381 TACTATCGCAATGCGA
1 GACTATCGCAACGCGA
1686397 TATTACTACG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (40 bp):
GACTATCGCAACGCGAATATGTAAATCGCAATGCGAGTAT
Found at i:1686397 original size:20 final size:20
Alignment explanation
Indices: 1686302--1686414 Score: 108
Period size: 20 Copynumber: 5.8 Consensus size: 20
1686292 TGATTTTTCG
1686302 ACTATCGCAATGCGAATATGT
1 ACTATCGCAATGCGAATAT-T
* * *
1686323 A-AATCGCAATGCGAGTATG
1 ACTATCGCAATGCGAATATT
* * *
1686342 GCTATCGCAACGTGAATATGT
1 ACTATCGCAATGCGAATAT-T
* *
1686363 A-AATCGCAATGCGATTATT
1 ACTATCGCAATGCGAATATT
1686382 ACTATCGCAATGCG-ATATT
1 ACTATCGCAATGCGAATATT
1686401 ACTA-CGCAATGCGA
1 ACTATCGCAATGCGA
1686415 TTCTGACTGT
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
18 9 0.12
19 10 0.14
20 52 0.72
21 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (20 bp):
ACTATCGCAATGCGAATATT
Found at i:1687299 original size:24 final size:24
Alignment explanation
Indices: 1687248--1687301 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1687238 GTATTCGAAA
*
1687248 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
1687272 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
1687296 TTTGAT
1 TTTGAT
1687302 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1689571 original size:18 final size:18
Alignment explanation
Indices: 1689548--1689582 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1689538 AGCAAAAGGC
*
1689548 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1689566 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1689583 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1689782 original size:20 final size:20
Alignment explanation
Indices: 1689757--1690069 Score: 156
Period size: 20 Copynumber: 16.9 Consensus size: 20
1689747 TTACACATTC
*
1689757 ATTTGACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1689777 ATTTGAATATCGCAACG-GG
1 ATTTGACTATCGCAACGCGA
*
1689796 A--T-A--ATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
**
1689811 AAATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1689831 ATTTGACTATCACAACG-GG
1 ATTTGACTATCGCAACGCGA
* *
1689850 A--T-A--ATCGCAATGCAA
1 ATTTGACTATCGCAACGCGA
**
1689865 AAATGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1689885 ATTTGACTATCGCAATG-GG
1 ATTTGACTATCGCAACGCGA
*
1689904 A--T-A--ATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
** *
1689919 AAATGACTATTGCAACGCGA
1 ATTTGACTATCGCAACGCGA
** * *
1689939 AAATAACTATCACAACGCGA
1 ATTTGACTATCGCAACGCGA
* **
1689959 ATTTAACCTA-CATAATCGCGA
1 ATTTGA-CTATCGCAA-CGCGA
*
1689980 ATTTGACTATCGCAACGAG-
1 ATTTGACTATCGCAACGCGA
1689999 A--T-A--ATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
1690014 A-ATGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
* *
1690033 ATTTGATTATCGCAACGGGA
1 ATTTGACTATCGCAACGCGA
1690053 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
1690070 AGAAAATCGC
Statistics
Matches: 226, Mismatches: 40, Indels: 54
0.71 0.12 0.17
Matches are distributed among these distances:
14 34 0.15
15 6 0.03
16 5 0.02
17 8 0.04
18 3 0.01
19 19 0.08
20 135 0.60
21 16 0.07
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1689949 original size:54 final size:54
Alignment explanation
Indices: 1689760--1689939 Score: 306
Period size: 54 Copynumber: 3.3 Consensus size: 54
1689750 CACATTCATT
* *
1689760 TGACTATCACAACGCGAATTTGAATATCGCAACGGGATAATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAA
* *
1689814 TGACTATCGCAACGCGAATTTGACTATCACAACGGGATAATCGCAATGCAAAAA
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAA
*
1689868 TGACTATCGCAACGCGAATTTGACTATCGCAATGGGATAATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAA
*
1689922 TGACTATTGCAACGCGAA
1 TGACTATCGCAACGCGAA
1689940 AATAACTATC
Statistics
Matches: 118, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 118 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (54 bp):
TGACTATCGCAACGCGAATTTGACTATCGCAACGGGATAATCGCAATGCGAAAA
Found at i:1690023 original size:33 final size:33
Alignment explanation
Indices: 1689975--1690102 Score: 121
Period size: 33 Copynumber: 3.6 Consensus size: 33
1689965 CCTACATAAT
1689975 CGCGAATTTGACTATCGCAACGAGATAATCGCAA
1 CGCGAA-TTGACTATCGCAACGAGATAATCGCAA
* *
1690009 CGCGAAATGACTATCGCAACACGAATTTGATTATCGCAA
1 CGCGAATTGACTATCGC-A-ACG-A---GATAATCGCAA
* *
1690048 CGGGAATTTGACTATCGCAACGAGAAAATCGCAA
1 CGCGAA-TTGACTATCGCAACGAGATAATCGCAA
* * *
1690082 AGTGTATTGACTATCGCAACG
1 CGCGAATTGACTATCGCAACG
1690103 CGAATATGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
33 25 0.32
34 19 0.24
35 3 0.04
36 1 0.01
37 1 0.01
38 3 0.04
39 16 0.21
40 10 0.13
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (33 bp):
CGCGAATTGACTATCGCAACGAGATAATCGCAA
Found at i:1690213 original size:54 final size:54
Alignment explanation
Indices: 1690148--1690298 Score: 293
Period size: 54 Copynumber: 2.8 Consensus size: 54
1690138 TTTACATTTC
1690148 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATAATCAACTTTT
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATAATCAACTTTT
1690202 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATAATCAACTTTT
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATAATCAACTTTT
*
1690256 AATCAATTAAACAAGCACAAATAAGAATTATTTGCACATCAAT
1 AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAAT
1690299 TAAACAAATA
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
54 96 1.00
ACGTcount: A:0.50, C:0.17, G:0.05, T:0.28
Consensus pattern (54 bp):
AATCAATTAAACAAGCACAAATAAGAATTATTTACACATCAATAATCAACTTTT
Found at i:1690297 original size:36 final size:34
Alignment explanation
Indices: 1690257--1690336 Score: 105
Period size: 30 Copynumber: 2.4 Consensus size: 34
1690247 TCAACTTTTA
*
1690257 ATCAATTAAACAAGCACAAATAAGAATTATTTGCAC
1 ATCAATTAAACAA--ACAAATAAGAATTATTTACAC
1690293 ATCAATT----AAACAAATAAGAATTATTTACAC
1 ATCAATTAAACAAACAAATAAGAATTATTTACAC
1690323 ATCAATTAAACAAA
1 ATCAATTAAACAAA
1690337 TCAACTCTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
30 27 0.69
32 2 0.05
34 3 0.08
36 7 0.18
ACGTcount: A:0.54, C:0.15, G:0.05, T:0.26
Consensus pattern (34 bp):
ATCAATTAAACAAACAAATAAGAATTATTTACAC
Found at i:1690306 original size:30 final size:30
Alignment explanation
Indices: 1690272--1690337 Score: 123
Period size: 30 Copynumber: 2.2 Consensus size: 30
1690262 TTAAACAAGC
*
1690272 ACAAATAAGAATTATTTGCACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
1690302 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
1690332 ACAAAT
1 ACAAAT
1690338 CAACTCTTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.53, C:0.14, G:0.05, T:0.29
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:1691764 original size:21 final size:22
Alignment explanation
Indices: 1691714--1691816 Score: 65
Period size: 21 Copynumber: 4.9 Consensus size: 22
1691704 AATGTTGGGA
* *
1691714 GGGACCTCTTCAAC-GATGACAG
1 GGGA-CTCTTGAACGGATGAGAG
* *
1691736 TGGCCTCTTGAACGG-TGAGAG
1 GGGACTCTTGAACGGATGAGAG
* *
1691757 GGGACTCTTG-AGGGATGATAG
1 GGGACTCTTGAACGGATGAGAG
* *
1691778 GGGCCTCTTGAAC-GAT-AGGG
1 GGGACTCTTGAACGGATGAGAG
*
1691798 GAGGCCTCTTGAAC-GATGA
1 G-GGACTCTTGAACGGATGA
1691817 CATGTGAGTC
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
20 6 0.09
21 53 0.83
22 5 0.08
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GGGACTCTTGAACGGATGAGAG
Found at i:1691816 original size:42 final size:42
Alignment explanation
Indices: 1691712--1691818 Score: 117
Period size: 42 Copynumber: 2.5 Consensus size: 42
1691702 AGAATGTTGG
* * * *
1691712 GAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGTGA
1 GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGA
* ** *
1691754 GAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGAT-A
1 GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGA
*
1691795 GGGGAGGCCTCTTGAACGATGACA
1 GAGG-GGCCTCTTGAACGATGACA
1691819 TGTGAGTCGG
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 4 0.08
42 47 0.92
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.21
Consensus pattern (42 bp):
GAGGGGCCTCTTGAACGATGACAGGGGCCTCTTGAACGATGA
Found at i:1692342 original size:20 final size:20
Alignment explanation
Indices: 1692317--1692412 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
1692307 TCGCAACACG
1692317 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
* *
1692337 AATGACTATCGAAATGCGAA
1 AATGACTATCGCAACGCGAA
1692357 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
1692377 AATGACCATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
1692397 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
1692413 AGAGAATCGC
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 68 1.00
ACGTcount: A:0.39, C:0.24, G:0.20, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:1692509 original size:20 final size:20
Alignment explanation
Indices: 1692455--1692522 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1692445 GCGATTCTTT
**
1692455 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
1692475 CGTTGCGATGGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
1692495 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTTCG
*
1692515 CGTGGCGA
1 CGTTGCGA
1692523 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.32
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1693047 original size:21 final size:20
Alignment explanation
Indices: 1693023--1693097 Score: 57
Period size: 21 Copynumber: 3.8 Consensus size: 20
1693013 GTGACAGAAT
1693023 AGGTGATGGCTCTCGTTGTGG
1 AGGTGATGGCTCTCGTTGT-G
* ** *
1693044 AGGTGTATAG-TCGGGTTGATC
1 AGGTG-ATGGCTCTCGTTG-TG
*
1693065 AGGTGATGGCTCT-G-GGTG
1 AGGTGATGGCTCTCGTTGTG
1693083 AGGTGATGGCTCTCG
1 AGGTGATGGCTCTCG
1693098 AAGTGGAGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
18 14 0.33
19 2 0.05
20 4 0.10
21 18 0.43
22 4 0.10
ACGTcount: A:0.13, C:0.13, G:0.43, T:0.31
Consensus pattern (20 bp):
AGGTGATGGCTCTCGTTGTG
Found at i:1694457 original size:20 final size:20
Alignment explanation
Indices: 1694432--1694470 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1694422 TCTTAAACTT
1694432 AAAATCGCAACACGAAAATC
1 AAAATCGCAACACGAAAATC
1694452 AAAATCGCAACACGAAAAT
1 AAAATCGCAACACGAAAAT
1694471 GACTATCGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.56, C:0.23, G:0.10, T:0.10
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATC
Found at i:1694478 original size:20 final size:20
Alignment explanation
Indices: 1694435--1694502 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1694425 TAAACTTAAA
* **
1694435 ATCGCAACACGAAAATCAAA
1 ATCGCAACACGAAAATGACT
1694455 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
1694475 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
*
1694495 ATTGCAAC
1 ATCGCAAC
1694503 GCGAGAATCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:1694946 original size:22 final size:22
Alignment explanation
Indices: 1694915--1694971 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
1694905 GATGGAGATA
1694915 GACAGATTTCGCCGGAGATGGG
1 GACAGATTTCGCCGGAGATGGG
* *
1694937 GACTGATTTCGTCGGAGATGGG
1 GACAGATTTCGCCGGAGATGGG
*
1694959 GACAGATGTCGCC
1 GACAGATTTCGCC
1694972 TTAGAGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.21, C:0.19, G:0.39, T:0.21
Consensus pattern (22 bp):
GACAGATTTCGCCGGAGATGGG
Found at i:1695177 original size:20 final size:20
Alignment explanation
Indices: 1695140--1695209 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1695130 TTTGAAAATT
* * *
1695140 GCATTGCGACAGTCAGAATC
1 GCATGGCGATAGTTAGAATC
*
1695160 GCGTGGCGATAGTTAGAATC
1 GCATGGCGATAGTTAGAATC
* * *
1695180 GCATTGCGATAGTAATAATC
1 GCATGGCGATAGTTAGAATC
*
1695200 GCATTGCGAT
1 GCATGGCGAT
1695210 TTACATATTC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (20 bp):
GCATGGCGATAGTTAGAATC
Found at i:1695209 original size:40 final size:40
Alignment explanation
Indices: 1695178--1695273 Score: 156
Period size: 40 Copynumber: 2.4 Consensus size: 40
1695168 ATAGTTAGAA
*
1695178 TCGCATTGCGATAGTAATAATCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
* * *
1695218 TCGCGTTGCGATAGCCATACTCGCATTGCGATTTACATAT
1 TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
1695258 TCGCATTGCGATAGTC
1 TCGCATTGCGATAGTC
1695274 GGAAAATCGC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (40 bp):
TCGCATTGCGATAGTCATAATCGCATTGCGATTTACATAT
Found at i:1695221 original size:20 final size:20
Alignment explanation
Indices: 1695178--1695269 Score: 105
Period size: 20 Copynumber: 4.6 Consensus size: 20
1695168 ATAGTTAGAA
* *
1695178 TCGCATTGCGATAGTA-ATAA
1 TCGCATTGCGAT-TTACATAT
1695198 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
* *** *
1695218 TCGCGTTGCGATAGCCATAC
1 TCGCATTGCGATTTACATAT
1695238 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
1695258 TCGCATTGCGAT
1 TCGCATTGCGAT
1695270 AGTCGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
19 2 0.03
20 57 0.97
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.34
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:1696671 original size:4 final size:4
Alignment explanation
Indices: 1696662--1696695 Score: 52
Period size: 4 Copynumber: 8.8 Consensus size: 4
1696652 AATATAGTAG
*
1696662 TTTA TTTA TTTA TTTA TTTA TTTA TGT- TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
1696696 CACTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 25 0.93
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1697036 original size:18 final size:17
Alignment explanation
Indices: 1697005--1697040 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1696995 TTTATAAAAA
1697005 TATAAAAAATATATATT
1 TATAAAAAATATATATT
1697022 TATAAAAAATAATATATT
1 TATAAAAAAT-ATATATT
1697040 T
1 T
1697041 TCTTGGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TATAAAAAATATATATT
Found at i:1697589 original size:18 final size:18
Alignment explanation
Indices: 1697548--1697582 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1697538 ATTTTATTCA
*
1697548 ATTATTTTTTTATCCTTT
1 ATTATTTTTATATCCTTT
1697566 ATTATTTTTATATCCTT
1 ATTATTTTTATATCCTT
1697583 ATATATTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTATTTTTATATCCTTT
Found at i:1699973 original size:20 final size:21
Alignment explanation
Indices: 1699950--1699996 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1699940 TTGCATTCGT
1699950 ATTTTTT-TCATTACATTTGC
1 ATTTTTTATCATTACATTTGC
** *
1699970 ATTTTTTATGTTTGCATTTGC
1 ATTTTTTATCATTACATTTGC
1699991 ATTTTT
1 ATTTTT
1699997 ATATTTTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.64
Consensus pattern (21 bp):
ATTTTTTATCATTACATTTGC
Found at i:1699987 original size:21 final size:20
Alignment explanation
Indices: 1699963--1700026 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 20
1699953 TTTTTCATTA
1699963 CATTTGCATTTTT-TATGTTT
1 CATTTGCATTTTTATAT-TTT
1699983 GCATTTGCATTTTTATATTTT
1 -CATTTGCATTTTTATATTTT
* *
1700004 CATTTAC-TTTTT-CATTTT
1 CATTTGCATTTTTATATTTT
1700022 CATTT
1 CATTT
1700027 TATATTTGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.25
19 5 0.12
20 6 0.15
21 16 0.40
22 3 0.08
ACGTcount: A:0.17, C:0.12, G:0.06, T:0.64
Consensus pattern (20 bp):
CATTTGCATTTTTATATTTT
Found at i:1699997 original size:20 final size:21
Alignment explanation
Indices: 1699963--1700008 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
1699953 TTTTTCATTA
*
1699963 CATTTGCATTTTTTATGTTTG
1 CATTTGCATTTTTTATATTTG
*
1699984 CATTTGCA-TTTTTATATTTT
1 CATTTGCATTTTTTATATTTG
1700004 CATTT
1 CATTT
1700009 ACTTTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.17, C:0.11, G:0.09, T:0.63
Consensus pattern (21 bp):
CATTTGCATTTTTTATATTTG
Found at i:1700015 original size:20 final size:20
Alignment explanation
Indices: 1699971--1700015 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1699961 TACATTTGCA
* *
1699971 TTTTTTATGTTTGCATTTGC
1 TTTTTTATATTTGCATTTAC
* *
1699991 ATTTTTATATTTTCATTTAC
1 TTTTTTATATTTGCATTTAC
1700011 TTTTT
1 TTTTT
1700016 CATTTTCATT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.16, C:0.09, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTTTTATATTTGCATTTAC
Found at i:1705441 original size:54 final size:53
Alignment explanation
Indices: 1705349--1705506 Score: 190
Period size: 54 Copynumber: 2.9 Consensus size: 53
1705339 TGATTGAGAA
* * *
1705349 ATCTAAGCAGAAGCCACAGGAAAGGATGAATGTATTGTCAAATGCTTTACAAAC
1 ATCTGAGCAGAAGCCACAGGAAA-GATGAATGTGTTGTCAAATGTTTTACAAAC
* * *
1705403 ATCTGGGCAGAAGCCACAGGAAAGAATGAATGTGTTGTCAAATGTTTTACGAGC
1 ATCTGAGCAGAAGCCACAGGAAAG-ATGAATGTGTTGTCAAATGTTTTACAAAC
* * * * *
1705457 ATCTGAGCAAAAACCATATGAGATGATGAATGTGTTGTCAAATGTTTTAC
1 ATCTGAGCAGAAGCCACAGGA-AAGATGAATGTGTTGTCAAATGTTTTAC
1705507 GAACCAGTTA
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
53 1 0.01
54 87 0.97
55 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.23, T:0.26
Consensus pattern (53 bp):
ATCTGAGCAGAAGCCACAGGAAAGATGAATGTGTTGTCAAATGTTTTACAAAC
Found at i:1705906 original size:22 final size:22
Alignment explanation
Indices: 1705878--1705940 Score: 90
Period size: 22 Copynumber: 2.9 Consensus size: 22
1705868 ATATCTACAT
*
1705878 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTATC
*
1705900 TCTTCAAAGATGATATATTATC
1 TCTTCAAAGATGATAGATTATC
* *
1705922 TTTTCAAAGATGAAAGATT
1 TCTTCAAAGATGATAGATT
1705941 TATTGGATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTATC
Found at i:1706271 original size:18 final size:17
Alignment explanation
Indices: 1706237--1706271 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1706227 CATTCATGCA
*
1706237 TGCATAAAAACATCATT
1 TGCATAAAAAAATCATT
1706254 TGCATAAAAAAATGCATT
1 TGCATAAAAAAAT-CATT
1706272 ACATTGATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.49, C:0.14, G:0.09, T:0.29
Consensus pattern (17 bp):
TGCATAAAAAAATCATT
Found at i:1706769 original size:45 final size:45
Alignment explanation
Indices: 1706720--1706833 Score: 129
Period size: 45 Copynumber: 2.5 Consensus size: 45
1706710 GGGAGCTTTT
* ** * * *
1706720 TGATATTTTCAAAACTTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTACA
*
1706765 TGATATTTTCAAAGCCTTCGGGTCATCCATAAGACCTACAGTACA
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTACA
* *
1706810 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATATTTTC-AAAA-CCTTCGGG
1706834 AGCTTTTTGA
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
45 46 0.81
46 3 0.05
47 8 0.14
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (45 bp):
TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGTACA
Found at i:1706779 original size:74 final size:73
Alignment explanation
Indices: 1706593--1706786 Score: 239
Period size: 74 Copynumber: 2.6 Consensus size: 73
1706583 CTATTTCCCA
* * *
1706593 CATCCATAAGACCTATAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTAAAG
1 CATCAATAAGACCTACAGTGCAGGATGTTTTC-AAAAGCCTTCGGGAGCTTTTTGATATTTAAAA
1706658 CCTCTGGGT
65 CCTCTGGGT
1706667 CATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCAATAAGACCTACAGTGCAGGATGTTTTC-AAAAGCCTTCGGGAGCTTTTTGATA-TTT-AA
*
1706732 AA-CTTTCGGGT
63 AACCTCT-GGGT
** * * * *
1706743 CATCTGTAAGCCCTTCAGTGCATGATATTTTC-AAAGCCTTCGGG
1 CATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAGCCTTCGGG
1706787 TCATCCATAA
Statistics
Matches: 107, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
74 68 0.64
75 6 0.06
76 33 0.31
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (73 bp):
CATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAGCCTTCGGGAGCTTTTTGATATTTAAAAC
CTCTGGGT
Found at i:1706845 original size:76 final size:74
Alignment explanation
Indices: 1706765--1706907 Score: 198
Period size: 76 Copynumber: 1.9 Consensus size: 74
1706755 CTTCAGTGCA
*
1706765 TGATATTTTCAAAGCCTTCGGGTCATCCATAAGACCTACAGTA-CAGGATGTTTTCAAAAAGCCT
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTACAG-AGCAGGATGTTTTC--AAAGCCT
1706829 TCGGGAGCTTTT
63 TCGGGAGCTTTT
** * * *
1706841 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCATGATGTTTTCAAAGCCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGAGCAGGATGTTTTCAAAGCCTTCG
1706906 GG
66 GG
1706908 TCATCTATAA
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
74 12 0.20
75 1 0.02
76 47 0.78
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (74 bp):
TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTACAGAGCAGGATGTTTTCAAAGCCTTCG
GGAGCTTTT
Found at i:1706868 original size:121 final size:121
Alignment explanation
Indices: 1706646--1706952 Score: 482
Period size: 121 Copynumber: 2.6 Consensus size: 121
1706636 GGGAGCTTTT
1706646 TGATA-TTT-AAAGCC-TCTGGGTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCT
1 TGATATTTTCAAAGCCTTC-GGGTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCT
* *
1706708 TCGGGAGCTTTTTGATATTTTCAAAACTTTCGGGTCATCTGTAAGCCCTTCAGTGCA
65 TCGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCA
* *
1706765 TGATATTTTCAAAGCCTTCGGGTCATCCATAAGACCTACAGTACAGGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAGCCTTCGGGTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1706830 CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCA
66 CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCA
* * * *
1706886 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAG-CCTTTCAGTGCATGATGTTTTC--AAAGCCT
1 TGATATTTTCAAAGCCTTCGGGTCATCAATAAGACC-TACAGTGCAGGATGTTTTCAAAAAGCCT
1706948 TCGGG
65 TCGGG
1706953 TCATCTGTAA
Statistics
Matches: 175, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
119 17 0.10
120 5 0.03
121 151 0.86
122 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (121 bp):
TGATATTTTCAAAGCCTTCGGGTCATCAATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
CGGGAGCTTTTTGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCA
Found at i:1706895 original size:45 final size:45
Alignment explanation
Indices: 1706841--1706999 Score: 219
Period size: 45 Copynumber: 3.5 Consensus size: 45
1706831 GGGAGCTTTT
* *
1706841 TGATATTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1706886 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCTTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1706931 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1706976 AGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
1707000 AGCTTTTTGA
Statistics
Matches: 101, Mismatches: 11, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
45 90 0.89
46 3 0.03
47 8 0.08
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1706999 original size:166 final size:165
Alignment explanation
Indices: 1706720--1707146 Score: 692
Period size: 166 Copynumber: 2.6 Consensus size: 165
1706710 GGGAGCTTTT
* * *
1706720 TGATATTTTCAAAACTTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATATTTTCAAAGCCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAAGCCTTCG
* *
1706785 GGTCATCCATAAGACCTACAGTACAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTT
65 GGTCATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTT
1706850 CAAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCA
130 CAAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCA
* *
1706886 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCTTTCAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCC-TTCAGTGCATGATGTTTTCAAAGCCTTCG
** *
1706951 GGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTT
65 GGTCATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTT
* *
1707016 CAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
130 CAAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCA
* *
1707052 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAACCTCCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAG-CCTTCAGTGCATGATGTTTTCAAAGCCTTCG
*
1707117 GGTCATCCATAAGACCTACATTGCAAGATG
65 GGTCATCCATAAGACCTACAGTGCAAGATG
1707147 ATAAGACCTC
Statistics
Matches: 240, Mismatches: 19, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
165 2 0.01
166 236 0.98
167 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (165 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCTTCAGTGCATGATGTTTTCAAAGCCTTCGG
GTCATCCATAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATATTTTC
AAAACCTTCGGGTCATCTGTAAGCCCTTCAGAGCA
Found at i:1707011 original size:121 final size:121
Alignment explanation
Indices: 1706886--1707110 Score: 405
Period size: 121 Copynumber: 1.9 Consensus size: 121
1706876 CTTCAGAGCA
* *
1706886 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCTTTCAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1706951 GGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
66 GGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
*
1707007 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
1707072 GGTCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAAA
66 GGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAA
1707111 CCTCCGGGTC
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
121 99 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (121 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTTCGGGAGCTTTT
Found at i:1707016 original size:76 final size:74
Alignment explanation
Indices: 1706931--1707073 Score: 241
Period size: 76 Copynumber: 1.9 Consensus size: 74
1706921 TTTCAGTGCA
1706931 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTC-AAAA-CCTT
1706996 CGGGAGCTTTT
64 CGGGAGCTTTT
* * *
1707007 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAACCTTCG
1707072 GG
66 GG
1707074 TCATCTGTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 8 0.12
75 4 0.06
76 52 0.81
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (74 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGACCTACAGTGCAAGATGTTTTCAAAACCTTCG
GGAGCTTTT
Found at i:1707056 original size:45 final size:45
Alignment explanation
Indices: 1707007--1707133 Score: 209
Period size: 45 Copynumber: 2.8 Consensus size: 45
1706997 GGGAGCTTTT
* *
1707007 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1707052 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* **
1707097 TGATGTTTTCAAAACCTCCGGGTCATCCATAAGACCT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCT
1707134 ACATTGCAAG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 77 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:1707321 original size:3 final size:3
Alignment explanation
Indices: 1707315--1707377 Score: 72
Period size: 3 Copynumber: 20.7 Consensus size: 3
1707305 ATTTTTTTTA
* * * * *
1707315 TAT TAT TAT TAT TAT TAT TAT TAA AAT TAA AAT TAT TAT TAA TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1707363 ATAT TAT TAT TAT TA
1 -TAT TAT TAT TAT TA
1707378 AATAAATAAT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:1709477 original size:17 final size:18
Alignment explanation
Indices: 1709455--1709488 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1709445 ATTTAATTCA
1709455 ATTATTTTT-TATCCTTT
1 ATTATTTTTATATCCTTT
1709472 ATTATTTTTATATCCTT
1 ATTATTTTTATATCCTT
1709489 ATATATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.68
Consensus pattern (18 bp):
ATTATTTTTATATCCTTT
Found at i:1709480 original size:18 final size:17
Alignment explanation
Indices: 1709455--1709488 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1709445 ATTTAATTCA
*
1709455 ATTATTTTTTATCCTTT
1 ATTATTTTATATCCTTT
1709472 ATTATTTTTATATCCTT
1 ATTA-TTTTATATCCTT
1709489 ATATATTAAT
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:0.21, C:0.12, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTATTTTATATCCTTT
Found at i:1711876 original size:20 final size:20
Alignment explanation
Indices: 1711853--1711918 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 20
1711843 TTGCATTCGT
*
1711853 ATTTTTTTCTTTACATTTGC
1 ATTTTTTTATTTACATTTGC
* *
1711873 ATTTTTTATGTTTGCATTTGC
1 ATTTTTT-TATTTACATTTGC
* * *
1711894 ATTTTTATATTTTCATTTAC
1 ATTTTTTTATTTACATTTGC
1711914 ATTTT
1 ATTTT
1711919 ATATTTGCAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
20 22 0.56
21 17 0.44
ACGTcount: A:0.18, C:0.11, G:0.06, T:0.65
Consensus pattern (20 bp):
ATTTTTTTATTTACATTTGC
Found at i:1714129 original size:18 final size:18
Alignment explanation
Indices: 1714102--1714154 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
1714092 GTTCAGTATT
*
1714102 TGTCCCGAAGGACCACTA
1 TGTCCGGAAGGACCACTA
1714120 TGTCCGGAAGGACCACTA
1 TGTCCGGAAGGACCACTA
*
1714138 TGTCAGGAAGGACCACT
1 TGTCCGGAAGGACCACT
1714155 GGATATATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.17
Consensus pattern (18 bp):
TGTCCGGAAGGACCACTA
Found at i:1714172 original size:22 final size:22
Alignment explanation
Indices: 1714144--1714304 Score: 241
Period size: 22 Copynumber: 7.3 Consensus size: 22
1714134 ACTATGTCAG
**
1714144 GAAGGACCACTGGATATATCCC
1 GAAGGACCACTGGATACGTCCC
*
1714166 GAAGGACCACTTGATACGTCCC
1 GAAGGACCACTGGATACGTCCC
* *
1714188 GAATGACCACTGTATACGTCCC
1 GAAGGACCACTGGATACGTCCC
*
1714210 GAAGGACCACTGGATACGTCCT
1 GAAGGACCACTGGATACGTCCC
*
1714232 GAAGGACTACTGGATACGTCCC
1 GAAGGACCACTGGATACGTCCC
*
1714254 GAAGGACTACTGGATACGTCCC
1 GAAGGACCACTGGATACGTCCC
*
1714276 GAATGACCACTGGATACGTCCC
1 GAAGGACCACTGGATACGTCCC
1714298 GAAGGAC
1 GAAGGAC
1714305 TAATATACCC
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 125 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.18
Consensus pattern (22 bp):
GAAGGACCACTGGATACGTCCC
Found at i:1717985 original size:17 final size:17
Alignment explanation
Indices: 1717950--1717987 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1717940 CAAAGCTTCC
*
1717950 TTTTCTTTTCATTTTCG
1 TTTTCTTTTCATTTACG
1717967 TTTTCTTTT-ACTTTACG
1 TTTTCTTTTCA-TTTACG
1717984 TTTT
1 TTTT
1717988 TATTGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 1 0.05
17 18 0.95
ACGTcount: A:0.08, C:0.16, G:0.05, T:0.71
Consensus pattern (17 bp):
TTTTCTTTTCATTTACG
Found at i:1729605 original size:60 final size:60
Alignment explanation
Indices: 1729492--1729606 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
1729482 ATATTCTATT
* * * * * * *
1729492 TTTTTAATTGGTCCTTAAACTTTTGAATATTTCAATTCCATCCCTACATTATGACTCTCA
1 TTTTAAATTAGTCCTTAAACTTTTGAACATTCCAATTCCATCCATAAACTATGACTCTCA
*
1729552 TTTTAAATTAGTCCTTAAACTTTT-AAGCATTCCAATTGCATCCATAAACTATGAC
1 TTTTAAATTAGTCCTTAAACTTTTGAA-CATTCCAATTCCATCCATAAACTATGAC
1729607 CCTCGGTCTA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 2 0.04
60 44 0.96
ACGTcount: A:0.30, C:0.21, G:0.07, T:0.42
Consensus pattern (60 bp):
TTTTAAATTAGTCCTTAAACTTTTGAACATTCCAATTCCATCCATAAACTATGACTCTCA
Found at i:1729619 original size:60 final size:60
Alignment explanation
Indices: 1729497--1729638 Score: 135
Period size: 60 Copynumber: 2.4 Consensus size: 60
1729487 CTATTTTTTT
* * * * * * * * *
1729497 AATTGGTCCTTAAACTTTTGAATATTTCAATTCCATCCCTACATTATGACTCTCATTTTA
1 AATTAGTCCTTAAACTTTTGAACATTCCAATTCCATCCATAAACTATGACCCTCAGTCTA
* *
1729557 AATTAGTCCTTAAACTTTT-AAGCATTCCAATTGCATCCATAAACTATGACCCTCGGTCTA
1 AATTAGTCCTTAAACTTTTGAA-CATTCCAATTCCATCCATAAACTATGACCCTCAGTCTA
* *
1729617 AATT-GATCCTCAAACATTTGAA
1 AATTAG-TCCTTAAACTTTTGAA
1729639 TTTTCTAATT
Statistics
Matches: 66, Mismatches: 13, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
59 3 0.05
60 61 0.92
61 2 0.03
ACGTcount: A:0.32, C:0.23, G:0.08, T:0.37
Consensus pattern (60 bp):
AATTAGTCCTTAAACTTTTGAACATTCCAATTCCATCCATAAACTATGACCCTCAGTCTA
Found at i:1729905 original size:60 final size:61
Alignment explanation
Indices: 1729788--1729933 Score: 161
Period size: 60 Copynumber: 2.4 Consensus size: 61
1729778 ATATACTTTG
* * * * *
1729788 GGATGAAATTGGAATGTTAAAAAAGGTTTAGAGACCAATTTAGAATGAAGTTCATAGTTT-A
1 GGATGAAATTGAAATGTT-AAAAAGATTGAGAGACCAATTTAGAATGAAGATAATAGTTTAA
* * *
1729849 GAGATGAAATTGAAATGTTCAAAAGATTGAG-GACTAATTTAGAATGATGATAATAGTTTAA
1 G-GATGAAATTGAAATGTTAAAAAGATTGAGAGACCAATTTAGAATGAAGATAATAGTTTAA
* * *
1729910 GGATGAAATTAAAATATTTAAAAG
1 GGATGAAATTGAAATGTTAAAAAG
1729934 CTAAGGGACC
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
60 44 0.61
61 12 0.17
62 16 0.22
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.31
Consensus pattern (61 bp):
GGATGAAATTGAAATGTTAAAAAGATTGAGAGACCAATTTAGAATGAAGATAATAGTTTAA
Found at i:1729948 original size:60 final size:60
Alignment explanation
Indices: 1729816--1729949 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
1729806 AAAAAAGGTT
* * * *
1729816 TAGA-GACCAATTTAGAATGAAGTTCATAGTTTAGAGATGAAATTGAAATGTTCAAAAGA
1 TAGAGGACCAATTTAGAATGAAGATAATAGTTTAGAGATGAAATTAAAATATTCAAAAGA
* * * * *
1729875 TTGAGGACTAATTTAGAATGATGATAATAGTTTA-AGGATGAAATTAAAATATTTAAAAGC
1 TAGAGGACCAATTTAGAATGAAGATAATAGTTTAGA-GATGAAATTAAAATATTCAAAAGA
1729935 TA-AGGGACCAATTTA
1 TAGA-GGACCAATTTA
1729950 AATTGATAGT
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
59 5 0.08
60 56 0.92
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (60 bp):
TAGAGGACCAATTTAGAATGAAGATAATAGTTTAGAGATGAAATTAAAATATTCAAAAGA
Found at i:1739724 original size:21 final size:22
Alignment explanation
Indices: 1739677--1739718 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1739667 ACATATAATT
*
1739677 ATAAATTAGTTAAAAATTAAAG
1 ATAAATTAGTTAAAAATAAAAG
*
1739699 ATAAATTA-TTTAAAATAAAA
1 ATAAATTAGTTAAAAATAAAA
1739719 AGTAAACTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (22 bp):
ATAAATTAGTTAAAAATAAAAG
Found at i:1742575 original size:19 final size:20
Alignment explanation
Indices: 1742542--1742583 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1742532 TACATTTTTC
*
1742542 ATTTCATATCAATTTGTTTA
1 ATTTCATATCAATTTATTTA
*
1742562 ATTT-ATATCCATTTATTTA
1 ATTTCATATCAATTTATTTA
1742581 ATT
1 ATT
1742584 AGCCCAATGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.31, C:0.10, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTCATATCAATTTATTTA
Found at i:1742704 original size:19 final size:21
Alignment explanation
Indices: 1742680--1742728 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 21
1742670 CACCGAAGTG
*
1742680 CCACATATTTGT-CC-AAGGA
1 CCACATATTTGTCCCGAAAGA
1742699 CCACATAGATTTGTCCCGAAAGA
1 CCACAT--ATTTGTCCCGAAAGA
1742722 CCACATA
1 CCACATA
1742729 GAACCCTTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
19 6 0.24
21 7 0.28
22 2 0.08
23 10 0.40
ACGTcount: A:0.35, C:0.29, G:0.14, T:0.22
Consensus pattern (21 bp):
CCACATATTTGTCCCGAAAGA
Found at i:1745262 original size:20 final size:20
Alignment explanation
Indices: 1745237--1745290 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1745227 CCTTGAAGTG
1745237 CATCGATACATTCTACAGTC
1 CATCGATACATTCTACAGTC
* *
1745257 CATCGATGCATTCTACAGTG
1 CATCGATACATTCTACAGTC
*
1745277 CATCAATACATTCT
1 CATCGATACATTCT
1745291 TTAACATGTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.30, C:0.28, G:0.11, T:0.31
Consensus pattern (20 bp):
CATCGATACATTCTACAGTC
Found at i:1745367 original size:64 final size:64
Alignment explanation
Indices: 1745299--1745435 Score: 168
Period size: 64 Copynumber: 2.1 Consensus size: 64
1745289 CTTTAACATG
* *
1745299 TGCATCGATGCACTACC-CATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTAAAGGGA
1 TGCATCGATGCACT-CCTCATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAAGGGA
* * * * ** * *
1745363 TGCATCGATGTACTCCTTATGCATCGATGCACCAATTGTATTCGATGTTTCCATTTTTAAGGGG
1 TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAAGGGA
1745427 TGCATCGAT
1 TGCATCGAT
1745436 ACACACTGAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
63 2 0.03
64 60 0.97
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (64 bp):
TGCATCGATGCACTCCTCATGCATCGATACACAAATTACATTCGATGTTTCCATTTTAAAGGGA
Found at i:1749504 original size:24 final size:20
Alignment explanation
Indices: 1749431--1749508 Score: 102
Period size: 20 Copynumber: 3.7 Consensus size: 20
1749421 TTCCACTTGA
*
1749431 AGTGCATCGATGCATTCTAT
1 AGTGCATCGATGCATTCTAC
*
1749451 AGTGAATCGATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
1749471 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1749494 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1749509 CTACCCATGC
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
20 34 0.67
22 1 0.02
23 3 0.06
24 13 0.25
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1749565 original size:64 final size:63
Alignment explanation
Indices: 1749496--1749657 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 63
1749486 TCTTTAACAT
* * * *
1749496 GTGCATCGATGCACTACCCATGCATCGATACACAAATTACCTTCGGTGTTTTC-ATTTTAAAGG-
1 GTGCATCGATGCACT-CCTATGCATCGATACACAAATTACATTCGATGTTTCCAATTTT-AAGGA
* * * *
1749559 GATGCATCAATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCCAATTTTAAGGA
1 G-TGCATCGATGCACTCC-TATGCATCGATACACAAATTACATTCGATGTTTCCAATTTTAAGGA
*
1749624 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
1749658 CTGAATAATT
Statistics
Matches: 82, Mismatches: 12, Indels: 9
0.80 0.12 0.09
Matches are distributed among these distances:
63 3 0.04
64 70 0.85
65 9 0.11
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAAATTACATTCGATGTTTCCAATTTTAAGGA
Found at i:1751831 original size:11 final size:11
Alignment explanation
Indices: 1751802--1751831 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
1751792 ATATATTACT
1751802 ATTTAAAAATA
1 ATTTAAAAATA
1751813 ATTGTAAAAATA
1 ATT-TAAAAATA
1751825 ATTTAAA
1 ATTTAAA
1751832 TTAAAAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (11 bp):
ATTTAAAAATA
Found at i:1756273 original size:24 final size:24
Alignment explanation
Indices: 1756212--1756271 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
1756202 TAATTTCCAC
1756212 GATGTAAACATTTAGTTAAATGTT
1 GATGTAAACATTTAGTTAAATGTT
1756236 GATGTAAACATTTAGTTAAATGTT
1 GATGTAAACATTTAGTTAAATGTT
1756260 GATGTAAA-ATTT
1 GATGTAAACATTT
1756272 TAATATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 4 0.11
24 32 0.89
ACGTcount: A:0.38, C:0.03, G:0.17, T:0.42
Consensus pattern (24 bp):
GATGTAAACATTTAGTTAAATGTT
Found at i:1756397 original size:15 final size:15
Alignment explanation
Indices: 1756379--1756411 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1756369 ATCAACATAT
1756379 ATAATTTTTATATAA
1 ATAATTTTTATATAA
*
1756394 ATAATTTTTATTTAA
1 ATAATTTTTATATAA
1756409 ATA
1 ATA
1756412 TTTAGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAATTTTTATATAA
Found at i:1756580 original size:19 final size:20
Alignment explanation
Indices: 1756556--1756596 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1756546 TTCTCAGTAA
* *
1756556 TTTTATT-TCTTTGGTAATC
1 TTTTATTCTCATTGATAATC
1756575 TTTTATTCTCATTGATAATC
1 TTTTATTCTCATTGATAATC
1756595 TT
1 TT
1756597 ACATTCCGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.20, C:0.12, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTATTCTCATTGATAATC
Found at i:1767645 original size:2 final size:2
Alignment explanation
Indices: 1767638--1767663 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1767628 AACCCATTTT
1767638 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
1767664 GAAGTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1769378 original size:3 final size:3
Alignment explanation
Indices: 1769370--1769396 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1769360 TAATGACCAA
1769370 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1769397 TGTGCTTTTT
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):
AAT
Found at i:1770187 original size:97 final size:98
Alignment explanation
Indices: 1770045--1770240 Score: 385
Period size: 98 Copynumber: 2.0 Consensus size: 98
1770035 AATTGACTCA
1770045 TACAGTTTACTAGCAGTTGAATTTTTAAGGTTTAGAAGT-AAAAAAAAAAAGTTTGCACGTCATT
1 TACAGTTTACTAGCAGTTGAATTTTTAAGGTTTAGAAGTAAAAAAAAAAAAGTTTGCACGTCATT
1770109 TGTTCTTATACGTTTTGCTTTGGAATTCGTCAT
66 TGTTCTTATACGTTTTGCTTTGGAATTCGTCAT
1770142 TACAGTTTACTAGCAGTTGAATTTTTAAGGTTTAGAAGTAAAAAAAAAAAAGTTTGCACGTCATT
1 TACAGTTTACTAGCAGTTGAATTTTTAAGGTTTAGAAGTAAAAAAAAAAAAGTTTGCACGTCATT
1770207 TGTTCTTATACGTTTTGCTTTGGAATTCGTCAT
66 TGTTCTTATACGTTTTGCTTTGGAATTCGTCAT
1770240 T
1 T
1770241 TGTTCTTATA
Statistics
Matches: 98, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
97 39 0.40
98 59 0.60
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.40
Consensus pattern (98 bp):
TACAGTTTACTAGCAGTTGAATTTTTAAGGTTTAGAAGTAAAAAAAAAAAAGTTTGCACGTCATT
TGTTCTTATACGTTTTGCTTTGGAATTCGTCAT
Found at i:1770243 original size:34 final size:34
Alignment explanation
Indices: 1770200--1770289 Score: 153
Period size: 34 Copynumber: 2.6 Consensus size: 34
1770190 AAAGTTTGCA
1770200 CGTCATTTGTTCTTATACGTTTTGCTTTGGAATT
1 CGTCATTTGTTCTTATACGTTTTGCTTTGGAATT
*
1770234 CGTCATTTGTTCTTATATGTTTTGCTTTGGAATT
1 CGTCATTTGTTCTTATACGTTTTGCTTTGGAATT
* *
1770268 CGTTATTTGTTCGTATACGTTT
1 CGTCATTTGTTCTTATACGTTT
1770290 GGAGAATTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.14, C:0.13, G:0.18, T:0.54
Consensus pattern (34 bp):
CGTCATTTGTTCTTATACGTTTTGCTTTGGAATT
Found at i:1773240 original size:42 final size:38
Alignment explanation
Indices: 1773152--1773243 Score: 112
Period size: 42 Copynumber: 2.3 Consensus size: 38
1773142 TTGAATTCGA
* *
1773152 ACTTACATGCATACCCATATCTGATACACCCAAATCTG
1 ACTTACATGCATACCCATATCTAATACACCCAAATCCG
* *
1773190 ACTGACATGCATACCTATATCTAATACACACACCCAAATCCG
1 ACTTACATGCATACCCATATCTAAT----ACACCCAAATCCG
1773232 ACTTACATGCAT
1 ACTTACATGCAT
1773244 GATGTTCAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
38 22 0.49
42 23 0.51
ACGTcount: A:0.36, C:0.32, G:0.08, T:0.25
Consensus pattern (38 bp):
ACTTACATGCATACCCATATCTAATACACCCAAATCCG
Found at i:1777878 original size:18 final size:16
Alignment explanation
Indices: 1777852--1777888 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
1777842 GATTATTCTA
1777852 TTTTTTTATTAAAGTCT
1 TTTTTTTATTAAAGT-T
1777869 TTTTTATTATTAAAGTT
1 TTTTT-TTATTAAAGTT
1777886 TTT
1 TTT
1777889 ATTAAAGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.24, C:0.03, G:0.05, T:0.68
Consensus pattern (16 bp):
TTTTTTTATTAAAGTT
Done.