Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168492.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_9, 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: 25814696
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 122000 characters in sequence are not A, C, G, or T
File 7 of 126
Found at i:1618244 original size:34 final size:33
Alignment explanation
Indices: 1618206--1618269 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1618196 ATGTTTTATG
*
1618206 TTGTATATTAAAT-TTAATAATTTATGTATTTGTA
1 TTGTATA--AAATATTAATAATTTATATATTTGTA
*
1618240 TTGTATAAAATATTGATAATTTATATATTT
1 TTGTATAAAATATTAATAATTTATATATTT
1618270 ATATCATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 4 0.15
33 16 0.59
34 7 0.26
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (33 bp):
TTGTATAAAATATTAATAATTTATATATTTGTA
Found at i:1622147 original size:66 final size:66
Alignment explanation
Indices: 1622039--1622172 Score: 169
Period size: 66 Copynumber: 2.0 Consensus size: 66
1622029 AAGCCTATCA
* * *
1622039 TATGACAAATTTAAAAAGAAAAATACAAGAAAATCTTGACTCTTATACCATATTAAACATCTAAC
1 TATGACAAATTTAAAAAGAAAAATACAAGAAAATCCTAACTCTGATACCATATTAAACATCTAAC
1622104 T
66 T
* *** * ** *
1622105 TATGACAAATTTGAAAAGGGCAATACAAGAAAGTCCTAACTCTGATATTATATTAAGCATCTAAC
1 TATGACAAATTTAAAAAGAAAAATACAAGAAAATCCTAACTCTGATACCATATTAAACATCTAAC
1622170 T
66 T
1622171 TA
1 TA
1622173 AAATTAATTG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 57 1.00
ACGTcount: A:0.46, C:0.15, G:0.10, T:0.29
Consensus pattern (66 bp):
TATGACAAATTTAAAAAGAAAAATACAAGAAAATCCTAACTCTGATACCATATTAAACATCTAAC
T
Found at i:1625064 original size:21 final size:21
Alignment explanation
Indices: 1625038--1625242 Score: 152
Period size: 21 Copynumber: 10.0 Consensus size: 21
1625028 TTCCAAAATA
*
1625038 AAAATTATATCAAAGGTTATC
1 AAAATTATATCAAAGGTTACC
* ** *
1625059 AAAATTATATTAAAACTTAAC
1 AAAATTATATCAAAGGTTACC
* * * *
1625080 AAAATTGTATCTATGATTACC
1 AAAATTATATCAAAGGTTACC
* * *
1625101 AAAATTGTATTAAAAGTTACC
1 AAAATTATATCAAAGGTTACC
* *
1625122 AAAATTATATCAAA-CTTACT
1 AAAATTATATCAAAGGTTACC
*
1625142 AAAATTTTATCAAAGGTTACC
1 AAAATTATATCAAAGGTTACC
**
1625163 AAAATTATAT-AAATGGTTATT
1 AAAATTATATCAAA-GGTTACC
* *
1625184 GAAATTATAACATAA-GTTACC
1 AAAATTATATCA-AAGGTTACC
* *
1625205 AAAA-TA-GT-AAAGATTACC
1 AAAATTATATCAAAGGTTACC
*
1625223 AAAATTATATTAAAGGTTAC
1 AAAATTATATCAAAGGTTAC
1625243 TAAATTTTTA
Statistics
Matches: 140, Mismatches: 36, Indels: 16
0.73 0.19 0.08
Matches are distributed among these distances:
17 2 0.01
18 10 0.07
19 2 0.01
20 23 0.16
21 100 0.71
22 1 0.01
23 2 0.01
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (21 bp):
AAAATTATATCAAAGGTTACC
Found at i:1625085 original size:42 final size:42
Alignment explanation
Indices: 1625038--1625311 Score: 168
Period size: 42 Copynumber: 6.7 Consensus size: 42
1625028 TTCCAAAATA
* *
1625038 AAAATTATATCAAAGGTTATCAAAATTATATTAAAACTTAAC
1 AAAATTATATCAAAGGTTATCAAAATTATATTAAAAGTTACC
* * * * * *
1625080 AAAATTGTATCTATGATTACCAAAATTGTATTAAAAGTTACC
1 AAAATTATATCAAAGGTTATCAAAATTATATTAAAAGTTACC
* * * *
1625122 AAAATTATATCAAA-CTTA-CTAAAATTTTATCAAAGGTTACC
1 AAAATTATATCAAAGGTTATC-AAAATTATATTAAAAGTTACC
** ** *
1625163 AAAATTATAT-AAATGGTTATTGAAATTATAACATAAGTTACC
1 AAAATTATATCAAA-GGTTATCAAAATTATATTAAAAGTTACC
* * * * *
1625205 AAAA-TA-GT-AAAGATTACCAAAATTATATTAAAGGTTACT
1 AAAATTATATCAAAGGTTATCAAAATTATATTAAAAGTTACC
* * * * * * * * *
1625244 AAATTTTTATGAAATGCTAT-AAAATTTTAATAAAGGTTACT
1 AAAATTATATCAAAGGTTATCAAAATTATATTAAAAGTTACC
* **
1625285 ACAA-TATATCAAAAATTATCAAAATTA
1 AAAATTATATCAAAGGTTATCAAAATTA
1625312 AAATTCTATA
Statistics
Matches: 175, Mismatches: 49, Indels: 17
0.73 0.20 0.07
Matches are distributed among these distances:
39 22 0.13
40 19 0.11
41 61 0.35
42 73 0.42
ACGTcount: A:0.49, C:0.09, G:0.07, T:0.35
Consensus pattern (42 bp):
AAAATTATATCAAAGGTTATCAAAATTATATTAAAAGTTACC
Found at i:1625467 original size:21 final size:20
Alignment explanation
Indices: 1625443--1625607 Score: 95
Period size: 21 Copynumber: 7.9 Consensus size: 20
1625433 GTATCTAAGA
1625443 TTACCAAAATCTTATTAAAAG
1 TTACCAAAAT-TTATTAAAAG
*
1625464 TTACCAAAATTATATT-AAAC
1 TTACCAAAATT-TATTAAAAG
* *
1625484 TTACTAAAATTTTATCAATAA-
1 TTACCAAAA-TTTATTAA-AAG
* *
1625505 TTACCATAA-TTATATAAATGG
1 TTACCAAAATTTAT-TAAA-AG
*
1625526 TTACTC-AAATTATATTATAAG
1 TTAC-CAAAATT-TATTAAAAG
* * *
1625547 TTACCAAAATAGTAATAAAGG
1 TTACCAAAAT-TTATTAAAAG
* *
1625568 TTACAAAAATTATATTAAAGG
1 TTACCAAAATT-TATTAAAAG
*
1625589 TTACTAAAATTTTATTAAA
1 TTACCAAAA-TTTATTAAA
1625608 TGCTATAAAA
Statistics
Matches: 112, Mismatches: 18, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
19 5 0.04
20 18 0.16
21 77 0.69
22 9 0.08
23 3 0.03
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (20 bp):
TTACCAAAATTTATTAAAAG
Found at i:1625551 original size:42 final size:40
Alignment explanation
Indices: 1625455--1625592 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 40
1625445 ACCAAAATCT
* * *
1625455 TATTAAAAGTTACCAAAATTATATTAAA-CTTACTAAAATTT
1 TATTATAAGTTACC-AAATTATA-TAAAGGTTACTAAAATTA
* *
1625496 TATCAATAA-TTACCATAATTATATAAATGGTTACTCAAATTA
1 TAT-TATAAGTTACCA-AATTATATAAA-GGTTACTAAAATTA
* *
1625538 TATTATAAGTTACCAAAATAGTAATAAAGGTTACAAAAATTA
1 TATTATAAGTTACCAAATTA-T-ATAAAGGTTACTAAAATTA
1625580 TATTA-AAGGTTAC
1 TATTATAA-GTTAC
1625593 TAAAATTTTA
Statistics
Matches: 80, Mismatches: 9, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
40 5 0.06
41 25 0.31
42 45 0.56
43 5 0.06
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (40 bp):
TATTATAAGTTACCAAATTATATAAAGGTTACTAAAATTA
Found at i:1637266 original size:17 final size:18
Alignment explanation
Indices: 1637227--1637267 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1637217 GATTATAATC
1637227 GATTTTTTAAAATGATTA
1 GATTTTTTAAAATGATTA
*
1637245 AATTTTTTAAAATGATT-
1 GATTTTTTAAAATGATTA
1637262 GATTTT
1 GATTTT
1637268 CGATTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (18 bp):
GATTTTTTAAAATGATTA
Found at i:1637429 original size:16 final size:17
Alignment explanation
Indices: 1637390--1637447 Score: 57
Period size: 16 Copynumber: 3.5 Consensus size: 17
1637380 AATTTTTTAG
* *
1637390 TAATTTAATTTAAATGA
1 TAATTAAATTTAAATTA
* *
1637407 CACTTAAATTTAAATT-
1 TAATTAAATTTAAATTA
*
1637423 TTATTAAA-TTAAATTA
1 TAATTAAATTTAAATTA
1637439 TAATTAAAT
1 TAATTAAAT
1637448 AAAAATAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
15 7 0.23
16 12 0.39
17 12 0.39
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (17 bp):
TAATTAAATTTAAATTA
Found at i:1643059 original size:13 final size:13
Alignment explanation
Indices: 1643041--1643066 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1643031 ATTAAGAGTT
1643041 AATTTAAATTTTA
1 AATTTAAATTTTA
1643054 AATTTAAATTTTA
1 AATTTAAATTTTA
1643067 TTTAATTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTAAATTTTA
Found at i:1643131 original size:18 final size:18
Alignment explanation
Indices: 1643105--1643141 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1643095 TTTAATTTAC
*
1643105 AAATATGAATATTTTAAT
1 AAATATGAATATTTAAAT
*
1643123 AAATTTGAATATTTAAAT
1 AAATATGAATATTTAAAT
1643141 A
1 A
1643142 GATAAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (18 bp):
AAATATGAATATTTAAAT
Found at i:1646962 original size:38 final size:38
Alignment explanation
Indices: 1646911--1646990 Score: 142
Period size: 38 Copynumber: 2.1 Consensus size: 38
1646901 TTTTTTGGAT
1646911 TGCTGCCCCCATTGTAAATCCTTCTCTGTACAAATGAA
1 TGCTGCCCCCATTGTAAATCCTTCTCTGTACAAATGAA
* *
1646949 TGCTGCCCTCATTGTAAATCCTTCTCTGTACAAATGAT
1 TGCTGCCCCCATTGTAAATCCTTCTCTGTACAAATGAA
1646987 TGCT
1 TGCT
1646991 TCATCTGTCC
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.35
Consensus pattern (38 bp):
TGCTGCCCCCATTGTAAATCCTTCTCTGTACAAATGAA
Found at i:1651572 original size:15 final size:16
Alignment explanation
Indices: 1651552--1651590 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1651542 AAACTTGCAC
1651552 ATTAAAAT-AAAAAAA
1 ATTAAAATCAAAAAAA
**
1651567 ATTAAAATCATTAAAA
1 ATTAAAATCAAAAAAA
1651583 ATTAAAAT
1 ATTAAAAT
1651591 TCGTGATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (16 bp):
ATTAAAATCAAAAAAA
Found at i:1652166 original size:21 final size:22
Alignment explanation
Indices: 1652142--1652187 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1652132 AAAATATAAA
* *
1652142 AAATATATTTTTTA-TTTTATT
1 AAATATATTTATAATTTTTATT
*
1652163 AAATTTATTTATAATTTTTATT
1 AAATATATTTATAATTTTTATT
1652185 AAA
1 AAA
1652188 ATTTTAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
AAATATATTTATAATTTTTATT
Found at i:1657380 original size:14 final size:14
Alignment explanation
Indices: 1657358--1657391 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1657348 TAAGAAAGAT
1657358 TTAAATAAAATTTG
1 TTAAATAAAATTTG
*
1657372 TTAAGTAAAATTTG
1 TTAAATAAAATTTG
*
1657386 TAAAAT
1 TTAAAT
1657392 TTTATGCTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (14 bp):
TTAAATAAAATTTG
Found at i:1657623 original size:13 final size:12
Alignment explanation
Indices: 1657590--1657614 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1657580 TTTAATTATA
1657590 AATAATATTTTT
1 AATAATATTTTT
1657602 AATAATATTTTT
1 AATAATATTTTT
1657614 A
1 A
1657615 CATATTATTG
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AATAATATTTTT
Found at i:1659813 original size:2 final size:2
Alignment explanation
Indices: 1659796--1659829 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1659786 CATCTTTTAC
* *
1659796 AT AT AT AC AT AC 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
1659830 CTTGCAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1663216 original size:10 final size:10
Alignment explanation
Indices: 1663201--1663230 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1663191 ACCAAATTTT
1663201 TATATTTTAA
1 TATATTTTAA
1663211 TATATTTTAA
1 TATATTTTAA
1663221 TA-ATTTTAA
1 TATATTTTAA
1663230 T
1 T
1663231 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATTTTAA
Found at i:1672122 original size:21 final size:21
Alignment explanation
Indices: 1672098--1672137 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1672088 AAAATATATT
*
1672098 AAAAAAT-ATGTGAAAAAAAG
1 AAAAAATAAAGTGAAAAAAAG
1672118 AAAAAATAAAGTGAAAAAAA
1 AAAAAATAAAGTGAAAAAAA
1672138 ATTATTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.12
Consensus pattern (21 bp):
AAAAAATAAAGTGAAAAAAAG
Found at i:1672823 original size:23 final size:24
Alignment explanation
Indices: 1672797--1672846 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
1672787 TATAATTTGA
*
1672797 ATAAATT-TAAAATTATCTAATTT
1 ATAAATTAAAAAATTATCTAATTT
*
1672820 AT-AATTAAAAAATTATCTTATTT
1 ATAAATTAAAAAATTATCTAATTT
1672843 -TAAA
1 ATAAA
1672847 AAAAAAAACT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATTAAAAAATTATCTAATTT
Found at i:1672851 original size:22 final size:23
Alignment explanation
Indices: 1672805--1672853 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1672795 GAATAAATTT
**
1672805 AAAATTATCTAATTTATAATTAA
1 AAAATTATCTAATTTATAAAAAA
*
1672828 AAAATTATCTTATTT-TAAAAAA
1 AAAATTATCTAATTTATAAAAAA
1672850 AAAA
1 AAAA
1672854 ACTATCCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAATTATCTAATTTATAAAAAA
Found at i:1679226 original size:6 final size:6
Alignment explanation
Indices: 1679218--1679264 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
1679208 GAGAAAGAGA
* *
1679218 GAAGAA GAAGAT GATGAGAT GAAGAT GAAGAT GAAGAC GAAGAT GAA
1 GAAGAT GAAGAT GA--AGAT GAAGAT GAAGAT GAAGAT GAAGAT GAA
1679265 AACAGAATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 30 0.83
8 6 0.17
ACGTcount: A:0.51, C:0.02, G:0.34, T:0.13
Consensus pattern (6 bp):
GAAGAT
Found at i:1680344 original size:3 final size:3
Alignment explanation
Indices: 1680336--1680364 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1680326 GTTAGATTTC
1680336 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1680365 CAGGCAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1684116 original size:2 final size:2
Alignment explanation
Indices: 1684111--1684146 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1684101 ACACACACAC
*
1684111 AT AT AT AT AT AT AC 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
1684147 TGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1687479 original size:10 final size:10
Alignment explanation
Indices: 1687464--1687493 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1687454 ACCAAATTTT
1687464 TATATTTTAA
1 TATATTTTAA
1687474 TATATTTTAA
1 TATATTTTAA
1687484 TA-ATTTTAA
1 TATATTTTAA
1687493 T
1 T
1687494 TAATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TATATTTTAA
Found at i:1690451 original size:68 final size:68
Alignment explanation
Indices: 1690340--1690470 Score: 192
Period size: 68 Copynumber: 1.9 Consensus size: 68
1690330 AAATTATCTT
*** * *
1690340 ATATATACAAAAGGTAATCATCCATTCATATACTTGTAGAAATAATTTTATAAACATCTTATTTA
1 ATATATACAAAAGGTAATCATCCATTCATATACTAACAAAAATAATTTTATAAACATCCTATTTA
1690405 TTC
66 TTC
*
1690408 ATATATACAGAAGGTAATCATCCACTT-ATATACTAACAAAAATAATTTTATAAACATCCTATT
1 ATATATACAAAAGGTAATCATCCA-TTCATATACTAACAAAAATAATTTTATAAACATCCTATT
1690471 CATTAGTATA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
68 54 0.96
69 2 0.04
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (68 bp):
ATATATACAAAAGGTAATCATCCATTCATATACTAACAAAAATAATTTTATAAACATCCTATTTA
TTC
Found at i:1690810 original size:13 final size:13
Alignment explanation
Indices: 1690794--1690841 Score: 87
Period size: 13 Copynumber: 3.7 Consensus size: 13
1690784 TCAATTATAT
1690794 GATTCAAAACCTA
1 GATTCAAAACCTA
*
1690807 GATTCAAAACCTT
1 GATTCAAAACCTA
1690820 GATTCAAAACCTA
1 GATTCAAAACCTA
1690833 GATTCAAAA
1 GATTCAAAA
1690842 TTGATTTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (13 bp):
GATTCAAAACCTA
Found at i:1693191 original size:524 final size:524
Alignment explanation
Indices: 1692200--1693240 Score: 1812
Period size: 524 Copynumber: 2.0 Consensus size: 524
1692190 ACTAAAAGAT
*
1692200 TATTGTCGTGACATTAGCTAGCAACTAAAACATTATTGCACTGATACCTCTAATGTTTTCCACAT
1 TATTGTCATGACATTAGCTAGCAACTAAAACATTATTGCACTGATACCTCTAATGTTTTCCACAT
** *
1692265 TTTTTCCTTCTTAGGATCCTACATTTCATGCCAATTTATATATTAATTGGTGCAAAGCTAGACAT
66 TTTTTCCTTCTTAACATCCGACATTTCATGCCAATTTATATATTAATTGGTGCAAAGCTAGACAT
*
1692330 TCTCACCATGCTACCAATGAGTCGAGTTAAAGAGCAAGATTCATCACCGATAGGTATAGCATCAT
131 TCTCACCATGCTACCAATGAATCGAGTTAAAGAGCAAGATTCATCACCGATAGGTATAGCATCAT
*
1692395 CATTGACCTTAACAATAACATACCCCCATTCTTCCAAATCCTAAATATTAGCCATACGTGTAGGA
196 CATTGACCTTAACAATAACATACCCCCATTCTTCCAAATCCTAAATATCAGCCATACGTGTAGGA
* * *
1692460 CCTCAAGCTTTTTTGTGTTGAACATTTCTTACATAGAAAAATTACATGTAAAGAAAGTAATTAAA
261 CCTCAAACTTTTTTATGTTGAACATTTCCTACATAGAAAAATTACATGTAAAGAAAGTAATTAAA
*
1692525 TTCATTAAAAACTTAAACAAGAACAACATTATAACACATAAAAAATTGTACTAACCTAATATAGT
326 TTCATTAAAAACTTAAACAAGAACAACATTATAACACATAAAAAATTGTACTAACATAATATAGT
* *
1692590 GTTTTTATACCTGAATTATGTCTAACTTGCTCATCTTGATTTTCATTATTTGTAGATTGAGAAAT
391 GTTTTTATACCTGAATTATGTCCAACTTGCTCATCTTGATCTTCATTATTTGTAGATTGAGAAAT
* *
1692655 TGGTTCTTGAGATTCCTGCAGAAGCTCATATTGTGAAGCTTCCGGATCTACATACACATGTTATT
456 TGGTTCTTGAGATTCCTGCAGAAACTCATATTGTGAAGCTTCCGAATCTACATACACATGTTATT
1692720 GTCA
521 GTCA
* * *
1692724 TATTGTCATGGCATTAGCTAGCAACTAAAACATTATTGTATTGATACCTCTAATGTTTTCCACAT
1 TATTGTCATGACATTAGCTAGCAACTAAAACATTATTGCACTGATACCTCTAATGTTTTCCACAT
1692789 TTTTTCCTTCTTAACATCCGACATTTCATGCCAATTTATATATTAATTGGTGCAAAGCTAGACAT
66 TTTTTCCTTCTTAACATCCGACATTTCATGCCAATTTATATATTAATTGGTGCAAAGCTAGACAT
*
1692854 TCTCACCATGCTACCAATGAATCGAGTTAAAGAGCAAGATTCATCACCGCTAGGTATAGCATCAT
131 TCTCACCATGCTACCAATGAATCGAGTTAAAGAGCAAGATTCATCACCGATAGGTATAGCATCAT
* *
1692919 CATTGACCTTAACAATAACATACCCCCCTTCTTCTAAATCCTAAATATCAGCCATACGTGTAGGA
196 CATTGACCTTAACAATAACATACCCCCATTCTTCCAAATCCTAAATATCAGCCATACGTGTAGGA
*
1692984 CCTCAAACTTTTTTATGTTGAACATTTCCTATATAGAAAAATTACATGTAAAGAAAGTAATTAAA
261 CCTCAAACTTTTTTATGTTGAACATTTCCTACATAGAAAAATTACATGTAAAGAAAGTAATTAAA
* *
1693049 TTCATTAAAAATTTAAACAAGAACAACATTATAACACATAAAGAATTGTACTAACATAATATAGT
326 TTCATTAAAAACTTAAACAAGAACAACATTATAACACATAAAAAATTGTACTAACATAATATAGT
*
1693114 GTTTTTATACTTGAATTATGTCCAACTTGCTCATCTTGATCTTCATTATTTGTAGATTGAGAAAT
391 GTTTTTATACCTGAATTATGTCCAACTTGCTCATCTTGATCTTCATTATTTGTAGATTGAGAAAT
* * * * * *
1693179 TGGTTTTTGAGATTCTTGTATAAACTCATATTGTGAAGCTTCTGAATCTATATACACATGTT
456 TGGTTCTTGAGATTCCTGCAGAAACTCATATTGTGAAGCTTCCGAATCTACATACACATGTT
1693241 GTTCTTCAGA
Statistics
Matches: 487, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
524 487 1.00
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (524 bp):
TATTGTCATGACATTAGCTAGCAACTAAAACATTATTGCACTGATACCTCTAATGTTTTCCACAT
TTTTTCCTTCTTAACATCCGACATTTCATGCCAATTTATATATTAATTGGTGCAAAGCTAGACAT
TCTCACCATGCTACCAATGAATCGAGTTAAAGAGCAAGATTCATCACCGATAGGTATAGCATCAT
CATTGACCTTAACAATAACATACCCCCATTCTTCCAAATCCTAAATATCAGCCATACGTGTAGGA
CCTCAAACTTTTTTATGTTGAACATTTCCTACATAGAAAAATTACATGTAAAGAAAGTAATTAAA
TTCATTAAAAACTTAAACAAGAACAACATTATAACACATAAAAAATTGTACTAACATAATATAGT
GTTTTTATACCTGAATTATGTCCAACTTGCTCATCTTGATCTTCATTATTTGTAGATTGAGAAAT
TGGTTCTTGAGATTCCTGCAGAAACTCATATTGTGAAGCTTCCGAATCTACATACACATGTTATT
GTCA
Found at i:1697037 original size:56 final size:55
Alignment explanation
Indices: 1696966--1697073 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 55
1696956 ATGAAACTGT
*
1696966 AATAATAATAAAATATA-TCTTAAAAAAAATTTA-TAAACAAAATAAAAATAAATTGC
1 AATAATAATAAAATATACT-TTAAAAAAAAGTTACTAAA-AAAATAAAAA-AAATTGC
* * *
1697022 AATAATAATAGAATATACTTTAGAAAAAAGTTACTGAAAAAATAAAAAAAAT
1 AATAATAATAAAATATACTTTAAAAAAAAGTTACTAAAAAAATAAAAAAAAT
1697074 GTATAACACA
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
55 4 0.09
56 38 0.83
57 4 0.09
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (55 bp):
AATAATAATAAAATATACTTTAAAAAAAAGTTACTAAAAAAATAAAAAAAATTGC
Found at i:1704071 original size:6 final size:6
Alignment explanation
Indices: 1704036--1704067 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1704026 AGAAGAAGAT
*
1704036 GATGAA GATGAA GATGAA GATGAA GACGAA GA
1 GATGAA GATGAA GATGAA GATGAA GATGAA GA
1704068 CGAAAACAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.50, C:0.03, G:0.34, T:0.12
Consensus pattern (6 bp):
GATGAA
Found at i:1705159 original size:3 final size:3
Alignment explanation
Indices: 1705151--1705206 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
1705141 GTTAGATTTC
1705151 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1705199 ATA ATA AT
1 ATA ATA AT
1705207 CAGGCAAAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1706332 original size:21 final size:21
Alignment explanation
Indices: 1706306--1706346 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1706296 TATAATGGAA
1706306 ATTATTATAAATT-AAATTTTG
1 ATTATTA-AAATTAAAATTTTG
1706327 ATTATTAAAATTAAAATTTT
1 ATTATTAAAATTAAAATTTT
1706347 AATACTCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
ATTATTAAAATTAAAATTTTG
Found at i:1708094 original size:61 final size:59
Alignment explanation
Indices: 1707964--1708241 Score: 388
Period size: 59 Copynumber: 4.7 Consensus size: 59
1707954 TTTTTTGTAG
*
1707964 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTT-GATTTCT-AA
1708023 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTTGGAAATTT-GATTTCT-AA
* ** *
1708084 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCCTTTTTTTGAAAATTT-ATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA-TATTTTTTTGGAAATTTGATTTCTAA
* *
1708143 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-GTTTTTGG-AATTTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTGATTTCTAA
*
1708200 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
1708242 TTAGAAATTT
Statistics
Matches: 201, Mismatches: 12, Indels: 13
0.89 0.05 0.06
Matches are distributed among these distances:
56 5 0.02
57 48 0.24
58 5 0.02
59 72 0.36
60 1 0.00
61 70 0.35
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.43
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTGATTTCTAA
Found at i:1708145 original size:120 final size:115
Alignment explanation
Indices: 1707964--1708240 Score: 393
Period size: 120 Copynumber: 2.4 Consensus size: 115
1707954 TTTTTTGTAG
*
1707964 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTCGATTTTCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTC-ATTTTCAAGGAAAA
*
1708029 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGGAAATTTCGATTT-TCAA
65 TTGATACTTTCAACTTTTCCCCAAAAATA--GTTTTTGG-AATTT-GATTTCT-AA
1708084 GGAAAATTGATACTTTCAACTTTT-CCTCAAAAACCCT-TTTTTTGAAAATTT-A-TTTCTAAGG
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAA---TATTTTTTGAAAATTTCATTTTC-AAGG
*
1708145 AAAATTGATACTTTCAACTTTTCCCCAAAAATAGTTTTTGGAATTTTATTTCTAA
61 AAAATTGATACTTTCAACTTTTCCCCAAAAATAGTTTTTGGAATTTGATTTCTAA
1708200 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTT
1708241 TTTAGAAATT
Statistics
Matches: 146, Mismatches: 3, Indels: 22
0.85 0.02 0.13
Matches are distributed among these distances:
113 1 0.01
114 6 0.04
116 35 0.24
117 9 0.06
118 7 0.05
119 7 0.05
120 67 0.46
122 13 0.09
123 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.43
Consensus pattern (115 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGAAAATTTCATTTTCAAGGAAAAT
TGATACTTTCAACTTTTCCCCAAAAATAGTTTTTGGAATTTGATTTCTAA
Found at i:1708356 original size:28 final size:28
Alignment explanation
Indices: 1708318--1708395 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 28
1708308 AACCTAATCT
* *
1708318 AATAAATAAAAATTAAAATAAA-CAAAGA
1 AATAAA-AAAAAATAAAAAAAATCAAAGA
1708346 AAT-AAAAAAAATAAAAAAAATTCAAAGA
1 AATAAAAAAAAATAAAAAAAA-TCAAAGA
* *
1708374 AAGAAGAAAAAAAAAAAAAAAA
1 AATAA-AAAAAAATAAAAAAAA
1708396 CCTGGAGCGG
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
26 13 0.31
27 2 0.05
28 11 0.26
29 1 0.02
30 15 0.36
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.12
Consensus pattern (28 bp):
AATAAAAAAAAATAAAAAAAATCAAAGA
Found at i:1708392 original size:36 final size:37
Alignment explanation
Indices: 1708318--1708391 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 37
1708308 AACCTAATCT
* *
1708318 AATAAATAAAAATTAAAATAAACAAAGAAATAAAAAA
1 AATAAATAAAAATTAAAAGAAACAAAGAAAAAAAAAA
* *
1708355 AATAAA-AAAAATTCAAAGAAA-GAAGAAAAAAAAAA
1 AATAAATAAAAATTAAAAGAAACAAAGAAAAAAAAAA
1708390 AA
1 AA
1708392 AAAACCTGGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 14 0.42
36 13 0.39
37 6 0.18
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (37 bp):
AATAAATAAAAATTAAAAGAAACAAAGAAAAAAAAAA
Found at i:1708752 original size:19 final size:20
Alignment explanation
Indices: 1708712--1708757 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1708702 GAACACCGGT
*
1708712 GCCGGATTCTGGAAAATGTC
1 GCCGGAATCTGGAAAATGTC
*
1708732 GCCGGAATCTGG-AAATTTC
1 GCCGGAATCTGGAAAATGTC
1708751 GCCGGAA
1 GCCGGAA
1708758 GTTGGCCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.54
20 11 0.46
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (20 bp):
GCCGGAATCTGGAAAATGTC
Found at i:1710262 original size:22 final size:22
Alignment explanation
Indices: 1710237--1710292 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
1710227 AGGGTTTTAT
1710237 GTTTTGAGTTTTAAAATTTAGA
1 GTTTTGAGTTTTAAAATTTAGA
* ** *
1710259 GTTTTGGGTTTTTGATTTTAGA
1 GTTTTGAGTTTTAAAATTTAGA
*
1710281 GTTTTGAATTTT
1 GTTTTGAGTTTT
1710293 GGGGTTTTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.21, C:0.00, G:0.21, T:0.57
Consensus pattern (22 bp):
GTTTTGAGTTTTAAAATTTAGA
Found at i:1710269 original size:29 final size:29
Alignment explanation
Indices: 1710221--1710278 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1710211 GTTGCATGCC
* *
1710221 AAATTTAGGGTTTTATG-TTTTGAGTTTTA
1 AAATTTAGAGTTTTAGGTTTTTGA-TTTTA
*
1710250 AAATTTAGAGTTTTGGGTTTTTGATTTTA
1 AAATTTAGAGTTTTAGGTTTTTGATTTTA
1710279 GAGTTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.24, C:0.00, G:0.21, T:0.55
Consensus pattern (29 bp):
AAATTTAGAGTTTTAGGTTTTTGATTTTA
Found at i:1710377 original size:30 final size:32
Alignment explanation
Indices: 1710343--1710433 Score: 91
Period size: 30 Copynumber: 2.9 Consensus size: 32
1710333 AATTTAAGGT
* *
1710343 TTTGATTTTTTAGTTTTAAA-AGTTTTAGGG-
1 TTTGATTTTTAAGGTTTAAAGAGTTTTAGGGC
*
1710373 TTTGA-TTTTAAGGTTTAAAGGGTTTTAGGGC
1 TTTGATTTTTAAGGTTTAAAGAGTTTTAGGGC
* * *
1710404 TTAGA-TTTTAGGGTTTGAAAGATTTTTAGG
1 TTTGATTTTTAAGGTTT-AAAGAGTTTTAGG
1710434 TTTCGAGATT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
29 12 0.24
30 14 0.27
31 14 0.27
32 11 0.22
ACGTcount: A:0.24, C:0.01, G:0.25, T:0.49
Consensus pattern (32 bp):
TTTGATTTTTAAGGTTTAAAGAGTTTTAGGGC
Found at i:1710419 original size:31 final size:31
Alignment explanation
Indices: 1710355--1710433 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
1710345 TGATTTTTTA
* *
1710355 GTTTTAAA-AGTTTTAGGGTTTGATTTTAAG
1 GTTTGAAAGAGTTTTAGGGTTAGATTTTAAG
* *
1710385 GTTT-AAAGGGTTTTAGGGCTTAGATTTTAGG
1 GTTTGAAAGAGTTTTAGGG-TTAGATTTTAAG
*
1710416 GTTTGAAAGATTTTTAGG
1 GTTTGAAAGAGTTTTAGG
1710434 TTTCGAGATT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.07
30 13 0.32
31 14 0.34
32 11 0.27
ACGTcount: A:0.25, C:0.01, G:0.28, T:0.46
Consensus pattern (31 bp):
GTTTGAAAGAGTTTTAGGGTTAGATTTTAAG
Found at i:1710624 original size:30 final size:31
Alignment explanation
Indices: 1710577--1710636 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
1710567 TTTAAAGTGT
1710577 AAAGGGTTTTAGAGTTTT-GATTTTAGGATTC
1 AAAGGGTTTTAGAGTTTTAG-TTTTAGGATTC
*
1710608 AAAGGG-TTTAGGGTTTTAGTTTTAGGATT
1 AAAGGGTTTTAGAGTTTTAGTTTTAGGATT
1710637 TGAAGAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.25, C:0.02, G:0.28, T:0.45
Consensus pattern (31 bp):
AAAGGGTTTTAGAGTTTTAGTTTTAGGATTC
Found at i:1710945 original size:19 final size:20
Alignment explanation
Indices: 1710907--1710947 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1710897 TTTTTATCAC
*
1710907 TTTATTCTTATTATCATTTT
1 TTTATTCTTATTAGCATTTT
*
1710927 TTTATT-TTTTTAGCATTTT
1 TTTATTCTTATTAGCATTTT
1710946 TT
1 TT
1710948 AGTTATTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.73
Consensus pattern (20 bp):
TTTATTCTTATTAGCATTTT
Found at i:1710966 original size:13 final size:12
Alignment explanation
Indices: 1710894--1710983 Score: 51
Period size: 14 Copynumber: 7.2 Consensus size: 12
1710884 AGTAGGAAAA
*
1710894 ATTT-TTTTATC
1 ATTTATTTTATT
1710905 ACTTTATTCTTATT
1 A-TTTATT-TTATT
* *
1710919 A-TCATTTTTTT
1 ATTTATTTTATT
**
1710930 ATTT-TTTTAGC
1 ATTTATTTTATT
*
1710941 ATTTTTTAGTTATT
1 ATTTATT--TTATT
1710955 ATTCTATTTTATTT
1 ATT-TATTTTA-TT
1710969 ATTTATTTTATT
1 ATTTATTTTATT
1710981 ATT
1 ATT
1710984 GTTTAAAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
11 14 0.23
12 15 0.25
13 12 0.20
14 16 0.27
15 3 0.05
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (12 bp):
ATTTATTTTATT
Found at i:1711902 original size:21 final size:20
Alignment explanation
Indices: 1711878--1711937 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
1711868 TATGTTTGTA
*
1711878 ATTTTTTTTTATTTTTTTGCT
1 ATTTTTTTTT-TTTTTTTACT
*
1711899 ATTTTTTGTTTTTTTTCTACT
1 ATTTTTT-TTTTTTTTTTACT
1711920 AGTTTTTTTTTTTTTTTT
1 A-TTTTTTTTTTTTTTTT
1711938 TTGCTTTCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 25 0.74
22 9 0.26
ACGTcount: A:0.08, C:0.05, G:0.05, T:0.82
Consensus pattern (20 bp):
ATTTTTTTTTTTTTTTTACT
Found at i:1714377 original size:12 final size:12
Alignment explanation
Indices: 1714363--1714419 Score: 55
Period size: 12 Copynumber: 4.7 Consensus size: 12
1714353 ATATTATTTT
1714363 AAATATAAATATA
1 AAAT-TAAATATA
1714376 AAATTAAATATA
1 AAATTAAATATA
1714388 TAAA--AATATATA
1 -AAATTAA-ATATA
* *
1714400 TAATTAAACATA
1 AAATTAAATATA
1714412 AAATTAAA
1 AAATTAAA
1714420 AAAATAACTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 4 0.11
12 24 0.65
13 9 0.24
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.32
Consensus pattern (12 bp):
AAATTAAATATA
Found at i:1714400 original size:14 final size:14
Alignment explanation
Indices: 1714363--1714401 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1714353 ATATTATTTT
*
1714363 AAATATAAATATAA
1 AAATATATATATAA
* *
1714377 AATTAAATATATAA
1 AAATATATATATAA
1714391 AAATATATATA
1 AAATATATATA
1714402 ATTAAACATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAATATATATATAA
Found at i:1717115 original size:27 final size:27
Alignment explanation
Indices: 1717085--1717139 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1717075 GATTGAATCT
1717085 TAAATTATAAGCCCTACAATGTTCTAA
1 TAAATTATAAGCCCTACAATGTTCTAA
1717112 TAAATTATAAGCCCTACAATGTTCTAA
1 TAAATTATAAGCCCTACAATGTTCTAA
1717139 T
1 T
1717140 GCAACCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (27 bp):
TAAATTATAAGCCCTACAATGTTCTAA
Found at i:1718381 original size:25 final size:25
Alignment explanation
Indices: 1718347--1718401 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
1718337 TTTCATTAAT
** *
1718347 TTTTTTTTAATTGTAGTTATAATAA
1 TTTTTTTTAATTACAATTATAATAA
*
1718372 TTTTTTTTAATTACAATTATGATAA
1 TTTTTTTTAATTACAATTATAATAA
1718397 TTTTT
1 TTTTT
1718402 ATTATTGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (25 bp):
TTTTTTTTAATTACAATTATAATAA
Found at i:1718556 original size:19 final size:18
Alignment explanation
Indices: 1718534--1718581 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
1718524 AAATTATAAT
*
1718534 AAAATATTTAATATAATAC
1 AAAATATTTAA-ATAAAAC
*
1718553 AAAA-ATTTAAATAAAAT
1 AAAATATTTAAATAAAAC
*
1718570 ATAATATTTAAA
1 AAAATATTTAAA
1718582 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 8 0.32
18 13 0.52
19 4 0.16
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAATATTTAAATAAAAC
Found at i:1721910 original size:37 final size:37
Alignment explanation
Indices: 1721860--1721934 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
1721850 ATTTTAAACC
1721860 ATTACTTGTAAAGTATAATTTTGTTCTTCTAGGTCAT
1 ATTACTTGTAAAGTATAATTTTGTTCTTCTAGGTCAT
1721897 ATTACTTGTAAAGTATAATTTTGTTCTTCTAGGTCAT
1 ATTACTTGTAAAGTATAATTTTGTTCTTCTAGGTCAT
1721934 A
1 A
1721935 AACCTTGCTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (37 bp):
ATTACTTGTAAAGTATAATTTTGTTCTTCTAGGTCAT
Found at i:1722741 original size:19 final size:19
Alignment explanation
Indices: 1722714--1722754 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1722704 TCATTTTTTT
1722714 TTTTAAATAATGCTGTAAA
1 TTTTAAATAATGCTGTAAA
* * *
1722733 TTTTCAATAATGTTGTGAA
1 TTTTAAATAATGCTGTAAA
1722752 TTT
1 TTT
1722755 CTAGATTACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (19 bp):
TTTTAAATAATGCTGTAAA
Found at i:1723659 original size:3 final size:3
Alignment explanation
Indices: 1723651--1723679 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1723641 GCCTTTCAAA
1723651 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1723680 AACCACAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1725643 original size:13 final size:14
Alignment explanation
Indices: 1725625--1725653 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1725615 TTAATTTAAA
1725625 TAAAATA-TATAAT
1 TAAAATATTATAAT
1725638 TAAAATATTATAAT
1 TAAAATATTATAAT
1725652 TA
1 TA
1725654 TATAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATATTATAAT
Found at i:1725684 original size:16 final size:16
Alignment explanation
Indices: 1725640--1725678 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1725630 TATATAATTA
*
1725640 AAATATTATAATTATAT
1 AAATA-TATATTTATAT
1725657 AAATATATATTTATAT
1 AAATATATATTTATAT
*
1725673 ATATAT
1 AAATAT
1725679 GAATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATATATATTTATAT
Found at i:1728383 original size:22 final size:24
Alignment explanation
Indices: 1728358--1728410 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
1728348 AAGCCTTAGA
*
1728358 AAAAACAAAAATT-AA-AATGACT
1 AAAAACAAAAATTCAACAATGAAT
*
1728380 AAAAATAAAAATTCAACAATGAAT
1 AAAAACAAAAATTCAACAATGAAT
1728404 AAGAAAC
1 AA-AAAC
1728411 TCAATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 12 0.48
23 2 0.08
24 8 0.32
25 3 0.12
ACGTcount: A:0.68, C:0.09, G:0.06, T:0.17
Consensus pattern (24 bp):
AAAAACAAAAATTCAACAATGAAT
Found at i:1729932 original size:2 final size:2
Alignment explanation
Indices: 1729925--1729953 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1729915 TAATGTGTAC
1729925 AT 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 AT A
1729954 CCAGGTGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1733579 original size:26 final size:26
Alignment explanation
Indices: 1733516--1733579 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
1733506 ATATTTTTTC
1733516 AATAAAAA-TAT-ATTAATATTAATT
1 AATAAAAATTATAATTAATATTAATT
* *
1733540 AATCTAAAATTATAATTTATATT-ATT
1 AAT-AAAAATTATAATTAATATTAATT
1733566 AATAAAAATCTATA
1 AATAAAAAT-TATA
1733580 TACTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
24 3 0.09
25 9 0.27
26 13 0.39
27 8 0.24
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (26 bp):
AATAAAAATTATAATTAATATTAATT
Found at i:1733816 original size:25 final size:24
Alignment explanation
Indices: 1733788--1733842 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
1733778 ATTTCTAATG
* *
1733788 ATATGCATGTTAGAGAGAATTTTAA
1 ATATGCAAGTTAGAGA-AAATTTAA
* *
1733813 ATATTGCAAGTTTGATAAAATTTAA
1 ATA-TGCAAGTTAGAGAAAATTTAA
1733838 ATATG
1 ATATG
1733843 TAATGTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
24 2 0.08
25 13 0.52
26 10 0.40
ACGTcount: A:0.42, C:0.04, G:0.16, T:0.38
Consensus pattern (24 bp):
ATATGCAAGTTAGAGAAAATTTAA
Found at i:1734103 original size:3 final size:3
Alignment explanation
Indices: 1734095--1734120 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
1734085 TTTTGCTTAT
1734095 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
1734121 TAAAGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1734591 original size:12 final size:12
Alignment explanation
Indices: 1734576--1734613 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1734566 TATATTTAAC
1734576 TATATTAAAAAT
1 TATATTAAAAAT
1734588 TATATT-AAAAT
1 TATATTAAAAAT
*
1734599 AATATATAAAAAT
1 TATAT-TAAAAAT
1734612 TA
1 TA
1734614 AAATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 9 0.41
12 7 0.32
13 6 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TATATTAAAAAT
Found at i:1751821 original size:18 final size:18
Alignment explanation
Indices: 1751775--1751825 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1751765 TATTATGTCT
*
1751775 ATATAAATTATAACATATA
1 ATATAAA-TATAAAATATA
* **
1751794 ATTTTTATATAAAATATA
1 ATATAAATATAAAATATA
1751812 ATATAAATATAAAA
1 ATATAAATATAAAA
1751826 ATTTTAATAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAATATAAAATATA
Found at i:1754312 original size:30 final size:30
Alignment explanation
Indices: 1754252--1754313 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
1754242 TCTTTGGCTT
* *
1754252 AATTGGGTGAAAATAGATGTTTAACTGTTC
1 AATTGGGTGAAAACAGATGTTTAACGGTTC
*
1754282 AATTGGGTGAAAACAGATGTTTAAGGGTTC
1 AATTGGGTGAAAACAGATGTTTAACGGTTC
1754312 AA
1 AA
1754314 CTGATTCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (30 bp):
AATTGGGTGAAAACAGATGTTTAACGGTTC
Found at i:1760165 original size:18 final size:18
Alignment explanation
Indices: 1760144--1760192 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 18
1760134 ACCCGAAATT
1760144 AATAAAATATTAATTTTTA
1 AATAAAATATT-ATTTTTA
1760163 ATATAAAATATTATTTTTA
1 A-ATAAAATATTATTTTTA
1760182 AATATAAATAT
1 AATA-AAATAT
1760193 AAAAAATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.11
19 15 0.54
20 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATAAAATATTATTTTTA
Found at i:1760180 original size:19 final size:21
Alignment explanation
Indices: 1760145--1760189 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
1760135 CCCGAAATTA
1760145 ATAAAATATTAATTTTT-AAT
1 ATAAAATATTAATTTTTAAAT
1760165 ATAAAATATT-ATTTTTAAAT
1 ATAAAATATTAATTTTTAAAT
1760185 ATAAA
1 ATAAA
1760190 TATAAAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATAAAATATTAATTTTTAAAT
Found at i:1760212 original size:26 final size:26
Alignment explanation
Indices: 1760183--1760261 Score: 87
Period size: 26 Copynumber: 3.2 Consensus size: 26
1760173 TTATTTTTAA
1760183 ATATAAATATAAAAAATTAAATAAAT
1 ATATAAATATAAAAAATTAAATAAAT
* * *
1760209 ATATAAATATATAATATAAAATTAAAT
1 ATATAAATATAAAAAATTAAA-TAAAT
1760236 A-A-AAA-ATAAAAAA-TAAA-AAAT
1 ATATAAATATAAAAAATTAAATAAAT
1760257 ATATA
1 ATATA
1760262 CAGGTCGGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 5 0.11
22 1 0.02
23 4 0.09
24 6 0.14
25 3 0.07
26 19 0.43
27 6 0.14
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (26 bp):
ATATAAATATAAAAAATTAAATAAAT
Found at i:1760242 original size:7 final size:7
Alignment explanation
Indices: 1760232--1760257 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1760222 ATATAAAATT
1760232 AAATAAA
1 AAATAAA
1760239 AAATAAA
1 AAATAAA
1760246 AAATAAA
1 AAATAAA
1760253 AAATA
1 AAATA
1760258 TATACAGGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAATAAA
Found at i:1772717 original size:22 final size:20
Alignment explanation
Indices: 1772692--1772731 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
1772682 TGATATTCAA
1772692 ATTTTAATATTTATAATTATTT
1 ATTTTAATA-TTA-AATTATTT
*
1772714 ATTTTATTATTAAATTAT
1 ATTTTAATATTAAATTAT
1772732 GATATTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 3 0.18
22 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTTAATATTAAATTATTT
Found at i:1773859 original size:21 final size:23
Alignment explanation
Indices: 1773833--1773875 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
1773823 TTTCTGAAAT
1773833 GCATAA-CAATCGACT-CTTTTA
1 GCATAAGCAATCGACTCCTTTTA
*
1773854 GCATAAGCAGTCGACTCCTTTT
1 GCATAAGCAATCGACTCCTTTT
1773876 TAGTTAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (23 bp):
GCATAAGCAATCGACTCCTTTTA
Found at i:1787171 original size:37 final size:37
Alignment explanation
Indices: 1787121--1787193 Score: 128
Period size: 37 Copynumber: 2.0 Consensus size: 37
1787111 CAGGTCCACG
**
1787121 TTATTTTCATCATCTAGTTATAATTCGGATTATATTC
1 TTATTTTCATCATCTAGTTATAATTCAAATTATATTC
1787158 TTATTTTCATCATCTAGTTATAATTCAAATTATATT
1 TTATTTTCATCATCTAGTTATAATTCAAATTATATT
1787194 AGCTAATCTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.52
Consensus pattern (37 bp):
TTATTTTCATCATCTAGTTATAATTCAAATTATATTC
Found at i:1789187 original size:18 final size:18
Alignment explanation
Indices: 1789139--1789213 Score: 79
Period size: 18 Copynumber: 4.4 Consensus size: 18
1789129 AATTAAAATA
*
1789139 AATAAAAAT-TATCATGC
1 AATAATAATATATCATGC
1789156 -A-AATAATAT-T-ATGC
1 AATAATAATATATCATGC
1789170 AATAATAATATATCATGC
1 AATAATAATATATCATGC
* *
1789188 AATTATAATATAATTATGC
1 AATAATAATAT-ATCATGC
1789207 AATAATA
1 AATAATA
1789214 TAATATATAA
Statistics
Matches: 48, Mismatches: 4, Indels: 10
0.77 0.06 0.16
Matches are distributed among these distances:
14 4 0.08
15 7 0.15
16 10 0.21
17 1 0.02
18 14 0.29
19 12 0.25
ACGTcount: A:0.52, C:0.08, G:0.05, T:0.35
Consensus pattern (18 bp):
AATAATAATATATCATGC
Found at i:1789197 original size:21 final size:21
Alignment explanation
Indices: 1789171--1789275 Score: 76
Period size: 21 Copynumber: 4.9 Consensus size: 21
1789161 ATATTATGCA
1789171 ATAATAATATATCATGCAATT
1 ATAATAATATATCATGCAATT
*
1789192 ATAAT-ATA-ATTATGCAATAAT
1 ATAATAATATATCATGCAAT--T
1789213 ATAATATATAAATTATCATGCAATT
1 ATAATA-AT--A-TATCATGCAATT
*
1789238 A-ATATAAAATATCATGCAATT
1 ATA-ATAATATATCATGCAATT
* *
1789259 A-ATTAATA-ATTATGCAA
1 ATAATAATATATCATGCAA
1789276 AAATATAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 20
0.73 0.06 0.21
Matches are distributed among these distances:
19 17 0.25
20 7 0.10
21 25 0.36
22 1 0.01
23 2 0.03
24 2 0.03
25 6 0.09
27 9 0.13
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (21 bp):
ATAATAATATATCATGCAATT
Found at i:1789214 original size:16 final size:16
Alignment explanation
Indices: 1789163--1789217 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 16
1789153 TGCAAATAAT
1789163 ATTATGCAATAATAATA
1 ATTATGCAATAAT-ATA
*
1789180 TATCATGCAATTATAATATA
1 -ATTATGC-A--ATAATATA
1789200 ATTATGCAATAATATA
1 ATTATGCAATAATATA
1789216 AT
1 AT
1789218 ATATAAATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
16 10 0.31
18 7 0.22
19 7 0.22
20 3 0.09
21 5 0.16
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTATGCAATAATATA
Found at i:1789275 original size:19 final size:21
Alignment explanation
Indices: 1789218--1789285 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
1789208 ATAATATAAT
*
1789218 ATATAAATTATCATGCAATTA
1 ATATAAAATATCATGCAATTA
1789239 ATATAAAATATCATGCAATTA
1 ATATAAAATATCATGCAATTA
*
1789260 AT-TAATAAT-T-ATGCAA-AA
1 ATATAA-AATATCATGCAATTA
1789278 ATATAAAA
1 ATATAAAA
1789286 AAAATCATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
18 5 0.12
19 9 0.21
20 4 0.09
21 25 0.58
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.34
Consensus pattern (21 bp):
ATATAAAATATCATGCAATTA
Found at i:1789407 original size:14 final size:13
Alignment explanation
Indices: 1789388--1789449 Score: 63
Period size: 14 Copynumber: 4.6 Consensus size: 13
1789378 CAAGAAATGG
1789388 AAATAAAATCAAA
1 AAATAAAATCAAA
1789401 AACATAAAATCAAA
1 AA-ATAAAATCAAA
*
1789415 AAATAAAAATAAAA
1 AAAT-AAAATCAAA
*
1789429 ATAAAAAAAT-AAA
1 A-AATAAAATCAAA
*
1789442 AAAGAAAA
1 AAATAAAA
1789450 AACCTACTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
12 6 0.14
13 8 0.19
14 27 0.63
15 2 0.05
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.13
Consensus pattern (13 bp):
AAATAAAATCAAA
Found at i:1789410 original size:33 final size:33
Alignment explanation
Indices: 1789373--1789442 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
1789363 AAACATATAA
* ** *
1789373 AAAATCAAGAAATGGAAAT-AAAATCAAAAACAT
1 AAAATCAAAAAATAAAAATAAAAAT-AAAAAAAT
1789406 AAAATCAAAAAATAAAAATAAAAATAAAAAAAT
1 AAAATCAAAAAATAAAAATAAAAATAAAAAAAT
1789439 AAAA
1 AAAA
1789443 AAGAAAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 27 0.84
34 5 0.16
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (33 bp):
AAAATCAAAAAATAAAAATAAAAATAAAAAAAT
Found at i:1789436 original size:27 final size:28
Alignment explanation
Indices: 1789388--1789450 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
1789378 CAAGAAATGG
*
1789388 AAAT-AAAATCAAAAAC-ATAAAATCAAA
1 AAATAAAAATCAAAAACAAAAAAAT-AAA
*
1789415 AAATAAAAAT-AAAAATAAAAAAATAAA
1 AAATAAAAATCAAAAACAAAAAAATAAA
*
1789442 AAAGAAAAA
1 AAATAAAAA
1789451 ACCTACTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 20 0.65
28 11 0.35
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.13
Consensus pattern (28 bp):
AAATAAAAATCAAAAACAAAAAAATAAA
Found at i:1789449 original size:20 final size:20
Alignment explanation
Indices: 1789392--1789443 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
1789382 AAATGGAAAT
*
1789392 AAAATCAAAAACATAAAATCAA
1 AAAAT-AAAAACA-AAAATAAA
*
1789414 AAAATAAAAATAAAAATAAA
1 AAAATAAAAACAAAAATAAA
1789434 AAAATAAAAA
1 AAAATAAAAA
1789444 AGAAAAAACC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 17 0.61
21 6 0.21
22 5 0.18
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAATAAAAACAAAAATAAA
Found at i:1820411 original size:2 final size:2
Alignment explanation
Indices: 1820404--1820431 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1820394 ACTACGACTT
1820404 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
1820432 AAGATTGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1822869 original size:6 final size:6
Alignment explanation
Indices: 1822858--1822888 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
1822848 AATCCAAGGC
*
1822858 AATTGA AATTGA AATTGA AACTGA AATTGA A
1 AATTGA AATTGA AATTGA AATTGA AATTGA A
1822889 GGTAAACGGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.29
Consensus pattern (6 bp):
AATTGA
Found at i:1824081 original size:13 final size:13
Alignment explanation
Indices: 1824063--1824116 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
1824053 TTTTTTATAT
1824063 TATTATCATATTA
1 TATTATCATATTA
*
1824076 TATTATCATATCA
1 TATTATCATATTA
*
1824089 TATTAT-ATTTTA
1 TATTATCATATTA
*
1824101 AATTATCATATT-
1 TATTATCATATTA
1824113 TATT
1 TATT
1824117 GTTAAATGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.35
13 22 0.65
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATCATATTA
Found at i:1824089 original size:18 final size:16
Alignment explanation
Indices: 1824057--1824097 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 16
1824047 TTCATATTTT
1824057 TTATATTATTATCATA
1 TTATATTATTATCATA
1824073 TTATATTATCATATCATA
1 TTATATTAT--TATCATA
1824091 TTATATT
1 TTATATT
1824098 TTAAATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.39
18 14 0.61
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (16 bp):
TTATATTATTATCATA
Found at i:1824109 original size:20 final size:20
Alignment explanation
Indices: 1824064--1824123 Score: 72
Period size: 18 Copynumber: 3.1 Consensus size: 20
1824054 TTTTTATATT
* *
1824064 ATTATCATATTATATTAT-C
1 ATTATCATATTATATTTTAA
1824083 A-TATCATATTATATTTTAA
1 ATTATCATATTATATTTTAA
1824102 ATTATCATATT-TATTGTTAA
1 ATTATCATATTATATT-TTAA
1824122 AT
1 AT
1824124 GTAATTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 15 0.42
19 6 0.17
20 15 0.42
ACGTcount: A:0.38, C:0.07, G:0.02, T:0.53
Consensus pattern (20 bp):
ATTATCATATTATATTTTAA
Found at i:1827286 original size:13 final size:13
Alignment explanation
Indices: 1827268--1827294 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1827258 AACCTTTTTG
1827268 ACAATTTGAAACT
1 ACAATTTGAAACT
1827281 ACAATTTGAAACT
1 ACAATTTGAAACT
1827294 A
1 A
1827295 TTTGAAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.07, T:0.30
Consensus pattern (13 bp):
ACAATTTGAAACT
Found at i:1827549 original size:20 final size:21
Alignment explanation
Indices: 1827524--1827562 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
1827514 TTAACATAAC
1827524 AAAAATAT-ATTAAA-ATAAGT
1 AAAAAT-TCATTAAATATAAGT
1827544 AAAAATTCATTAAATATAA
1 AAAAATTCATTAAATATAA
1827563 TATAACTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.06
20 12 0.71
21 4 0.24
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (21 bp):
AAAAATTCATTAAATATAAGT
Found at i:1828798 original size:3 final size:3
Alignment explanation
Indices: 1828773--1828816 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
1828763 AAATAAATTT
* *
1828773 TTA TTT TTA TT- TAA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1828817 ATTTAACATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
2 3 0.09
3 32 0.91
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1832411 original size:20 final size:19
Alignment explanation
Indices: 1832376--1832427 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
1832366 ATAACATGAA
*
1832376 ATTAACATAATAAAAATAT-
1 ATTAAAATAATAAAAAT-TC
1832395 ATTAAAATAAGTAAAAATTC
1 ATTAAAATAA-TAAAAATTC
1832415 ATTAAAAATAATA
1 ATT-AAAATAATA
1832428 TAACTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.34
20 12 0.41
21 7 0.24
ACGTcount: A:0.63, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
ATTAAAATAATAAAAATTC
Found at i:1841395 original size:20 final size:19
Alignment explanation
Indices: 1841360--1841411 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 19
1841350 ATAACATAAA
*
1841360 ATTAATATAATAAAAATAT-
1 ATTAAAATAATAAAAAT-TC
1841379 ATTAAAATAAGTAAAAATTC
1 ATTAAAATAA-TAAAAATTC
1841399 ATTAAAAATAATA
1 ATT-AAAATAATA
1841412 TAACTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 10 0.34
20 12 0.41
21 7 0.24
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (19 bp):
ATTAAAATAATAAAAATTC
Found at i:1843508 original size:23 final size:23
Alignment explanation
Indices: 1843477--1843528 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
1843467 AATTTGATAC
* *
1843477 TTTTA-TATATTTTTTATATTAT-
1 TTTTATTATA-TTATTATATCATA
1843499 TTTTATTATATTATTATATCATA
1 TTTTATTATATTATTATATCATA
1843522 TTTTATT
1 TTTTATT
1843529 TTAAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 15 0.58
23 11 0.42
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTATTATATTATTATATCATA
Found at i:1843509 original size:14 final size:13
Alignment explanation
Indices: 1843477--1843513 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1843467 AATTTGATAC
1843477 TTTTATA-TA-TT
1 TTTTATATTATTT
1843488 TTTTATATTATTT
1 TTTTATATTATTT
1843501 TTATTATATTATT
1 TT-TTATATTATT
1843514 ATATCATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 7 0.30
12 2 0.09
13 4 0.17
14 10 0.43
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTATATTATTT
Found at i:1847032 original size:21 final size:20
Alignment explanation
Indices: 1847001--1847078 Score: 67
Period size: 21 Copynumber: 3.9 Consensus size: 20
1846991 ATAAATTATT
1847001 AATAT-TTTATATAATATAA
1 AATATATTTATATAATATAA
1847020 AATTATATTTATAT-ATAATTAA
1 AA-TATATTTATATAAT-A-TAA
*
1847042 AATATAATTTATATTAA-AAAA
1 AATAT-ATTTATA-TAATATAA
1847063 AATAT-TTTATA-AATAT
1 AATATATTTATATAATAT
1847079 TATATTAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
17 2 0.04
18 1 0.02
19 8 0.16
20 5 0.10
21 18 0.37
22 13 0.27
23 1 0.02
24 1 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATATATTTATATAATATAA
Found at i:1847062 original size:19 final size:21
Alignment explanation
Indices: 1847004--1847073 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 21
1846994 AATTATTAAT
*
1847004 ATTT-TATATAATATAAAATTA
1 ATTTATATATAATA-AAAAATA
*
1847025 TATTTATATATAATTAAAATATA
1 -ATTTATATATAA-TAAAAAATA
1847048 ATTTATAT-TAA-AAAAAATA
1 ATTTATATATAATAAAAAATA
*
1847067 TTTTATA
1 ATTTATA
1847074 AATATTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
19 13 0.31
21 3 0.07
22 12 0.29
23 12 0.29
24 2 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
ATTTATATATAATAAAAAATA
Found at i:1848383 original size:12 final size:12
Alignment explanation
Indices: 1848364--1848402 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1848354 TTAATTTAAA
1848364 TATATTAAAATT
1 TATATTAAAATT
* *
1848376 TTTATTAAAATAA
1 TATATTAAAAT-T
1848389 TATATTAAAATT
1 TATATTAAAATT
1848401 TA
1 TA
1848403 AAAATTGATA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TATATTAAAATT
Found at i:1849798 original size:12 final size:12
Alignment explanation
Indices: 1849781--1849813 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1849771 TTAAATTATA
1849781 AATAATATTTTT
1 AATAATATTTTT
1849793 AATAAT-TTTTT
1 AATAATATTTTT
1849804 ATATAATATT
1 A-ATAATATT
1849814 AATTTTTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.32
12 11 0.58
13 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
AATAATATTTTT
Found at i:1850450 original size:7 final size:7
Alignment explanation
Indices: 1850432--1850464 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1850422 CAATGTTTGG
1850432 ATTAAAA
1 ATTAAAA
1850439 A-TAAAA
1 ATTAAAA
1850445 ATTAAAAA
1 ATT-AAAA
1850453 ATTAAAA
1 ATTAAAA
1850460 ATTAA
1 ATTAA
1850465 CAATAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 6 0.25
7 11 0.46
8 7 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
ATTAAAA
Found at i:1850458 original size:15 final size:14
Alignment explanation
Indices: 1850435--1850464 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1850425 TGTTTGGATT
1850435 AAAAATAAAAATTA
1 AAAAATAAAAATTA
1850449 AAAAATTAAAAATTA
1 AAAAA-TAAAAATTA
1850464 A
1 A
1850465 CAATAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAATAAAAATTA
Found at i:1850948 original size:1 final size:1
Alignment explanation
Indices: 1850942--1850966 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
1850932 CAAAGCCAAG
1850942 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
1850967 CTGTTACTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1853327 original size:2 final size:2
Alignment explanation
Indices: 1853322--1853356 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1853312 TATATATATA
*
1853322 TG TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1853357 TAATTATTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1860606 original size:16 final size:16
Alignment explanation
Indices: 1860574--1860616 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
1860564 GATACTAATA
* *
1860574 AAATATAACA-TATAT
1 AAATATAAAATTAAAT
1860589 AAATATAAAATTAAAT
1 AAATATAAAATTAAAT
1860605 AAATAATAAAAT
1 AAAT-ATAAAAT
1860617 ATATATTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 9 0.38
16 8 0.33
17 7 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AAATATAAAATTAAAT
Found at i:1860610 original size:20 final size:22
Alignment explanation
Indices: 1860571--1860610 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
1860561 TAAGATACTA
*
1860571 ATAAAATATAACATATATAAAT
1 ATAAAATATAACATAAATAAAT
1860593 ATAAAAT-TAA-ATAAATAA
1 ATAAAATATAACATAAATAA
1860611 TAAAATATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 3 0.18
22 7 0.41
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (22 bp):
ATAAAATATAACATAAATAAAT
Found at i:1861760 original size:19 final size:21
Alignment explanation
Indices: 1861738--1861776 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1861728 CTTTTAAAAA
1861738 ATTAAA-A-ATAAAAATTTTT
1 ATTAAATATATAAAAATTTTT
1861757 ATTAAATATATAAAAATTTT
1 ATTAAATATATAAAAATTTT
1861777 AAAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATTAAATATATAAAAATTTTT
Found at i:1864975 original size:19 final size:19
Alignment explanation
Indices: 1864907--1864975 Score: 54
Period size: 18 Copynumber: 3.7 Consensus size: 19
1864897 TTCAACCAAA
1864907 TATTTAAAAATATT--AAAT
1 TATTT-AAAATATTAAAAAT
*
1864925 TATATTAAAATAATAAAAA-
1 TAT-TTAAAATATTAAAAAT
* * *
1864944 AATTTTAAGTATTAAAAAT
1 TATTTAAAATATTAAAAAT
*
1864963 TATTTGAAATATT
1 TATTTAAAATATT
1864976 TAATATTTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
18 22 0.56
19 14 0.36
20 3 0.08
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
TATTTAAAATATTAAAAAT
Found at i:1865418 original size:2 final size:2
Alignment explanation
Indices: 1865411--1865442 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1865401 AGTATAGATT
1865411 AG AG AG 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 AG AG AG
1865443 GGTTAACTTA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1865788 original size:6 final size:6
Alignment explanation
Indices: 1865777--1865802 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1865767 TAATACTCAC
1865777 CCCATA CCCATA CCCATA CCCATA CC
1 CCCATA CCCATA CCCATA CCCATA CC
1865803 TTACACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCATA
Found at i:1865935 original size:24 final size:23
Alignment explanation
Indices: 1865883--1865936 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1865873 AATTAAAATT
* *
1865883 AATATATTTTGTTAAATATATT-
1 AATATATTTTATTAAAAATATTA
1865905 AATATATATTTATTAAAAATTATCTA
1 AATATAT-TTTATTAAAAA-TAT-TA
1865931 AATATA
1 AATATA
1865937 CAAGATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 7 0.27
23 9 0.35
24 3 0.12
25 1 0.04
26 6 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (23 bp):
AATATATTTTATTAAAAATATTA
Found at i:1865957 original size:9 final size:9
Alignment explanation
Indices: 1865943--1865972 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
1865933 TATACAAGAT
1865943 AAAAATTAA
1 AAAAATTAA
1865952 AAAAATT-A
1 AAAAATTAA
1865960 AAAAATTAA
1 AAAAATTAA
1865969 AAAA
1 AAAA
1865973 TTATTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (9 bp):
AAAAATTAA
Found at i:1865962 original size:8 final size:8
Alignment explanation
Indices: 1865943--1865975 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
1865933 TATACAAGAT
1865943 AAAAATTAA
1 AAAAATT-A
1865952 AAAAATTA
1 AAAAATTA
1865960 AAAAATTA
1 AAAAATTA
1865968 AAAAATTA
1 AAAAATTA
1865976 TTTTTTTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAAATTA
Found at i:1866484 original size:19 final size:18
Alignment explanation
Indices: 1866453--1866522 Score: 54
Period size: 19 Copynumber: 3.8 Consensus size: 18
1866443 TAAAATTTGG
1866453 AATT-TAATAAGATAAAAGT
1 AATTATAAT-AGATAAAA-T
1866472 AATTATAATAGAT-AAAT
1 AATTATAATAGATAAAAT
* * * *
1866489 AATGATATTAAAGAAAACT
1 AATTATAATAGATAAAA-T
*
1866508 AATTATCATAGATAA
1 AATTATAATAGATAA
1866523 TTAATGATAT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
17 10 0.26
18 6 0.15
19 19 0.49
20 4 0.10
ACGTcount: A:0.57, C:0.03, G:0.09, T:0.31
Consensus pattern (18 bp):
AATTATAATAGATAAAAT
Found at i:1866519 original size:36 final size:36
Alignment explanation
Indices: 1866466--1866538 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
1866456 TTAATAAGAT
*
1866466 AAAAGTAATTATAATAGATAAATAATGATATTAAAG
1 AAAACTAATTATAATAGATAAATAATGATATTAAAG
* *
1866502 AAAACTAATTATCATAGATAATTAATGATATTAAAG
1 AAAACTAATTATAATAGATAAATAATGATATTAAAG
1866538 A
1 A
1866539 TAGAAAAAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.56, C:0.03, G:0.10, T:0.32
Consensus pattern (36 bp):
AAAACTAATTATAATAGATAAATAATGATATTAAAG
Found at i:1870877 original size:21 final size:21
Alignment explanation
Indices: 1870853--1870923 Score: 54
Period size: 21 Copynumber: 3.2 Consensus size: 21
1870843 TAAAGATTTA
1870853 CTAAGATTGAGAATTAACTAT
1 CTAAGATTGAGAATTAACTAT
** * *
1870874 CTAATCTTGA-AATTGTAAAGATTT
1 CTAAGATTGAGAA-T-T-AA-CTAT
1870898 ACTAAGATTGAGAATTAACTAT
1 -CTAAGATTGAGAATTAACTAT
1870920 CTAA
1 CTAA
1870924 TCTTGTACCG
Statistics
Matches: 36, Mismatches: 8, Indels: 12
0.64 0.14 0.21
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
22 3 0.08
23 4 0.11
24 3 0.08
25 9 0.25
26 2 0.06
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (21 bp):
CTAAGATTGAGAATTAACTAT
Found at i:1870903 original size:46 final size:46
Alignment explanation
Indices: 1870836--1870928 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
1870826 CTACTTGCTG
1870836 GAAATTGTAAAGATTTACTAAGATTGAGAATTAACTATCTAATCTT
1 GAAATTGTAAAGATTTACTAAGATTGAGAATTAACTATCTAATCTT
1870882 GAAATTGTAAAGATTTACTAAGATTGAGAATTAACTATCTAATCTT
1 GAAATTGTAAAGATTTACTAAGATTGAGAATTAACTATCTAATCTT
1870928 G
1 G
1870929 TACCGGGATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.37
Consensus pattern (46 bp):
GAAATTGTAAAGATTTACTAAGATTGAGAATTAACTATCTAATCTT
Found at i:1887643 original size:17 final size:18
Alignment explanation
Indices: 1887621--1887654 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1887611 CATATAATAT
*
1887621 TTGTATTTTTAT-TTGTA
1 TTGTATTATTATATTGTA
1887638 TTGTATTATTATATTGT
1 TTGTATTATTATATTGT
1887655 GTTTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.21, C:0.00, G:0.12, T:0.68
Consensus pattern (18 bp):
TTGTATTATTATATTGTA
Found at i:1900631 original size:12 final size:12
Alignment explanation
Indices: 1900614--1900647 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1900604 AACATTGAAC
1900614 TACAAAAGAAGT
1 TACAAAAGAAGT
*
1900626 TACAAAAGGAGT
1 TACAAAAGAAGT
*
1900638 TAAAAAAGAA
1 TACAAAAGAA
1900648 TTTGATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.62, C:0.06, G:0.18, T:0.15
Consensus pattern (12 bp):
TACAAAAGAAGT
Found at i:1901122 original size:17 final size:17
Alignment explanation
Indices: 1901089--1901122 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1901079 TAAATATAAT
* *
1901089 ATAATAATATGATAAAA
1 ATAATAATATAAAAAAA
1901106 ATAATAATATAAAAAAA
1 ATAATAATATAAAAAAA
1901123 TTATGAAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
ATAATAATATAAAAAAA
Found at i:1901131 original size:25 final size:24
Alignment explanation
Indices: 1901080--1901132 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
1901070 TGATAATTTT
* *
1901080 AAATATAATATAATAATATGATAA
1 AAATATAATATAAAAAAATGATAA
* *
1901104 AAATAATAATATAAAAAAATTATGA
1 AAAT-ATAATATAAAAAAATGATAA
1901129 AAAT
1 AAAT
1901133 GATACAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATATAATATAAAAAAATGATAA
Found at i:1902263 original size:62 final size:61
Alignment explanation
Indices: 1902185--1902309 Score: 223
Period size: 62 Copynumber: 2.0 Consensus size: 61
1902175 GTTACAGATC
*
1902185 AAATGGGAAATGTAGGCAGCATGATTTATTGTAGACCTTTTTGGTCTGTGCTGTATTAATTG
1 AAATGGGAAATGTAGGCAGCATGATATATTGTAGACCTTTTTGGTCTGTGCTGTA-TAATTG
*
1902247 AAATGGGAAATTTAGGCAGCATGATATATTGTAGACCTTTTTGGTCTGTGCTGTATAATTG
1 AAATGGGAAATGTAGGCAGCATGATATATTGTAGACCTTTTTGGTCTGTGCTGTATAATTG
1902308 AA
1 AA
1902310 TCTAAGTTAT
Statistics
Matches: 61, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
61 8 0.13
62 53 0.87
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (61 bp):
AAATGGGAAATGTAGGCAGCATGATATATTGTAGACCTTTTTGGTCTGTGCTGTATAATTG
Found at i:1904199 original size:33 final size:34
Alignment explanation
Indices: 1904150--1904214 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
1904140 TATAAAAAAT
1904150 TATTTTTAATTATTTATCTAAATTTAAATTTATA
1 TATTTTTAATTATTTATCTAAATTTAAATTTATA
* * * *
1904184 TATTTTTTA-TATTTATTTAATTTTATATTTA
1 TATTTTTAATTATTTATCTAAATTTAAATTTA
1904215 CATTAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 19 0.70
34 8 0.30
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (34 bp):
TATTTTTAATTATTTATCTAAATTTAAATTTATA
Found at i:1904209 original size:16 final size:16
Alignment explanation
Indices: 1904160--1904214 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1904150 TATTTTTAAT
* *
1904160 TATTTATCTAAATTTA
1 TATTTATATAATTTTA
* *
1904176 AATTTATATATTTTTTA
1 TATTTATATA-ATTTTA
*
1904193 TATTTATTTAATTTTA
1 TATTTATATAATTTTA
1904209 TATTTA
1 TATTTA
1904215 CATTAAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
16 19 0.61
17 12 0.39
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATTTATATAATTTTA
Found at i:1905109 original size:11 final size:10
Alignment explanation
Indices: 1905068--1905109 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
1905058 TAATTATAAT
*
1905068 TTAAAATTTT
1 TTAAAATTTA
1905078 TTAAAATTTA
1 TTAAAATTTA
1905088 TTAAAATTTTA
1 TTAAAA-TTTA
1905099 TATAAAATTTA
1 T-TAAAATTTA
1905110 CACTTATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 15 0.52
11 9 0.31
12 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
TTAAAATTTA
Found at i:1906339 original size:12 final size:12
Alignment explanation
Indices: 1906314--1906349 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
1906304 ATATATAAAA
1906314 AATTATTT-TTT
1 AATTATTTATTT
1906325 AATTATTTATTT
1 AATTATTTATTT
*
1906337 AATTATATATTT
1 AATTATTTATTT
1906349 A
1 A
1906350 TAATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 8 0.35
12 15 0.65
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
AATTATTTATTT
Found at i:1906370 original size:19 final size:21
Alignment explanation
Indices: 1906341--1906390 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1906331 TTATTTAATT
1906341 ATATATTTATA-AT-AAAAATA
1 ATAT-TTTATATATAAAAAATA
* *
1906361 ATTTTTTATATTTAAAAAATA
1 ATATTTTATATATAAAAAATA
1906382 ATATTTTAT
1 ATATTTTAT
1906391 TAATTTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 6 0.24
20 4 0.16
21 15 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATTTTATATATAAAAAATA
Done.