Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A11
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: 114316535
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4920000 characters in sequence are not A, C, G, or T
File 9 of 356
Found at i:3140900 original size:41 final size:41
Alignment explanation
Indices: 3140796--3140902 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
3140786 TACTTTTTTG
* * *
3140796 CGGCGTTTTTCCAAAAGCACCACTAAAACCTCGATCTATAG
1 CGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATAC
* * *
3140837 CAGCGTTTTTTCAAAAGTGCCGCTAAAACCTCGATCTATAC
1 CGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATAC
3140878 CGGCGTTTTTCCAAAAGCGCCGCTA
1 CGGCGTTTTTCCAAAAGCGCCGCTA
3140903 TTGTTCAGTT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.26
Consensus pattern (41 bp):
CGGCGTTTTTCCAAAAGCGCCGCTAAAACCTCGATCTATAC
Found at i:3146536 original size:35 final size:35
Alignment explanation
Indices: 3146488--3146821 Score: 393
Period size: 35 Copynumber: 9.5 Consensus size: 35
3146478 GACAAAGTGC
*
3146488 GAAATGTAGGTATGGTATTAACCATACCGAGTTGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
* * * *
3146523 GAAACGTAAGTATGGTATTAACCATACCGAGATGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
* * *
3146558 GAAACGTAGCTATGGTATCATCCATACCGAGTTGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
* * * * * *
3146593 GACATGTAGATATGGTATCATTCTTACCGGGTTGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
* * *
3146628 GAAATGTAGGTATGGTATCATCCATACCGAATTGA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
* * *
3146663 AAAATGTAGATATGGTATTATCCATACTGAGTTGT
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
* * * *
3146698 GAAACGTAGGTATGGTATCATCCATGCCGAGTTGA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
* **
3146733 GAAATGTAGGTATGGTATTATCCATACTGAGTTAA
1 GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
3146768 GAAATGTAGGTAT-GTCATT-TCCCATACCGAGTTGT
1 GAAATGTAGGTATGGT-ATTAT-CCATACCGAGTTGT
3146803 GAAATGTAGGTATGGTATT
1 GAAATGTAGGTATGGTATT
3146822 TCAATGAGGA
Statistics
Matches: 254, Mismatches: 42, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
34 3 0.01
35 249 0.98
36 2 0.01
ACGTcount: A:0.31, C:0.13, G:0.24, T:0.32
Consensus pattern (35 bp):
GAAATGTAGGTATGGTATTATCCATACCGAGTTGT
Found at i:3148373 original size:30 final size:30
Alignment explanation
Indices: 3148337--3148399 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
3148327 ACTTAACAAG
*
3148337 CAAATGTCTCTAAAATAATAATAAAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
* *
3148367 CAAATGTCTTTAAAATAATAACATAATTAA
1 CAAATGTCTCTAAAATAATAACAAAATTAA
3148397 CAA
1 CAA
3148400 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.30
Consensus pattern (30 bp):
CAAATGTCTCTAAAATAATAACAAAATTAA
Found at i:3157981 original size:16 final size:16
Alignment explanation
Indices: 3157960--3158016 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
3157950 TTTGGTTCGC
*
3157960 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
3157976 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
3157992 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
3158008 TGTAATGGA
1 TGTAATGGA
3158017 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:3158283 original size:18 final size:17
Alignment explanation
Indices: 3158262--3158296 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
3158252 TTATTATTAA
*
3158262 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
3158280 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
3158297 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:3158433 original size:16 final size:16
Alignment explanation
Indices: 3158396--3158437 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3158386 TTAATCATAT
*
3158396 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
3158412 TT-AAATATATTATAA
1 TTAAAATATATTATAA
3158427 TTAAAATATAT
1 TTAAAATATAT
3158438 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:3158435 original size:154 final size:156
Alignment explanation
Indices: 3158149--3158462 Score: 560
Period size: 154 Copynumber: 2.0 Consensus size: 156
3158139 TAGAATACCC
3158149 TTAGCAGAAATTTGTTTTGGTAAATGATTATAGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATAGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
3158214 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
*
3158279 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAAAAA
* * *
3158306 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATAGTTATTGTTATTTAAATTTTAATAAGATTATAT
3158369 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
3158434 ATATAATTTAATAAAATTCTTAAAAA
131 ATATAATTTAATAAAATTCTTAAAAA
3158460 TTA
1 TTA
3158463 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
154 92 0.61
155 1 0.01
157 59 0.39
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (156 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATAGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAAAAA
Found at i:3158444 original size:14 final size:15
Alignment explanation
Indices: 3158405--3158446 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3158395 TTTAAACATA
*
3158405 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3158420 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
3158434 A-TATAATTTAATA
1 ATTATAATTAAATA
3158447 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3158533 original size:120 final size:121
Alignment explanation
Indices: 3158394--3158690 Score: 462
Period size: 120 Copynumber: 2.5 Consensus size: 121
3158384 ATTTAATCAT
*
3158394 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAA-A
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* * *
3158458 AATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAA
66 AA-TAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGA-AA
3158516 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
3158579 AATAAAATTCTTCTATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
66 AATAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
* *
3158635 ATTTCAA-ATAATTAATATTAAATATGATT-TAATT-AAATATATGATTTAATAAAATT
1 ATTTCAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATT
3158691 TAAAATTATT
Statistics
Matches: 165, Mismatches: 6, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
119 24 0.15
120 130 0.79
121 10 0.06
122 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (121 bp):
ATTTCAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
AATAAAATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAGAAA
Found at i:3158564 original size:14 final size:15
Alignment explanation
Indices: 3158515--3158566 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
3158505 GTAAAATATA
3158515 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
3158530 TATTAAATATATTAT
1 AATTAAATATATTAT
3158545 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
3158558 AATTTAATA
1 AATTAAATA
3158567 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:3158581 original size:44 final size:43
Alignment explanation
Indices: 3158492--3158582 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
3158482 CTCAAATCAT
* * *
3158492 AATATATGATACTGTAAAATATAAATTAACATAATTATTATTA
1 AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
* * *
3158535 AATATATTATAAT-TAAAATATATAATTTAATAAAATTCTTAATA
1 AATATATGATAATGTAAAATATA-AA-TTAACAAAATTATTAATA
3158579 AATA
1 AATA
3158583 AAATTCTTCT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
42 9 0.22
43 13 0.32
44 18 0.45
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (43 bp):
AATATATGATAATGTAAAATATAAATTAACAAAATTATTAATA
Found at i:3158617 original size:59 final size:59
Alignment explanation
Indices: 3158434--3158617 Score: 148
Period size: 59 Copynumber: 3.1 Consensus size: 59
3158424 TAATTAAAAT
3158434 ATATAATTTAATAAAATTCTTAA-AAATTAATATTCTTATATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAA-TAATATTCTTATATGAATTTACTCAAATCATA
* * * * * * * *
3158493 ATAT-ATGATACTGTAAAA-TATAAATTAACATAATTATTATTAAAT-ATATTATAATTAAA--A
1 ATATAAT-TTA--ATAAAATTCTTAA-TAA-ATAA-TATTCTTATATGA-ATT-TACTCAAATCA
3158553 T-
58 TA
* *
3158554 ATATAATTTAATAAAATTCTTAATAAATAAAATTCTTCTATGAATTTACTCAAATCATA
1 ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
3158613 ATATA
1 ATATA
3158618 TGATACTATA
Statistics
Matches: 92, Mismatches: 18, Indels: 30
0.66 0.13 0.21
Matches are distributed among these distances:
56 6 0.07
57 10 0.11
58 9 0.10
59 19 0.21
60 8 0.09
61 11 0.12
62 10 0.11
63 13 0.14
64 6 0.07
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATAAATAATATTCTTATATGAATTTACTCAAATCATA
Found at i:3158671 original size:15 final size:15
Alignment explanation
Indices: 3158651--3158689 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
3158641 AATAATTAAT
3158651 ATTAAATATGATTTA
1 ATTAAATATGATTTA
3158666 ATTAAATATATGATTTA
1 ATT-AA-ATATGATTTA
*
3158683 ATAAAAT
1 ATTAAAT
3158690 TTAAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATTAAATATGATTTA
Found at i:3158676 original size:17 final size:17
Alignment explanation
Indices: 3158656--3158689 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3158646 TTAATATTAA
*
3158656 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
3158673 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
3158690 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:3158832 original size:93 final size:92
Alignment explanation
Indices: 3158722--3158916 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
3158712 GATTATAGTT
* * *
3158722 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
3158785 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
3158815 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
3158880 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
3158907 TATGAATTTA
1 TATGAATTTA
3158917 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:3160331 original size:11 final size:11
Alignment explanation
Indices: 3160317--3160343 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3160307 AAAAATCAAT
3160317 ACAAAAGTTTC
1 ACAAAAGTTTC
3160328 ACAAAAGTTTC
1 ACAAAAGTTTC
3160339 ACAAA
1 ACAAA
3160344 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:3168849 original size:21 final size:21
Alignment explanation
Indices: 3168823--3168863 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
3168813 AGACGAGCAA
*
3168823 TACTCCACAACAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
3168844 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
3168864 TTGAGCAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:3172804 original size:29 final size:28
Alignment explanation
Indices: 3172755--3172827 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
3172745 CTAGAACCTG
3172755 AATTTTAAAATATAGAAAATAAA-AGGACTA
1 AATTTTAAAA-ATA-AAAATAAAGA-GACTA
*
3172785 AATTCTTAAAAATAAAAATACAGAGACTA
1 AATT-TTAAAAATAAAAATAAAGAGACTA
*
3172814 AATTTTAAATATAA
1 AATTTTAAAAATAA
3172828 GAAAAGTACA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
28 9 0.23
29 16 0.41
30 8 0.21
31 6 0.15
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (28 bp):
AATTTTAAAAATAAAAATAAAGAGACTA
Found at i:3190577 original size:9 final size:9
Alignment explanation
Indices: 3190563--3190587 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3190553 TATAATGAAT
3190563 AAAGAATTG
1 AAAGAATTG
3190572 AAAGAATTG
1 AAAGAATTG
3190581 AAAGAAT
1 AAAGAAT
3190588 CCATCCATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (9 bp):
AAAGAATTG
Found at i:3199567 original size:46 final size:46
Alignment explanation
Indices: 3199549--3199751 Score: 209
Period size: 46 Copynumber: 4.3 Consensus size: 46
3199539 TGACAAGTGG
* * *
3199549 AAAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
*
3199595 AAAGTGATAAGTGATAGCT-TCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* * *
3199641 AAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* *
3199693 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
3199738 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
3199752 CATACGTAAG
Statistics
Matches: 143, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
44 14 0.10
45 5 0.03
46 79 0.55
47 1 0.01
52 44 0.31
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
Found at i:3199568 original size:52 final size:50
Alignment explanation
Indices: 3199497--3199751 Score: 303
Period size: 52 Copynumber: 5.2 Consensus size: 50
3199487 ATCAAGTGAC
* **
3199497 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGT
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
* *
3199547 GGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC----
1 --AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
3199595 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
* *
3199645 GAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC----
1 --AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
** *
3199693 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AGGGACAAGT
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
3199742 GATAAGTGAT
1 -A-AAGTGAT
3199752 CATACGTAAG
Statistics
Matches: 178, Mismatches: 13, Indels: 25
0.82 0.06 0.12
Matches are distributed among these distances:
45 5 0.03
46 80 0.45
50 1 0.01
51 7 0.04
52 85 0.48
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (50 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
Found at i:3199603 original size:98 final size:98
Alignment explanation
Indices: 3199483--3199751 Score: 452
Period size: 98 Copynumber: 2.8 Consensus size: 98
3199473 TTTGAGTACT
*
3199483 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
3199548 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
3199581 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* *
3199646 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
3199679 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AGGGACAAGT-
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
3199742 GATAAGTGAT
66 GA-AAGTGAT
3199752 CATACGTAAG
Statistics
Matches: 160, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
96 1 0.01
97 16 0.10
98 143 0.89
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:3201066 original size:49 final size:49
Alignment explanation
Indices: 3201005--3201148 Score: 225
Period size: 49 Copynumber: 2.9 Consensus size: 49
3200995 ATGTGAACAT
* *
3201005 GTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAA
1 GTGA-TATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
3201055 GTGATATGTGATTTCGTGTAAGACCATAGTTGGGCTATGGCATCGGTAT
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
* *
3201104 GTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCG
3201149 AGAAAACGAA
Statistics
Matches: 88, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
49 84 0.95
50 4 0.05
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.33
Consensus pattern (49 bp):
GTGATATGTGATTACGTGTAAGACCATAGTTGGGCTATGGCATCGGTAA
Found at i:3204359 original size:46 final size:46
Alignment explanation
Indices: 3204341--3204543 Score: 209
Period size: 46 Copynumber: 4.3 Consensus size: 46
3204331 TGACAAGTGG
* * *
3204341 AAAGTGATAAGTAATAGCT-TCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
*
3204387 AAAGTGATAAGTGATAGCT-TCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* * *
3204433 AAGTGAAAAGTGATAAGTGATAGCT-TCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTAT-AGCTACACTTATCTGATCAAGTGAC
* *
3204485 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AGGGAC
1 AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
3204530 -AAGTGATAAGTGAT
1 AAAGTGATAAGTGAT
3204544 CATACGTAAG
Statistics
Matches: 143, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
44 14 0.10
45 5 0.03
46 79 0.55
47 1 0.01
52 44 0.31
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTATAGCTACACTTATCTGATCAAGTGAC
Found at i:3204360 original size:52 final size:50
Alignment explanation
Indices: 3204289--3204543 Score: 303
Period size: 52 Copynumber: 5.2 Consensus size: 50
3204279 ATCAAGTGAC
* **
3204289 AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGT
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
* *
3204339 GGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC----
1 --AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
3204387 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
* *
3204437 GAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC----
1 --AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
** *
3204485 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AGGGACAAGT
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
3204534 GATAAGTGAT
1 -A-AAGTGAT
3204544 CATACGTAAG
Statistics
Matches: 178, Mismatches: 13, Indels: 25
0.82 0.06 0.12
Matches are distributed among these distances:
45 5 0.03
46 80 0.45
50 1 0.01
51 7 0.04
52 85 0.48
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.29
Consensus pattern (50 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGT
Found at i:3204395 original size:98 final size:98
Alignment explanation
Indices: 3204275--3204543 Score: 452
Period size: 98 Copynumber: 2.8 Consensus size: 98
3204265 TTTGAGTACT
*
3204275 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
3204340 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
3204373 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
* *
3204438 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
3204471 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AGGGACAAGT-
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
3204534 GATAAGTGAT
66 GA-AAGTGAT
3204544 CATACGTAAG
Statistics
Matches: 160, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
96 1 0.01
97 16 0.10
98 143 0.89
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:3206152 original size:16 final size:16
Alignment explanation
Indices: 3206131--3206161 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3206121 TTTGTTTGCA
3206131 ATTTTTATAAATTATT
1 ATTTTTATAAATTATT
*
3206147 ATTTTTCTAAATTAT
1 ATTTTTATAAATTAT
3206162 CATAAATTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
ATTTTTATAAATTATT
Found at i:3208648 original size:21 final size:21
Alignment explanation
Indices: 3208601--3208652 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
3208591 TGATAAAAAA
*
3208601 ATATTTAAGATTTTTTGAATTT
1 ATATTT-AGATTTTTTGAATAT
*
3208623 TTATTTAGATTTTTT-ACATAT
1 ATATTTAGATTTTTTGA-ATAT
3208644 ATATTTAGA
1 ATATTTAGA
3208653 ATATTTATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 1 0.04
21 20 0.77
22 5 0.19
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.58
Consensus pattern (21 bp):
ATATTTAGATTTTTTGAATAT
Found at i:3210424 original size:20 final size:20
Alignment explanation
Indices: 3210399--3210448 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
3210389 TGGCTTAAAA
3210399 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
3210419 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
3210436 GTGGTAGTGGATT
1 TTGGTAGTGGATT
3210449 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:3215063 original size:20 final size:20
Alignment explanation
Indices: 3215038--3215087 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
3215028 TGGCTTAAAA
3215038 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
3215058 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
3215075 GTGGTAGTGGATT
1 TTGGTAGTGGATT
3215088 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:3220659 original size:23 final size:22
Alignment explanation
Indices: 3220621--3220674 Score: 74
Period size: 24 Copynumber: 2.4 Consensus size: 22
3220611 CTTCATCTCG
*
3220621 TATTTTTTATTAATTA-TTTAA
1 TATTTTTTTTTAATTATTTTAA
3220642 TATTTTTTTTCTATATTATTTTAA
1 TATTTTTTTT-TA-ATTATTTTAA
3220666 TATTTTTTT
1 TATTTTTTT
3220675 AAATTAATCC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 9 0.31
22 2 0.07
23 4 0.14
24 14 0.48
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (22 bp):
TATTTTTTTTTAATTATTTTAA
Found at i:3231422 original size:13 final size:13
Alignment explanation
Indices: 3231404--3231430 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3231394 GGCAAAAGAC
3231404 AGGAGAGAGGACA
1 AGGAGAGAGGACA
3231417 AGGAGAGAGGACA
1 AGGAGAGAGGACA
3231430 A
1 A
3231431 TGAAGACCAA
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:0.07, G:0.44, T:0.00
Consensus pattern (13 bp):
AGGAGAGAGGACA
Found at i:3238257 original size:24 final size:24
Alignment explanation
Indices: 3238230--3238275 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
3238220 TAATGTATTC
* *
3238230 TATATTTTTTATATTATATATTTT
1 TATAATTTTTAAATTATATATTTT
*
3238254 TATAATTTTTAAATTATTTATT
1 TATAATTTTTAAATTATATATT
3238276 GACATAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATAATTTTTAAATTATATATTTT
Found at i:3238467 original size:22 final size:24
Alignment explanation
Indices: 3238427--3238476 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
3238417 TGTTTAATTT
*
3238427 AATTCAAAAAGATATTAAAAGCTA-
1 AATTCAAAAAAATATTAAAA-CTAC
3238451 AATT-AAAAAAATA-TAAAACTAC
1 AATTCAAAAAAATATTAAAACTAC
3238473 AATT
1 AATT
3238477 TATTATTATG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 3 0.12
22 9 0.38
23 8 0.33
24 4 0.17
ACGTcount: A:0.62, C:0.08, G:0.04, T:0.26
Consensus pattern (24 bp):
AATTCAAAAAAATATTAAAACTAC
Found at i:3242112 original size:14 final size:15
Alignment explanation
Indices: 3242093--3242127 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
3242083 ATAATTAGTA
3242093 TTATTAAAATT-ATT
1 TTATTAAAATTAATT
*
3242107 TTATTAAATTTAATT
1 TTATTAAAATTAATT
3242122 TTATTA
1 TTATTA
3242128 TTATATGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTATTAAAATTAATT
Found at i:3243010 original size:3 final size:3
Alignment explanation
Indices: 3243002--3243027 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3242992 CCGTCTTGCT
3243002 GAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GA
3243028 GACTACTCCA
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:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:3249887 original size:4 final size:4
Alignment explanation
Indices: 3249878--3249908 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3249868 AATGTTTATA
3249878 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
3249909 ATTTGGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:3251703 original size:33 final size:33
Alignment explanation
Indices: 3251664--3251729 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
3251654 TTCATCGCAG
* *
3251664 ACCTTCAAATTTTTCTCTTAGATTATGTTTGTT
1 ACCTTCAAATTGTACTCTTAGATTATGTTTGTT
*
3251697 ACCTTCATATTGTACTCTTAGATTATGTTTGTT
1 ACCTTCAAATTGTACTCTTAGATTATGTTTGTT
3251730 TGGTCGTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.21, C:0.15, G:0.11, T:0.53
Consensus pattern (33 bp):
ACCTTCAAATTGTACTCTTAGATTATGTTTGTT
Found at i:3251789 original size:9 final size:9
Alignment explanation
Indices: 3251775--3251799 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3251765 TCCCTTTCTT
3251775 TTTTTTTTC
1 TTTTTTTTC
3251784 TTTTTTTTC
1 TTTTTTTTC
3251793 TTTTTTT
1 TTTTTTT
3251800 AATATTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:3266220 original size:19 final size:19
Alignment explanation
Indices: 3266196--3266234 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
3266186 GATCCAGAGG
3266196 GGACACCTGAAAAGTAGGT
1 GGACACCTGAAAAGTAGGT
3266215 GGACACCTGAAAAGTAGGT
1 GGACACCTGAAAAGTAGGT
3266234 G
1 G
3266235 AACTGGCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.33, T:0.15
Consensus pattern (19 bp):
GGACACCTGAAAAGTAGGT
Found at i:3270967 original size:5 final size:5
Alignment explanation
Indices: 3270959--3270992 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
3270949 TAAAGGAAAG
3270959 AAATA AAATA AAATA AAATA AAATA AAAGTA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA-TA AAA
3270993 CTGAGTATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:3271111 original size:24 final size:24
Alignment explanation
Indices: 3271084--3271158 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
3271074 AGAAAATCAA
3271084 ATATGTAAAAGGAACGAGAATAAC
1 ATATGTAAAAGGAACGAGAATAAC
* * * *
3271108 ATATATAAAA--AATAGAGATGTGA-
1 ATATGTAAAAGGAA-CGAGA-ATAAC
3271131 ATATGTAAAAGGAACGAGAATAAC
1 ATATGTAAAAGGAACGAGAATAAC
3271155 ATAT
1 ATAT
3271159 ATGGAAAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
22 2 0.05
23 15 0.39
24 19 0.50
25 2 0.05
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.21
Consensus pattern (24 bp):
ATATGTAAAAGGAACGAGAATAAC
Found at i:3271113 original size:26 final size:26
Alignment explanation
Indices: 3271084--3271166 Score: 70
Period size: 26 Copynumber: 3.4 Consensus size: 26
3271074 AGAAAATCAA
3271084 ATATGTAAAAGGAACGAGAATAACAT
1 ATATGTAAAAGGAACGAGAATAACAT
* ***
3271110 ATA--TAAAA--AA-TAGAGATGTGA-
1 ATATGTAAAAGGAACGAGA-ATAACAT
3271131 ATATGTAAAAGGAACGAGAATAACAT
1 ATATGTAAAAGGAACGAGAATAACAT
*
3271157 ATATGGAAAA
1 ATATGTAAAA
3271167 TAGAGATATG
Statistics
Matches: 41, Mismatches: 9, Indels: 14
0.64 0.14 0.22
Matches are distributed among these distances:
21 6 0.15
22 5 0.12
23 5 0.12
24 5 0.12
25 5 0.12
26 15 0.37
ACGTcount: A:0.55, C:0.05, G:0.19, T:0.20
Consensus pattern (26 bp):
ATATGTAAAAGGAACGAGAATAACAT
Found at i:3271120 original size:47 final size:48
Alignment explanation
Indices: 3271069--3271170 Score: 145
Period size: 47 Copynumber: 2.2 Consensus size: 48
3271059 GAGTATATGG
3271069 AAAATAGAAAAT-CAAATATGTAAAAGGAACGAGAATAACATATATAA
1 AAAATAGAAAATGCAAATATGTAAAAGGAACGAGAATAACATATATAA
* ** **
3271116 AAAATAG-AGATGTGAATATGTAAAAGGAACGAGAATAACATATATGG
1 AAAATAGAAAATGCAAATATGTAAAAGGAACGAGAATAACATATATAA
3271163 AAAATAGA
1 AAAATAGA
3271171 GATATGAAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
46 3 0.06
47 45 0.94
ACGTcount: A:0.58, C:0.05, G:0.18, T:0.20
Consensus pattern (48 bp):
AAAATAGAAAATGCAAATATGTAAAAGGAACGAGAATAACATATATAA
Found at i:3271171 original size:47 final size:47
Alignment explanation
Indices: 3271083--3271178 Score: 165
Period size: 47 Copynumber: 2.0 Consensus size: 47
3271073 TAGAAAATCA
*
3271083 AATATGTAAAAGGAACGAGAATAACATATATAAAAAATAGAGATGTG
1 AATATGTAAAAGGAACGAGAATAACATATATAAAAAATAGAGATATG
**
3271130 AATATGTAAAAGGAACGAGAATAACATATATGGAAAATAGAGATATG
1 AATATGTAAAAGGAACGAGAATAACATATATAAAAAATAGAGATATG
3271177 AA
1 AA
3271179 AGGAAATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.55, C:0.04, G:0.20, T:0.21
Consensus pattern (47 bp):
AATATGTAAAAGGAACGAGAATAACATATATAAAAAATAGAGATATG
Found at i:3272404 original size:15 final size:15
Alignment explanation
Indices: 3272384--3272431 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3272374 GATTTTAATG
*
3272384 GAATGTAATTCTTTA
1 GAATGTAATTCTTGA
* *
3272399 GAATGTGATTGTTGA
1 GAATGTAATTCTTGA
* *
3272414 AAATGTAATTGTTGA
1 GAATGTAATTCTTGA
3272429 GAA
1 GAA
3272432 ATTTACTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.23, T:0.40
Consensus pattern (15 bp):
GAATGTAATTCTTGA
Found at i:3275063 original size:101 final size:103
Alignment explanation
Indices: 3274921--3275204 Score: 400
Period size: 101 Copynumber: 2.8 Consensus size: 103
3274911 CAAATAAAAT
* *
3274921 TACATTA--AAAAAATCATAAAACATTAAACTAAACACTAACAAATTATATAACCTAATCATAAA
1 TACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAAATT-TATAACCTAATCATAAA
3274984 TTACTAACAAAATAACTAT-AAAAT-TAT-TTTTTTAAA
65 TTACTAACAAAATAACTATAAAAATATATATTTTTTAAA
* * *
3275020 TACATTACTAAAAGATCACAAAACACTAAACTAAACACTAACAATTTGTATAATCTAATCATAAA
1 TACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAAATT-TATAACCTAATCATAAA
* *
3275085 TCACTAGCAAAATAACTATAAAAATATATATTTTTTAAA
65 TTACTAACAAAATAACTATAAAAATATATATTTTTTAAA
* *
3275124 TCACATTACTAAAAAATCACAAAACCCTAAACTTAACACTAAC-AATTTATAACCTAATCCCATA
1 T-ACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAAATTTATAACCTAAT--CATA
3275188 AATTACTAACAAAATAA
63 AATTACTAACAAAATAA
3275205 ATAACTATAA
Statistics
Matches: 162, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
99 7 0.04
101 67 0.41
102 5 0.03
103 13 0.08
104 13 0.08
105 57 0.35
ACGTcount: A:0.53, C:0.17, G:0.01, T:0.29
Consensus pattern (103 bp):
TACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAAATTTATAACCTAATCATAAAT
TACTAACAAAATAACTATAAAAATATATATTTTTTAAA
Found at i:3275224 original size:105 final size:102
Alignment explanation
Indices: 3274921--3275224 Score: 347
Period size: 105 Copynumber: 3.0 Consensus size: 102
3274911 CAAATAAAAT
* *
3274921 TACATTA--AAAAAATCATAAAACATTAAACTAAACACTAACAAATTATATAACCTAATCATAAA
1 TACATTACTAAAAAATCACAAAACACTAAACTAAACACTAAC-AATTATATAACCTAATCATAAA
3274984 TTACTAAC---A-AAATAACTATAAAATTATTTTTTTAAA
65 TTACTAACAAAATAAATAACTATAAAA-T-TTTTTTTAAA
* * *
3275020 TACATTACTAAAAGATCACAAAACACTAAACTAAACACTAACAATTTGTATAATCTAATCATAAA
1 TACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAA-TTATATAACCTAATCATAAA
* * * *
3275085 TCACTAGCAAAATAACT-A-TAAAAATATATATTTTTTAAA
65 TTACTAACAAAATAAATAACTATAAA-AT-T-TTTTTTAAA
* *
3275124 TCACATTACTAAAAAATCACAAAACCCTAAACTTAACACTAACAATT-TATAACCTAATCCCATA
1 T-ACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAATTATATAACCTAAT--CATA
3275188 AATTACTAACAAAATAAATAACTATAACAATTTTTTT
63 AATTACTAACAAAATAAATAACTATAA-AATTTTTTT
3275225 AAAAGGAATT
Statistics
Matches: 173, Mismatches: 17, Indels: 24
0.81 0.08 0.11
Matches are distributed among these distances:
99 7 0.04
100 2 0.01
101 54 0.31
103 18 0.10
104 15 0.09
105 68 0.39
106 2 0.01
107 6 0.03
108 1 0.01
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.30
Consensus pattern (102 bp):
TACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAATTATATAACCTAATCATAAAT
TACTAACAAAATAAATAACTATAAAATTTTTTTTAAA
Found at i:3275360 original size:27 final size:27
Alignment explanation
Indices: 3275303--3275354 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3275293 TACTAACAGC
* *
3275303 TAGGAGTCACCAGTGACACCTATCATG
1 TAGGAGTCACCACTGACACCTACCATG
* *
3275330 TAGGAGTCACCACTGGCGCCTACCA
1 TAGGAGTCACCACTGACACCTACCA
3275355 GATAGGCATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.27, C:0.31, G:0.23, T:0.19
Consensus pattern (27 bp):
TAGGAGTCACCACTGACACCTACCATG
Found at i:3275494 original size:17 final size:18
Alignment explanation
Indices: 3275460--3275495 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
3275450 AGACACCACT
*
3275460 AATAAAATAATATTAAAA
1 AATAAAATAATATAAAAA
3275478 AATAAAA-AATATAAAAA
1 AATAAAATAATATAAAAA
3275495 A
1 A
3275496 GGTGGTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (18 bp):
AATAAAATAATATAAAAA
Found at i:3291885 original size:4 final size:4
Alignment explanation
Indices: 3291878--3291903 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3291868 ACACACACAC
3291878 ACGT ACGT ACGT ACGT ACGT ACGT AC
1 ACGT ACGT ACGT ACGT ACGT ACGT AC
3291904 ATTAGCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (4 bp):
ACGT
Found at i:3292993 original size:32 final size:30
Alignment explanation
Indices: 3292953--3293020 Score: 82
Period size: 32 Copynumber: 2.2 Consensus size: 30
3292943 AAATAATAAA
*
3292953 AATAAAATTATATTTTAACCCTCTCTAAAAAT
1 AATAAAATTATAATTTAACCCT-T-TAAAAAT
* **
3292985 AATAAAATTTTAATTTATTCCTTTAAAAAT
1 AATAAAATTATAATTTAACCCTTTAAAAAT
3293015 AATAAA
1 AATAAA
3293021 TATATAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 13 0.41
31 1 0.03
32 18 0.56
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (30 bp):
AATAAAATTATAATTTAACCCTTTAAAAAT
Found at i:3293607 original size:9 final size:9
Alignment explanation
Indices: 3293585--3293627 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
3293575 GATTTGTCAG
*
3293585 CTTTTTATA
1 CTTTTTTTA
*
3293594 TTTTTTTTA
1 CTTTTTTTA
3293603 CTTTTTTTA
1 CTTTTTTTA
3293612 C-TTTTTTA
1 CTTTTTTTA
3293620 CCTTTTTT
1 -CTTTTTT
3293628 CTTATATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
8 7 0.24
9 17 0.59
10 5 0.17
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (9 bp):
CTTTTTTTA
Found at i:3293691 original size:18 final size:18
Alignment explanation
Indices: 3293670--3293716 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
3293660 TTTTTTAAGT
3293670 TTTATATTATTT-TCCTAA
1 TTTATATTATTTAT-CTAA
* * *
3293688 TTTATTTTGTTTATTTAA
1 TTTATATTATTTATCTAA
3293706 TTTATATTATT
1 TTTATATTATT
3293717 AATTTTAAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTATATTATTTATCTAA
Found at i:3293775 original size:21 final size:21
Alignment explanation
Indices: 3293719--3293792 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
3293709 ATATTATTAA
* * * *
3293719 TTTTAAAAAATTTGTAATATA
1 TTTTTAAAATTTTATAATATT
*
3293740 TATTTAAAATGTTTTATAATATT
1 TTTTTAAAA--TTTTATAATATT
*
3293763 TTTTTAAAATTTTA-ATTATT
1 TTTTTAAAATTTTATAATATT
3293783 ATTTTTAAAA
1 -TTTTTAAAA
3293793 ATATTTTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 5 0.12
21 21 0.49
23 17 0.40
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
TTTTTAAAATTTTATAATATT
Found at i:3293793 original size:22 final size:23
Alignment explanation
Indices: 3293706--3293794 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 23
3293696 GTTTATTTAA
* *
3293706 TTTATATTATTAATTTTAAAAAA
1 TTTATATTATTATTTTTAAAAAT
* * * *
3293729 TTTGTAATA-TATATTTAAAATGT
1 TTTATATTATTATTTTTAAAA-AT
*
3293752 TTTATAATATT-TTTTT-AAAAT
1 TTTATATTATTATTTTTAAAAAT
3293773 TTTA-ATTATTATTTTTAAAAAT
1 TTTATATTATTATTTTTAAAAAT
3293795 ATTTTTTAAC
Statistics
Matches: 52, Mismatches: 10, Indels: 9
0.73 0.14 0.13
Matches are distributed among these distances:
20 5 0.10
21 10 0.19
22 17 0.33
23 19 0.37
24 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
TTTATATTATTATTTTTAAAAAT
Found at i:3294323 original size:26 final size:27
Alignment explanation
Indices: 3294274--3294336 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 27
3294264 TTTTAAATAC
* * *
3294274 AATTTTTAAATACATTTAAAAAATTAT
1 AATTTTTTAATACATATAAAAAATCAT
*
3294301 AATTTTTTAATA-ATATAAGAAATCAT
1 AATTTTTTAATACATATAAAAAATCAT
*
3294327 AATATTTTAA
1 AATTTTTTAA
3294337 ATATTTTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
26 20 0.65
27 11 0.35
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (27 bp):
AATTTTTTAATACATATAAAAAATCAT
Found at i:3294506 original size:21 final size:21
Alignment explanation
Indices: 3294467--3294510 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3294457 ATTTAAAATG
3294467 TTTTATAATATATTTTTTACAA
1 TTTTATAATATATTTTTTA-AA
3294489 TTTTA-AATAT-TATTTTTAAA
1 TTTTATAATATAT-TTTTTAAA
3294509 TT
1 TT
3294511 CTTTTTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 5 0.24
21 11 0.52
22 5 0.24
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATAATATATTTTTTAAA
Found at i:3294635 original size:18 final size:18
Alignment explanation
Indices: 3294612--3294659 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
3294602 GTGACTATTA
3294612 ATAAATTTAAATATAAAT
1 ATAAATTTAAATATAAAT
*
3294630 ATAAATTTTAA-A-AAAT
1 ATAAATTTAAATATAAAT
*
3294646 ATATA-TTAAATATA
1 ATAAATTTAAATATA
3294660 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 4 0.16
16 9 0.36
17 2 0.08
18 10 0.40
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAAATTTAAATATAAAT
Found at i:3295680 original size:10 final size:10
Alignment explanation
Indices: 3295665--3295690 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3295655 TGGTGTCAAA
3295665 TTGAACTTGC
1 TTGAACTTGC
3295675 TTGAACTTGC
1 TTGAACTTGC
3295685 TTGAAC
1 TTGAAC
3295691 CAATCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (10 bp):
TTGAACTTGC
Found at i:3295891 original size:22 final size:23
Alignment explanation
Indices: 3295866--3295911 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3295856 CAACCAAATC
3295866 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3295888 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3295911 A
1 A
3295912 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3295917 original size:23 final size:23
Alignment explanation
Indices: 3295873--3295917 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3295863 ATCAATTCAA
*
3295873 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
3295896 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
3295918 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:3303638 original size:22 final size:23
Alignment explanation
Indices: 3303613--3303658 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3303603 CAACCAAATC
3303613 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3303635 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3303658 A
1 A
3303659 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3303664 original size:23 final size:23
Alignment explanation
Indices: 3303620--3303664 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3303610 ATCAATTCAA
*
3303620 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
3303643 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
3303665 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:3307766 original size:46 final size:44
Alignment explanation
Indices: 3307662--3307776 Score: 158
Period size: 44 Copynumber: 2.6 Consensus size: 44
3307652 TGTCTTTGAC
** * *
3307662 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATAAT
* *
3307706 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATA--TATAAT
3307752 ATGGACTTACATGGCTCATTCCTGT
1 ATGGACTTACATGGCTCATTCCTGT
3307777 TCTGTCCTGT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
44 33 0.53
46 29 0.47
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (44 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATAAT
Found at i:3308145 original size:30 final size:30
Alignment explanation
Indices: 3308109--3308166 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
3308099 CCTCGACTCT
*
3308109 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
3308139 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
3308167 AAGGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:3308788 original size:5 final size:5
Alignment explanation
Indices: 3308775--3308846 Score: 62
Period size: 5 Copynumber: 14.4 Consensus size: 5
3308765 TTGTTTTATG
3308775 TATATA TATAA TATAA TATAA TAT-A T-TAA TGATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
3308823 CATAA TCATTAC TATAA TATAA TA
1 TATAA T-A-TAA TATAA TATAA TA
3308847 ATATTTTTTT
Statistics
Matches: 56, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 34 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (5 bp):
TATAA
Found at i:3308800 original size:19 final size:19
Alignment explanation
Indices: 3308776--3308818 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3308766 TGTTTTATGT
3308776 ATATATATAAT-ATAATATA
1 ATATAT-TAATGATAATATA
3308795 ATATATTAATGATAATATA
1 ATATATTAATGATAATATA
3308814 ATATA
1 ATATA
3308819 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
ATATATTAATGATAATATA
Found at i:3308828 original size:24 final size:24
Alignment explanation
Indices: 3308782--3308847 Score: 71
Period size: 24 Copynumber: 2.7 Consensus size: 24
3308772 ATGTATATAT
* * *
3308782 ATAATATAATATAATATATTAATG
1 ATAATATAATATAATAAAATAATC
3308806 ATAATATAATATAA-AAACATAATC
1 ATAATATAATATAATAAA-ATAATC
*
3308830 ATTACTATAATATAATAA
1 A-TAATATAATATAATAA
3308848 TATTTTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
23 2 0.06
24 19 0.54
25 12 0.34
26 2 0.06
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
ATAATATAATATAATAAAATAATC
Found at i:3313656 original size:14 final size:13
Alignment explanation
Indices: 3313622--3313663 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 13
3313612 ACTTGAAATG
3313622 TATTTTTTA-AAA
1 TATTTTTTATAAA
*
3313634 -ATGTTTTATAATA
1 TATTTTTTATAA-A
3313647 TATTTTTTATAAA
1 TATTTTTTATAAA
3313660 TATT
1 TATT
3313664 AAAAATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 7 0.28
12 2 0.08
13 6 0.24
14 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TATTTTTTATAAA
Found at i:3313698 original size:33 final size:34
Alignment explanation
Indices: 3313628--3313717 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 34
3313618 AATGTATTTT
*
3313628 TTAAAAATGTTTTAT-AATA-TATTTTTTATAAATA
1 TTAAAAATATTTT-TCAATATTA-TTTTTATAAATA
3313662 TTAAAAATATATTTTCAA-ATTATTTTT-TAAATA
1 TTAAAAATAT-TTTTCAATATTATTTTTATAAATA
* *
3313695 TTAAATATATTTTTTAATATTAT
1 TTAAAAATATTTTTCAATATTAT
3313718 AAAACATTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
32 6 0.12
33 20 0.41
34 16 0.33
35 7 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (34 bp):
TTAAAAATATTTTTCAATATTATTTTTATAAATA
Found at i:3313700 original size:19 final size:19
Alignment explanation
Indices: 3313678--3313716 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
3313668 ATATATTTTC
3313678 AAAT-TATTTTTTAAATATT
1 AAATATATTTTTT-AATATT
3313697 AAATATATTTTTTAATATT
1 AAATATATTTTTTAATATT
3313716 A
1 A
3313717 TAAAACATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
AAATATATTTTTTAATATT
Found at i:3313743 original size:29 final size:29
Alignment explanation
Indices: 3313710--3313771 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
3313700 TATATTTTTT
3313710 AATATTATAAAACATTTAAAATGATTTAA
1 AATATTATAAAACATTTAAAATGATTTAA
* ** * * *
3313739 AATATTTTTTAATATTTTAAATGATTTTA
1 AATATTATAAAACATTTAAAATGATTTAA
3313768 AATA
1 AATA
3313772 GAATTTTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (29 bp):
AATATTATAAAACATTTAAAATGATTTAA
Found at i:3313755 original size:19 final size:19
Alignment explanation
Indices: 3313682--3313766 Score: 75
Period size: 20 Copynumber: 4.3 Consensus size: 19
3313672 ATTTTCAAAT
3313682 TATTTTTTAA-ATATTAAATA
1 TATTTTTTAATAT-TTAAA-A
3313702 TATTTTTTAATATTATAAAA
1 TATTTTTTAATATT-TAAAA
* **
3313722 CA-TTTAAAATGATTTAAAA
1 TATTTTTTAAT-ATTTAAAA
*
3313741 TATTTTTTAATATTTTAAA
1 TATTTTTTAATATTTAAAA
3313760 TGATTTT
1 T-ATTTT
3313767 AAATAGAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
19 20 0.38
20 27 0.51
21 6 0.11
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (19 bp):
TATTTTTTAATATTTAAAA
Found at i:3313765 original size:20 final size:20
Alignment explanation
Indices: 3313670--3313766 Score: 74
Period size: 20 Copynumber: 4.8 Consensus size: 20
3313660 TATTAAAAAT
3313670 ATATTTTCAAATTATTTTTTA
1 ATATTTT-AAATTATTTTTTA
*
3313691 A-ATATTAAATATATTTTTTA
1 ATATTTTAAAT-TATTTTTTA
* ** **
3313711 ATATTATAAAACA-TTTAAA
1 ATATTTTAAATTATTTTTTA
*
3313730 ATGA-TTTAAAATATTTTTTA
1 AT-ATTTTAAATTATTTTTTA
*
3313750 ATATTTTAAATGATTTT
1 ATATTTTAAATTATTTT
3313767 AAATAGAATT
Statistics
Matches: 58, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
19 18 0.31
20 33 0.57
21 7 0.12
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (20 bp):
ATATTTTAAATTATTTTTTA
Found at i:3314502 original size:37 final size:36
Alignment explanation
Indices: 3314432--3314502 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
3314422 AATAATTATT
*
3314432 TTTTTAAAATTTTAAAAAATTAATTTGAAAAATACA
1 TTTTTAAAATTTTAAAAAATTAATTTCAAAAATACA
*
3314468 TTTTTAAAATTTATAAATAAA-TAATTTCACAAATA
1 TTTTTAAAATTT-TAAA-AAATTAATTTCAAAAATA
3314503 TATATAAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 12 0.39
37 16 0.52
38 3 0.10
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.42
Consensus pattern (36 bp):
TTTTTAAAATTTTAAAAAATTAATTTCAAAAATACA
Found at i:3314563 original size:21 final size:23
Alignment explanation
Indices: 3314523--3314582 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
3314513 TAAAAAATAT
*
3314523 TTTTAAAAATAATA--ATTAAA-A
1 TTTTAAAAA-AATATTATAAAACA
3314544 TTTTAAAAAAATATTATAAAACA
1 TTTTAAAAAAATATTATAAAACA
* *
3314567 TTTTAAATATATATTA
1 TTTTAAAAAAATATTA
3314583 CAATTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
20 4 0.12
21 9 0.27
22 5 0.15
23 15 0.45
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
TTTTAAAAAAATATTATAAAACA
Found at i:3314639 original size:36 final size:37
Alignment explanation
Indices: 3314599--3314672 Score: 100
Period size: 36 Copynumber: 2.0 Consensus size: 37
3314589 TTTTAAAATT
*
3314599 AATAATAT-AAA-TTAAATAAGTAAAATAAATC-AAGAA
1 AATAATATAAAACTTAAAAAAG-AAAA-AAATCTAAGAA
3314635 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
1 AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
3314672 A
1 A
3314673 GAGACAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
36 13 0.38
37 13 0.38
38 8 0.24
ACGTcount: A:0.69, C:0.04, G:0.05, T:0.22
Consensus pattern (37 bp):
AATAATATAAAACTTAAAAAAGAAAAAAATCTAAGAA
Found at i:3314644 original size:18 final size:18
Alignment explanation
Indices: 3314594--3314645 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
3314584 AATTTTTTTA
* *
3314594 AAATTAATAATATAAATT
1 AAATAAATAATATAAATC
* *
3314612 AAATAAGTAAAATAAATC
1 AAATAAATAATATAAATC
3314630 AAGA-AAATAATATAAA
1 AA-ATAAATAATATAAA
3314646 ACTTAAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 26 0.96
19 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATAAATAATATAAATC
Found at i:3314702 original size:9 final size:9
Alignment explanation
Indices: 3314688--3314729 Score: 75
Period size: 9 Copynumber: 4.7 Consensus size: 9
3314678 AAAATATAAG
3314688 AAAAAAGTA
1 AAAAAAGTA
*
3314697 AAAAAAGTT
1 AAAAAAGTA
3314706 AAAAAAGTA
1 AAAAAAGTA
3314715 AAAAAAGTA
1 AAAAAAGTA
3314724 AAAAAA
1 AAAAAA
3314730 ATATAAGAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (9 bp):
AAAAAAGTA
Found at i:3316626 original size:10 final size:10
Alignment explanation
Indices: 3316611--3316637 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
3316601 CTTCAAATCA
3316611 CGAATTTTAT
1 CGAATTTTAT
3316621 CGAATTTTAT
1 CGAATTTTAT
3316631 CGAATTT
1 CGAATTT
3316638 CATTCATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.48
Consensus pattern (10 bp):
CGAATTTTAT
Found at i:3317037 original size:173 final size:173
Alignment explanation
Indices: 3316743--3317269 Score: 1045
Period size: 173 Copynumber: 3.0 Consensus size: 173
3316733 TTTTGTAACT
3316743 TTCTCTTATAACTTGTTGAGTATCAAAAGACTAGTTTGAAGCAAACATTATGTACAAAGAGGTTT
1 TTCT-TTATAACTTGTTGAGTATCAAAAGACTAGTTTGAAGCAAACATTATGTACAAAGAGGTTT
3316808 GGTTCATTGTAATGATTACTTGTTTCAAGCATAGATATGTGAAAATTTTTATTTGCATTTTATCA
65 GGTTCATTGTAATGATTACTTGTTTCAAGCATAGATATGTGAAAATTTTTATTTGCATTTTATCA
3316873 TTATTATGTCTATCTTTACTAACCATTGATTCATGTTAACAAGA
130 TTATTATGTCTATCTTTACTAACCATTGATTCATGTTAACAAGA
3316917 TTCTTTATAACTTGTTGAGTATCAAAAGACTAGTTTGAAGCAAACATTATGTACAAAGAGGTTTG
1 TTCTTTATAACTTGTTGAGTATCAAAAGACTAGTTTGAAGCAAACATTATGTACAAAGAGGTTTG
3316982 GTTCATTGTAATGATTACTTGTTTCAAGCATAGATATGTGAAAATTTTTATTTGCATTTTATCAT
66 GTTCATTGTAATGATTACTTGTTTCAAGCATAGATATGTGAAAATTTTTATTTGCATTTTATCAT
3317047 TATTATGTCTATCTTTACTAACCATTGATTCATGTTAACAAGA
131 TATTATGTCTATCTTTACTAACCATTGATTCATGTTAACAAGA
3317090 TTCTTTATAACTTGTTGAGTATCAAAAGACTAGTTTGAAGCAAACATTATGTACAAAGAGGTTTG
1 TTCTTTATAACTTGTTGAGTATCAAAAGACTAGTTTGAAGCAAACATTATGTACAAAGAGGTTTG
3317155 GTTCATTGTAATGATTACTTGTTTCAAGCATAGATATGTGAAAATTTTTATTTGCATTTTATCAT
66 GTTCATTGTAATGATTACTTGTTTCAAGCATAGATATGTGAAAATTTTTATTTGCATTTTATCAT
3317220 TATTATGTCTATCTTTACTAACCATTGATTCATGTTAACAAGA
131 TATTATGTCTATCTTTACTAACCATTGATTCATGTTAACAAGA
3317263 TTCTTTA
1 TTCTTTA
3317270 ATTTAAAAAA
Statistics
Matches: 353, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
173 349 0.99
174 4 0.01
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (173 bp):
TTCTTTATAACTTGTTGAGTATCAAAAGACTAGTTTGAAGCAAACATTATGTACAAAGAGGTTTG
GTTCATTGTAATGATTACTTGTTTCAAGCATAGATATGTGAAAATTTTTATTTGCATTTTATCAT
TATTATGTCTATCTTTACTAACCATTGATTCATGTTAACAAGA
Found at i:3320046 original size:20 final size:19
Alignment explanation
Indices: 3320010--3320050 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
3320000 TCTTTACCAA
*
3320010 AATTTTTAAATTTTTTTTT
1 AATTTTTAAATTATTTTTT
*
3320029 AATTTTTTAATGTATTTTTT
1 AATTTTTAAAT-TATTTTTT
3320049 AA
1 AA
3320051 ATTTACAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
AATTTTTAAATTATTTTTT
Found at i:3330002 original size:20 final size:20
Alignment explanation
Indices: 3329977--3330016 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
3329967 CGGAAAATGA
3329977 TTTCTGAAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
*
3329997 TTTCTGGAAAATGATTTACT
1 TTTCTGAAAAATGATTTACT
3330017 GAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (20 bp):
TTTCTGAAAAATGATTTACT
Found at i:3330022 original size:34 final size:33
Alignment explanation
Indices: 3329962--3330026 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
3329952 TAGTAAAATG
3329962 TTTTCCGGAAAATGATTTCTGAAAAATGATTTAC
1 TTTTCCGGAAAATGATTTCTGAAAAAT-ATTTAC
*
3329996 TTTTCTGGAAAATGATTTACTG-AAAATATTT
1 TTTTCCGGAAAATGATTT-CTGAAAAATATTT
3330027 TTTGATGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 4 0.14
34 22 0.76
35 3 0.10
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (33 bp):
TTTTCCGGAAAATGATTTCTGAAAAATATTTAC
Found at i:3330142 original size:20 final size:20
Alignment explanation
Indices: 3330117--3330155 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3330107 TTTATTACAT
3330117 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
3330137 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
3330156 TTTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:3332722 original size:2 final size:2
Alignment explanation
Indices: 3332710--3332766 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
3332700 ACATACATAT
*
3332710 AC AC AC TC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3332752 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
3332767 TATATATACC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:3333026 original size:40 final size:40
Alignment explanation
Indices: 3332982--3333067 Score: 172
Period size: 40 Copynumber: 2.1 Consensus size: 40
3332972 CCCGAATGTC
3332982 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
1 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
3333022 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
1 ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
3333062 ATTCCA
1 ATTCCA
3333068 CATCAAATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.26, C:0.30, G:0.23, T:0.21
Consensus pattern (40 bp):
ATTCCAGCACGAAGCCTGCGGGTCTTTAAGCCCGGATACA
Found at i:3336831 original size:17 final size:17
Alignment explanation
Indices: 3336811--3336894 Score: 82
Period size: 17 Copynumber: 5.1 Consensus size: 17
3336801 ACATATTTTC
3336811 ACAGCTCACACATTACT
1 ACAGCTCACACATTACT
3336828 ACAGCTCACACATTAC-
1 ACAGCTCACACATTACT
* * * *
3336844 ACAACTCGCACATCATT
1 ACAGCTCACACATTACT
** *
3336861 GTAGCTCACACGTTAC-
1 ACAGCTCACACATTACT
*
3336877 ACAGCTCACACATCACT
1 ACAGCTCACACATTACT
3336894 A
1 A
3336895 TGACTCGCAA
Statistics
Matches: 50, Mismatches: 15, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
16 24 0.48
17 26 0.52
ACGTcount: A:0.35, C:0.36, G:0.08, T:0.21
Consensus pattern (17 bp):
ACAGCTCACACATTACT
Found at i:3336856 original size:33 final size:33
Alignment explanation
Indices: 3336810--3336894 Score: 107
Period size: 33 Copynumber: 2.6 Consensus size: 33
3336800 CACATATTTT
*
3336810 CACAGCTCACACATTACTACAGCTCACACATTA
1 CACAGCTCACACATCACTACAGCTCACACATTA
* * * ** *
3336843 CACAACTCGCACATCATTGTAGCTCACACGTTA
1 CACAGCTCACACATCACTACAGCTCACACATTA
3336876 CACAGCTCACACATCACTA
1 CACAGCTCACACATCACTA
3336895 TGACTCGCAA
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.34, C:0.36, G:0.08, T:0.21
Consensus pattern (33 bp):
CACAGCTCACACATCACTACAGCTCACACATTA
Found at i:3337701 original size:20 final size:20
Alignment explanation
Indices: 3337676--3337725 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
3337666 TGGCTTAAAA
3337676 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
3337696 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
3337713 GTGGTAGTGGATT
1 TTGGTAGTGGATT
3337726 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:3342341 original size:20 final size:20
Alignment explanation
Indices: 3342316--3342365 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
3342306 TGGCTTAAAA
3342316 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
3342336 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
3342353 GTGGTAGTGGATT
1 TTGGTAGTGGATT
3342366 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:3345525 original size:16 final size:16
Alignment explanation
Indices: 3345504--3345599 Score: 93
Period size: 16 Copynumber: 5.9 Consensus size: 16
3345494 AGTCATAGTG
3345504 ATGTGTGAGCTGTGTA
1 ATGTGTGAGCTGTGTA
*** *
3345520 ATGTGTGAGCTACAATG
1 ATGTGTGAGCT-GTGTA
* *
3345537 ATGTGCGAGTTGTGTA
1 ATGTGTGAGCTGTGTA
** *
3345553 ATGTGCAAGCTATGTA
1 ATGTGTGAGCTGTGTA
3345569 ATGTGTGAGCTGTAGTA
1 ATGTGTGAGCTGT-GTA
3345586 ATGTGTGAGCTGTG
1 ATGTGTGAGCTGTG
3345600 AAAATATGTG
Statistics
Matches: 62, Mismatches: 16, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
16 36 0.58
17 26 0.42
ACGTcount: A:0.23, C:0.08, G:0.34, T:0.34
Consensus pattern (16 bp):
ATGTGTGAGCTGTGTA
Found at i:3345564 original size:33 final size:33
Alignment explanation
Indices: 3345502--3345590 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 33
3345492 CGAGTCATAG
* **
3345502 TGATGTGTGAGCTGTGTAATGTGTGAGCTACAA
1 TGATGTGCGAGCTGTGTAATGTGCAAGCTACAA
* **
3345535 TGATGTGCGAGTTGTGTAATGTGCAAGCTA-TG
1 TGATGTGCGAGCTGTGTAATGTGCAAGCTACAA
* *
3345567 TAATGTGTGAGCTGTAGTAATGTG
1 TGATGTGCGAGCTGT-GTAATGTG
3345591 TGAGCTGTGA
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
32 12 0.26
33 34 0.74
ACGTcount: A:0.24, C:0.08, G:0.34, T:0.35
Consensus pattern (33 bp):
TGATGTGCGAGCTGTGTAATGTGCAAGCTACAA
Found at i:3348981 original size:22 final size:20
Alignment explanation
Indices: 3348938--3348976 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3348928 CAATTTAAAA
*
3348938 TATAAAAATTTATTAATATG
1 TATATAAATTTATTAATATG
3348958 TATATAAATTTATTAATAT
1 TATATAAATTTATTAATAT
3348977 ATGTAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATAAATTTATTAATATG
Found at i:3349102 original size:20 final size:20
Alignment explanation
Indices: 3349077--3349116 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
3349067 AAATATTTTC
3349077 AGTAAATCATTTTCCAAAAA
1 AGTAAATCATTTTCCAAAAA
3349097 AGTAAATCATTTTCCAAAAA
1 AGTAAATCATTTTCCAAAAA
3349117 TCATTTTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.05, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAAAAA
Found at i:3349345 original size:29 final size:28
Alignment explanation
Indices: 3349290--3349353 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
3349280 ATTTAATATA
* *
3349290 AATATATATAAATATAATTATTATTTA-
1 AATATATATAAATACAAATATTATTTAT
* *
3349317 ACATATATAATTAATACAAATATTTTTTAT
1 A-ATATAT-ATAAATACAAATATTATTTAT
3349347 AATATAT
1 AATATAT
3349354 TCGGGTCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 1 0.03
28 6 0.20
29 22 0.73
30 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
AATATATATAAATACAAATATTATTTAT
Found at i:3357728 original size:14 final size:17
Alignment explanation
Indices: 3357696--3357731 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
3357686 TAGTTTTCAT
3357696 ATTTATTTTGTTATCTA
1 ATTTATTTTGTTATCTA
3357713 ATTT-TTTTGTT-T-TA
1 ATTTATTTTGTTATCTA
3357727 ATTTA
1 ATTTA
3357732 ATTTCAATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
14 6 0.33
15 1 0.06
16 7 0.39
17 4 0.22
ACGTcount: A:0.22, C:0.03, G:0.06, T:0.69
Consensus pattern (17 bp):
ATTTATTTTGTTATCTA
Found at i:3362362 original size:13 final size:12
Alignment explanation
Indices: 3362343--3362381 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3362333 TGAGTATGTA
3362343 TTTTTTATATAT
1 TTTTTTATATAT
3362355 TATTTTTATA-AT
1 T-TTTTTATATAT
*
3362367 TTTTTCATATAT
1 TTTTTTATATAT
3362379 TTT
1 TTT
3362382 AATGATCGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
11 7 0.29
12 9 0.38
13 8 0.33
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TTTTTTATATAT
Found at i:3368949 original size:15 final size:15
Alignment explanation
Indices: 3368931--3368960 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3368921 AAATTTTAAT
*
3368931 TTTTTATAGTTTATA
1 TTTTTATAATTTATA
3368946 TTTTTATAATTTATA
1 TTTTTATAATTTATA
3368961 AAGGATTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (15 bp):
TTTTTATAATTTATA
Found at i:3374285 original size:31 final size:31
Alignment explanation
Indices: 3374247--3374306 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
3374237 AGAAATCAAA
3374247 TATTTCATGTTATTTAAGATATTTAATATGG
1 TATTTCATGTTATTTAAGATATTTAATATGG
* *
3374278 TATTTCATTTTGTTTAAGATATTTAATAT
1 TATTTCATGTTATTTAAGATATTTAATAT
3374307 AAAAGAGAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTTCATGTTATTTAAGATATTTAATATGG
Found at i:3376784 original size:30 final size:31
Alignment explanation
Indices: 3376744--3376803 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
3376734 AACTGGACTA
* * *
3376744 TTTTTGAAAAAGTTGATGGTCAAATTTAACC
1 TTTTTAAAAAAATTGAGGGTCAAATTTAACC
3376775 TTTTTAAAAAAATTGAGGGTCAAATTTAA
1 TTTTTAAAAAAATTGAGGGTCAAATTTAA
3376804 TTAAAAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (31 bp):
TTTTTAAAAAAATTGAGGGTCAAATTTAACC
Found at i:3383160 original size:31 final size:31
Alignment explanation
Indices: 3383131--3383224 Score: 79
Period size: 32 Copynumber: 3.0 Consensus size: 31
3383121 TTTCTATTTG
3383131 ATATTATAACACATTTAATTTTTAATATTTAC
1 ATATTATAACA-ATTTAATTTTTAATATTTAC
* * *
3383163 ATATTTTATCAATTTAA-TTTTAAT-TTTAA
1 ATATTATAACAATTTAATTTTTAATATTTAC
* *
3383192 ATAATT-CAACAAACTTAACTTTTTAA-ATTTAC
1 AT-ATTATAAC-AATTTAA-TTTTTAATATTTAC
3383224 A
1 A
3383225 AATTCTATCT
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
29 8 0.16
30 16 0.32
31 6 0.12
32 20 0.40
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (31 bp):
ATATTATAACAATTTAATTTTTAATATTTAC
Found at i:3386048 original size:3 final size:3
Alignment explanation
Indices: 3386040--3386077 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3386030 CATTGATAAA
3386040 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
3386078 ATGAATTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:3386757 original size:20 final size:21
Alignment explanation
Indices: 3386732--3386772 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3386722 AATTTATATT
3386732 ATTTTT-AATATATATT-TTAA
1 ATTTTTAAATA-ATATTATTAA
3386752 ATTTTTAAATAATATTATTAA
1 ATTTTTAAATAATATTATTAA
3386773 TTAAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTTAAATAATATTATTAA
Found at i:3386774 original size:20 final size:20
Alignment explanation
Indices: 3386728--3386774 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
3386718 CTCTAATTTA
3386728 TATT-ATTTTTAATATATAT
1 TATTAATTTTTAATATATAT
3386747 T-TTAAATTTTTAA-ATAATAT
1 TATT-AATTTTTAATAT-ATAT
3386767 TATTAATT
1 TATTAATT
3386775 AAATATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 17 0.71
21 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATTAATTTTTAATATATAT
Found at i:3396033 original size:30 final size:30
Alignment explanation
Indices: 3395997--3396082 Score: 86
Period size: 30 Copynumber: 2.9 Consensus size: 30
3395987 TATGAGTACG
3395997 TTTAGGAACTTGAGAAGACTCGATATCTTA
1 TTTAGGAACTTGAGAAGACTCGATATCTTA
* * * *
3396027 TTTAGG-AGTTTAGGAAGACTGGATATCTTG
1 TTTAGGAACTTGA-GAAGACTCGATATCTTA
* *
3396057 TTTAGGATCTTGGGAAGA-TCTGATAT
1 TTTAGGAACTTGAGAAGACTC-GATAT
3396083 TTCATTTTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
29 5 0.11
30 37 0.84
31 2 0.05
ACGTcount: A:0.29, C:0.09, G:0.26, T:0.36
Consensus pattern (30 bp):
TTTAGGAACTTGAGAAGACTCGATATCTTA
Found at i:3397121 original size:14 final size:15
Alignment explanation
Indices: 3397102--3397131 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3397092 CTACATCAAC
3397102 AAATAAT-ATAAAAA
1 AAATAATAATAAAAA
3397116 AAATAATAATAAAAA
1 AAATAATAATAAAAA
3397131 A
1 A
3397132 GCTACTCTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (15 bp):
AAATAATAATAAAAA
Found at i:3404239 original size:16 final size:16
Alignment explanation
Indices: 3404218--3404267 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
3404208 TACTCCCTTC
3404218 ATTAAATATAATTATA
1 ATTAAATATAATTATA
3404234 ATTAAATTATAATT-TA
1 ATTAAA-TATAATTATA
*
3404250 AATAAA-ATATATTATA
1 ATTAAATATA-ATTATA
3404266 AT
1 AT
3404268 CAACTAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
14 3 0.10
15 3 0.10
16 16 0.55
17 7 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAAATATAATTATA
Found at i:3405073 original size:21 final size:23
Alignment explanation
Indices: 3405020--3405074 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 23
3405010 TTTCTGACAC
*
3405020 ATTTTTGT-TTTCTTTTTCTTTT
1 ATTTTTATATTTCTTTTTCTTTT
*
3405042 ATTTTCATATTTC-TTTT-TTTT
1 ATTTTTATATTTCTTTTTCTTTT
*
3405063 ATTTTTTTATTT
1 ATTTTTATATTT
3405075 TGTTCCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 14 0.50
22 10 0.36
23 4 0.14
ACGTcount: A:0.11, C:0.07, G:0.02, T:0.80
Consensus pattern (23 bp):
ATTTTTATATTTCTTTTTCTTTT
Found at i:3405114 original size:9 final size:8
Alignment explanation
Indices: 3405089--3405160 Score: 54
Period size: 8 Copynumber: 8.4 Consensus size: 8
3405079 CCTTAATAAA
*
3405089 TTTTATCT
1 TTTTATTT
3405097 TTTTATTT
1 TTTTATTT
3405105 TTTTACTTT
1 TTTTA-TTT
*
3405114 TTTGATTGT
1 TTTTATT-T
* *
3405123 TTTTCTTA
1 TTTTATTT
*
3405131 TTTCATTT
1 TTTTATTT
3405139 TGTTTATTTT
1 T-TTTA-TTT
3405149 GTTTTATTT
1 -TTTTATTT
3405158 TTT
1 TTT
3405161 ATTATTAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
8 23 0.46
9 19 0.38
10 7 0.14
11 1 0.02
ACGTcount: A:0.11, C:0.06, G:0.06, T:0.78
Consensus pattern (8 bp):
TTTTATTT
Found at i:3405212 original size:28 final size:29
Alignment explanation
Indices: 3405176--3405237 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
3405166 TAAATTTAAA
3405176 ATGATATAATATAATA-TTTTTTTTAATT
1 ATGATATAATATAATATTTTTTTTTAATT
3405204 ATGATATAATATAATATTTTTTTTTAATT
1 ATGATATAATATAATATTTTTTTTTAATT
3405233 ATGAT
1 ATGAT
3405238 TGGTTTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (29 bp):
ATGATATAATATAATATTTTTTTTTAATT
Found at i:3406159 original size:18 final size:17
Alignment explanation
Indices: 3406096--3406160 Score: 78
Period size: 18 Copynumber: 3.6 Consensus size: 17
3406086 AGTTAATAAT
3406096 AAAAAATAAAACAAAAT-
1 AAAAAATAAAA-AAAATC
*
3406113 AAAATAAGAAAAAAAATC
1 AAAA-AATAAAAAAAATC
3406131 AAAAAAGTAAAAAAAATC
1 AAAAAA-TAAAAAAAATC
3406149 AAAAAGATAAAA
1 AAAAA-ATAAAA
3406161 TTTATTAAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
17 11 0.26
18 30 0.71
19 1 0.02
ACGTcount: A:0.80, C:0.05, G:0.05, T:0.11
Consensus pattern (17 bp):
AAAAAATAAAAAAAATC
Found at i:3406206 original size:16 final size:17
Alignment explanation
Indices: 3406171--3406261 Score: 80
Period size: 17 Copynumber: 5.5 Consensus size: 17
3406161 TTTATTAAGG
* *
3406171 AACAAAATAAAAAAGTAA
1 AACAAAAGAAAAATG-AA
*
3406189 AA-AAATGAAAAATGAA
1 AACAAAAGAAAAATGAA
* *
3406205 AATAAAAGAAAAA-AAA
1 AACAAAAGAAAAATGAA
*
3406221 AACAAAAGAAATATGAA
1 AACAAAAGAAAAATGAA
**
3406238 AATGAAAGAAAAA-GAA
1 AACAAAAGAAAAATGAA
3406254 AACAAAAG
1 AACAAAAG
3406262 GTGTCAGAAG
Statistics
Matches: 58, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
16 26 0.45
17 30 0.52
18 2 0.03
ACGTcount: A:0.77, C:0.03, G:0.11, T:0.09
Consensus pattern (17 bp):
AACAAAAGAAAAATGAA
Found at i:3406217 original size:33 final size:33
Alignment explanation
Indices: 3406180--3406261 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
3406170 GAACAAAATA
*
3406180 AAAAAGTAAAA-AAATGAAAAATGAAAATAAAAG
1 AAAAAG-AAAACAAAAGAAAAATGAAAATAAAAG
* * *
3406213 AAAAAAAAAACAAAAGAAATATGAAAATGAAAG
1 AAAAAGAAAACAAAAGAAAAATGAAAATAAAAG
3406246 AAAAAGAAAACAAAAG
1 AAAAAGAAAACAAAAG
3406262 GTGTCAGAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 4 0.09
33 39 0.91
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (33 bp):
AAAAAGAAAACAAAAGAAAAATGAAAATAAAAG
Found at i:3406541 original size:29 final size:29
Alignment explanation
Indices: 3406484--3406543 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
3406474 CACTTTTTAC
*
3406484 TTAAAAAAATGAGTTATTTTTGTATTTAA
1 TTAAAAAAATGAGTTATTTTTGTAATTAA
**
3406513 TTAAAAATGTGAGTTA-TTTTGATAATTAA
1 TTAAAAAAATGAGTTATTTTTG-TAATTAA
3406542 TT
1 TT
3406544 TATTTTTTGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (29 bp):
TTAAAAAAATGAGTTATTTTTGTAATTAA
Found at i:3411158 original size:23 final size:23
Alignment explanation
Indices: 3411132--3411176 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3411122 TGGGTATGTG
*
3411132 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
3411155 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
3411177 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:3412050 original size:22 final size:23
Alignment explanation
Indices: 3412025--3412070 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
3412015 CAACCAAACC
3412025 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
3412047 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
3412070 A
1 A
3412071 CATCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:3416487 original size:17 final size:17
Alignment explanation
Indices: 3416467--3416500 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3416457 ATGTTTAGGT
3416467 TTAAAAATTTTAATTAA
1 TTAAAAATTTTAATTAA
**
3416484 TTAAATTTTTTAATTAA
1 TTAAAAATTTTAATTAA
3416501 AAATCTATTT
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTAAAAATTTTAATTAA
Found at i:3426677 original size:19 final size:20
Alignment explanation
Indices: 3426640--3426678 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3426630 AAATTATGAA
3426640 AAAAAATTCAAAATATTTAT
1 AAAAAATTCAAAATATTTAT
3426660 AAAAAA-TCTAAAAT-TTTAT
1 AAAAAATTC-AAAATATTTAT
3426679 CTTTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAAATTCAAAATATTTAT
Done.