Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, 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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 95 of 121
Found at i:16109459 original size:46 final size:46
Alignment explanation
Indices: 16109386--16109510 Score: 153
Period size: 46 Copynumber: 2.7 Consensus size: 46
16109376 TATTATGTTA
* * * * *
16109386 TATTTTCAAAAGTTGTGAAACCTCTAATGAAATGAGCTTTTCA-ATT
1 TATTTTCAAAAGTTATGGAGCCTCTAATGAAAGGAGCTTTT-ATATC
*
16109432 TATTTTCAAAAGTTATGGAGCCACTAATGAAAGGAGCTTTTATATC
1 TATTTTCAAAAGTTATGGAGCCTCTAATGAAAGGAGCTTTTATATC
* * *
16109478 TATTTTCAAAAATTATAGAGCCTTTAATGAAAG
1 TATTTTCAAAAGTTATGGAGCCTCTAATGAAAG
16109511 TAGTTTTTCA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
45 1 0.01
46 67 0.99
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (46 bp):
TATTTTCAAAAGTTATGGAGCCTCTAATGAAAGGAGCTTTTATATC
Found at i:16109547 original size:19 final size:21
Alignment explanation
Indices: 16109523--16109565 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
16109513 GTTTTTCAAG
16109523 AATTCAA-AAAAT-AAAAAAA
1 AATTCAAGAAAATCAAAAAAA
16109542 AATTCAAGAAAATCCAAAAAAA
1 AATTCAAGAAAAT-CAAAAAAA
16109564 AA
1 AA
16109566 AACAAAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
22 9 0.43
ACGTcount: A:0.74, C:0.09, G:0.02, T:0.14
Consensus pattern (21 bp):
AATTCAAGAAAATCAAAAAAA
Found at i:16115460 original size:63 final size:62
Alignment explanation
Indices: 16115365--16115484 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 62
16115355 AATGATCCCA
* **
16115365 AAAAAATGGAAAGGGATTATTGAAGGTGTTTTTGACAAAAAAATACCTTGAATAATCCCCTCT
1 AAAAAATGGAAAAGGATTATTGAAGGCATTTTTGAC-AAAAAATACCTTGAATAATCCCCTCT
* * * *
16115428 AAAAAATTGAAAAGGATTATTCG-AGGCATTTTTTACCAAAAATGCCTTGAATAATCC
1 AAAAAATGGAAAAGGATTATT-GAAGGCATTTTTGACAAAAAATACCTTGAATAATCC
16115485 ATTCACAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
62 19 0.39
63 29 0.59
64 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (62 bp):
AAAAAATGGAAAAGGATTATTGAAGGCATTTTTGACAAAAAATACCTTGAATAATCCCCTCT
Found at i:16115495 original size:63 final size:62
Alignment explanation
Indices: 16115403--16115552 Score: 158
Period size: 62 Copynumber: 2.4 Consensus size: 62
16115393 TTTTTGACAA
* ** * *
16115403 AAAAATACCTTGAATAATCCCCTC-TAAAAAATTGAAAAGGATTATTCGAGGCATTTTTTACC
1 AAAAATGCCTTGAATAATCCATTCACAAAAAATT-AAAAGGATTATTCAAGGCATTTTTTACC
* * * *
16115465 AAAAATGCCTTGAATAATCCATTCACAAAAAATTTAAGGGGTTATTCAAGGCATTTTTTACT
1 AAAAATGCCTTGAATAATCCATTCACAAAAAATTAAAAGGATTATTCAAGGCATTTTTTACC
* * * *
16115527 AGAAACGTCTTTAATAATCCTATTCA
1 AAAAATGCCTTGAATAATCC-ATTCA
16115553 ATTTTTTATA
Statistics
Matches: 73, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
62 60 0.82
63 13 0.18
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (62 bp):
AAAAATGCCTTGAATAATCCATTCACAAAAAATTAAAAGGATTATTCAAGGCATTTTTTACC
Found at i:16116479 original size:25 final size:25
Alignment explanation
Indices: 16116449--16116504 Score: 103
Period size: 25 Copynumber: 2.2 Consensus size: 25
16116439 TTATTGTTTT
16116449 AATTTAAGATTTTAAATTAAATATA
1 AATTTAAGATTTTAAATTAAATATA
*
16116474 AATTTAAGTTTTTAAATTAAATATA
1 AATTTAAGATTTTAAATTAAATATA
16116499 AATTTA
1 AATTTA
16116505 TTACCAAGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (25 bp):
AATTTAAGATTTTAAATTAAATATA
Found at i:16122898 original size:56 final size:55
Alignment explanation
Indices: 16122639--16122933 Score: 180
Period size: 55 Copynumber: 5.5 Consensus size: 55
16122629 TATAATAAAA
* * * *** *
16122639 AAAATTAAAACATATAAGTCTATACTGACA-ATCTCTAATTGTCGGTATAGGTAAG
1 AAAATTAAAACATACAAGTCTATACTGACAGGT-GCTAACCATCGGTATAGATAAG
* * * * * * *
16122694 AAAATTAAAGCATACAATTCTATAATG--ATGTCTCTAACCATCAGTATAGGTACA-
1 AAAATTAAAACATACAAGTCTATACTGACAGGT-GCTAACCATCGGTATAGATA-AG
* * * **** * * *
16122748 AAAATTAAAAAATACAAGTCTATATTGA-TGGATGCTAAGTGCCGCTATGGGTAAG
1 AAAATTAAAACATACAAGTCTATACTGACAGG-TGCTAACCATCGGTATAGATAAG
* * * *
16122803 ---A--AAAA-TTACAAGTCTATACTGACAGGTGTTAACCGTCGGTATAGGTAAG
1 AAAATTAAAACATACAAGTCTATACTGACAGGTGCTAACCATCGGTATAGATAAG
* * *
16122852 AAAAATTAAAACATATAAGTCTATACTGACAGGTGCTAGCCATCGGTATAGATGAG
1 -AAAATTAAAACATACAAGTCTATACTGACAGGTGCTAACCATCGGTATAGATAAG
*
16122908 AAAATTAAAACATACAAATCTATACT
1 AAAATTAAAACATACAAGTCTATACT
16122934 AATGGGCTTT
Statistics
Matches: 186, Mismatches: 41, Indels: 26
0.74 0.16 0.10
Matches are distributed among these distances:
49 32 0.17
50 6 0.03
52 1 0.01
53 2 0.01
54 42 0.23
55 65 0.35
56 38 0.20
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (55 bp):
AAAATTAAAACATACAAGTCTATACTGACAGGTGCTAACCATCGGTATAGATAAG
Found at i:16124555 original size:13 final size:13
Alignment explanation
Indices: 16124539--16124590 Score: 59
Period size: 13 Copynumber: 3.8 Consensus size: 13
16124529 TTTATTAAAC
*
16124539 TTAATTATTATTT
1 TTAATTTTTATTT
*
16124552 TTAATTTTTACATAT
1 TTAATTTTT--ATTT
*
16124567 ATAATTTTTATTT
1 TTAATTTTTATTT
16124580 TTAATTTTTAT
1 TTAATTTTTAT
16124591 ATATATGTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
13 21 0.66
15 11 0.34
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TTAATTTTTATTT
Found at i:16124560 original size:7 final size:7
Alignment explanation
Indices: 16124539--16124589 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
16124529 TTTATTAAAC
*
16124539 TTAATTA
1 TTAATTT
16124546 TT-ATTT
1 TTAATTT
16124552 TTAATTT
1 TTAATTT
*
16124559 TTACATAT
1 TTA-ATTT
*
16124567 ATAATTT
1 TTAATTT
16124574 TT-ATTT
1 TTAATTT
16124580 TTAATTT
1 TTAATTT
16124587 TTA
1 TTA
16124590 TATATATGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
6 11 0.31
7 20 0.56
8 5 0.14
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (7 bp):
TTAATTT
Found at i:16124571 original size:28 final size:28
Alignment explanation
Indices: 16124540--16124596 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
16124530 TTATTAAACT
16124540 TAATTATTATTTTTAATTTTTACATATA
1 TAATTATTATTTTTAATTTTTACATATA
* *
16124568 TAATTTTTATTTTTAATTTTTATATATA
1 TAATTATTATTTTTAATTTTTACATATA
16124596 T
1 T
16124597 GTAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
TAATTATTATTTTTAATTTTTACATATA
Found at i:16128662 original size:21 final size:21
Alignment explanation
Indices: 16128636--16128677 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16128626 TTCCTAACCC
*
16128636 CAGATTTCATATCTCAAACGT
1 CAGATTTCAGATCTCAAACGT
*
16128657 CAGATTTCAGATTTCAAACGT
1 CAGATTTCAGATCTCAAACGT
16128678 TTGAAAAAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (21 bp):
CAGATTTCAGATCTCAAACGT
Found at i:16130229 original size:16 final size:16
Alignment explanation
Indices: 16130182--16130233 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
16130172 TTTTGATTTT
* *
16130182 TTTTGTATTTTTTGTTA
1 TTTT-TATTTTATATTA
* *
16130199 TTTTTAATATAATATTA
1 TTTTT-ATTTTATATTA
16130216 TTTTTATTTTATATTA
1 TTTTTATTTTATATTA
16130232 TT
1 TT
16130234 ACTAATAATA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 12 0.43
17 16 0.57
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (16 bp):
TTTTTATTTTATATTA
Found at i:16130263 original size:4 final size:4
Alignment explanation
Indices: 16130254--16130326 Score: 51
Period size: 4 Copynumber: 17.5 Consensus size: 4
16130244 ATTTTTTTAG
16130254 AAAT AAAT AAAT AAAT AAAT AAA- ATAA- AAAT AAAATT GAAAT AAAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT -AAA-T -AAAT -AAAT
* ** *
16130301 AAAG ACTT AAAA AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
16130327 TTTAATAATA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
3 3 0.05
4 40 0.73
5 8 0.15
6 4 0.07
ACGTcount: A:0.74, C:0.01, G:0.03, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:16130286 original size:11 final size:11
Alignment explanation
Indices: 16130270--16130303 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
16130260 ATAAATAAAT
16130270 AAATAAAATAA
1 AAATAAAATAA
**
16130281 AAATAAAATTG
1 AAATAAAATAA
16130292 AAATAAAATAA
1 AAATAAAATAA
16130303 A
1 A
16130304 GACTTAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:16130316 original size:38 final size:37
Alignment explanation
Indices: 16130269--16130359 Score: 94
Period size: 38 Copynumber: 2.4 Consensus size: 37
16130259 AATAAATAAA
16130269 TAAATAAAATAAAAATAAAATTGAAATAA-AATAAAGACT
1 TAAA-AAAATAAAAA-AAAATT-AAATAATAATAAAGACT
* * **
16130308 TAAAAAAATAAATAAATAATTTAATAATAATAACTACT
1 TAAAAAAATAAA-AAAAAATTAAATAATAATAAAGACT
16130346 TAAAATAAATAAAA
1 TAAAA-AAATAAAA
16130360 TTTTATTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
37 5 0.11
38 27 0.60
39 13 0.29
ACGTcount: A:0.68, C:0.03, G:0.02, T:0.26
Consensus pattern (37 bp):
TAAAAAAATAAAAAAAAATTAAATAATAATAAAGACT
Found at i:16130450 original size:17 final size:17
Alignment explanation
Indices: 16130430--16130479 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
16130420 TAATTTTTGC
16130430 TAAAAAATAATAAATTA
1 TAAAAAATAATAAATTA
*
16130447 TAAAAAATGATAAA-TA
1 TAAAAAATAATAAATTA
16130463 -AAATAAA-AATAAATTA
1 TAAA-AAATAATAAATTA
16130479 T
1 T
16130480 TTAAATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 8 0.29
16 7 0.25
17 13 0.46
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (17 bp):
TAAAAAATAATAAATTA
Found at i:16136553 original size:49 final size:49
Alignment explanation
Indices: 16136481--16136582 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
16136471 TTGTAATTCG
16136481 CTTTAAGATTGTAAAGCATTTTGACAGGAGTTGTAGAGAATAATGGATT
1 CTTTAAGATTGTAAAGCATTTTGACAGGAGTTGTAGAGAATAATGGATT
16136530 CTTTAAGATTGTAAAGCATTTTGACAGGAGTTGTAGAGAATAATGGATT
1 CTTTAAGATTGTAAAGCATTTTGACAGGAGTTGTAGAGAATAATGGATT
16136579 CTTT
1 CTTT
16136583 CTTGGTTGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (49 bp):
CTTTAAGATTGTAAAGCATTTTGACAGGAGTTGTAGAGAATAATGGATT
Found at i:16140795 original size:20 final size:22
Alignment explanation
Indices: 16140756--16140796 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16140746 AAGTCATATA
*
16140756 ATTATAATTTAGATTTTTTTAG
1 ATTATAATTTAGAGTTTTTTAG
16140778 ATTATAATTT-G-GTTTTTTA
1 ATTATAATTTAGAGTTTTTTA
16140797 CGGATATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (22 bp):
ATTATAATTTAGAGTTTTTTAG
Found at i:16140913 original size:14 final size:13
Alignment explanation
Indices: 16140888--16140912 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16140878 ATTTTTTAGG
16140888 AATCAAATTTTTC
1 AATCAAATTTTTC
16140901 AATCAAATTTTT
1 AATCAAATTTTT
16140913 TGGATTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (13 bp):
AATCAAATTTTTC
Found at i:16142069 original size:17 final size:17
Alignment explanation
Indices: 16142047--16142079 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
16142037 TTATGTCACG
16142047 TCAAGGGGATAAGATAA
1 TCAAGGGGATAAGATAA
16142064 TCAAGGGGATAAGATA
1 TCAAGGGGATAAGATA
16142080 TAGGGGATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.30, T:0.18
Consensus pattern (17 bp):
TCAAGGGGATAAGATAA
Found at i:16142086 original size:14 final size:16
Alignment explanation
Indices: 16142049--16142089 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
16142039 ATGTCACGTC
16142049 AAGGGGATAAGATAAT
1 AAGGGGATAAGATAAT
16142065 CAAGGGGATAAGAT-AT
1 -AAGGGGATAAGATAAT
16142081 -AGGGGATAA
1 AAGGGGATAA
16142090 CGTCTAGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.38
16 2 0.08
17 13 0.54
ACGTcount: A:0.46, C:0.02, G:0.34, T:0.17
Consensus pattern (16 bp):
AAGGGGATAAGATAAT
Found at i:16150024 original size:30 final size:30
Alignment explanation
Indices: 16149990--16150064 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
16149980 TAGACACTCA
* *
16149990 AAATAAACACTTAGTTTTTAATTTATACT-T
1 AAATAAACTCTTAATTTTTAATTTATA-TGT
* *
16150020 AAATAAATTTTTAATTTTTAATTTATATGT
1 AAATAAACTCTTAATTTTTAATTTATATGT
16150050 AAATAAACTCTTAAT
1 AAATAAACTCTTAAT
16150065 ATAAATTAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 1 0.03
30 37 0.97
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.48
Consensus pattern (30 bp):
AAATAAACTCTTAATTTTTAATTTATATGT
Found at i:16153031 original size:22 final size:22
Alignment explanation
Indices: 16152994--16153044 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
16152984 TCAAAATTCA
*
16152994 ATAAAAATAGTATTTTTAAAAT
1 ATAAAAATAGTATTTTAAAAAT
*
16153016 A-AAAATATAGTTTTTTAAAAAT
1 ATAAAA-ATAGTATTTTAAAAAT
16153038 ATAAAAA
1 ATAAAAA
16153045 AATAAATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 4 0.16
22 17 0.68
23 4 0.16
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (22 bp):
ATAAAAATAGTATTTTAAAAAT
Found at i:16153086 original size:17 final size:18
Alignment explanation
Indices: 16153004--16153086 Score: 51
Period size: 18 Copynumber: 4.2 Consensus size: 18
16152994 ATAAAAATAG
*
16153004 TATTTTTAAAATAAAAATA
1 TATTTTTAAAATTAAAA-A
16153023 TAGTTTTTTAAAAATATAAAAAAA
1 TA--TTTTT-AAAAT-T--AAAAA
* *
16153047 TAAATTTTTAAAATTCAACA
1 T--ATTTTTAAAATTAAAAA
16153067 TATTTTTAAAA-TAAAAA
1 TATTTTTAAAATTAAAAA
16153084 TAT
1 TAT
16153087 AATTTTTGTT
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
17 7 0.14
18 10 0.20
19 2 0.04
20 4 0.08
21 5 0.10
22 6 0.12
23 5 0.10
24 7 0.14
25 4 0.08
26 1 0.02
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (18 bp):
TATTTTTAAAATTAAAAA
Found at i:16153128 original size:16 final size:15
Alignment explanation
Indices: 16153102--16153135 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
16153092 TTGTTAAAAA
16153102 TATAAAAAATTATAT
1 TATAAAAAATTATAT
*
16153117 TATAATAAAATTTTAT
1 TATAA-AAAATTATAT
16153133 TAT
1 TAT
16153136 CATATATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAAAAAATTATAT
Found at i:16161773 original size:4 final size:4
Alignment explanation
Indices: 16161764--16161788 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
16161754 TGTGCCTTGT
16161764 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
16161789 CCCTCGGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:16165301 original size:33 final size:33
Alignment explanation
Indices: 16165259--16165323 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
16165249 AGATGAGATG
*
16165259 TCCTTTTGATTAATTAATTATTAACTTTAGCAC
1 TCCTTTTGATTAATTAATCATTAACTTTAGCAC
* *
16165292 TCCTTTTGATTAATTGATCATTATCTTTAGCA
1 TCCTTTTGATTAATTAATCATTAACTTTAGCA
16165324 TTATTTGGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (33 bp):
TCCTTTTGATTAATTAATCATTAACTTTAGCAC
Found at i:16167505 original size:13 final size:12
Alignment explanation
Indices: 16167474--16167657 Score: 106
Period size: 13 Copynumber: 14.5 Consensus size: 12
16167464 CATATCAAAC
*
16167474 CCTAACCCTAAA
1 CCTAAACCTAAA
16167486 CCT-AACCTAAA
1 CCTAAACCTAAA
*
16167497 TCCTAAACCT-AG
1 -CCTAAACCTAAA
* *
16167509 CTTAAACCCCAAA
1 CCTAAA-CCTAAA
*
16167522 TCTTAAACCTAAA
1 -CCTAAACCTAAA
*
16167535 CCCTAAACCTTAAG
1 -CCTAAACC-TAAA
*
16167549 CTTAAACCCT-AA
1 CCTAAA-CCTAAA
16167561 CCTAAACCCTAAA
1 CCTAAA-CCTAAA
16167574 CTCT-AACCTAAA
1 C-CTAAACCTAAA
*
16167586 CTCCAAACCTTAAA
1 C-CTAAACC-TAAA
16167600 CCTAAACCCTAAA
1 CCTAAA-CCTAAA
* *
16167613 CCTAACCCTACAC
1 CCTAAACCTA-AA
16167626 CCTAAACCTTAAA
1 CCTAAACC-TAAA
* *
16167639 CCTAATCATAAA
1 CCTAAACCTAAA
16167651 CTCTAAA
1 C-CTAAA
16167658 TGAAACCCTA
Statistics
Matches: 136, Mismatches: 21, Indels: 29
0.73 0.11 0.16
Matches are distributed among these distances:
11 12 0.09
12 37 0.27
13 65 0.48
14 22 0.16
ACGTcount: A:0.42, C:0.35, G:0.01, T:0.21
Consensus pattern (12 bp):
CCTAAACCTAAA
Found at i:16167566 original size:32 final size:31
Alignment explanation
Indices: 16167527--16167641 Score: 110
Period size: 32 Copynumber: 3.6 Consensus size: 31
16167517 CCAAATCTTA
*
16167527 AACCTAAACCCTAAACCTTAAGCTTAAACCCT
1 AACCTAAACCCTAAACCTTAA-CCTAAACCCT
*
16167559 AACCTAAACCCTAAA-CTCTAACCTAAACTCCA
1 AACCTAAACCCTAAACCT-TAACCTAAAC-CCT
*
16167591 AACCTTAAA-CCTAAACCCTAAACCT-AACCCT
1 AACC-TAAACCCTAAA-CCTTAACCTAAACCCT
*
16167622 ACACCCTAAACCTTAAACCT
1 A-A-CCTAAACCCTAAACCT
16167642 AATCATAAAC
Statistics
Matches: 70, Mismatches: 5, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
31 11 0.16
32 41 0.59
33 16 0.23
34 2 0.03
ACGTcount: A:0.42, C:0.37, G:0.01, T:0.20
Consensus pattern (31 bp):
AACCTAAACCCTAAACCTTAACCTAAACCCT
Found at i:16167602 original size:39 final size:40
Alignment explanation
Indices: 16167525--16167656 Score: 132
Period size: 39 Copynumber: 3.4 Consensus size: 40
16167515 CCCCAAATCT
* * * * * *
16167525 TAAA-CCTAAACCCTAAACCTTAAGCTTAAACCCT-AACC
1 TAAACCCTAAACTCTAACCCTAAACCCTAAACCTTAAACC
16167563 TAAACCCTAAACTCTAA-CCTAAACTCC-AAACCTTAAACC
1 TAAACCCTAAACTCTAACCCTAAAC-CCTAAACCTTAAACC
*
16167602 TAAACCCTAAAC-CTAACCCTACACCCTAAACCTTAAACC
1 TAAACCCTAAACTCTAACCCTAAACCCTAAACCTTAAACC
* *
16167641 T-AATCATAAACTCTAA
1 TAAACCCTAAACTCTAA
16167657 ATGAAACCCT
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
38 29 0.36
39 51 0.64
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.21
Consensus pattern (40 bp):
TAAACCCTAAACTCTAACCCTAAACCCTAAACCTTAAACC
Found at i:16167643 original size:32 final size:32
Alignment explanation
Indices: 16167530--16167657 Score: 86
Period size: 32 Copynumber: 4.0 Consensus size: 32
16167520 AATCTTAAAC
* * *
16167530 CTAAACCCTAAACCTTAAGCTTAAACCCT-AAC
1 CTAAA-CCTAAACCCTAACCCTAAACCCTAAAC
*
16167562 CTAAACCCTAAACTCTAA-CCTAAACTCC-AAAC
1 CTAAA-CCTAAACCCTAACCCTAAAC-CCTAAAC
* *
16167594 CTTAAACCTAAACCCTAAACCT-AACCCTACACC
1 C-TAAACCTAAACCCTAACCCTAAACCCTA-AAC
* * *
16167627 CTAAACCTTAAA-CCTAATCATAAACTCTAAA
1 CTAAACC-TAAACCCTAACCCTAAACCCTAAA
16167658 TGAAACCCTA
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
31 8 0.10
32 51 0.65
33 20 0.25
ACGTcount: A:0.43, C:0.35, G:0.01, T:0.21
Consensus pattern (32 bp):
CTAAACCTAAACCCTAACCCTAAACCCTAAAC
Found at i:16167657 original size:7 final size:6
Alignment explanation
Indices: 16167474--16167657 Score: 106
Period size: 7 Copynumber: 29.0 Consensus size: 6
16167464 CATATCAAAC
* * * *
16167474 CCTAAC CCTAAA CCT-AA CCTAAA TCCTAAA CCT-AG CTTAAA CCCCAAA
1 CCTAAA CCTAAA CCTAAA CCTAAA -CCTAAA CCTAAA CCTAAA -CCTAAA
* * *
16167522 TCTTAAA CCTAAA CCCTAAA CCTTAAG CTTAAA CCCT-AA CCTAAA CCCTAAA
1 -CCTAAA CCTAAA -CCTAAA CC-TAAA CCTAAA -CCTAAA CCTAAA -CCTAAA
* * *
16167574 CTCT-AA CCTAAA CTCCAAA CCTTAAA CCTAAA CCCTAAA CCTAAC CCTACAC
1 C-CTAAA CCTAAA C-CTAAA CC-TAAA CCTAAA -CCTAAA CCTAAA CCTA-AA
* *
16167626 CCTAAA CCTTAAA CCTAAT CATAAA CTCTAAA
1 CCTAAA CC-TAAA CCTAAA CCTAAA C-CTAAA
16167658 TGAAACCCTA
Statistics
Matches: 139, Mismatches: 22, Indels: 33
0.72 0.11 0.17
Matches are distributed among these distances:
5 13 0.09
6 60 0.43
7 66 0.47
ACGTcount: A:0.42, C:0.35, G:0.01, T:0.21
Consensus pattern (6 bp):
CCTAAA
Found at i:16168544 original size:16 final size:17
Alignment explanation
Indices: 16168523--16168556 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
16168513 ATTATGCTAC
*
16168523 CAAGAAATAA-AGCCAA
1 CAAGAAAGAAGAGCCAA
16168539 CAAGAAAGAAGAGCCAA
1 CAAGAAAGAAGAGCCAA
16168556 C
1 C
16168557 CATCCTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.59, C:0.21, G:0.18, T:0.03
Consensus pattern (17 bp):
CAAGAAAGAAGAGCCAA
Found at i:16179829 original size:16 final size:17
Alignment explanation
Indices: 16179808--16179840 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16179798 TACCAACATA
16179808 TTAAAAAATAT-ATTGG
1 TTAAAAAATATAATTGG
*
16179824 TTAAAAATTATAATTGG
1 TTAAAAAATATAATTGG
16179841 AAAAATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (17 bp):
TTAAAAAATATAATTGG
Found at i:16181575 original size:21 final size:22
Alignment explanation
Indices: 16181536--16181576 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
16181526 TAGTAAAATT
* *
16181536 AAATATTATAATGATAATATTA
1 AAATATTATAATAAAAATATTA
16181558 AAAT-TTATAATAAAAATAT
1 AAATATTATAATAAAAATAT
16181577 ATATTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AAATATTATAATAAAAATATTA
Found at i:16181645 original size:14 final size:14
Alignment explanation
Indices: 16181606--16181647 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
16181596 ATGATGAAAT
*
16181606 AAATTATAATAAAA
1 AAATTATATTAAAA
16181620 AAATTATATTAAAA
1 AAATTATATTAAAA
* *
16181634 ATATTATTTTAAAA
1 AAATTATATTAAAA
16181648 TTTATATGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAATTATATTAAAA
Found at i:16183459 original size:15 final size:15
Alignment explanation
Indices: 16183412--16183459 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
16183402 AATTAAAATT
* *
16183412 TTATTATTTTTTAAA
1 TTATAATTTTTTATA
16183427 TTATAATTATTTTATA
1 TTATAATT-TTTTATA
*
16183443 TTATAATTTTTTGTA
1 TTATAATTTTTTATA
16183458 TT
1 TT
16183460 TGCAAATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 15 0.52
16 14 0.48
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATAATTTTTTATA
Found at i:16186513 original size:26 final size:24
Alignment explanation
Indices: 16186449--16186523 Score: 66
Period size: 26 Copynumber: 3.0 Consensus size: 24
16186439 TAAAATTTTC
*
16186449 TAATA-TTTTAATCTTTTAAAAAA
1 TAATATTTTTAATTTTTTAAAAAA
16186472 TAATATTTCTTGAATTTTTTAGAAAAA
1 TAATATTT-TT-AATTTTTTA-AAAAA
*
16186499 -AATACTGTTTTAA-TTTTAAAAAAA
1 TAATA-T-TTTTAATTTTTTAAAAAA
16186523 T
1 T
16186524 TCAAAATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
23 5 0.12
24 7 0.16
25 7 0.16
26 14 0.33
27 8 0.19
28 2 0.05
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (24 bp):
TAATATTTTTAATTTTTTAAAAAA
Found at i:16186669 original size:24 final size:24
Alignment explanation
Indices: 16186625--16186676 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
16186615 ATTTCTTTTA
**
16186625 TTTTTTAAAAAGTTAGATTTCAAT
1 TTTTTTAAAAAAATAGATTTCAAT
* *
16186649 TTTTTTAAAAAAATAGTTTTCAGT
1 TTTTTTAAAAAAATAGATTTCAAT
16186673 TTTT
1 TTTT
16186677 AGAATTTAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.54
Consensus pattern (24 bp):
TTTTTTAAAAAAATAGATTTCAAT
Found at i:16191672 original size:200 final size:201
Alignment explanation
Indices: 16191282--16191695 Score: 517
Period size: 200 Copynumber: 2.1 Consensus size: 201
16191272 TGTGAATCTA
* * * * *
16191282 AGGTGACAGTAAAATTAAACATCAACTTATACTTTTTTTTTGTGATGTTAGATTTCGTCAGCTAT
1 AGGTGACAATAAAATCAAACATCAACTTATACTTTTTTCTTGTGACGTTAGATTTCATCAGCTAT
*
16191347 ATATGAAAAAAAATGTCATTAAATGCTATAATCATCACAAAATAAATGATAAAATATGATATATT
66 ATATGAAAAAAAA-GTCATTAAAGGCTATAATCATCACAAAATAAATGATAAAATATGATATATT
* * * * * * ***
16191412 AGTGACGAAAGGTAAATCGTTATAGTGTTGGTGACACAATTAATGTCATTTATAATTGTAAGATA
130 AGTGACAAAAGGTAAATCGTCACAATATTGGTGACACAATTAAAGTCACCAATAATTGTAAGATA
16191477 ACGTCAC
195 ACGTCAC
* * * * * *
16191484 AGGTGATAATAAAATCAAATATCACCTTATGC-TTTTTCTTGTGACGTTAGATTTCATTAGTTAT
1 AGGTGACAATAAAATCAAACATCAACTTATACTTTTTTCTTGTGACGTTAGATTTCATCAGCTAT
* ** * *
16191548 ATATGAAAAACACA-TCATTAAAGGCTATAATTGTCACAAAATAAATTATAAAATCTGATATATT
66 ATATGAAAAA-AAAGTCATTAAAGGCTATAATCATCACAAAATAAATGATAAAATATGATATATT
* *
16191612 AGTGACAAAAGGTAAATTGTCACAATATTGGTGACACAATTAAAGTCACCAATGATTGTAAGATA
130 AGTGACAAAAGGTAAATCGTCACAATATTGGTGACACAATTAAAGTCACCAATAATTGTAAGATA
* *
16191677 ATGTCAA
195 ACGTCAC
*
16191684 ACGTGACAATAA
1 AGGTGACAATAA
16191696 GTAAAACATC
Statistics
Matches: 179, Mismatches: 32, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
200 114 0.64
201 37 0.21
202 28 0.16
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (201 bp):
AGGTGACAATAAAATCAAACATCAACTTATACTTTTTTCTTGTGACGTTAGATTTCATCAGCTAT
ATATGAAAAAAAAGTCATTAAAGGCTATAATCATCACAAAATAAATGATAAAATATGATATATTA
GTGACAAAAGGTAAATCGTCACAATATTGGTGACACAATTAAAGTCACCAATAATTGTAAGATAA
CGTCAC
Found at i:16194756 original size:19 final size:19
Alignment explanation
Indices: 16194721--16194760 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
16194711 AATTTGTCGA
*
16194721 TTGAAGTTTTCGACCAAAT
1 TTGAAGTTTTAGACCAAAT
16194740 TTGAAGTTTCTAG-CCAAAT
1 TTGAAGTTT-TAGACCAAAT
16194759 TT
1 TT
16194761 CGGCAAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (19 bp):
TTGAAGTTTTAGACCAAAT
Found at i:16196089 original size:25 final size:24
Alignment explanation
Indices: 16196060--16196109 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
16196050 CTCTTACTTG
* * *
16196060 TATTTTATTTATTTGTTCATTTATT
1 TATTTTATATATCTG-TCATTCATT
16196085 TATTTTATATATCTGTCATTCATT
1 TATTTTATATATCTGTCATTCATT
16196109 T
1 T
16196110 GCATATGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.66
Consensus pattern (24 bp):
TATTTTATATATCTGTCATTCATT
Found at i:16202473 original size:3 final size:3
Alignment explanation
Indices: 16202441--16202488 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
16202431 AAATAGTTAA
* * * *
16202441 TAT TAA TAT TAA TAT TAA TAT TAA TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
16202487 TA
1 TA
16202489 GGTTCATATT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:16202483 original size:6 final size:6
Alignment explanation
Indices: 16202432--16202481 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
16202422 AATTTCCTTA
* *
16202432 AATAGTT AATATT AATATT AATATT AATATT AATATT ATTATT ATTATT
1 AATA-TT AATATT AATATT AATATT AATATT AATATT AATATT AATATT
16202481 A
1 A
16202482 TTTATTAGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
6 38 0.90
7 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AATATT
Found at i:16203109 original size:19 final size:21
Alignment explanation
Indices: 16203085--16203126 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16203075 GATTGAAAAA
16203085 TTTTA-TTCTCG-AAATTTTT
1 TTTTATTTCTCGAAAATTTTT
*
16203104 TTTTATTTCTGGAAAATTTTT
1 TTTTATTTCTCGAAAATTTTT
16203125 TT
1 TT
16203127 GACTTTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTTATTTCTCGAAAATTTTT
Found at i:16203947 original size:32 final size:34
Alignment explanation
Indices: 16203867--16203948 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 34
16203857 TGACCGAGGT
*
16203867 TATGAAACTTTAAAAATGGCTCCTCTGACCAAAAGC
1 TATGAAACTTT--AAATGGCTCCTCTGAACAAAAGC
* *
16203903 TATGAAATTTTAAATGGCT-CTCT-AACTAAAG-
1 TATGAAACTTTAAATGGCTCCTCTGAACAAAAGC
16203934 TAATGAAACTTTAAA
1 T-ATGAAACTTTAAA
16203949 ATAAAATCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 1 0.02
32 18 0.44
33 4 0.10
34 8 0.20
36 10 0.24
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.30
Consensus pattern (34 bp):
TATGAAACTTTAAATGGCTCCTCTGAACAAAAGC
Found at i:16212472 original size:14 final size:14
Alignment explanation
Indices: 16212453--16212494 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
16212443 TTCAATTGGG
16212453 TTTTTTTCTTTTCT
1 TTTTTTTCTTTTCT
*
16212467 TTTTTTT-TTTTCC
1 TTTTTTTCTTTTCT
* *
16212480 TCTATTTCTTTTCT
1 TTTTTTTCTTTTCT
16212494 T
1 T
16212495 ACAATAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTTTCTTTTCT
Found at i:16213622 original size:200 final size:200
Alignment explanation
Indices: 16213167--16213936 Score: 861
Period size: 200 Copynumber: 3.8 Consensus size: 200
16213157 TATACTTTTT
* * * * *
16213167 TTTTTTTTGTGATGTTAGATTTCGTTAGCTATATAAAAAAAAAAATGTAATTAAATGCTATAATC
1 TTTTTTTTGTGACGTTAGATTTCATTAGCTATAT--ATAAAAAAATGTTATTAAAGGCTATAATC
* * * * *
16213232 ATCACAAAATAAATGATAAAATATGATATATTAGTGACGAAAGGTAAATCGTTACAATGTTGGTA
64 ATCACAAAATAAATGATAAAATATGATATATTAGTGACAAAAGGTAAATCGTCACAATATTGATG
* * * * * *
16213297 ACATAATTAATGTCACTTATGATTGTAAGATAACGTCACAGGTGATAATAAAATCAAATATCACC
129 ACACAATTAATGTCACCTATGATTGTAAGATAACGTCAAATGTGACAAT-AAGTCAAATATCACC
16213362 TTATGCTC
193 TTATGCTC
* * * *
16213370 --TTTTTTGTGACGTTAGATTTTATTAGTTATATATAAAAAACACGTTATTAAAGGCTATAATTA
1 TTTTTTTTGTGACGTTAGATTTCATTAGCTATATATAAAAAA-ATGTTATTAAAGGCTATAATCA
* * *
16213433 TCACAAAATAAATTATAAAATATGATATATTAGTGACAAAAGGTAAATTC-TCATAATATTGGTG
65 TCACAAAATAAATGATAAAATATGATATATTAGTGACAAAAGGTAAA-TCGTCACAATATTGATG
* * * * *
16213497 ACACAATTAAAGTCACCAATGATTGTAAGATAATGTCAAATGTGACAATAAGTAAAACATCACCT
129 ACACAATTAATGTCACCTATGATTGTAAGATAACGTCAAATGTGACAATAAGTCAAATATCACCT
16213562 TATGCTC
194 TATGCTC
* * * * ** * *
16213569 TTTTTTTTGTGATGTTAGGTTTC-GTCGACTATATAGGAAAAAATGTCATTAAAGGCTATAATCG
1 TTTTTTTTGTGACGTTAGATTTCATTAG-CTATATATAAAAAAATGTTATTAAAGGCTATAATCA
* * * *
16213633 TCACAAAATAAATGATAAAATTTGATATATTAGTGACAAAAGGTAAATCATCACAGTATTAATGA
65 TCACAAAATAAATGATAAAATATGATATATTAGTGACAAAAGGTAAATCGTCACAATATTGATGA
* * * * * * *
16213698 CTCAATTAATGTTACTTATGATTGTAAGATAACATCAAATGTGACAATAGGATCAAATGTTACCT
130 CACAATTAATGTCACCTATGATTGTAAGATAACGTCAAATGTGACAATAAG-TCAAATATCACCT
16213763 TATG--C
194 TATGCTC
* * *
16213768 TTTTTTTTGTGACGTTA-AGTTTCATTAGCTATATATGAAAAAACTGTTATTAAATGCTATAATT
1 TTTTTTTTGTGACGTTAGA-TTTCATTAGCTATATAT-AAAAAAATGTTATTAAAGGCTATAATC
* * * * * ** * * *
16213832 GTCATAAAATAAATGATAAAATCTAATATGTTAGTGATGAAAGATAAGTCGTCACAATATTGACG
64 ATCACAAAATAAATGATAAAATATGATATATTAGTGACAAAAGGTAAATCGTCACAATATTGATG
*
16213897 ACACAATTAATGTCACCTATGATTGTAAAATAACGTCAAA
129 ACACAATTAATGTCACCTATGATTGTAAGATAACGTCAAA
16213937 CATAACAATA
Statistics
Matches: 474, Mismatches: 83, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
199 57 0.12
200 345 0.73
201 72 0.15
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (200 bp):
TTTTTTTTGTGACGTTAGATTTCATTAGCTATATATAAAAAAATGTTATTAAAGGCTATAATCAT
CACAAAATAAATGATAAAATATGATATATTAGTGACAAAAGGTAAATCGTCACAATATTGATGAC
ACAATTAATGTCACCTATGATTGTAAGATAACGTCAAATGTGACAATAAGTCAAATATCACCTTA
TGCTC
Found at i:16213947 original size:400 final size:401
Alignment explanation
Indices: 16213167--16213948 Score: 1018
Period size: 400 Copynumber: 2.0 Consensus size: 401
16213157 TATACTTTTT
* *
16213167 TTTTTTTTGTGATGTTAGATTTCGTTAGCTATATAAAAAAAAAAATGTAATTAAATGCTATAATC
1 TTTTTTTTGTGATGTTAGATTTCGTGAGCTATAT-AAAAAAAAAATGTAATTAAAGGCTATAATC
* * * * **
16213232 ATCACAAAATAAATGATAAAATATGATATATTAGTGACGAAAGGTAAATCGTTACAATGTTGGTA
65 ATCACAAAATAAATGATAAAATATGATATATTAGTGACAAAAGGTAAATCATCACAATATTAATA
* * *
16213297 ACATAATTAATGTCACTTATGATTGTAAGATAACGTCACAGGTGATAATAAAATCAAATATCACC
130 ACATAATTAATGTCACTTATGATTGTAAGATAACATCAAAGGTGACAATAAAATCAAATATCACC
* *
16213362 TTATGCTCTTTTTTGTGACGTTAGATTTTATTAGTTATATATAAAAAACACGTTATTAAAGGCTA
195 TTATGCTCTTTTTTGTGACGTTAGATTTCATTAGCTATATATAAAAAACACGTTATTAAAGGCTA
* * * * *
16213427 TAATTATCACAAAATAAATTATAAAATATGATATATTAGTGACAAAAGGTAAATTCTCATAATAT
260 TAATTATCACAAAATAAATGATAAAATATAATATATTAGTGACAAAAGATAAAGTCTCACAATAT
** * * ** *
16213492 TGGTGACACAATTAAAGTCACCAATGATTGTAAGATAATGTCAAATGTGACAATAAGTAAAACAT
325 TGACGACACAATTAAAGTCACCAATGATTGTAAAATAACGTCAAACATAACAATAAGTAAAACAT
16213557 CACCTTATGCTC
390 CACCTTATGCTC
* ** *
16213569 TTTTTTTTGTGATGTTAGGTTTCGTCGA-CTATAT-AGGAAAAAATGTCATTAAAGGCTATAATC
1 TTTTTTTTGTGATGTTAGATTTCGT-GAGCTATATAAAAAAAAAATGTAATTAAAGGCTATAATC
* * * *
16213632 GTCACAAAATAAATGATAAAATTTGATATATTAGTGACAAAAGGTAAATCATCACAGTATTAATG
65 ATCACAAAATAAATGATAAAATATGATATATTAGTGACAAAAGGTAAATCATCACAATATTAATA
* * ** * *
16213697 AC-TCAATTAATGTTACTTATGATTGTAAGATAACATCAAATGTGACAATAGGATCAAATGTTAC
130 ACAT-AATTAATGTCACTTATGATTGTAAGATAACATCAAAGGTGACAATAAAATCAAATATCAC
* * *
16213761 CTTATGCTTTTTTTTGTGACGTTA-AGTTTCATTAGCTATATATGAAAAAAC-TGTTATTAAATG
194 CTTATGCTCTTTTTTGTGACGTTAGA-TTTCATTAGCTATATAT-AAAAAACACGTTATTAAAGG
* * * * **
16213824 CTATAATTGTCATAAAATAAATGATAAAATCTAATATGTTAGTGATGAAAGAT-AAGTCGTCACA
257 CTATAATTATCACAAAATAAATGATAAAATATAATATATTAGTGACAAAAGATAAAGTC-TCACA
* *
16213888 ATATTGACGACACAATTAATGTCACCTATGATTGTAAAATAACGTCAAACATAACAATAAG
321 ATATTGACGACACAATTAAAGTCACCAATGATTGTAAAATAACGTCAAACATAACAATAAG
16213949 ATCAGACATA
Statistics
Matches: 325, Mismatches: 50, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
399 6 0.02
400 281 0.86
401 7 0.02
402 30 0.09
403 1 0.00
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (401 bp):
TTTTTTTTGTGATGTTAGATTTCGTGAGCTATATAAAAAAAAAATGTAATTAAAGGCTATAATCA
TCACAAAATAAATGATAAAATATGATATATTAGTGACAAAAGGTAAATCATCACAATATTAATAA
CATAATTAATGTCACTTATGATTGTAAGATAACATCAAAGGTGACAATAAAATCAAATATCACCT
TATGCTCTTTTTTGTGACGTTAGATTTCATTAGCTATATATAAAAAACACGTTATTAAAGGCTAT
AATTATCACAAAATAAATGATAAAATATAATATATTAGTGACAAAAGATAAAGTCTCACAATATT
GACGACACAATTAAAGTCACCAATGATTGTAAAATAACGTCAAACATAACAATAAGTAAAACATC
ACCTTATGCTC
Found at i:16215238 original size:13 final size:13
Alignment explanation
Indices: 16215220--16215244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16215210 TGTTATGTAT
16215220 ATATAATATATAC
1 ATATAATATATAC
16215233 ATATAATATATA
1 ATATAATATATA
16215245 TAATGCATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATAATATATAC
Found at i:16217158 original size:18 final size:17
Alignment explanation
Indices: 16217124--16217156 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
16217114 CTATTTGGGG
16217124 ATTTTTTTATGAATTTA
1 ATTTTTTTATGAATTTA
16217141 ATTTTTTTATGAATTT
1 ATTTTTTTATGAATTT
16217157 TACCAAACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
ATTTTTTTATGAATTTA
Found at i:16217985 original size:25 final size:24
Alignment explanation
Indices: 16217953--16218002 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
16217943 CTCTTACTTA
* * *
16217953 TATTTTATTTATTTGTTCATTTATT
1 TATTTTATATATCTG-TCATTCATT
16217978 TATTTTATATATCTGTCATTCATT
1 TATTTTATATATCTGTCATTCATT
16218002 T
1 T
16218003 GCATATGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.66
Consensus pattern (24 bp):
TATTTTATATATCTGTCATTCATT
Found at i:16223553 original size:15 final size:14
Alignment explanation
Indices: 16223527--16223569 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
16223517 ACTTTGGTGA
*
16223527 AATTTATAGAAAAT
1 AATTTTTAGAAAAT
*
16223541 ATTTATTTAGAAAAT
1 AATT-TTTAGAAAAT
*
16223556 AATTTTGAGAAAAT
1 AATTTTTAGAAAAT
16223570 TGACCATTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (14 bp):
AATTTTTAGAAAAT
Found at i:16224337 original size:3 final size:3
Alignment explanation
Indices: 16224318--16224364 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
16224308 AAATAGTTAA
*
16224318 TAT TA- TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
16224363 TA
1 TA
16224365 GGTTCATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:16224463 original size:3 final size:3
Alignment explanation
Indices: 16224420--16224449 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
16224410 AAAGAATAAC
16224420 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16224450 CCAAAACAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:16225720 original size:42 final size:40
Alignment explanation
Indices: 16225670--16225755 Score: 93
Period size: 41 Copynumber: 2.1 Consensus size: 40
16225660 ACAATTTTTG
*
16225670 AAAATTAAAAAGG-CTCATCTAACCAGAGATAATGATACTTT
1 AAAATT-AAAAGGCCTC-TCTAACCAGAGATAATGAAACTTT
* * * *
16225711 AAAATTTAAAAGGCCTCTTTGACCAGAGGTTATGAAACTTT
1 AAAA-TTAAAAGGCCTCTCTAACCAGAGATAATGAAACTTT
16225752 AAAA
1 AAAA
16225756 ATGGCTCCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
41 33 0.87
42 5 0.13
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (40 bp):
AAAATTAAAAGGCCTCTCTAACCAGAGATAATGAAACTTT
Found at i:16225772 original size:36 final size:36
Alignment explanation
Indices: 16225730--16225825 Score: 115
Period size: 34 Copynumber: 2.7 Consensus size: 36
16225720 AAGGCCTCTT
*
16225730 TGACCAGAGGTTATGAAACTTTAAAAATGGCTCCTC
1 TGACCAGAAGTTATGAAACTTTAAAAATGGCTCCTC
* * *
16225766 TGACCAGAAGTTGTGAAA-TTT-TAAATGGCTTCTC
1 TGACCAGAAGTTATGAAACTTTAAAAATGGCTCCTC
* * *
16225800 TAACTAGAAGTAATGAAACTTTAAAA
1 TGACCAGAAGTTATGAAACTTTAAAA
16225826 TAAAAATCTG
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
34 25 0.51
35 6 0.12
36 18 0.37
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.30
Consensus pattern (36 bp):
TGACCAGAAGTTATGAAACTTTAAAAATGGCTCCTC
Found at i:16235168 original size:19 final size:19
Alignment explanation
Indices: 16235133--16235172 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
16235123 AATTTGTCGA
*
16235133 TTGAAGTTTTCGACCAAAT
1 TTGAAGTTTTAGACCAAAT
16235152 TTGAAGTTTCTAG-CCAAAT
1 TTGAAGTTT-TAGACCAAAT
16235171 TT
1 TT
16235173 CGGCAAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (19 bp):
TTGAAGTTTTAGACCAAAT
Found at i:16236494 original size:25 final size:24
Alignment explanation
Indices: 16236465--16236514 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
16236455 CTCTTACTTG
* * *
16236465 TATTTTATTTATTTGTTCATTTATT
1 TATTTTATATATCTG-TCATTCATT
16236490 TATTTTATATATCTGTCATTCATT
1 TATTTTATATATCTGTCATTCATT
16236514 T
1 T
16236515 GCATATGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 9 0.41
25 13 0.59
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.66
Consensus pattern (24 bp):
TATTTTATATATCTGTCATTCATT
Found at i:16242820 original size:6 final size:6
Alignment explanation
Indices: 16242806--16242855 Score: 64
Period size: 6 Copynumber: 8.0 Consensus size: 6
16242796 AATTTCCTTA
* *
16242806 AATAGTT AATATT AATATT AATATT AATATT AATTATT ATTATT ATTATT
1 AATA-TT AATATT AATATT AATATT AATATT AA-TATT AATATT AATATT
16242856 TATTAGGTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
6 32 0.78
7 9 0.22
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (6 bp):
AATATT
Found at i:16243478 original size:19 final size:21
Alignment explanation
Indices: 16243454--16243495 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
16243444 GATTGAAAAA
16243454 TTTTA-TTCTCG-AAATTTTT
1 TTTTATTTCTCGAAAATTTTT
*
16243473 TTTTATTTCTGGAAAATTTTT
1 TTTTATTTCTCGAAAATTTTT
16243494 TT
1 TT
16243496 GACTTTGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 5 0.25
21 10 0.50
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.64
Consensus pattern (21 bp):
TTTTATTTCTCGAAAATTTTT
Found at i:16244266 original size:36 final size:36
Alignment explanation
Indices: 16244224--16244322 Score: 112
Period size: 34 Copynumber: 2.8 Consensus size: 36
16244214 TAAAAGGGTT
* *
16244224 CTCTGACCGGAGGTTATGAAACTTTAAAAATGGCTC
1 CTCTGACCAGAAGTTATGAAACTTTAAAAATGGCTC
* * *
16244260 CTCTGACCAGAAGTTGTGAAA-TTT-TAAATGGCTT
1 CTCTGACCAGAAGTTATGAAACTTTAAAAATGGCTC
* * *
16244294 CTCTAACTAGAAGTAATGAAACTTTAAAA
1 CTCTGACCAGAAGTTATGAAACTTTAAAA
16244323 TAAAAATCTG
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
34 25 0.49
35 6 0.12
36 20 0.39
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.30
Consensus pattern (36 bp):
CTCTGACCAGAAGTTATGAAACTTTAAAAATGGCTC
Found at i:16256151 original size:7 final size:7
Alignment explanation
Indices: 16256125--16256216 Score: 54
Period size: 7 Copynumber: 13.7 Consensus size: 7
16256115 TAATTAATAG
16256125 ATTTAATT
1 ATTT-ATT
*
16256133 AATTATTT
1 ATTTA-TT
16256141 ATTTATT
1 ATTTATT
16256148 ATTTATT
1 ATTTATT
* *
16256155 -GTGATT
1 ATTTATT
*
16256161 ATTT-TA
1 ATTTATT
16256167 ATTT-TT
1 ATTTATT
16256173 -TGTTATT
1 AT-TTATT
*
16256180 ATTTACT
1 ATTTATT
16256187 ATTTATT
1 ATTTATT
16256194 ATTT-TT
1 ATTTATT
*
16256200 ATCT-TT
1 ATTTATT
16256206 -TTTATT
1 ATTTATT
16256212 ATTTA
1 ATTTA
16256217 AATGAATAAT
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
5 3 0.05
6 21 0.32
7 31 0.48
8 10 0.15
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.68
Consensus pattern (7 bp):
ATTTATT
Found at i:16256180 original size:32 final size:32
Alignment explanation
Indices: 16256142--16256216 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
16256132 TAATTATTTA
*
16256142 TTTATTATTTA-T-TGTGATTATTTTAATTTTT
1 TTTATTATTTACTAT-TGATTATTTTAATCTTT
* *
16256173 TGTTATTATTTACTATTTATTATTTTTATCTTT
1 T-TTATTATTTACTATTGATTATTTTAATCTTT
16256206 TTTATTATTTA
1 TTTATTATTTA
16256217 AATGAATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
31 1 0.03
32 20 0.53
33 16 0.42
34 1 0.03
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.71
Consensus pattern (32 bp):
TTTATTATTTACTATTGATTATTTTAATCTTT
Found at i:16256773 original size:3 final size:3
Alignment explanation
Indices: 16256767--16256822 Score: 62
Period size: 3 Copynumber: 19.3 Consensus size: 3
16256757 GATGATGATG
* * *
16256767 ATA ATA ATA ATA ATA ATA GTG ATA ATA ATA ATA ATA AT- ATC ATA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
16256813 AAA ATA ATA A
1 ATA ATA ATA A
16256823 ATAAATAAAT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:16256789 original size:21 final size:20
Alignment explanation
Indices: 16256764--16256822 Score: 84
Period size: 21 Copynumber: 3.0 Consensus size: 20
16256754 GATGATGATG
16256764 ATGATAATAATAATAATAAT
1 ATGATAATAATAATAATAAT
16256784 AGTGATAATAATAATAATAAT
1 A-TGATAATAATAATAATAAT
* *
16256805 ATCATAA-AAAAATAATAA
1 ATGATAATAATAATAATAA
16256823 ATAAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 20 0.56
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.31
Consensus pattern (20 bp):
ATGATAATAATAATAATAAT
Found at i:16256833 original size:28 final size:25
Alignment explanation
Indices: 16256767--16256843 Score: 64
Period size: 27 Copynumber: 2.9 Consensus size: 25
16256757 GATGATGATG
** *
16256767 ATAATAATAATAATAATAGTGATAATA
1 ATAATAATAATAA-AATA-AAAAAATA
**
16256794 ATAATAATAATATCATAAAAAAATA
1 ATAATAATAATAAAATAAAAAAATA
16256819 ATAAATAAATAAATAAAATAAAAAA
1 AT-AAT-AAT-AATAAAATAAAAAA
16256844 GAAAAAGAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
25 7 0.17
26 6 0.15
27 15 0.38
28 12 0.30
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (25 bp):
ATAATAATAATAAAATAAAAAAATA
Found at i:16257305 original size:36 final size:37
Alignment explanation
Indices: 16257258--16257332 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
16257248 CATATTTTGT
16257258 AAAGCAGTTTTACT-AAAAAAAAAAATTAAATGCCCA
1 AAAGCAGTTTTACTAAAAAAAAAAAATTAAATGCCCA
16257294 AAAGCAGTTTTACTAAAAAAAAAAAATTAAATGCCCA
1 AAAGCAGTTTTACTAAAAAAAAAAAATTAAATGCCCA
16257331 AA
1 AA
16257333 TCAAAAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 14 0.37
37 24 0.63
ACGTcount: A:0.57, C:0.13, G:0.08, T:0.21
Consensus pattern (37 bp):
AAAGCAGTTTTACTAAAAAAAAAAAATTAAATGCCCA
Found at i:16257373 original size:18 final size:20
Alignment explanation
Indices: 16257339--16257375 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
16257329 CAAATCAAAA
16257339 AATTTTATTTTTGTTTTTAG
1 AATTTTATTTTTGTTTTTAG
16257359 AATTTT-TTTTT-TTTTTA
1 AATTTTATTTTTGTTTTTA
16257376 CTTTATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (20 bp):
AATTTTATTTTTGTTTTTAG
Found at i:16262254 original size:4 final size:4
Alignment explanation
Indices: 16262234--16262276 Score: 50
Period size: 4 Copynumber: 10.2 Consensus size: 4
16262224 TCAAGGACTG
* *
16262234 AGAA AGAA ATGAG AGAA AGAA AGAA AGAG AGAA AGGAA AGAA A
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA A-GAA AGAA A
16262277 ACGAATAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 26 0.79
5 7 0.21
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (4 bp):
AGAA
Found at i:16262256 original size:17 final size:16
Alignment explanation
Indices: 16262234--16262276 Score: 68
Period size: 17 Copynumber: 2.6 Consensus size: 16
16262224 TCAAGGACTG
16262234 AGAAAGAAATGAGAGAA
1 AGAAAGAAA-GAGAGAA
16262251 AGAAAGAAAGAGAGAA
1 AGAAAGAAAGAGAGAA
16262267 AGGAAAGAAA
1 A-GAAAGAAA
16262277 ACGAATAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 8 0.32
17 17 0.68
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.02
Consensus pattern (16 bp):
AGAAAGAAAGAGAGAA
Found at i:16265068 original size:2 final size:2
Alignment explanation
Indices: 16265061--16265104 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
16265051 AAGCTGTATG
16265061 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16265103 TA
1 TA
16265105 AACCTTAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16266752 original size:14 final size:14
Alignment explanation
Indices: 16266733--16266762 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
16266723 AAAAACTACT
16266733 TACATATATATATA
1 TACATATATATATA
16266747 TACATATATATATA
1 TACATATATATATA
16266761 TA
1 TA
16266763 TAACAAGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (14 bp):
TACATATATATATA
Found at i:16269476 original size:12 final size:12
Alignment explanation
Indices: 16269446--16269488 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
16269436 TTAGTTTTTA
* *
16269446 TGTGTGCATGCA
1 TGTGTGCGTGCG
*
16269458 TGCGTGCGTGCG
1 TGTGTGCGTGCG
*
16269470 TGTGTGCGTGTG
1 TGTGTGCGTGCG
16269482 TGTGTGC
1 TGTGTGC
16269489 ATGTGTCCGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.05, C:0.16, G:0.44, T:0.35
Consensus pattern (12 bp):
TGTGTGCGTGCG
Found at i:16280476 original size:115 final size:115
Alignment explanation
Indices: 16280270--16280500 Score: 444
Period size: 115 Copynumber: 2.0 Consensus size: 115
16280260 ATCTCAATTC
16280270 CCAAATAGATGAAAAGATTCGAATATGTGTTGGTTACCATGATCTGAATAGGGCAAACCTAGATG
1 CCAAATAGATGAAAAGATTCGAATATGTGTTGGTTACCATGATCTGAATAGGGCAAACCTAGATG
16280335 ATAACTTTTTTTTACCTCATACCAACACTTTAATGGATAATACAACTAGG
66 ATAACTTTTTTTTACCTCATACCAACACTTTAATGGATAATACAACTAGG
*
16280385 CCAAATAGATGAAAAGATTCGAATATGTGTTGGTTACCATGATCTGAATAGGGCAAGCCTAGATG
1 CCAAATAGATGAAAAGATTCGAATATGTGTTGGTTACCATGATCTGAATAGGGCAAACCTAGATG
*
16280450 ATAACTTTTTTTTACCTCATATCAACACTTTAATGGATAATACAACTAGG
66 ATAACTTTTTTTTACCTCATACCAACACTTTAATGGATAATACAACTAGG
16280500 C
1 C
16280501 ATTCCATGTT
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
115 114 1.00
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (115 bp):
CCAAATAGATGAAAAGATTCGAATATGTGTTGGTTACCATGATCTGAATAGGGCAAACCTAGATG
ATAACTTTTTTTTACCTCATACCAACACTTTAATGGATAATACAACTAGG
Found at i:16284297 original size:41 final size:40
Alignment explanation
Indices: 16284198--16284570 Score: 278
Period size: 41 Copynumber: 9.2 Consensus size: 40
16284188 AAGTTTTTAA
* * * * *
16284198 AAATTTTCAAAATTGTATGCATTTGTTTTGAATGAGCCTTT
1 AAATTTTCAAAGTTGTGTGCTTTTATTTTGAAAGAG-CTTT
* *
16284239 AAAATTTTCAAAG-TGTGTGCTTTTGTTTTGAAGGAGCTTT
1 -AAATTTTCAAAGTTGTGTGCTTTTATTTTGAAAGAGCTTT
* ** *
16284279 AAACTTTTAAAAGTTGTGTG-TTTTCGCTTTGAAGGAG-TCTT
1 AAA-TTTTCAAAGTTGTGTGCTTTT-ATTTTGAAAGAGCT-TT
* * * **
16284320 AAATTTTTCAAAGTTGTATACCTTCGTTTTGAAAGAGCTTT
1 AAA-TTTTCAAAGTTGTGTGCTTTTATTTTGAAAGAGCTTT
* * * *
16284361 -AATTTTCAATGTTGTGTG-TCTTCATTTTGAAGGAGTATTT
1 AAATTTTCAAAGTTGTGTGCT-TTTATTTTGAAAGAG-CTTT
* * * *
16284401 AAATTTTTCAAAGTTGTATGCCTTTATTTTGAAAGAACCTT
1 AAA-TTTTCAAAGTTGTGTGCTTTTATTTTGAAAGAGCTTT
* * *
16284442 AAA-TTTCAAAGTTATGTGCTTTCATTTTAAAAGAGCTTT
1 AAATTTTCAAAGTTGTGTGCTTTTATTTTGAAAGAGCTTT
* * * *
16284481 AAACTTTTAAAAGTTGTGTGCATTTATTTTGAAAAAGCCTTA
1 AAA-TTTTCAAAGTTGTGTGCTTTTATTTTGAAAGAG-CTTT
* *
16284523 AAATTTTCAAAGTTGTGTGCCTTCT-TTTTG-AAGGGCTTT
1 AAATTTTCAAAGTTGTGTG-CTTTTATTTTGAAAGAGCTTT
16284562 -AATTTTCAA
1 AAATTTTCAA
16284571 GAGCCCTAAT
Statistics
Matches: 267, Mismatches: 49, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
38 9 0.03
39 64 0.24
40 25 0.09
41 120 0.45
42 49 0.18
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (40 bp):
AAATTTTCAAAGTTGTGTGCTTTTATTTTGAAAGAGCTTT
Found at i:16284330 original size:81 final size:81
Alignment explanation
Indices: 16284223--16284556 Score: 316
Period size: 81 Copynumber: 4.1 Consensus size: 81
16284213 TATGCATTTG
* * * * * * * *
16284223 TTTTGAATGAGCCTTTAAAATTTTCAAAG-TGTGTGCTTTTGTTTTGAAGGAGCTTTAAACTTTT
1 TTTTGAAGGAGTC-TTAAATTTTTCAAAGTTGTATGCCTTTATTTTGAAAGAGCCTTAAA-TTTT
* *
16284287 AAAAGTTGTGTGTTTTCG
64 CAAAGTTGTGTGTTTTCA
* * ** *
16284305 CTTTGAAGGAGTCTTAAATTTTTCAAAGTTGTATACCTTCGTTTTGAAAGAG-CTTTAATTTTCA
1 TTTTGAAGGAGTCTTAAATTTTTCAAAGTTGTATGCCTTTATTTTGAAAGAGCCTTAAATTTTCA
* *
16284369 ATGTTGTGTGTCTTCA
66 AAGTTGTGTGTTTTCA
* *
16284385 TTTTGAAGGAGTATTTAAATTTTTCAAAGTTGTATGCCTTTATTTTGAAAGAACCTTAAA-TTTC
1 TTTTGAAGGAGT-CTTAAATTTTTCAAAGTTGTATGCCTTTATTTTGAAAGAGCCTTAAATTTTC
* *
16284449 AAAGTTATGTGCTTTCA
65 AAAGTTGTGTGTTTTCA
* * * * * * *
16284466 TTTTAAAAGAG-CTTTAAACTTTTAAAAGTTGTGTGCATTTATTTTGAAAAAGCCTTAAAATTTT
1 TTTTGAAGGAGTC-TTAAATTTTTCAAAGTTGTATGCCTTTATTTTGAAAGAGCCTT-AAATTTT
** *
16284530 CAAAGTTGTGTGCCTTCT
64 CAAAGTTGTGTGTTTTCA
16284548 TTTTGAAGG
1 TTTTGAAGG
16284557 GCTTTAATTT
Statistics
Matches: 206, Mismatches: 40, Indels: 12
0.80 0.16 0.05
Matches are distributed among these distances:
80 66 0.32
81 82 0.40
82 58 0.28
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (81 bp):
TTTTGAAGGAGTCTTAAATTTTTCAAAGTTGTATGCCTTTATTTTGAAAGAGCCTTAAATTTTCA
AAGTTGTGTGTTTTCA
Found at i:16291836 original size:16 final size:16
Alignment explanation
Indices: 16291813--16291854 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
16291803 ATGGTCTCAT
16291813 GTTTTTTT-GGTGTTG
1 GTTTTTTTGGGTGTTG
*
16291828 GTTTGTTTTGGGTGTTC
1 GTTT-TTTTGGGTGTTG
*
16291845 TTTTTTTTGG
1 GTTTTTTTGG
16291855 AAGAAGGCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 4 0.17
16 10 0.43
17 9 0.39
ACGTcount: A:0.00, C:0.02, G:0.31, T:0.67
Consensus pattern (16 bp):
GTTTTTTTGGGTGTTG
Found at i:16292686 original size:2 final size:2
Alignment explanation
Indices: 16292679--16292704 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16292669 AATAATGTAG
16292679 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
16292705 GCTTACTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16301371 original size:16 final size:17
Alignment explanation
Indices: 16301350--16301384 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
16301340 AATTGGACCC
16301350 AATATTAAAAAAT-TAA
1 AATATTAAAAAATATAA
*
16301366 AATATTTAAAAATATAA
1 AATATTAAAAAATATAA
16301383 AA
1 AA
16301385 AATAACAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AATATTAAAAAATATAA
Found at i:16307249 original size:11 final size:11
Alignment explanation
Indices: 16307233--16307257 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16307223 TCAGCCCTCC
16307233 CATCCCTTGCA
1 CATCCCTTGCA
16307244 CATCCCTTGCA
1 CATCCCTTGCA
16307255 CAT
1 CAT
16307258 ACTGAGTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.44, G:0.08, T:0.28
Consensus pattern (11 bp):
CATCCCTTGCA
Found at i:16310026 original size:12 final size:12
Alignment explanation
Indices: 16310009--16310033 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
16309999 GACTGTGTTT
16310009 TATTTTTTTTTA
1 TATTTTTTTTTA
16310021 TATTTTTTTTTA
1 TATTTTTTTTTA
16310033 T
1 T
16310034 TTATTGTTTG
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TATTTTTTTTTA
Found at i:16310690 original size:132 final size:132
Alignment explanation
Indices: 16310449--16310718 Score: 414
Period size: 132 Copynumber: 2.0 Consensus size: 132
16310439 TTTAGGGCTG
* * *
16310449 GCTCTAATATCACTTGTCACGGGTCGAGACTTAAGCTTCGAACCCGCGTGGCTCCAGGACCCGGG
1 GCTCTGATATCACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCAGGACCCGGG
* * *
16310514 CATTCATCCTTTCAGCGTCCCAGATCAGCCTTCCTACTGCGGTTCACACCCTTGTGAGGTATTGT
66 CATTCACCCTTTCAGAGTCCCAGATCAGCCTTCCTACTACGGTTCACACCCTTGTGAGGTATTGT
16310579 CC
131 CC
* ** *
16310581 GCTCTGATATCACTTGTCACGGGTTGAGACTTAAGCTCCGAACCCGCGCGGCTCTGGGACTCGGG
1 GCTCTGATATCACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCAGGACCCGGG
* * *
16310646 CATTCACCCTTTCGGAGTCTCAGATCAGCCTTCCTACTATGGTTCACACCCTTGTGAGGTATTGT
66 CATTCACCCTTTCAGAGTCCCAGATCAGCCTTCCTACTACGGTTCACACCCTTGTGAGGTATTGT
16310711 CC
131 CC
*
16310713 GTTCTG
1 GCTCTG
16310719 GCCCCTCTGG
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
132 124 1.00
ACGTcount: A:0.17, C:0.31, G:0.24, T:0.28
Consensus pattern (132 bp):
GCTCTGATATCACTTGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTCCAGGACCCGGG
CATTCACCCTTTCAGAGTCCCAGATCAGCCTTCCTACTACGGTTCACACCCTTGTGAGGTATTGT
CC
Found at i:16311040 original size:503 final size:503
Alignment explanation
Indices: 16310092--16311089 Score: 1385
Period size: 503 Copynumber: 2.0 Consensus size: 503
16310082 AGGGTTCTAG
** * *
16310092 TGTCACGGGTCGAGACTTAAGCTCCGAATTCGTGCGGCTTCGGGATTCGGACATTCACCCTTTCG
1 TGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTTCGGGACTCGGACATTCACCCTTTCG
* * * * *
16310157 ATTTCTCGGATCAGCCTGACCGCCACGGTTCACATCCTTGTGAGATATTGTCTGCTCTAGCCCCC
66 ATGTCTCAGATCAGCCTGACCACCACGGTTCACACCCTTGTGAGATATTGTCCGCTCTAGCCCCC
* *
16310222 CTAGTCTCACGGTTTTATCCTACAAAAGGCACCTCACAAGGCGGAGATGGTGTGAACACTTTTAT
131 CTAGCCTCACGGTTTTATCCTACAAAAAGCACCTCACAAGGCGGAGATGGTGTGAACACTTTTAT
16310287 ACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAGGACTCCCCCTTAGGTCCGTGACATT
196 ACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAGGACTCCCCCTTAGGTCCGTGACATT
* ** * ** *
16310352 CTTCCGCACCCAACCTTGTGACGCCCTCGTCATAGAGGCTGGTCACCCTGCCTACCTCCCCCGAG
261 CTCCCGCACCCAACCTCATGACGCCCTCGTCACAGAGGCTGACCACCCTACCTACCTCCCCCGAG
* * *
16310417 GTGCTTGGCGTGGATCGAACGGTTTAGGGCTGGCTCTAATATCACTTGTCACGGGTCGAGACTTA
326 GTGCTTGGCGTGGATCGAACGATTTAGGGCTGGCTCTAATACCACTTGTCACGGGTCGAGACTCA
* * * * * * *
16310482 AGCTTCGAACCCGCGTGGCTCCAGGACCCGGGCATTCATCCTTTCAGCGTCCCAGATCAGCCT-T
391 AGCTTCAAACCCGCGCGACTCCAGGACCCGGGCATTCACCCTTCCAACGTCCCAGATCAGCCTGA
**
16310546 CCTACTGCGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGATATCACT
456 CC-ACCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGATATCACT
* *
16310595 TGTCACGGGTTGAGACTTAAGCTCCGAACCCGCGCGGC-TCTGGGACTCGGGCATTCACCCTTTC
1 TGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTTC-GGGACTCGGACATTCACCCTTTC
* * * * * *
16310659 GGA-GTCTCAGATCAGCCT-TCCTACTATGGTTCACACCCTTGTGAGGTATTGTCCGTTCTGGCC
65 -GATGTCTCAGATCAGCCTGACC-ACCACGGTTCACACCCTTGTGAGATATTGTCCGCTCTAGCC
* * * * *
16310722 CCTCTGGCCTCACGGTTTTGTCCTACAAAAAGCGCCTCACAAGGCGGAGATGGTGTGAACCCTTT
128 CCCCTAGCCTCACGGTTTTATCCTACAAAAAGCACCTCACAAGGCGGAGATGGTGTGAACACTTT
* ** *
16310787 TATACCCCAGTGACCTTCCTATTATGTTCGATGTGGGATTCAGGACTCTTCCTTAGGTCTGTGAC
193 TATACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAGGACTCCCCCTTAGGTCCGTGAC
* * * **
16310852 ATTCTCCCGCACCCAACCTCATGACGCCCTCGTCACGGAGGCTGACCACCCTACCTGCCTCTCTT
258 ATTCTCCCGCACCCAACCTCATGACGCCCTCGTCACAGAGGCTGACCACCCTACCTACCTCCCCC
* *
16310917 GAGGTGCTTGGCGTGGCTCGAACGATTTAGGGCTGGCTCTGATACCACTTGTCACGGGTCGAGAC
323 GAGGTGCTTGGCGTGGATCGAACGATTTAGGGCTGGCTCTAATACCACTTGTCACGGGTCGAGAC
* *
16310982 TCAAGCTTCAAACCCGCGCGACTCC-GAGACTCGGGCATTCACCCTTCCAACTTCCCAGATCAGC
388 TCAAGCTTCAAACCCGCGCGACTCCAG-GACCCGGGCATTCACCCTTCCAACGTCCCAGATCAGC
* * *
16311046 CTGACCGCCACGGTTTACACCCTTGTGAGGTATTGTCTGCTCTG
452 CTGACCACCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTG
16311090 GCCCCCTTAG
Statistics
Matches: 431, Mismatches: 59, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
502 5 0.01
503 422 0.98
504 4 0.01
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (503 bp):
TGTCACGGGTCGAGACTTAAGCTCCGAACCCGCGCGGCTTCGGGACTCGGACATTCACCCTTTCG
ATGTCTCAGATCAGCCTGACCACCACGGTTCACACCCTTGTGAGATATTGTCCGCTCTAGCCCCC
CTAGCCTCACGGTTTTATCCTACAAAAAGCACCTCACAAGGCGGAGATGGTGTGAACACTTTTAT
ACCCCAGTGACCCTCCTATTATGTTCGATGTGGGATTCAGGACTCCCCCTTAGGTCCGTGACATT
CTCCCGCACCCAACCTCATGACGCCCTCGTCACAGAGGCTGACCACCCTACCTACCTCCCCCGAG
GTGCTTGGCGTGGATCGAACGATTTAGGGCTGGCTCTAATACCACTTGTCACGGGTCGAGACTCA
AGCTTCAAACCCGCGCGACTCCAGGACCCGGGCATTCACCCTTCCAACGTCCCAGATCAGCCTGA
CCACCACGGTTCACACCCTTGTGAGGTATTGTCCGCTCTGATATCACT
Found at i:16312092 original size:19 final size:18
Alignment explanation
Indices: 16312043--16312099 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
16312033 TTTTTTAAAC
*
16312043 AAAATAGAAATAGAAATA
1 AAAATAAAAATAGAAATA
*
16312061 AAAATAAATAATAGTAATA
1 AAAATAAA-AATAGAAATA
*
16312080 ACAATAATAAATA-AAATA
1 AAAATAA-AAATAGAAATA
16312098 AA
1 AA
16312100 CTAAATAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 12 0.38
19 19 0.59
20 1 0.03
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (18 bp):
AAAATAAAAATAGAAATA
Found at i:16312563 original size:16 final size:16
Alignment explanation
Indices: 16312544--16312586 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
16312534 TTTGTTTTCA
16312544 TTTTTTATTTT-CTTAT
1 TTTTTTATTTTCCTT-T
16312560 TTTTTTATTTTCCTTT
1 TTTTTTATTTTCCTTT
*
16312576 TTTTTTGTTTT
1 TTTTTTATTTT
16312587 TTAATTTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 22 0.88
17 3 0.12
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (16 bp):
TTTTTTATTTTCCTTT
Found at i:16312565 original size:29 final size:29
Alignment explanation
Indices: 16312515--16312578 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
16312505 GTTTTTCTCT
* *
16312515 TTTTTTAATTTTGTTTTGTTTTGTTTTCA
1 TTTTTTAATTTTCTTTTGTTTTATTTTCA
* *
16312544 TTTTTT-ATTTTCTTATTTTTTTATTTTCC
1 TTTTTTAATTTTCTT-TTGTTTTATTTTCA
16312573 TTTTTT
1 TTTTTT
16312579 TTTGTTTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 7 0.23
29 23 0.77
ACGTcount: A:0.09, C:0.06, G:0.05, T:0.80
Consensus pattern (29 bp):
TTTTTTAATTTTCTTTTGTTTTATTTTCA
Found at i:16312867 original size:21 final size:21
Alignment explanation
Indices: 16312841--16312880 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
16312831 ATTTTGCCCG
* *
16312841 GAGGTCTTATAGATTATGCTC
1 GAGGTCTAAGAGATTATGCTC
16312862 GAGGTCTAAGAGATTATGC
1 GAGGTCTAAGAGATTATGC
16312881 CTGGAGGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (21 bp):
GAGGTCTAAGAGATTATGCTC
Found at i:16313237 original size:22 final size:22
Alignment explanation
Indices: 16313212--16313297 Score: 70
Period size: 22 Copynumber: 3.9 Consensus size: 22
16313202 TGAAATGTTT
16313212 TGCCTATAGGTCTTACAAATTA
1 TGCCTATAGGTCTTACAAATTA
* **
16313234 TGCCTAGAGACCTTA-AAGATTA
1 TGCCTATAGGTCTTACAA-ATTA
* *
16313256 TGCCCGA-AGGGT-TTAGAAATTA
1 TG-CCTATA-GGTCTTACAAATTA
*
16313278 TGCCTATAGGTTTTACAAAT
1 TGCCTATAGGTCTTACAAAT
16313298 CTCAATATCT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
21 8 0.16
22 36 0.72
23 6 0.12
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (22 bp):
TGCCTATAGGTCTTACAAATTA
Found at i:16313265 original size:126 final size:125
Alignment explanation
Indices: 16312801--16313265 Score: 431
Period size: 126 Copynumber: 3.7 Consensus size: 125
16312791 CCTCCCAATT
* * * * *
16312801 AAAGGCGTTGAAACTTTAAAATTTTAAAATATTTTGCC-CGGAGGTCTTATAGATTATG-CTCGA
1 AAAGGCATTGAAACTTTGAAATTTTAAAATATTTT-CCTC-AAGGTCTTATAAATTATGCCTAGA
* * * * *
16312864 GGTC-TAAGAGATTATGCCTGGAGGACTTACAAATCTCAACATATTTGAATGTTCATCGTATC
64 GGTCTTAA-AGATTATGCCCGAAGGTCTTACAAATCTCAACATATTTGAATGCTCTTCGTATC
** **
16312926 AAAGGTGTTGAAACTTTGAAATTTTAAAATATTTTTATCAAAGGTCTTATAAATTATGCCTAGAG
1 AAAGGCATTGAAACTTTGAAATTTTAAAATATTTTCCTC-AAGGTCTTATAAATTATGCCTAGAG
* * * * * *
16312991 GTTTTAGAGAATATGCTC-AGAGATCTTACAAATCTCAACATTTTTGAATGCT-TCTCGTATC
65 GTCTTAAAGATTATGCCCGA-AGGTCTTACAAATCTCAACATATTTGAATGCTCT-TCGTATC
* * * * * *
16313052 ATAGGCATTGAAACTTTAAAATTTTAAAATATTTTACCTCAAGATTTTATAGATTATGCATAGAG
1 AAAGGCATTGAAACTTTGAAATTTTAAAATATTTT-CCTCAAGGTCTTATAAATTATGCCTAGAG
**** * * *
16313117 GTCTTACAA-ATTATATTTGAAGGTCTTACAAATCTCAACATCTTTGAATGCTCTTTGTTTC
65 GTCTTA-AAGATTATGCCCGAAGGTCTTACAAATCTCAACATATTTGAATGCTCTTCGTATC
* * * * *
16313178 AGAGGCATTGAAGCTTTGAAATTTTGAAATGTTTTGCCT-ATAGGTCTTACAAATTATGCCTAGA
1 AAAGGCATTGAAACTTTGAAATTTTAAAATATTTT-CCTCA-AGGTCTTATAAATTATGCCTAGA
**
16313242 GACCTTAAAGATTATGCCCGAAGG
64 GGTCTTAAAGATTATGCCCGAAGG
16313266 GTTTAGAAAT
Statistics
Matches: 273, Mismatches: 56, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
125 53 0.19
126 213 0.78
127 7 0.03
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (125 bp):
AAAGGCATTGAAACTTTGAAATTTTAAAATATTTTCCTCAAGGTCTTATAAATTATGCCTAGAGG
TCTTAAAGATTATGCCCGAAGGTCTTACAAATCTCAACATATTTGAATGCTCTTCGTATC
Found at i:16313474 original size:32 final size:32
Alignment explanation
Indices: 16313405--16313474 Score: 95
Period size: 32 Copynumber: 2.2 Consensus size: 32
16313395 TTTGATTAAA
* * *
16313405 CTTAGTTTGATCTGAGTGCTAGCTAGGCTAGG
1 CTTAGTTTGATCTAAGTGCCAGCTAGACTAGG
*
16313437 CTTAGTTTGATCTAAGTGCCAGCTAGACTGGG
1 CTTAGTTTGATCTAAGTGCCAGCTAGACTAGG
*
16313469 TTTAGT
1 CTTAGT
16313475 GTGTTCGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.36
Consensus pattern (32 bp):
CTTAGTTTGATCTAAGTGCCAGCTAGACTAGG
Found at i:16313637 original size:22 final size:22
Alignment explanation
Indices: 16313612--16313693 Score: 87
Period size: 22 Copynumber: 3.7 Consensus size: 22
16313602 TTAAGGTGCT
* *
16313612 AACTAATTTGGGCTTAGGTGTC
1 AACTAATCTAGGCTTAGGTGTC
*
16313634 AACTGATCTAGGCTTAGGTGGT-
1 AACTAATCTAGGCTTAGGT-GTC
*
16313656 AACTAATCTAGGCTTAGGT-AC
1 AACTAATCTAGGCTTAGGTGTC
*
16313677 TAGCTAATCTAGGCTTA
1 -AACTAATCTAGGCTTA
16313694 AAGTGCCAGC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
22 49 0.96
23 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (22 bp):
AACTAATCTAGGCTTAGGTGTC
Found at i:16313653 original size:44 final size:44
Alignment explanation
Indices: 16313605--16313743 Score: 136
Period size: 44 Copynumber: 3.1 Consensus size: 44
16313595 TTTGAACTTA
* * *
16313605 AGGTGCTAACTAATTTGGGCTTAGGTGTCAACTGATCTAGGCTT
1 AGGTGCTAACTAATTTGGGCTTAGGTGACAGCTAATCTAGGCTT
* * *
16313649 AGGTGGTAACTAATCTAGGCTTAGGT-ACTAGCTAATCTAGGCTT
1 AGGTGCTAACTAATTTGGGCTTAGGTGAC-AGCTAATCTAGGCTT
* * * * * *
16313693 AAAGTGCCAGCTAATTTGGGCTTAAGTGCCAGTTAATCTAGGCTT
1 -AGGTGCTAACTAATTTGGGCTTAGGTGACAGCTAATCTAGGCTT
*
16313738 GGGTGC
1 AGGTGC
16313744 CAGTTGATCT
Statistics
Matches: 75, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
43 1 0.01
44 40 0.53
45 33 0.44
46 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (44 bp):
AGGTGCTAACTAATTTGGGCTTAGGTGACAGCTAATCTAGGCTT
Found at i:16313748 original size:22 final size:22
Alignment explanation
Indices: 16313639--16313746 Score: 99
Period size: 22 Copynumber: 4.9 Consensus size: 22
16313629 GTGTCAACTG
* ** *
16313639 ATCTAGGCTTAGGTGGTAACTA
1 ATCTAGGCTTAAGTGCCAGCTA
* * *
16313661 ATCTAGGCTTAGGTACTAGCTA
1 ATCTAGGCTTAAGTGCCAGCTA
16313683 ATCTAGGCTTAAAGTGCCAGCTA
1 ATCTAGGCTT-AAGTGCCAGCTA
* * *
16313706 ATTTGGGCTTAAGTGCCAGTTA
1 ATCTAGGCTTAAGTGCCAGCTA
**
16313728 ATCTAGGCTTGGGTGCCAG
1 ATCTAGGCTTAAGTGCCAG
16313747 TTGATCTAAA
Statistics
Matches: 72, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
22 55 0.76
23 17 0.24
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (22 bp):
ATCTAGGCTTAAGTGCCAGCTA
Found at i:16314030 original size:25 final size:24
Alignment explanation
Indices: 16313988--16314053 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 24
16313978 CTACAAGTAC
* *
16313988 TTTTTATATAATGCAAATGTAAATG
1 TTTTT-TATGATGCAAATGCAAATG
*
16314013 TCTTTTTATGATGCAAATGCGAATG
1 T-TTTTTATGATGCAAATGCAAATG
16314038 TTTTAGTTATGATGCA
1 TTTT--TTATGATGCA
16314054 TATGATGTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 3 0.09
25 18 0.51
26 14 0.40
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.44
Consensus pattern (24 bp):
TTTTTTATGATGCAAATGCAAATG
Found at i:16314093 original size:41 final size:41
Alignment explanation
Indices: 16314048--16314126 Score: 95
Period size: 41 Copynumber: 1.9 Consensus size: 41
16314038 TTTTAGTTAT
* * * *
16314048 GATGCATATGATGTAAATGCAAATAGCTTTCTCATGATATA
1 GATGCAAATGAAGCAAATACAAATAGCTTTCTCATGATATA
* * *
16314089 GATGCAAATGAAGCAACTACAAATATCTTTTTCATGAT
1 GATGCAAATGAAGCAAATACAAATAGCTTTCTCATGAT
16314127 GTATATGTGA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (41 bp):
GATGCAAATGAAGCAAATACAAATAGCTTTCTCATGATATA
Found at i:16315448 original size:145 final size:150
Alignment explanation
Indices: 16315219--16315488 Score: 347
Period size: 145 Copynumber: 1.8 Consensus size: 150
16315209 AAAAGCCATG
** *
16315219 TGTCTTTCTATTTTTGCTCTTTCTTTTTTTTTTGAAATATTTGTCTTCAACTTTAGCATTTTATT
1 TGTCTTTCTATTTTTGCTCTTTC-TTTTTTTTAAAAATATTTGGCTTCAACTTTAGCATTTTATT
* * *
16315284 TTCTTAAATTCTATCTTTTTTTTTAT-TGGGGT-TTCAACTGAAGCTTAATTCACTTTTTATCCC
65 TTCTCAAATTCTATCTTTTTTTTTATATGAGATCTT-AACTGAAGCTTAATTCACTTTTTATCCC
16315347 GGATCTTTATCTTCTAGGTGCA
129 GGATCTTTATCTTCTAGGTGCA
* *
16315369 TGTC-TTCT-TTTTTG-TCTTTC-TTTTTTTAAAAATATTTGGCTTTAAGTTTAGCATTTTATTT
1 TGTCTTTCTATTTTTGCTCTTTCTTTTTTTTAAAAATATTTGGCTTCAACTTTAGCATTTTATTT
** * * *
16315430 TCTC-CCTATCTTTTTTTTTTTTTATATGAGATCTTAACTGAAGCTTTATTCACTTTTTA
66 TCTCAAAT-TCTATCTTTTTTTTTATATGAGATCTTAACTGAAGCTTAATTCACTTTTTA
16315489 CCTAGAATTT
Statistics
Matches: 104, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
144 1 0.01
145 54 0.52
146 27 0.26
147 8 0.08
148 6 0.06
149 4 0.04
150 4 0.04
ACGTcount: A:0.19, C:0.15, G:0.10, T:0.57
Consensus pattern (150 bp):
TGTCTTTCTATTTTTGCTCTTTCTTTTTTTTAAAAATATTTGGCTTCAACTTTAGCATTTTATTT
TCTCAAATTCTATCTTTTTTTTTATATGAGATCTTAACTGAAGCTTAATTCACTTTTTATCCCGG
ATCTTTATCTTCTAGGTGCA
Found at i:16318425 original size:12 final size:12
Alignment explanation
Indices: 16318403--16318432 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16318393 GCTCATTTTT
16318403 TTTAA-TTTTAA
1 TTTAATTTTTAA
16318414 TTTAATTTTTAA
1 TTTAATTTTTAA
16318426 TTTAATT
1 TTTAATT
16318433 ATTTTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 5 0.28
12 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTAATTTTTAA
Found at i:16318448 original size:3 final size:3
Alignment explanation
Indices: 16318430--16318570 Score: 78
Period size: 3 Copynumber: 45.7 Consensus size: 3
16318420 TTTTAATTTA
* * *
16318430 ATT ATT TTT CATT ATT ATT ATG ATT ATT ATT ATT GTT ATT ATT ATTT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
*
16318477 ATCT ATT AAT ATT -TT -TT ATTT ATTT ATCT ATT ATT ATT ATT -TT -TT
1 AT-T ATT ATT ATT ATT ATT A-TT A-TT AT-T ATT ATT ATT ATT ATT ATT
* * * *
16318522 AGTT ATCT ATT AAT A-T ATT -TA ATT ATTT ATCT ATT ATT TTT ATT TTT
1 A-TT AT-T ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT ATT ATT ATT
16318569 AT
1 AT
16318571 CTTTATCCTT
Statistics
Matches: 110, Mismatches: 15, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
2 11 0.10
3 69 0.63
4 30 0.27
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:16318495 original size:24 final size:25
Alignment explanation
Indices: 16318441--16318567 Score: 127
Period size: 24 Copynumber: 5.1 Consensus size: 25
16318431 TTATTTTTCA
* *
16318441 TTATTATTATGAT-TATTATTATTGTT
1 TTATTATT-T-ATCTATTAATATTATT
16318467 ATTATTATTTATCTATTAATATT-TT
1 -TTATTATTTATCTATTAATATTATT
*
16318492 TTATTTATTTATCTATTATTATTATT
1 TTA-TTATTTATCTATTAATATTATT
*
16318518 TT-TTAGTTATCTATTAATA-TATT
1 TTATTATTTATCTATTAATATTATT
* * *
16318541 TAATTATTTATCTATTATTTTTATT
1 TTATTATTTATCTATTAATATTATT
16318566 TT
1 TT
16318568 TATCTTTATC
Statistics
Matches: 86, Mismatches: 9, Indels: 12
0.80 0.08 0.11
Matches are distributed among these distances:
23 5 0.06
24 32 0.37
25 27 0.31
26 14 0.16
27 8 0.09
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.66
Consensus pattern (25 bp):
TTATTATTTATCTATTAATATTATT
Found at i:16318509 original size:48 final size:47
Alignment explanation
Indices: 16318453--16318570 Score: 157
Period size: 48 Copynumber: 2.5 Consensus size: 47
16318443 ATTATTATGA
* * * *
16318453 TTAT-TATTATTGTTATTATTATTTATCTATTAATATTTTTTATTTAT
1 TTATCTATTATTATTATTTTTATTTATCTATTAATA-TATTTAATTAT
*
16318500 TTATCTATTATTATTATTTTTTAGTTATCTATTAATATATTTAATTAT
1 TTATCTATTATTATTA-TTTTTATTTATCTATTAATATATTTAATTAT
*
16318548 TTATCTATTATTTTTATTTTTAT
1 TTATCTATTATTATTATTTTTAT
16318571 CTTTATCCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
47 10 0.16
48 34 0.55
49 18 0.29
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (47 bp):
TTATCTATTATTATTATTTTTATTTATCTATTAATATATTTAATTAT
Found at i:16318943 original size:18 final size:19
Alignment explanation
Indices: 16318908--16318944 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
16318898 GATTCTGGTA
*
16318908 GAATTTTTCGGTGAACTTT
1 GAATTTTTCAGTGAACTTT
16318927 GAATTTTTCAGTG-ACTTT
1 GAATTTTTCAGTGAACTTT
16318945 TCTAGCATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.49
Consensus pattern (19 bp):
GAATTTTTCAGTGAACTTT
Found at i:16319435 original size:3 final size:3
Alignment explanation
Indices: 16319427--16319474 Score: 78
Period size: 3 Copynumber: 15.7 Consensus size: 3
16319417 CTTTCTCATT
*
16319427 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTG TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
16319473 TT
1 TT
16319475 TATTGAATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:16319662 original size:14 final size:14
Alignment explanation
Indices: 16319630--16319664 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
16319620 AATTTTTCTT
*
16319630 AAAAATAAAATTTT
1 AAAAATAAAATTTA
*
16319644 TAAAATAAAATTTA
1 AAAAATAAAATTTA
16319658 AAAAATA
1 AAAAATA
16319665 TATATTTTAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAATAAAATTTA
Found at i:16319684 original size:73 final size:71
Alignment explanation
Indices: 16319580--16319779 Score: 259
Period size: 73 Copynumber: 2.8 Consensus size: 71
16319570 AAACAAAAGG
*
16319580 TTTAAAAAATATATATTTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTTT
1 TTTAAAAAATATATA-TTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAA-TTTC
16319645 AAAATAAAA
64 AAAAT-AAA
* *
16319654 TTTAAAAAATATATATTTTAG-GAAAAAGTTGAAAGTATGAATTTTTCTTAAAATTAAAATTTCA
1 TTTAAAAAATATATATTTTAGAG-AAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCA
*
16319718 AAATTAA
65 AAATAAA
* *
16319725 ---AAAAAATATAT-TTTTAGAGAAAAGTTGGAAGTA-CATATTTTCCTTAAAAATAAAA
1 TTTAAAAAATATATATTTTAGAGAAAAGTTGAAAGTATCA-ATTTTTCTTAAAAATAAAA
16319780 ATTATCAAGA
Statistics
Matches: 115, Mismatches: 8, Indels: 13
0.85 0.06 0.10
Matches are distributed among these distances:
66 1 0.01
67 36 0.31
68 12 0.10
71 2 0.02
72 9 0.08
73 40 0.35
74 15 0.13
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.38
Consensus pattern (71 bp):
TTTAAAAAATATATATTTTAGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAA
AATAAA
Found at i:16319840 original size:60 final size:55
Alignment explanation
Indices: 16319735--16319884 Score: 142
Period size: 55 Copynumber: 2.6 Consensus size: 55
16319725 AAAAAATATA
* * *
16319735 TTTTTAGAGAAAAGTTGGAAGTA-CATATTTTCCTTAAAAATAAAAATTATCAAGAAAAACG
1 TTTTGAGA-AAAAGTTGAAAGTATCA-ATTTTCCTTAAAAATAAAAACT-TC----AAAACG
* * * *
16319796 TTTTGAGAAAAAGTTGAAAGTATCAATTTT-TTTTAAAATAAAAAACTTCTAAATG
1 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAAACTTCAAAACG
*
16319851 CTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTT
1 TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTT
16319885 GTACAAAAGC
Statistics
Matches: 77, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
55 33 0.43
56 2 0.03
59 9 0.12
60 24 0.31
61 9 0.12
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (55 bp):
TTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAAACTTCAAAACG
Found at i:16331441 original size:43 final size:41
Alignment explanation
Indices: 16331364--16331483 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 41
16331354 TCAAGCAGCA
* * *
16331364 ATTTA-TTTTTTCAAAGTTTTGTT-GCTCTATTTAGAAGAACC
1 ATTTATTTTTTTAAAAG-TTTGTTACCTCTGTTTAGAAG-ACC
*
16331405 ATTTATTTTTTTAAAAGTTCTGTTACCTCTGTTTAGAAGAGC
1 ATTTATTTTTTTAAAAGTT-TGTTACCTCTGTTTAGAAGACC
16331447 -TTTATTTATTTTAAAAG-TTGTTGAGCCTCTGTTTAGA
1 ATTTATTT-TTTTAAAAGTTTGTT-A-CCTCTGTTTAGA
16331484 GGAGTTTTAT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
40 4 0.06
41 16 0.23
42 37 0.54
43 12 0.17
ACGTcount: A:0.26, C:0.11, G:0.14, T:0.49
Consensus pattern (41 bp):
ATTTATTTTTTTAAAAGTTTGTTACCTCTGTTTAGAAGACC
Found at i:16331476 original size:42 final size:43
Alignment explanation
Indices: 16331412--16331881 Score: 461
Period size: 42 Copynumber: 11.1 Consensus size: 43
16331402 ACCATTTATT
*
16331412 TTTTTAAAAGTTCTGTT-A-CCTCTGTTTAGAAGAGCTTTATTTA
1 TTTTTAAAAG-TC-GTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
* *
16331455 -TTTTAAAAGTTGTTGAGCCTCTGTTTAGAGGAGTTTTATTTA
1 TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
* * * *
16331497 TTTTTTCAAAGTCATTGAGCCTCTGTTTAGATGAGC--AATTTA
1 -TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
* *
16331539 CTTTTCAAAAATCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
1 -TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
*
16331583 -TTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTTTA
1 TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
* * *
16331625 TTTTTCTAAAA-TCGTTGAACCTCTGTTTAAAGGAGC--AATTTA
1 -TTTT-TAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
** *
16331667 CTTTCCAAAAGTCGTTGAGCCTCTATTTAGAGGAGCTTTATTTA
1 -TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
* *
16331711 -TTTTAAAAGTCGTTGAGCCTCTGTTTACAGGAGCTTTGTTTA
1 TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
* *
16331753 TTTTTCCAAAGTCGTTGAGCCTCTGTTTAGTA--A--TTTA---C
1 TTTTT-AAAAGTCGTTGAGCCTCTGTTTAG-AGGAGCTTTATTTA
* * * *
16331791 TTTCTAAAAGTCTTTGAGCCTCTGTTTATAGGAGCTTTGTTTA
1 TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
* * ** * *
16331834 TTTTTCAAAAGTTGTTGAGCTTCTACTTAGAAGAGCTTTGTTTA
1 TTTTT-AAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
16331878 TTTT
1 TTTT
16331882 ACTTAAAGTC
Statistics
Matches: 351, Mismatches: 53, Indels: 45
0.78 0.12 0.10
Matches are distributed among these distances:
36 1 0.00
37 21 0.06
38 5 0.01
40 6 0.02
41 9 0.03
42 172 0.49
43 9 0.03
44 122 0.35
45 6 0.02
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (43 bp):
TTTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTA
Found at i:16331508 original size:86 final size:85
Alignment explanation
Indices: 16331430--16331882 Score: 487
Period size: 86 Copynumber: 5.4 Consensus size: 85
16331420 AGTTCTGTTA
* *
16331430 CCTCTGTTTAGAAGAGCTTTATTTATTTTAAAAGTTGTTGAGCCTCTGTTTAGAGGAGTTTTATT
1 CCTCTGTTTAGAAGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATT
*
16331495 TATTTTTTCAAAGTCATTGAG
66 TA-TTTTTCAAAGTCGTTGAG
* * *
16331516 CCTCTGTTTAGATGAGC--AATTTACTTTTCAAAAATCGTTGAGCCTCTGTTTAGAGGAGCTTTA
1 CCTCTGTTTAGAAGAGCTTTATTTA-TTTT-AAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTA
*
16331579 TTTA-TTTTAAAAGTCGTTGAG
64 TTTATTTTTCAAAGTCGTTGAG
* * * * *
16331600 CCTCTGTTTAGAGGAGCTTTGTTTATTTTTCTAAAA-TCGTTGAACCTCTGTTTAAAGGAGC--A
1 CCTCTGTTTAGAAGAGCTTTATTTA--TTT-TAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTT
* *
16331662 ATTTACTTTCCAAAAGTCGTTGAG
63 ATTTATTTTTC-AAAGTCGTTGAG
* * * *
16331686 CCTCTATTTAGAGGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTACAGGAGCTTTGTT
1 CCTCTGTTTAGAAGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATT
16331751 TATTTTTCCAAAGTCGTTGAG
66 TATTTTT-CAAAGTCGTTGAG
* * * * * *
16331772 CCTCTGTTTAGTA-A--TTTA-CT-TTCTAAAAGTCTTTGAGCCTCTGTTTATAGGAGCTTTGTT
1 CCTCTGTTTAGAAGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATT
*
16331832 TATTTTTCAAAAGTTGTTGAG
66 TATTTTTC-AAAGTCGTTGAG
* ** *
16331853 CTTCTACTTAGAAGAGCTTTGTTTATTTTA
1 CCTCTGTTTAGAAGAGCTTTATTTATTTTA
16331883 CTTAAAGTCA
Statistics
Matches: 310, Mismatches: 39, Indels: 36
0.81 0.10 0.09
Matches are distributed among these distances:
80 1 0.00
81 64 0.21
82 2 0.01
83 9 0.03
84 70 0.23
85 9 0.03
86 146 0.47
87 8 0.03
88 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (85 bp):
CCTCTGTTTAGAAGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATT
TATTTTTCAAAGTCGTTGAG
Found at i:16331592 original size:128 final size:128
Alignment explanation
Indices: 16331430--16331896 Score: 617
Period size: 128 Copynumber: 3.7 Consensus size: 128
16331420 AGTTCTGTTA
* * * *
16331430 CCTCTGTTTAGAAGAGCTTTATTTATTTTAAAAGTTGTTGAGCCTCTGTTTAGAGGAGTTTTATT
1 CCTCTGTTTAGAGGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTT
*
16331495 TATTTTTTCAAAGTCATTGAGCCTCTGTTTAGATGAGCAATTTACTTTTCAAAAATCGTTGAG
66 TATTTTTTCAAAGTCATTGAGCCTCTGTTTAGATGAGCAATTTACTTTTCAAAAGTCGTTGAG
16331558 CCTCTGTTTAGAGGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTT
1 CCTCTGTTTAGAGGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTT
* * * * * *
16331623 TA-TTTTTCTAAAATCGTTGAACCTCTGTTTAAAGGAGCAATTTACTTTCCAAAAGTCGTTGAG
66 TATTTTTTC-AAAGTCATTGAGCCTCTGTTTAGATGAGCAATTTACTTTTCAAAAGTCGTTGAG
* *
16331686 CCTCTATTTAGAGGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTACAGGAGCTTTGTT
1 CCTCTGTTTAGAGGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTT
* * *
16331751 TATTTTTCCAAAGTCGTTGAGCCTCTGTTTAG-T----AATTTAC-TTTCTAAAAGTCTTTGAG
66 TATTTTTTCAAAGTCATTGAGCCTCTGTTTAGATGAGCAATTTACTTTTC-AAAAGTCGTTGAG
* * * * ** *
16331809 CCTCTGTTTATAGGAGCTTTGTTTATTTTTCAAAAGTTGTTGAGCTTCTACTTAGAAGAGCTTTG
1 CCTCTGTTTAGAGGAGCTTTATTTA-TTTT-AAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTG
16331874 TTTATTTTACTT-AAAGTCATTGA
64 TTTATTTT--TTCAAAGTCATTGA
16331897 ACTTTTACTT
Statistics
Matches: 301, Mismatches: 31, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
122 3 0.01
123 41 0.14
124 4 0.01
125 36 0.12
126 10 0.03
127 7 0.02
128 195 0.65
129 5 0.02
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.43
Consensus pattern (128 bp):
CCTCTGTTTAGAGGAGCTTTATTTATTTTAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTGTT
TATTTTTTCAAAGTCATTGAGCCTCTGTTTAGATGAGCAATTTACTTTTCAAAAGTCGTTGAG
Found at i:16331817 original size:81 final size:79
Alignment explanation
Indices: 16331706--16331853 Score: 242
Period size: 81 Copynumber: 1.8 Consensus size: 79
16331696 GAGGAGCTTT
*
16331706 ATTTATTTTAAAAGTCGTTGAGCCTCTGTTTACAGGAGCTTTGTTTATTTTTCCAAAGTCGTTGA
1 ATTTATTTTAAAAGTCGTTGAGCCTCTGTTTACAGGAGCTTTGTTTATTTTTCAAAAGTCGTTGA
16331771 GCCTCTGTTTAGTA
66 GCCTCTGTTTAGTA
* * *
16331785 ATTTACTTTCTAAAAGTCTTTGAGCCTCTGTTTATAGGAGCTTTGTTTATTTTTCAAAAGTTGTT
1 ATTTA-TTT-TAAAAGTCGTTGAGCCTCTGTTTACAGGAGCTTTGTTTATTTTTCAAAAGTCGTT
16331850 GAGC
64 GAGC
16331854 TTCTACTTAG
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
79 5 0.08
80 3 0.05
81 55 0.87
ACGTcount: A:0.22, C:0.14, G:0.18, T:0.45
Consensus pattern (79 bp):
ATTTATTTTAAAAGTCGTTGAGCCTCTGTTTACAGGAGCTTTGTTTATTTTTCAAAAGTCGTTGA
GCCTCTGTTTAGTA
Found at i:16331908 original size:45 final size:43
Alignment explanation
Indices: 16331822--16331918 Score: 113
Period size: 45 Copynumber: 2.2 Consensus size: 43
16331812 CTGTTTATAG
* ** *
16331822 GAGCTTTGTTTATTTTTCAAAAGTTGTTGAGCTTCTACTTAGAA
1 GAGCTTTGTTTATTTTACAAAAGTCATTGAACTTCTACTTAG-A
* *
16331866 GAGCTTTGTTTATTTTACTTAAAGTCATTGAACTTTTACTTAGA
1 GAGCTTTGTTTATTTTAC-AAAAGTCATTGAACTTCTACTTAGA
16331910 GAAGCTTTG
1 G-AGCTTTG
16331919 ATCAAAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
44 19 0.42
45 26 0.58
ACGTcount: A:0.26, C:0.11, G:0.18, T:0.45
Consensus pattern (43 bp):
GAGCTTTGTTTATTTTACAAAAGTCATTGAACTTCTACTTAGA
Found at i:16331949 original size:11 final size:10
Alignment explanation
Indices: 16331933--16331973 Score: 57
Period size: 10 Copynumber: 4.0 Consensus size: 10
16331923 AAATTTTAAC
16331933 CAAAAAAACAA
1 CAAAAAAA-AA
16331944 C-AAAAAAAA
1 CAAAAAAAAA
16331953 CAAAAAAAAA
1 CAAAAAAAAA
16331963 GCAAAAAAAAA
1 -CAAAAAAAAA
16331974 AAAGGTCGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 3 0.11
10 14 0.50
11 11 0.39
ACGTcount: A:0.85, C:0.12, G:0.02, T:0.00
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:16331949 original size:12 final size:11
Alignment explanation
Indices: 16331934--16331974 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
16331924 AATTTTAACC
16331934 AAAAAAACAACA
1 AAAAAAACAA-A
16331946 AAAAAAACAAA
1 AAAAAAACAAA
*
16331957 AAAAAAGCAAA
1 AAAAAAACAAA
16331968 AAAAAAA
1 AAAAAAA
16331975 AAGGTCGAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAA
Found at i:16331958 original size:20 final size:20
Alignment explanation
Indices: 16331933--16331976 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
16331923 AAATTTTAAC
16331933 CAAAAAAACAA-CAAAAAAAA
1 CAAAAAAA-AAGCAAAAAAAA
16331953 CAAAAAAAAAGCAAAAAAAA
1 CAAAAAAAAAGCAAAAAAAA
16331973 -AAAA
1 CAAAA
16331977 GGTCGAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (20 bp):
CAAAAAAAAAGCAAAAAAAA
Found at i:16332136 original size:5 final size:5
Alignment explanation
Indices: 16332128--16332171 Score: 70
Period size: 5 Copynumber: 8.4 Consensus size: 5
16332118 CATTTTTCTT
16332128 TTTAA TTTAAA TTTAA TTTAA TTTAA TTTTAA TTTAA TTTAA TT
1 TTTAA TTT-AA TTTAA TTTAA TTTAA -TTTAA TTTAA TTTAA TT
16332172 ATTTTTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 27 0.73
6 10 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TTTAA
Found at i:16332144 original size:11 final size:11
Alignment explanation
Indices: 16332128--16332169 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
16332118 CATTTTTCTT
16332128 TTTAATTTAAA
1 TTTAATTTAAA
16332139 TTTAATTT-AA
1 TTTAATTTAAA
*
16332149 TTTAATTTTAA
1 TTTAATTTAAA
16332160 TTTAATTTAA
1 TTTAATTTAA
16332170 TTATTTTTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 10 0.34
11 19 0.66
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:16332152 original size:21 final size:21
Alignment explanation
Indices: 16332128--16332171 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
16332118 CATTTTTCTT
16332128 TTTAATTTAAATTTAATTTAA
1 TTTAATTTAAATTTAATTTAA
*
16332149 TTTAATTTTAATTTAATTTAA
1 TTTAATTTAAATTTAATTTAA
16332170 TT
1 TT
16332172 ATTTTTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTAATTTAAATTTAATTTAA
Found at i:16332170 original size:16 final size:16
Alignment explanation
Indices: 16332128--16332171 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
16332118 CATTTTTCTT
*
16332128 TTTAATTTAAATTTAA
1 TTTAATTTAATTTTAA
16332144 TTTAATTTAATTTTAA
1 TTTAATTTAATTTTAA
16332160 TTTAATTTAATT
1 TTTAATTTAATT
16332172 ATTTTTCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATTTAATTTTAA
Found at i:16332187 original size:3 final size:3
Alignment explanation
Indices: 16332169--16332308 Score: 92
Period size: 3 Copynumber: 45.7 Consensus size: 3
16332159 ATTTAATTTA
* *
16332169 ATT ATT TTT CATT ATT ATT ATG ATT ATT ATT ATT ATT ATT ATTT ATCT
1 ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T
* * * *
16332217 ATT AAT ATT -TT TTT ATT -TT TTT ATCT ATT ATT ATT ATT -TT TTT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT
* * *
16332260 AGTT ATCT ATT AAT A-T ATT -TT ATT ATTT ATCT ATT ATT TTT ATT TTT
1 A-TT AT-T ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT ATT ATT ATT
16332307 AT
1 AT
16332309 CTTTTTTCTT
Statistics
Matches: 110, Mismatches: 14, Indels: 26
0.73 0.09 0.17
Matches are distributed among these distances:
2 10 0.09
3 77 0.70
4 23 0.21
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:16332228 original size:51 final size:50
Alignment explanation
Indices: 16332166--16332305 Score: 144
Period size: 51 Copynumber: 2.8 Consensus size: 50
16332156 TTAATTTAAT
*
16332166 TTAATTATTTTTCATTATTATTAT-GATTATTATTATTATTATTATTTATCTA
1 TTAA-TATTTTT-ATTATTATTATCGATTATTATTATT-TTATTAGTTATCTA
* * *
16332218 TTAATATTTTT-TTATTTTTTTATCTATTATTATTATTTTTTTAGTTATCTA
1 TTAATATTTTTATTA--TTATTATCGATTATTATTATTTTATTAGTTATCTA
* *
16332269 TTAATATATTTTATTA-T-TTATCTATTATTTTTATTTT
1 TTAATAT-TTTTATTATTATTATCGATTATTATTATTTT
16332306 TATCTTTTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 13
0.81 0.05 0.14
Matches are distributed among these distances:
49 22 0.28
50 1 0.01
51 32 0.41
52 20 0.26
53 3 0.04
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.68
Consensus pattern (50 bp):
TTAATATTTTTATTATTATTATCGATTATTATTATTTTATTAGTTATCTA
Done.