Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008228.1 Hibiscus syriacus cultivar Beakdansim tig00110864_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3739947
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 20
Found at i:1299816 original size:402 final size:402
Alignment explanation
Indices: 1299071--1299829 Score: 1011
Period size: 402 Copynumber: 1.9 Consensus size: 402
1299061 TCGTTCACAG
* * * * *
1299071 CATAGCTCAAGGCTAGAAGGTTTATCTGTCAATGAAAACTTTTGAGTTCGATTCCATTCAGCTCG
1 CATAGCTCAAGGCGAGAAGGGTTATCTATCAATGAAAACTTTTAAGTTCGATTCCATTCAGATCG
* * * * ** * *
1299136 ATAGTGTATCAACCGCATTGTAGTAGTGAGGAACTACTTTCTGGTTGAAGTTTAAACTGAGGTCT
66 AGAGCGTATCAACCGCATGGTAGCAGCAAGGAACTACTTTCCGGTTGAAGTTTAAACCGAGGTCT
* * **
1299201 TTTAGTCAAGAAGAAGGCTTAGGTTCGATGTGATTTAGCAACGAGAAACTATCTCCCAGCCTAAT
131 TTAAGTCAAGAAGAAGACTTAGGTTCGATACGATTTAGCAACGAGAAACTATCTCCCAGCCTAAT
* * ** *
1299266 TTATAGCATAGCTCAAGACGAGAAGGGTTATCTGTCAACGAAAACTTTCAAGTTTGATTCCATTC
196 TTACAACATAGCTCAAGACGAGAAAAGTTATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTC
* * * *
1299331 ATCTCGAGGGTGTATCAACTGCAAGGTAGCAGCGAGGAACTACTTCCCGATTGAAGTTTAAACCG
261 AGCTCGAGGGTGTATCAACTGCAAGGTAGCAGCGAAGAACTACTTCCAGATTGAAGTTTAAACCA
* * * *
1299396 AGGTATTTAAGTCAAGAAGAAGACCTAGGTTGGCTGCGATTTAGCAATAATGAACTATCTCCTAG
326 AGATATTTAAGCCAAGAAGAAAACCAAGGTTGGCTGCGATTTAGCAATAATGAACTATCTCCTAG
1299461 CCTAATTTACAA
391 CCTAATTTACAA
*
1299473 CATAGCTCAAGGCGAGAAGGGTTATCTATCAATGAAAACTTTTAAGTTTGATTCCATTCAGATCG
1 CATAGCTCAAGGCGAGAAGGGTTATCTATCAATGAAAACTTTTAAGTTCGATTCCATTCAGATCG
* *
1299538 AGGGCGTATCAACTGCATGGTAGCAGCAAGGAACTACTTTCCGGTTGAAGTTTAAACCGAGGTCT
66 AGAGCGTATCAACCGCATGGTAGCAGCAAGGAACTACTTTCCGGTTGAAGTTTAAACCGAGGTCT
* * * *
1299603 TTAAGTCAAGAAGAAGACTTAGGTTGGCTACGATTTAGCAACTAGGAACTATCTCCCAGCCTAAT
131 TTAAGTCAAGAAGAAGACTTAGGTTCGATACGATTTAGCAACGAGAAACTATCTCCCAGCCTAAT
* * ** * * * * *
1299668 TTACAACATCGCTTAAGTTGATAAAAGTTGTTTGTCAATGAAAACTTTCGAGTTCGATTCCATTC
196 TTACAACATAGCTCAAGACGAGAAAAGTTATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTC
* * * *
1299733 AGGTCGAGGGCT-TATCAA-TCGCATGGTAGCAGCGAAGAACTACTTTTCAG-TTGAATTTTAAA
261 AGCTCGAGGG-TGTATCAACT-GCAAGGTAGCAGCGAAGAACTAC-TTCCAGATTGAAGTTTAAA
*
1299795 CCAAGATCTTTAAGCCAAGAAGAAAACCAAGGTTG
323 CCAAGATATTTAAGCCAAGAAGAAAACCAAGGTTG
1299830 ACTAAGATTT
Statistics
Matches: 303, Mismatches: 51, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
401 1 0.00
402 297 0.98
403 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (402 bp):
CATAGCTCAAGGCGAGAAGGGTTATCTATCAATGAAAACTTTTAAGTTCGATTCCATTCAGATCG
AGAGCGTATCAACCGCATGGTAGCAGCAAGGAACTACTTTCCGGTTGAAGTTTAAACCGAGGTCT
TTAAGTCAAGAAGAAGACTTAGGTTCGATACGATTTAGCAACGAGAAACTATCTCCCAGCCTAAT
TTACAACATAGCTCAAGACGAGAAAAGTTATCTGTCAACGAAAACTTTCAAGTTCGATTCCATTC
AGCTCGAGGGTGTATCAACTGCAAGGTAGCAGCGAAGAACTACTTCCAGATTGAAGTTTAAACCA
AGATATTTAAGCCAAGAAGAAAACCAAGGTTGGCTGCGATTTAGCAATAATGAACTATCTCCTAG
CCTAATTTACAA
Found at i:1300522 original size:27 final size:27
Alignment explanation
Indices: 1300479--1300684 Score: 134
Period size: 27 Copynumber: 7.8 Consensus size: 27
1300469 ACATTTAATA
* *
1300479 TATTA-TTATATAGTATATACATATAT
1 TATTAGTTATATATTATATATATATAT
1300505 TATTAGTTATATA-T-TATATAT-TAT
1 TATTAGTTATATATTATATATATATAT
*
1300529 TATTAGTTATATCTATATTATATATATATT
1 TATTAGTTATATAT-TA-TATATATATA-T
* *
1300559 ATATTAGTAATATATTATATTTAGTATA-
1 -TATTAGTTATATATTATATATA-TATAT
*
1300587 TATTA-TTATTATATTATAGTATTTATA-
1 TATTAGTTA-TATATTATA-TATATATAT
*
1300614 TATATA-TTATAT-TTATAT-TTTATA-
1 TAT-TAGTTATATATTATATATATATAT
* * *
1300638 AATTGGTATATGTATTATATATAT-TAT
1 TATTAGT-TATATATTATATATATATAT
*
1300665 TATTA-TTAT-TATTTTATATA
1 TATTAGTTATATATTATATATA
1300685 CTTTTATTTA
Statistics
Matches: 148, Mismatches: 15, Indels: 36
0.74 0.08 0.18
Matches are distributed among these distances:
23 1 0.01
24 34 0.23
25 14 0.09
26 23 0.16
27 36 0.24
28 14 0.09
29 7 0.05
30 7 0.05
31 12 0.08
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (27 bp):
TATTAGTTATATATTATATATATATAT
Found at i:1300540 original size:44 final size:39
Alignment explanation
Indices: 1300476--1300676 Score: 130
Period size: 36 Copynumber: 5.3 Consensus size: 39
1300466 GACACATTTA
1300476 ATATATTATTATATAGTATATACATATATTATTAGTTATATATT
1 ATATATTATTATATAGTATAT-C-TATATTA-TA--TATATATT
1300520 ATATATTATTAT-TAGTTATATCTATATTATATATATA-T
1 ATATATTATTATATAG-TATATCTATATTATATATATATT
*
1300558 -TATATTA--GTA-A-TATAT-TATATT-TAGTATATATT
1 ATATATTATTATATAGTATATCTATATTATA-TATATATT
1300591 AT-TATTA-TATTATAGTAT-T-TATA-TATATATTATATT
1 ATATATTATTA-TATAGTATATCTATATTATATA-TATATT
* * * * *
1300627 -TATATT-TTATAAATTGGTATATGTATTATATATATTATT
1 ATATATTATTATATAGT-ATATCTATATTATATATA-TATT
1300666 AT-TATTATTAT
1 ATATATTATTAT
1300677 TTTATATACT
Statistics
Matches: 131, Mismatches: 6, Indels: 44
0.72 0.03 0.24
Matches are distributed among these distances:
31 2 0.02
32 12 0.09
33 11 0.08
34 1 0.01
35 12 0.09
36 21 0.16
37 11 0.08
38 6 0.05
39 20 0.15
40 5 0.04
41 2 0.02
42 7 0.05
43 4 0.03
44 17 0.13
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (39 bp):
ATATATTATTATATAGTATATCTATATTATATATATATT
Found at i:1300551 original size:11 final size:10
Alignment explanation
Indices: 1300514--1300683 Score: 107
Period size: 11 Copynumber: 16.0 Consensus size: 10
1300504 TTATTAGTTA
1300514 TATATTATA-
1 TATATTATAT
1300523 TATTATTATTAGT
1 TA-TATTA-TA-T
1300536 TATATCTATAT
1 TATAT-TATAT
1300547 TATATATATAT
1 TATAT-TATAT
*
1300558 TATATTAGTAA
1 TATATTA-TAT
1300569 TATATTATAT
1 TATATTATAT
1300579 T-TAGTATATAT
1 TATA-T-TATAT
1300590 TATTATTATAT
1 TA-TATTATAT
*
1300601 TATAGTAT-T
1 TATATTATAT
1300610 TATATATATAT
1 TATAT-TATAT
1300621 TATATTTATAT
1 TATA-TTATAT
* *
1300632 TTTA-TAAAT
1 TATATTATAT
* *
1300641 TGGTATATGTAT
1 T-ATAT-TATAT
1300653 TATA-TATAT
1 TATATTATAT
1300662 TATTATTATTAT
1 TA-TATTA-TAT
*
1300674 TATTTTATAT
1 TATATTATAT
1300684 ACTTTTATTT
Statistics
Matches: 129, Mismatches: 13, Indels: 37
0.72 0.07 0.21
Matches are distributed among these distances:
9 20 0.16
10 26 0.20
11 61 0.47
12 16 0.12
13 6 0.05
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.58
Consensus pattern (10 bp):
TATATTATAT
Found at i:1300595 original size:74 final size:73
Alignment explanation
Indices: 1300476--1300637 Score: 190
Period size: 74 Copynumber: 2.2 Consensus size: 73
1300466 GACACATTTA
*
1300476 ATATAT-TATTATATAGTATATACATATATTATTAGTTATATATTA-TATATTATTATTAGTTAT
1 ATATATATATTATATAGTATATACATATATTATTAGTTATATATTATTATATTA-TAGTAGTTAT
*
1300539 ATCTATATT
65 ATATATATT
* *
1300548 ATATATATATTATATTAGTA-ATATAT-TA-TATTTAGTATATATTATTATTATATTATAGTATT
1 ATATATATATTATA-TAGTATATACATATATTA-TTAGT-TATA-TATTATTATATTATAGTAGT
1300610 TATATATATATT
62 TATATATATATT
* *
1300622 ATATTTATATTTTATA
1 ATATATATATTATATA
1300638 AATTGGTATA
Statistics
Matches: 78, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
71 2 0.03
72 13 0.17
73 18 0.23
74 38 0.49
75 7 0.09
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.56
Consensus pattern (73 bp):
ATATATATATTATATAGTATATACATATATTATTAGTTATATATTATTATATTATAGTAGTTATA
TATATATT
Found at i:1300636 original size:13 final size:14
Alignment explanation
Indices: 1300511--1300684 Score: 71
Period size: 15 Copynumber: 12.0 Consensus size: 14
1300501 ATATTATTAG
*
1300511 TTATATATTATATA
1 TTATATTTTATATA
1300525 TTATTATTAGTTATAT-
1 TTA-TATT--TTATATA
*
1300541 CTATATTATATATATA
1 TTATATT-T-TATATA
*
1300557 TTATATTAGTAATATA
1 TTATATT--TTATATA
1300573 TTATA-TTTAGTATA
1 TTATATTTTA-TATA
*
1300587 -TAT-TATTATTATA
1 TTATATTTTA-TATA
1300600 TTATAGTATTTATATA
1 TTATA-T-TTTATATA
1300616 -TATA--TTATAT-
1 TTATATTTTATATA
*
1300626 TTATATTTTATAAA
1 TTATATTTTATATA
* *
1300640 TTGGTATATGTAT-TA
1 TT-ATAT-TTTATATA
1300655 TATATATTATTAT-TA
1 T-TATATT-TTATATA
1300670 TTATTATTTTATATA
1 TTA-TATTTTATATA
1300685 CTTTTATTTA
Statistics
Matches: 122, Mismatches: 16, Indels: 43
0.67 0.09 0.24
Matches are distributed among these distances:
11 10 0.08
13 17 0.14
14 20 0.16
15 37 0.30
16 28 0.23
17 10 0.08
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (14 bp):
TTATATTTTATATA
Found at i:1300637 original size:38 final size:39
Alignment explanation
Indices: 1300500--1300676 Score: 122
Period size: 38 Copynumber: 4.5 Consensus size: 39
1300490 AGTATATACA
* * *
1300500 TATATTATTAGTTATATATTATA-TATTATTATTAGTTATAT
1 TATATTA-TATTTATATATTATATTAGTAATA-TA-TTATAT
1300541 CTATATTATA--TATATATTATATTAGTAATATATTATAT
1 -TATATTATATTTATATATTATATTAGTAATATATTATAT
* *
1300579 T-TAGTATATATTAT-TATTATATTA-TAGTAT-TTATAT
1 TATATTATAT-TTATATATTATATTAGTAATATATTATAT
* * *
1300615 ATATATTATATTTATATTTTATAAATTGGTATATGTATTATA-
1 -TATATTATATTTATATATTAT--ATTAGTA-ATATATTATAT
1300657 TATATTAT-TATTAT-TATTAT
1 TATATTATAT-TTATATATTAT
1300677 TTTATATACT
Statistics
Matches: 112, Mismatches: 10, Indels: 28
0.75 0.07 0.19
Matches are distributed among these distances:
36 12 0.11
37 11 0.10
38 28 0.25
39 16 0.14
40 15 0.13
41 16 0.14
42 9 0.08
43 5 0.04
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.57
Consensus pattern (39 bp):
TATATTATATTTATATATTATATTAGTAATATATTATAT
Found at i:1302121 original size:11 final size:10
Alignment explanation
Indices: 1302105--1302157 Score: 58
Period size: 11 Copynumber: 5.4 Consensus size: 10
1302095 GTTTAATCCT
1302105 TTTAATTTTAA
1 TTTAATTTT-A
1302116 TTTAATTTT-
1 TTTAATTTTA
*
1302125 TTTTA-TTTA
1 TTTAATTTTA
1302134 TTTAATTTTTA
1 TTTAA-TTTTA
1302145 TTTAATTTT-
1 TTTAATTTTA
1302154 TTTA
1 TTTA
1302158 TTAATATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
8 3 0.08
9 12 0.32
10 4 0.11
11 18 0.49
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTAATTTTA
Found at i:1302141 original size:23 final size:23
Alignment explanation
Indices: 1302111--1302183 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
1302101 TCCTTTTAAT
*
1302111 TTTAATTTAATTTTTTTTATTTA
1 TTTAATTTAATTTATTTTATTTA
*
1302134 TTTAATTTTTATTTAATTTT-TTTA
1 TTTAA-TTTAATTT-ATTTTATTTA
*
1302158 -TTAATATTAATTTGTTTTATTT-
1 TTTAAT-TTAATTTATTTTATTTA
1302180 TTTA
1 TTTA
1302184 GGGACAATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
22 5 0.12
23 21 0.51
24 11 0.27
25 4 0.10
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (23 bp):
TTTAATTTAATTTATTTTATTTA
Found at i:1302141 original size:29 final size:28
Alignment explanation
Indices: 1302105--1302170 Score: 96
Period size: 29 Copynumber: 2.3 Consensus size: 28
1302095 GTTTAATCCT
*
1302105 TTTAATTTTAATTTAATTTTTTTTATTTA
1 TTTAATTTTAATTTAA-TTTTTTTATTAA
*
1302134 TTTAATTTTTATTTAATTTTTTTATTAA
1 TTTAATTTTAATTTAATTTTTTTATTAA
1302162 TATTAATTT
1 T-TTAATTT
1302171 GTTTTATTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 12 0.35
29 22 0.65
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (28 bp):
TTTAATTTTAATTTAATTTTTTTATTAA
Found at i:1302176 original size:28 final size:28
Alignment explanation
Indices: 1302105--1302182 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
1302095 GTTTAATCCT
*
1302105 TTTAATTT-TAATTTAATTTTTTTTATTTA
1 TTTAATTTGT-ATTTAA-TTTTTTTATTAA
*
1302134 TTTAATTTTTATTTAATTTTTTTATTAA
1 TTTAATTTGTATTTAATTTTTTTATTAA
1302162 TATTAATTTGT-TTT-ATTTTTT
1 T-TTAATTTGTATTTAATTTTTT
1302183 AGGGACAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 7 0.16
28 15 0.33
29 22 0.49
30 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (28 bp):
TTTAATTTGTATTTAATTTTTTTATTAA
Found at i:1302182 original size:29 final size:28
Alignment explanation
Indices: 1302105--1302182 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
1302095 GTTTAATCCT
*
1302105 TTTAATTT-TAATTTAATTTTTTTTATTTA
1 TTTAATTTGT-ATTT-ATTTTTTTTATTAA
* *
1302134 TTTAATTTTTATTTAATTTTTTTATTAA
1 TTTAATTTGTATTTATTTTTTTTATTAA
1302162 TATTAATTTGT-TTTATTTTTT
1 T-TTAATTTGTATTTATTTTTT
1302183 AGGGACAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
28 22 0.51
29 20 0.47
30 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.01, T:0.73
Consensus pattern (28 bp):
TTTAATTTGTATTTATTTTTTTTATTAA
Found at i:1307296 original size:2 final size:2
Alignment explanation
Indices: 1307289--1307324 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1307279 AATTCATTGG
1307289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1307325 TCTGCTTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1309029 original size:16 final size:16
Alignment explanation
Indices: 1309008--1309070 Score: 92
Period size: 16 Copynumber: 3.9 Consensus size: 16
1308998 TTACCCGACC
1309008 TGTTTTCAACCTGACT
1 TGTTTTCAACCTGACT
*
1309024 TGTTTTCAACATGACT
1 TGTTTTCAACCTGACT
*
1309040 TGTTTTCAACCTGACA
1 TGTTTTCAACCTGACT
1309056 TG-TTTCTAACCTGAC
1 TGTTTTC-AACCTGAC
1309071 CTGTAAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
15 4 0.09
16 39 0.91
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (16 bp):
TGTTTTCAACCTGACT
Found at i:1309281 original size:22 final size:25
Alignment explanation
Indices: 1309251--1309308 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 25
1309241 AAATAAACCT
*
1309251 ATTATATAAAATTATTTA-ATA-AA
1 ATTAGATAAAATTATTTACATATAA
1309274 ATTA-ATAAAATTATTTACATATAA
1 ATTAGATAAAATTATTTACATATAA
1309298 ATTAGATAAAA
1 ATTAGATAAAA
1309309 CATTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
22 13 0.41
23 7 0.22
24 6 0.19
25 6 0.19
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (25 bp):
ATTAGATAAAATTATTTACATATAA
Found at i:1312669 original size:99 final size:101
Alignment explanation
Indices: 1312444--1312773 Score: 441
Period size: 102 Copynumber: 3.3 Consensus size: 101
1312434 ATGAACAACG
** * * *
1312444 AACAGTAG-TAACAAATTAATTAGTTTATTTAAACTATAAATATAGGAAGTTAACAACCTTATAA
1 AACAGTAGCT-ACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGAAGCTAACAACCTTATAA
1312508 AAGCAATATGAATGAACAACTAACAACACAAACAAATC
65 AAGCAATATGAATGAACAAC-AACAACACAAACAAATC
* * * * *
1312546 AACAGTAGCAACAAATTGAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAAGAACCTTATAGA
1 AACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGAAGCTAACAACCTTATAAA
** ** *
1312611 AGTTATCCGAATGAA-AA-ACCAACACAAACAAATC
66 AGCAATATGAATGAACAACAACAACACAAACAAATC
* * *
1312645 AACAGTAACTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGTAGCTAATAACCTTATAAA
1 AACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGAAGCTAACAACCTTATAAA
*
1312710 AGCAATTTGAATGAACAACCAACAACACAAACAAATC
66 AGCAATATGAATGAACAA-CAACAACACAAACAAATC
1312747 AACAGTAGCTACAAATTAAACAGTTTA
1 AACAGTAGCTACAAATTAAACAGTTTA
1312774 GTTACTTCTT
Statistics
Matches: 197, Mismatches: 27, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
99 86 0.44
100 2 0.01
101 2 0.01
102 107 0.54
ACGTcount: A:0.50, C:0.16, G:0.10, T:0.24
Consensus pattern (101 bp):
AACAGTAGCTACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGAAGCTAACAACCTTATAAA
AGCAATATGAATGAACAACAACAACACAAACAAATC
Found at i:1317244 original size:3 final size:3
Alignment explanation
Indices: 1317236--1317264 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1317226 GAATTGGGTT
1317236 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1317265 TGGGTCAGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:1318758 original size:20 final size:19
Alignment explanation
Indices: 1318735--1318839 Score: 88
Period size: 20 Copynumber: 5.1 Consensus size: 19
1318725 GGTTACATAT
*
1318735 ATAGTTTATATAACATATAA
1 ATAGTTTATAT-ACATATAC
1318755 ATAGATTGTATATATACATATAC
1 ATAG--T-T-TATATACATATAC
*
1318778 TATAGGTTATAT--ATATAC
1 -ATAGTTTATATACATATAC
1318796 ATAGTTTATATACACTATAC
1 ATAGTTTATATACA-TATAC
1318816 ATAGTTTATACATACATGATAC
1 ATAGTTTAT--ATACAT-ATAC
1318838 AT
1 AT
1318840 GTACTATAAG
Statistics
Matches: 71, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
17 10 0.14
18 6 0.08
19 1 0.01
20 23 0.32
21 2 0.03
22 12 0.17
23 8 0.11
24 9 0.13
ACGTcount: A:0.43, C:0.10, G:0.08, T:0.40
Consensus pattern (19 bp):
ATAGTTTATATACATATAC
Found at i:1318770 original size:24 final size:24
Alignment explanation
Indices: 1318741--1318798 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
1318731 ATATATAGTT
*
1318741 TATATA-ACATATA-AATAGATTG
1 TATATATACATATACAATAGATTA
* *
1318763 TATATATACATATACTATAGGTTA
1 TATATATACATATACAATAGATTA
1318787 TATATATACATA
1 TATATATACATA
1318799 GTTTATATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 6 0.19
23 7 0.23
24 18 0.58
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (24 bp):
TATATATACATATACAATAGATTA
Found at i:1318876 original size:37 final size:37
Alignment explanation
Indices: 1318828--1318898 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1318818 AGTTTATACA
*
1318828 TACATGATACATGTACTATAAGTTACA-TATATAGTT
1 TACATGATACATATACTATAAGTTACATTATATAGTT
* *
1318864 TACATGTATACATATATTATAGGTTACATTATATA
1 TACATG-ATACATATACTATAAGTTACATTATATA
1318899 TATTAACTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 6 0.20
37 18 0.60
38 6 0.20
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (37 bp):
TACATGATACATATACTATAAGTTACATTATATAGTT
Found at i:1318890 original size:24 final size:23
Alignment explanation
Indices: 1318857--1318901 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1318847 AAGTTACATA
*
1318857 TATAGTTTACATGTATACATATAT
1 TATAGGTTACAT-TATACATATAT
*
1318881 TATAGGTTACATTATATATAT
1 TATAGGTTACATTATACATAT
1318902 TAACTATTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (23 bp):
TATAGGTTACATTATACATATAT
Found at i:1318926 original size:7 final size:7
Alignment explanation
Indices: 1318916--1318982 Score: 55
Period size: 7 Copynumber: 9.7 Consensus size: 7
1318906 TATTGTTTAT
1318916 GTTTAGG
1 GTTTAGG
1318923 GTTTAGG
1 GTTTAGG
*
1318930 GTTTATG
1 GTTTAGG
* **
1318937 ATGAAGG
1 GTTTAGG
*
1318944 GTTTA-T
1 GTTTAGG
1318950 GTTTAGG
1 GTTTAGG
**
1318957 GTTTAAA
1 GTTTAGG
*
1318964 ATTTAGG
1 GTTTAGG
1318971 GTTTAGG
1 GTTTAGG
1318978 GTTTA
1 GTTTA
1318983 TGCTTTATAT
Statistics
Matches: 43, Mismatches: 16, Indels: 2
0.70 0.26 0.03
Matches are distributed among these distances:
6 5 0.12
7 38 0.88
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.45
Consensus pattern (7 bp):
GTTTAGG
Found at i:1318971 original size:27 final size:27
Alignment explanation
Indices: 1318923--1318975 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1318913 TATGTTTAGG
**
1318923 GTTTAGGGTTTATGATGAAGGGTTTAT
1 GTTTAGGGTTTAAAATGAAGGGTTTAT
**
1318950 GTTTAGGGTTTAAAATTTAGGGTTTA
1 GTTTAGGGTTTAAAATGAAGGGTTTA
1318976 GGGTTTATGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (27 bp):
GTTTAGGGTTTAAAATGAAGGGTTTAT
Found at i:1318989 original size:14 final size:14
Alignment explanation
Indices: 1318924--1318975 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
1318914 ATGTTTAGGG
1318924 TTTAGGGTTTATGA
1 TTTAGGGTTTATGA
**
1318938 TGAAGGGTTTATG-
1 TTTAGGGTTTATGA
**
1318951 TTTAGGGTTTAAAA
1 TTTAGGGTTTATGA
1318965 TTTAGGGTTTA
1 TTTAGGGTTTA
1318976 GGGTTTATGC
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
13 9 0.29
14 22 0.71
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTATGA
Found at i:1319157 original size:42 final size:42
Alignment explanation
Indices: 1319104--1319213 Score: 184
Period size: 42 Copynumber: 2.6 Consensus size: 42
1319094 TAGTTTATAC
* *
1319104 ATACATGTACTATAAGTTACATATATAGTTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACACGT
1319146 ATACATATACTATAAGTTACATATATAGTTTACATTACACGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACACGT
* *
1319188 ATACACATACTATAAGTTATATATAT
1 ATACATATACTATAAGTTACATATAT
1319214 TAACTATTGT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (42 bp):
ATACATATACTATAAGTTACATATATAGTTTACATTACACGT
Found at i:1319438 original size:2 final size:2
Alignment explanation
Indices: 1319431--1319565 Score: 90
Period size: 2 Copynumber: 69.0 Consensus size: 2
1319421 TCTTTAATAG
*
1319431 AT AT AT AT AT AT AT AT AT AT -T ACT -T AT AT -T AGT -T AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT
* * * *
1319471 AC AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AC AT AT AA
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1319510 ACT AT AT AT -T TT AT AT AGT TT AT AT AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT
1319553 AT AT AT ACT AT AT
1 AT AT AT A-T AT AT
1319566 TAATATAAAT
Statistics
Matches: 106, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
1 9 0.08
2 89 0.84
3 8 0.08
ACGTcount: A:0.46, C:0.05, G:0.01, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1319539 original size:13 final size:13
Alignment explanation
Indices: 1319521--1319743 Score: 73
Period size: 13 Copynumber: 16.5 Consensus size: 13
1319511 CTATATATTT
1319521 TATATAGTTTATA
1 TATATAGTTTATA
*
1319534 TATATA-TATATA
1 TATATAGTTTATA
*
1319546 TATATA-TATATA
1 TATATAGTTTATA
*
1319558 TACTATA-TTAATA
1 TA-TATAGTTTATA
* * *
1319571 TAAATAATATTTTA
1 TATATAGT-TTATA
* * *
1319585 TAAACTA-TATACTT
1 TATA-TAGTTTA-TA
*
1319599 TTTATAGTTTATACA
1 TATATAGTTTAT--A
1319614 TATATAGTTTATA
1 TATATAGTTTATA
* *
1319627 TACATAGCTTATA
1 TATATAGTTTATA
*
1319640 TATATAGTTCACATA
1 TATATAGTT--TATA
* * *
1319655 AACATAATTTATA
1 TATATAGTTTATA
1319668 TATATAGCTTATAATAA
1 TATATAG-TT-T-AT-A
1319685 TTATATAGTTTATA
1 -TATATAGTTTATA
**
1319699 -ATATA-AATATA
1 TATATAGTTTATA
* *
1319710 GTTTATAATTT-TA
1 -TATATAGTTTATA
1319723 TATTCATAGTTTATA
1 TA-T-ATAGTTTATA
1319738 TATATA
1 TATATA
1319744 ATGCAAATAA
Statistics
Matches: 156, Mismatches: 33, Indels: 42
0.68 0.14 0.18
Matches are distributed among these distances:
11 4 0.03
12 28 0.18
13 57 0.37
14 25 0.16
15 29 0.19
16 3 0.02
17 3 0.02
18 7 0.04
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:1319539 original size:31 final size:32
Alignment explanation
Indices: 1319513--1319594 Score: 77
Period size: 31 Copynumber: 2.7 Consensus size: 32
1319503 CATATAAACT
* *
1319513 ATATATTTTATATAGT-TTATA-T-ATATATAT
1 ATATATTTTATATA-TACTATATTAATATAAAT
*
1319543 ATATATATATATATATACTATATTAATATAAAT
1 ATATAT-TTTATATATACTATATTAATATAAAT
1319576 A-ATATTTTATA-A-ACTATAT
1 ATATATTTTATATATACTATAT
1319595 ACTTTTTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
29 7 0.16
30 8 0.18
31 16 0.36
32 5 0.11
33 8 0.18
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (32 bp):
ATATATTTTATATATACTATATTAATATAAAT
Found at i:1319559 original size:78 final size:79
Alignment explanation
Indices: 1319455--1319632 Score: 243
Period size: 78 Copynumber: 2.2 Consensus size: 79
1319445 ATATATTACT
* *
1319455 TATATTAGTTATACATACATATATATACTATATTAATATAAATTATAACATATAAACTATATA-T
1 TATA-TAG-TATATATACATATATATACTATATTAATATAAATAATAACATATAAACTATATACT
*
1319519 TTTATATAGTTTATATA
64 TTT-TATAGTTTATACA
* ***
1319536 TATATA-TATATATATATATATATACTATATTAATATAAATAATATTTTATAAACTATATACTTT
1 TATATAGTATATATACATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTT
1319600 TTATAGTTTATACA
66 TTATAGTTTATACA
*
1319614 TATATAGTTTATATACATA
1 TATATAGTATATATACATA
1319633 GCTTATATAT
Statistics
Matches: 86, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
78 66 0.77
79 14 0.16
80 2 0.02
81 4 0.05
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (79 bp):
TATATAGTATATATACATATATATACTATATTAATATAAATAATAACATATAAACTATATACTTT
TTATAGTTTATACA
Found at i:1319681 original size:26 final size:25
Alignment explanation
Indices: 1319613--1319681 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 25
1319603 TAGTTTATAC
* *
1319613 ATATATAGTTTATATACATAGCTTAT
1 ATATATAG-TTATAAACATAACTTAT
*
1319639 ATATATAGTTCACATAAACATAATTTAT
1 ATATATAGTT---ATAAACATAACTTAT
1319667 ATATATAGCTTATAA
1 ATATATAG-TTATAA
1319682 TAATTATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
25 2 0.06
26 12 0.33
28 20 0.56
29 2 0.06
ACGTcount: A:0.43, C:0.09, G:0.06, T:0.42
Consensus pattern (25 bp):
ATATATAGTTATAAACATAACTTAT
Found at i:1319708 original size:18 final size:18
Alignment explanation
Indices: 1319664--1319821 Score: 83
Period size: 18 Copynumber: 9.3 Consensus size: 18
1319654 AAACATAATT
* *
1319664 TATATATATAGCTTATAA
1 TATAAATATAGTTTATAA
*
1319682 TA-ATTATATAGTTTATAA
1 TATA-AATATAGTTTATAA
1319700 TATAAATATAGTTTATAA
1 TATAAATATAGTTTATAA
* *
1319718 TTTTATATTCATAGTTTAT-A
1 -TATA-AAT-ATAGTTTATAA
**
1319738 TAT--ATA-A---TGCAA
1 TATAAATATAGTTTATAA
*
1319750 -ATAAATATAATTTAT-A
1 TATAAATATAGTTTATAA
1319766 TAT--ATATAGTTTATAA
1 TATAAATATAGTTTATAA
* *
1319782 TA-ATTATATAGTTGATAA
1 TATA-AATATAGTTTATAA
1319800 TATAAATATAGTTTAT-A
1 TATAAATATAGTTTATAA
1319817 TATAA
1 TATAA
1319822 TTTTATATTA
Statistics
Matches: 108, Mismatches: 14, Indels: 37
0.68 0.09 0.23
Matches are distributed among these distances:
11 3 0.03
12 1 0.01
13 3 0.03
14 2 0.02
15 11 0.10
16 5 0.05
17 10 0.09
18 54 0.50
19 7 0.06
20 3 0.03
21 9 0.08
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.47
Consensus pattern (18 bp):
TATAAATATAGTTTATAA
Found at i:1319731 original size:98 final size:100
Alignment explanation
Indices: 1319621--1319816 Score: 306
Period size: 100 Copynumber: 2.0 Consensus size: 100
1319611 ACATATATAG
* * *
1319621 TTTATATACATAGCTTATATATATAGTTCACATAAACATAA-TT-TATATATATAGCTTATAATA
1 TTTATATACATAGCTTATATATATAATGCAAATAAACATAATTTATATATATATAGCTTATAATA
*
1319684 ATTATATAGTTTATAATATAAATATAGTTTATAAT
66 ATTATATAGTTGATAATATAAATATAGTTTATAAT
* * * *
1319719 TTTATATTCATAGTTTATATATATAATGCAAATAAATATAATTTATATATATATAGTTTATAATA
1 TTTATATACATAGCTTATATATATAATGCAAATAAACATAATTTATATATATATAGCTTATAATA
1319784 ATTATATAGTTGATAATATAAATATAGTTTATA
66 ATTATATAGTTGATAATATAAATATAGTTTATA
1319817 TATAATTTTA
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
98 35 0.40
99 2 0.02
100 51 0.58
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (100 bp):
TTTATATACATAGCTTATATATATAATGCAAATAAACATAATTTATATATATATAGCTTATAATA
ATTATATAGTTGATAATATAAATATAGTTTATAAT
Found at i:1319772 original size:15 final size:15
Alignment explanation
Indices: 1319734--1319837 Score: 59
Period size: 15 Copynumber: 6.7 Consensus size: 15
1319724 ATTCATAGTT
**
1319734 TATATATATAATGCA
1 TATATATATAATTTA
* *
1319749 AATAAATATAATTTA
1 TATATATATAATTTA
*
1319764 TATATATATAGTTTA
1 TATATATATAATTTA
* *
1319779 TAATAATTATATAGTTGA
1 T-AT-A-TATATAATTTA
*
1319797 TA-ATATA-AATATA
1 TATATATATAATTTA
*
1319810 GTTTATATATAATTTTA
1 -TATATATATAA-TTTA
1319827 TATTATATATA
1 TA-TATATATA
1319838 TATTATATTT
Statistics
Matches: 67, Mismatches: 14, Indels: 14
0.71 0.15 0.15
Matches are distributed among these distances:
13 3 0.04
14 5 0.07
15 30 0.45
16 5 0.07
17 13 0.19
18 11 0.16
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.47
Consensus pattern (15 bp):
TATATATATAATTTA
Found at i:1319839 original size:36 final size:37
Alignment explanation
Indices: 1319762--1319839 Score: 108
Period size: 36 Copynumber: 2.2 Consensus size: 37
1319752 AAATATAATT
*
1319762 TATATATATATAGTTTATAATAATTATATAGTTGATA
1 TATATAAATATAGTTTATAATAATTATATAGTTGATA
*
1319799 -ATATAAATATAGTTTATATATAATTTTATA-TT-ATA
1 TATATAAATATAGTTTATA-ATAATTATATAGTTGATA
1319834 TATATA
1 TATATA
1319840 TTATATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
35 3 0.08
36 24 0.65
37 10 0.27
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (37 bp):
TATATAAATATAGTTTATAATAATTATATAGTTGATA
Found at i:1319840 original size:98 final size:98
Alignment explanation
Indices: 1319624--1319840 Score: 287
Period size: 100 Copynumber: 2.2 Consensus size: 98
1319614 TATATAGTTT
* * * * *
1319624 ATATACATAGCTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAATTAT
1 ATATTCATAGTTTATATATATAATGCAAATAAACATAATTTATATATATAGCTTATAATAATTAT
* * *
1319689 ATAGTTTATAATATAAATATAGTTTATAATTTT
66 ATAGTTGATAATATAAATATAGTTTATAATATA
* *
1319722 ATATTCATAGTTTATATATATAATGCAAATAAATATAATTTATATATATATAGTTTATAATAATT
1 ATATTCATAGTTTATATATATAATGCAAATAAACATAA-TT-TATATATATAGCTTATAATAATT
1319787 ATATAGTTGATAATATAAATATAGTTTAT-ATATA
64 ATATAGTTGATAATATAAATATAGTTTATAATATA
*
1319821 AT-TTTATA-TTATATATATAT
1 ATATTCATAGTT-TATATATAT
1319841 TATATTTTTT
Statistics
Matches: 105, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
97 2 0.02
98 46 0.44
99 7 0.07
100 50 0.48
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.47
Consensus pattern (98 bp):
ATATTCATAGTTTATATATATAATGCAAATAAACATAATTTATATATATAGCTTATAATAATTAT
ATAGTTGATAATATAAATATAGTTTATAATATA
Found at i:1322435 original size:36 final size:35
Alignment explanation
Indices: 1322388--1322784 Score: 206
Period size: 36 Copynumber: 11.4 Consensus size: 35
1322378 TTCAAAAACC
*
1322388 TATATAATATATATTTTCAAAAGTATTTTAAAATTA
1 TATATTATATATATTTTCAAAAGTATTTTAAAA-TA
* * * *
1322424 TATATTATATATTTTTTTAAAAATATTTTCAAA-A
1 TATATTATATATATTTTCAAAAGTATTTTAAAATA
* *
1322458 T-TA-TATA-GT-TTTTAAAAATGT-TTTTAAAACTA
1 TATATTATATATATTTTCAAAA-GTATTTTAAAA-TA
* *
1322490 TATACTATATA-ATTTTTCAAAA-TGATTTCAAAATTA
1 TATATTATATATA-TTTTCAAAAGT-ATTTTAAAA-TA
* * *
1322526 TATAATATATATGTTTTCAAAATGT-TTTT-TAA-A
1 TATATTATATATATTTTCAAAA-GTATTTTAAAATA
* *
1322559 -A-ACTATATATATTTTCAAAATGT-TTTT-TAA-A
1 TATATTATATATATTTTCAAAA-GTATTTTAAAATA
* *
1322590 -A-ACTATATATATTTTCAAAA-TGTTTTAAAA-A
1 TATATTATATATATTTTCAAAAGTATTTTAAAATA
* * *
1322621 CTATATAATATATATTTTTAAAAATATTTTAAAAATTA
1 -TATATTATATATATTTTCAAAAGTATTTT-AAAA-TA
* *
1322659 TATATTATATTTATTTTCAAAATGTTTTTTAAAACTA
1 TATATTATATATATTTTCAAAA-GTATTTTAAAA-TA
* * * *
1322696 TATAATATATAAATGTTTTCAAACATGT-TTTCAAAACCA
1 TAT-AT-TATATATATTTTCAAA-A-GTATTTTAAAA-TA
* * * *
1322735 TATATTATATATGTTTTTAAAAATATTTTCAAACTA
1 TATATTATATATATTTTCAAAAGTATTTT-AAAATA
*
1322771 TATACTATATATAT
1 TATATTATATATAT
1322785 ATATATATAT
Statistics
Matches: 290, Mismatches: 43, Indels: 56
0.75 0.11 0.14
Matches are distributed among these distances:
29 1 0.00
30 19 0.07
31 53 0.18
32 7 0.02
33 6 0.02
34 23 0.08
35 8 0.03
36 88 0.30
37 45 0.16
38 11 0.04
39 25 0.09
40 4 0.01
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.48
Consensus pattern (35 bp):
TATATTATATATATTTTCAAAAGTATTTTAAAATA
Found at i:1322481 original size:29 final size:30
Alignment explanation
Indices: 1322427--1322493 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
1322417 AAAATTATAT
*
1322427 ATTATATATTTTTTTAAAAATATTTTCAAA
1 ATTATATATGTTTTTAAAAATATTTTCAAA
* *
1322457 ATTATATA-GTTTTTAAAAATGTTTTTAAA
1 ATTATATATGTTTTTAAAAATATTTTCAAA
*
1322486 ACTATATA
1 ATTATATA
1322494 CTATATAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
29 25 0.76
30 8 0.24
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATTATATATGTTTTTAAAAATATTTTCAAA
Found at i:1322535 original size:102 final size:102
Alignment explanation
Indices: 1322382--1322763 Score: 356
Period size: 102 Copynumber: 3.7 Consensus size: 102
1322372 AAAAAATTCA
* * * *
1322382 AAAACCTATAT-A-ATATATATTTTCAAAA-GTATTTTAAAATTATATATTATATATTTTTTTAA
1 AAAA-CTATATAATATATATATTTTCAAAATG-ATTTCAAAACTATATAATATATATGTTTTTAA
*
1322444 AAATATTTTCAAAATTATATAGT-TTTTAAAAATGTTTTT
64 AAATATTTTAAAAATTATATA-TATTTTAAAAATGTTTTT
* * *
1322483 AAAACTATATACTATATA-ATTTTTCAAAATGATTTCAAAATTATATAATATATATGTTTTCAAA
1 AAAACTATATAATATATATA-TTTTCAAAATGATTTCAAAACTATATAATATATATGTTTTTAAA
* * * *
1322547 ATGTTTTTTAAAAACTATATATATTTTCAAAATGTTTTT
65 A-ATATTTTAAAAATTATATATATTTTAAAAATGTTTTT
* * * *
1322586 -TAA--A-A-ACTATATATATTTTCAAAATGTTTTAAAAACTATATAATATATA--TTTTTAAAA
1 AAAACTATATAATATATATATTTTCAAAATGATTTCAAAACTATATAATATATATGTTTTTAAAA
1322644 ATATTTTAAAAATTATATATTATATTTATTTTCAAAATGTTTTTT
66 ATATTTTAAAAATTATATA-TAT-TTTA-----AAAATG-TTTTT
* * * *
1322689 AAAACTATATAATATATAAATGTTTTCAAACATGTTTTCAAAACCATATATTATATATGTTTTTA
1 AAAACTATATAATATAT--ATATTTTCAAA-ATGATTTCAAAACTATATAATATATATGTTTTTA
1322754 AAAATATTTT
63 AAAATATTTT
1322764 CAAACTATAT
Statistics
Matches: 231, Mismatches: 25, Indels: 38
0.79 0.09 0.13
Matches are distributed among these distances:
95 16 0.07
96 11 0.05
97 3 0.01
98 39 0.17
99 2 0.01
100 7 0.03
101 5 0.02
102 53 0.23
103 36 0.16
104 2 0.01
106 1 0.00
107 1 0.00
108 6 0.03
110 10 0.04
111 23 0.10
113 16 0.07
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (102 bp):
AAAACTATATAATATATATATTTTCAAAATGATTTCAAAACTATATAATATATATGTTTTTAAAA
ATATTTTAAAAATTATATATATTTTAAAAATGTTTTT
Found at i:1322566 original size:31 final size:31
Alignment explanation
Indices: 1322531--1322627 Score: 171
Period size: 31 Copynumber: 3.2 Consensus size: 31
1322521 AATTATATAA
*
1322531 TATATATGTTTTCAAAATGTTTTTTAAAAAC
1 TATATATATTTTCAAAATGTTTTTTAAAAAC
1322562 TATATATATTTTCAAAATGTTTTTTAAAAAC
1 TATATATATTTTCAAAATGTTTTTTAAAAAC
1322593 TATATATATTTTCAAAATG--TTTTAAAAAC
1 TATATATATTTTCAAAATGTTTTTTAAAAAC
1322622 TATATA
1 TATATA
1322628 ATATATATTT
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 16 0.25
31 49 0.75
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.47
Consensus pattern (31 bp):
TATATATATTTTCAAAATGTTTTTTAAAAAC
Found at i:1322674 original size:37 final size:37
Alignment explanation
Indices: 1322593--1322784 Score: 178
Period size: 37 Copynumber: 5.2 Consensus size: 37
1322583 TTTTAAAAAC
* *
1322593 TATATATA-TTTTCAAAATGTTTTAAAAACTATATA-
1 TATATATATTTTTAAAAATATTTTAAAAACTATATAT
*
1322628 -ATATATATTTTTAAAAATATTTTAAAAATTATATAT
1 TATATATATTTTTAAAAATATTTTAAAAACTATATAT
* * * * *
1322664 TATATTTA-TTTTCAAAATGTTTTTTAAAACTATATAA
1 TATATATATTTTTAAAAAT-ATTTTAAAAACTATATAT
* * * * *
1322701 TATATAAATGTTTTCAAACATGTTTTCAAAACCATATAT
1 TATATATAT-TTTT-AAAAATATTTTAAAAACTATATAT
* * *
1322740 TATATATGTTTTTAAAAATATTTT-CAAACTATATAC
1 TATATATATTTTTAAAAATATTTTAAAAACTATATAT
1322776 TATATATAT
1 TATATATAT
1322785 ATATATATAT
Statistics
Matches: 125, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
34 7 0.06
35 24 0.19
36 26 0.21
37 35 0.28
38 4 0.03
39 25 0.20
40 4 0.03
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (37 bp):
TATATATATTTTTAAAAATATTTTAAAAACTATATAT
Found at i:1322732 original size:39 final size:38
Alignment explanation
Indices: 1322593--1322784 Score: 175
Period size: 35 Copynumber: 5.2 Consensus size: 38
1322583 TTTTAAAAAC
*
1322593 TATATATATTTTCAAAATGTTTTAAAAACTATAT-A-A
1 TATATATGTTTTCAAAATGTTTTAAAAACTATATAATA
* * *
1322629 TATATAT-TTTTAAAAATATTTTAAAAATTATAT-AT-
1 TATATATGTTTTCAAAATGTTTTAAAAACTATATAATA
* * *
1322664 TATATTTATTTTCAAAATGTTTTTTAAAACTATATAATA
1 TATATATGTTTTCAAAATG-TTTTAAAAACTATATAATA
* * *
1322703 TATAAATGTTTTCAAACATGTTTTCAAAACCATAT-AT-
1 TATATATGTTTTCAAA-ATGTTTTAAAAACTATATAATA
* * * *
1322740 TATATATGTTTTTAAAAATATTTT-CAAACTATATACTA
1 TATATATG-TTTTCAAAATGTTTTAAAAACTATATAATA
1322778 TATATAT
1 TATATAT
1322785 ATATATATAT
Statistics
Matches: 128, Mismatches: 19, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
35 30 0.23
36 24 0.19
37 27 0.21
38 18 0.14
39 26 0.20
40 3 0.02
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (38 bp):
TATATATGTTTTCAAAATGTTTTAAAAACTATATAATA
Found at i:1325134 original size:40 final size:41
Alignment explanation
Indices: 1325090--1325175 Score: 120
Period size: 40 Copynumber: 2.1 Consensus size: 41
1325080 ACGAATAGGT
*
1325090 AAATCGCAACGTGAATTTATAAA-TCGCAACACAGTTTCCA
1 AAATCGCAACGCGAATTTATAAATTCGCAACACAGTTTCCA
* * * *
1325130 AAATCGCAACGCGAATTTTTAAATTCGTAACACATTTTTCA
1 AAATCGCAACGCGAATTTATAAATTCGCAACACAGTTTCCA
1325171 AAATC
1 AAATC
1325176 ACGTTGCGAT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 21 0.52
41 19 0.47
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (41 bp):
AAATCGCAACGCGAATTTATAAATTCGCAACACAGTTTCCA
Found at i:1325153 original size:20 final size:20
Alignment explanation
Indices: 1325070--1325153 Score: 64
Period size: 20 Copynumber: 4.2 Consensus size: 20
1325060 ACAGGTTCCA
***
1325070 AAATCGCAACACGAATAGGT
1 AAATCGCAACACGAATTTAT
**
1325090 AAATCGCAACGTGAATTTAT
1 AAATCGCAACACGAATTTAT
*
1325110 AAATCGCAACAC-AGTTTCCA-
1 AAATCGCAACACGAATTT--AT
* *
1325130 AAATCGCAACGCGAATTTTT
1 AAATCGCAACACGAATTTAT
1325150 AAAT
1 AAAT
1325154 TCGTAACACA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
19 4 0.08
20 40 0.82
21 5 0.10
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (20 bp):
AAATCGCAACACGAATTTAT
Found at i:1325258 original size:57 final size:57
Alignment explanation
Indices: 1325170--1325467 Score: 427
Period size: 57 Copynumber: 5.2 Consensus size: 57
1325160 CACATTTTTC
* ** *
1325170 AAAATCACGTTGCGATAACACTGTTTACCTATATCGGTAATTAGCGTTGCAAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
* * * *
1325227 AAAATCGCGTTGCAATAGTAGTGTTTACCTATGTCGGTAATTAGCATTGCGAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
* *
1325284 AAAATCGCGTTGTGATAGTATTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
* * *
1325341 AAAAT-GACGTTGCGATAGTACTGTTTATCTACATCGGTAATTAGCGTTGCGATTTTGG
1 AAAATCG-CGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTT-G
** *
1325399 AAAATCGCGTTGCGATAACACTTTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1 AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
1325456 AAAATCGCGTTG
1 AAAATCGCGTTG
1325468 TGAATTTGTA
Statistics
Matches: 214, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
56 1 0.00
57 163 0.76
58 49 0.23
59 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (57 bp):
AAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCGAATTTG
Found at i:1325467 original size:20 final size:20
Alignment explanation
Indices: 1325442--1325490 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
1325432 TCGGTAATTA
1325442 GCGTTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
* *
1325462 GCGTTGTGAATTTGTAAATC
1 GCGTTGCGAATTTGAAAATC
1325482 GCGTTGCGA
1 GCGTTGCGA
1325491 TAGTACTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:1325531 original size:77 final size:77
Alignment explanation
Indices: 1325388--1325602 Score: 322
Period size: 77 Copynumber: 2.8 Consensus size: 77
1325378 TAATTAGCGT
* ** * *
1325388 TGCGATTTTGGAAAATCGCGTTGCGATAACACTTTTTACCTATATCGGTAATTAGCGTTGCGAAT
1 TGCGAATTT-GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCAAAT
*
1325453 TTGAAAATCGCGT
65 TTGAAAATCGCGC
* * * *
1325466 TGTGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATGTCAGTAATTAGCGTTGCAAATT
1 TGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCAAATT
*
1325531 TGAAAATCTCGC
66 TGAAAATCGCGC
1325543 TGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGC
1 TGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGC
1325603 GATTTACATA
Statistics
Matches: 122, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
77 115 0.94
78 7 0.06
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (77 bp):
TGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCGTTGCAAATT
TGAAAATCGCGC
Found at i:1325566 original size:20 final size:20
Alignment explanation
Indices: 1325519--1325567 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1325509 TCAGTAATTA
*
1325519 GCGTTGCAAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
* *
1325539 TCGCTGCGAATTTGAAAATC
1 GCGTTGCGAATTTGAAAATC
1325559 GCGTTGCGA
1 GCGTTGCGA
1325568 TAGTACTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (20 bp):
GCGTTGCGAATTTGAAAATC
Found at i:1325621 original size:20 final size:20
Alignment explanation
Indices: 1325596--1325687 Score: 184
Period size: 20 Copynumber: 4.6 Consensus size: 20
1325586 TCGGTAATTA
1325596 GCGTTGCGATTTACATATTC
1 GCGTTGCGATTTACATATTC
1325616 GCGTTGCGATTTACATATTC
1 GCGTTGCGATTTACATATTC
1325636 GCGTTGCGATTTACATATTC
1 GCGTTGCGATTTACATATTC
1325656 GCGTTGCGATTTACATATTC
1 GCGTTGCGATTTACATATTC
1325676 GCGTTGCGATTT
1 GCGTTGCGATTT
1325688 TGGAACCTGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 72 1.00
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
GCGTTGCGATTTACATATTC
Found at i:1325624 original size:77 final size:76
Alignment explanation
Indices: 1325379--1325645 Score: 315
Period size: 77 Copynumber: 3.5 Consensus size: 76
1325369 CTACATCGGT
* * ** *
1325379 AATTAGCGTTGCGATTTTGGAAAATCGCGTTGCGATAACACTTTTTACCTATATCGGTAATTAGC
1 AATTCGCGTTGCGAATTT-GAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGC
1325444 GTTGCGAATTTGA
65 GTTGCG-ATTTGA
* * * * *
1325457 AAATCGCGTTGTGAATTTGTAAATCGCGTTGCGATAGTACTGTTTACCTATGTCAGTAATTAGCG
1 AATTCGCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
*
1325522 TTGCAAATTTGA
66 TTGC-GATTTGA
* * *
1325534 AAATCTCGCTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
1 AATTCGCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
1325599 TTGCGATTT-A
66 TTGCGATTTGA
*
1325609 CATATTCGCGTTGCG-ATTT-ACATATTCGCGTTGCGAT
1 -A-ATTCGCGTTGCGAATTTGA-A-AATCGCGTTGCGAT
1325646 TTACATATTC
Statistics
Matches: 162, Mismatches: 22, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
75 2 0.01
76 10 0.06
77 136 0.84
78 14 0.09
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (76 bp):
AATTCGCGTTGCGAATTTGAAAATCGCGTTGCGATAGTACTGTTTACCTATATCGGTAATTAGCG
TTGCGATTTGA
Found at i:1327584 original size:16 final size:16
Alignment explanation
Indices: 1327563--1327595 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1327553 AAGATTTTGA
*
1327563 AATCAAGTTTTAAATT
1 AATCAAGTTTGAAATT
1327579 AATCAAGTTTGAAATT
1 AATCAAGTTTGAAATT
1327595 A
1 A
1327596 CTCCCTCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.09, T:0.39
Consensus pattern (16 bp):
AATCAAGTTTGAAATT
Found at i:1327633 original size:8 final size:8
Alignment explanation
Indices: 1327622--1327661 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
1327612 CACTTCTCCC
1327622 CCTTAACA
1 CCTTAACA
1327630 CCTTAACA
1 CCTTAACA
1327638 -CTTAA-A
1 CCTTAACA
1327644 CACTTAACA
1 C-CTTAACA
1327653 CCTTAACA
1 CCTTAACA
1327661 C
1 C
1327662 TTCTTCCCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 5 0.17
8 21 0.72
9 2 0.07
ACGTcount: A:0.40, C:0.35, G:0.00, T:0.25
Consensus pattern (8 bp):
CCTTAACA
Found at i:1327649 original size:15 final size:15
Alignment explanation
Indices: 1327622--1327663 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
1327612 CACTTCTCCC
1327622 CCTTAACACCTTAACA
1 CCTTAACA-CTTAACA
1327638 -CTTAAACACTTAACA
1 CCTT-AACACTTAACA
1327653 CCTTAACACTT
1 CCTTAACACTT
1327664 CTTCCCCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 17 0.71
16 7 0.29
ACGTcount: A:0.38, C:0.33, G:0.00, T:0.29
Consensus pattern (15 bp):
CCTTAACACTTAACA
Found at i:1329780 original size:19 final size:20
Alignment explanation
Indices: 1329751--1329788 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1329741 CAGACCCCAT
1329751 GGGGGATATCGATTCCCCTA
1 GGGGGATATCGATTCCCCTA
*
1329771 GGGGGA-ATCGGTTCCCCT
1 GGGGGATATCGATTCCCCT
1329789 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.16, C:0.26, G:0.34, T:0.24
Consensus pattern (20 bp):
GGGGGATATCGATTCCCCTA
Found at i:1329800 original size:23 final size:22
Alignment explanation
Indices: 1329770--1329837 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 22
1329760 CGATTCCCCT
*
1329770 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTGC-A
*
1329793 AGGGGGAATCTGTTCCCCTGCA
1 AGGGGGAATCGGTTCCCCTGCA
* *
1329815 AGGGGGTATCGATTCCCTCTGCA
1 AGGGGGAATCGGTTCCC-CTGCA
1329838 CCAAAATGCT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 15 0.38
23 24 0.62
ACGTcount: A:0.19, C:0.26, G:0.31, T:0.24
Consensus pattern (22 bp):
AGGGGGAATCGGTTCCCCTGCA
Found at i:1336840 original size:96 final size:95
Alignment explanation
Indices: 1336679--1336956 Score: 400
Period size: 96 Copynumber: 2.9 Consensus size: 95
1336669 TAATAGGTGT
* *
1336679 TGCTGATT-CAACTCCATATGTGAAGAATCGAGC--TAATGACAATGTTGATGATACTGATCCAA
1 TGCTG-TTCCAACTCCATATGTGAAGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAA
1336741 CTCCGTATGCGATGGATGAGCCAAGTACTGG
65 CTCCGTATGCGATGGATGAGCCAAGTACTGG
* *
1336772 TGCTGTTCCAACTCCATATGTGAAGGAATCGAGCAAGAATGACAATGTTTATGATGTTGATCCAA
1 TGCTGTTCCAACTCCATATGTGAA-GAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAA
*
1336837 CTCCGTATGCGATGGATGAGCCAAGTATTGG
65 CTCCGTATGCGATGGATGAGCCAAGTACTGG
* * * * *
1336868 TGTTGTTCCAACTCCGTATGTTAAAGAATTGAGCAAGAATTACAATGTTGATGATGCTGATCCAA
1 TGCTGTTCCAACTCCATATG-TGAAGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAA
* *
1336933 CTCCGTATGTGATGGATAAGCCAA
65 CTCCGTATGCGATGGATGAGCCAA
1336957 AATCCAGTGA
Statistics
Matches: 166, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
92 2 0.01
93 21 0.13
94 9 0.05
96 131 0.79
97 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (95 bp):
TGCTGTTCCAACTCCATATGTGAAGAATCGAGCAAGAATGACAATGTTGATGATGCTGATCCAAC
TCCGTATGCGATGGATGAGCCAAGTACTGG
Found at i:1337203 original size:120 final size:121
Alignment explanation
Indices: 1336972--1337232 Score: 389
Period size: 120 Copynumber: 2.2 Consensus size: 121
1336962 AGTGATGTTT
* * *
1336972 CAACTTCTTATGCACTGGATGAAAGTGTCGATCCACCTCCTTATGTGATGGAATCGAATGAGATG
1 CAACTCCTTATACACTGGATGAAAGTATCGATCCACCTCCTTATGTGATGGAATCGAATGAGATG
* * *
1337037 TTGGTGCTGATCTACCTCATTTTGTGATAGAATCAAGCAAAAAGTTGATACTGATC
66 TTAGTGCTGATCTACCTCATTCTGTGATAGAATCAAGCAAAAAGTTGATACTGATA
* * *
1337093 CAACTCCTTATACGCTGGATGAAAGTATTGATCCACCTCCTTCTGTGATGGAATCG-ATGAGATG
1 CAACTCCTTATACACTGGATGAAAGTATCGATCCACCTCCTTATGTGATGGAATCGAATGAGATG
* * *
1337157 TTAGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGCAAAAAGTTGATGCTGATA
66 TTAGTGCTGATCTACCTCATTCTGTGATAGAATCAAGCAAAAAGTTGATACTGATA
* *
1337213 CAACTCCTTATGCAATGGAT
1 CAACTCCTTATACACTGGAT
1337233 TTAAGCGAAA
Statistics
Matches: 125, Mismatches: 15, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
120 75 0.60
121 50 0.40
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (121 bp):
CAACTCCTTATACACTGGATGAAAGTATCGATCCACCTCCTTATGTGATGGAATCGAATGAGATG
TTAGTGCTGATCTACCTCATTCTGTGATAGAATCAAGCAAAAAGTTGATACTGATA
Found at i:1337762 original size:37 final size:37
Alignment explanation
Indices: 1337721--1337944 Score: 145
Period size: 37 Copynumber: 6.1 Consensus size: 37
1337711 ATTTTAAGAG
*
1337721 AAACTCTCTCGAGTGAGATAAATTTTGTTTCGAGGGA
1 AAACTCTCTCGAGTGAGATAAATTTTGTTTCAAGGGA
* * * * * *
1337758 AAACTGTCTTC-AGCGAGACAAATTTGGTTTTAA-GAA
1 AAACTCTC-TCGAGTGAGATAAATTTTGTTTCAAGGGA
*
1337794 AAAC-CATCTCGAGTTAGATAAATTTTGTTTCAAGGGA
1 AAACTC-TCTCGAGTGAGATAAATTTTGTTTCAAGGGA
* * ** * * * *
1337831 AAACTGTCTCAAGTGAGACGAAGTTGGTTTTAA-GAA
1 AAACTCTCTCGAGTGAGATAAATTTTGTTTCAAGGGA
1337867 AAAC-CATCTCGAGTGAGATAAAATTTCTTGTTTCAAGGG-
1 AAACTC-TCTCGAGTGAGAT-AAA-TT-TTGTTTCAAGGGA
* * ** * * *
1337906 AAACTGTCTCAAAAGAGACAAAATATGTTTCAAGGGA
1 AAACTCTCTCGAGTGAGATAAATTTTGTTTCAAGGGA
1337943 AA
1 AA
1337945 TGATCTTAAA
Statistics
Matches: 137, Mismatches: 38, Indels: 24
0.69 0.19 0.12
Matches are distributed among these distances:
35 2 0.01
36 53 0.39
37 55 0.40
38 6 0.04
39 20 0.15
40 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (37 bp):
AAACTCTCTCGAGTGAGATAAATTTTGTTTCAAGGGA
Found at i:1337805 original size:73 final size:74
Alignment explanation
Indices: 1337712--1337927 Score: 289
Period size: 73 Copynumber: 2.9 Consensus size: 74
1337702 AAGAAACATA
* *
1337712 TTTTAAGAGAAACTC-TCTCGAGTGAGATAAATTTTGTTTCGAGGGAAAACTGTCTTC-AGCGAG
1 TTTTAAGAAAAAC-CATCTCGAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTTCAAGCGAG
*
1337775 ACAAATTTGG
65 ACAAAGTTGG
* *
1337785 TTTTAAGAAAAACCATCTCGAGTTAGATAAATTTTGTTTCAAGGGAAAACTGTC-TCAAGTGAGA
1 TTTTAAGAAAAACCATCTCGAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTTCAAGCGAGA
*
1337849 CGAAGTTGG
66 CAAAGTTGG
**
1337858 TTTTAAGAAAAACCATCTCGAGTGAGATAAAATTTCTTGTTTCAAGGG-AAACTGTC-TCAAAAG
1 TTTTAAGAAAAACCATCTCGAGTGAGAT-AAA-TT-TTGTTTCAAGGGAAAACTGTCTTCAAGCG
1337921 AGACAAA
63 AGACAAA
1337928 ATATGTTTCA
Statistics
Matches: 128, Mismatches: 10, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
72 3 0.02
73 89 0.70
74 3 0.02
75 21 0.16
76 12 0.09
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (74 bp):
TTTTAAGAAAAACCATCTCGAGTGAGATAAATTTTGTTTCAAGGGAAAACTGTCTTCAAGCGAGA
CAAAGTTGG
Found at i:1338632 original size:15 final size:15
Alignment explanation
Indices: 1338612--1338654 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
1338602 AATAAGAATT
1338612 GAGAAAGAATCAAGA
1 GAGAAAGAATCAAGA
1338627 GAGAAAGAATCAAGA
1 GAGAAAGAATCAAGA
*
1338642 GAGAAAGCATCAA
1 GAGAAAGAATCAA
1338655 ACCTCAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.58, C:0.09, G:0.26, T:0.07
Consensus pattern (15 bp):
GAGAAAGAATCAAGA
Found at i:1340517 original size:21 final size:21
Alignment explanation
Indices: 1340467--1340518 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
1340457 CAAGAGTTCA
*
1340467 TGATGATCATCAAAAGAAAAT
1 TGATGATCTTCAAAAGAAAAT
*
1340488 TAATGATCTTCAAAAGAAAAT
1 TGATGATCTTCAAAAGAAAAT
1340509 TGATGATCTT
1 TGATGATCTT
1340519 AAAGCTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (21 bp):
TGATGATCTTCAAAAGAAAAT
Found at i:1344137 original size:23 final size:21
Alignment explanation
Indices: 1344084--1344137 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
1344074 CCCCTTGCTA
1344084 TGTATCGATACACCTTGAATG
1 TGTATCGATACACCTTGAATG
* *
1344105 TATA-CTGATACATTCTTTGAATG
1 TGTATC-GATACA--CCTTGAATG
1344128 TGTATCGATA
1 TGTATCGATA
1344138 GCCCTATAGG
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.04
21 9 0.35
23 15 0.58
24 1 0.04
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (21 bp):
TGTATCGATACACCTTGAATG
Found at i:1348004 original size:21 final size:21
Alignment explanation
Indices: 1347966--1348006 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1347956 AATGGGAAGA
* *
1347966 AAAAAATTTCATTGCATTGTC
1 AAAAAATCTCATTACATTGTC
*
1347987 AAAAAATCTGATTACATTGT
1 AAAAAATCTCATTACATTGT
1348007 TCTTAGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (21 bp):
AAAAAATCTCATTACATTGTC
Found at i:1348091 original size:10 final size:9
Alignment explanation
Indices: 1348076--1348109 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1348066 GATTTGTACA
1348076 TTTTTCTGTT
1 TTTTTCT-TT
*
1348086 TTTTTCTTA
1 TTTTTCTTT
1348095 TTTTTCTTT
1 TTTTTCTTT
1348104 TTTTTC
1 TTTTTC
1348110 AAAATAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:1348579 original size:96 final size:96
Alignment explanation
Indices: 1348428--1348724 Score: 406
Period size: 96 Copynumber: 3.1 Consensus size: 96
1348418 GTTGCTGATT
* * *
1348428 CAACTCCATATGTG-AAGAATCGAGC--TAATGAA-AATGTTGATGATGCTGATCCAACTCCGTA
1 CAACTCCATATGTGAAAGAATCAACCAAGAAT-AACAATGTTGATGATGCTGATCCAACTCCGTA
1348489 TGCGATGGATGAGCCAAGTAGTGGTGTTGTTC
65 TGCGATGGATGAGCCAAGTAGTGGTGTTGTTC
* * *
1348521 CAACTCTATATGTGAAGGAATCAACCAAGAATAACAATGCTGATGATGCTGATCCAACTCCGTAT
1 CAACTCCATATGTGAAAGAATCAACCAAGAATAACAATGTTGATGATGCTGATCCAACTCCGTAT
*
1348586 GCGATGGATGAGCCAAGTATTGGTGTTGTTC
66 GCGATGGATGAGCCAAGTAGTGGTGTTGTTC
* * * *
1348617 CAACTCCGTATGTGAAAGAATCGAGCAAGAATAACAATGTTGATGATGTTGATCCAACTCCGTAT
1 CAACTCCATATGTGAAAGAATCAACCAAGAATAACAATGTTGATGATGCTGATCCAACTCCGTAT
* * *
1348682 GCGATAGATGAGCCAA-AAGTCGGTGATGTTC
66 GCGATGGATGAGCCAAGTAGT-GGTGTTGTTC
*
1348713 CAACTCCTTATG
1 CAACTCCATATG
1348725 CGCTGGATGA
Statistics
Matches: 180, Mismatches: 19, Indels: 7
0.87 0.09 0.03
Matches are distributed among these distances:
93 13 0.07
94 8 0.04
95 4 0.02
96 155 0.86
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (96 bp):
CAACTCCATATGTGAAAGAATCAACCAAGAATAACAATGTTGATGATGCTGATCCAACTCCGTAT
GCGATGGATGAGCCAAGTAGTGGTGTTGTTC
Found at i:1348852 original size:121 final size:121
Alignment explanation
Indices: 1348711--1349315 Score: 701
Period size: 121 Copynumber: 4.9 Consensus size: 121
1348701 TCGGTGATGT
* *
1348711 TCCAACTCCTTATGCGCTGGATGAAAGTGTCGATCCACCTCCTTCTGTGATAGAATTGAACGAGA
1 TCCAACTCCTTATGCGCTGGATGAAAGTGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGA
* *
1348776 TGTTGGTGTTGATCTACCTCCTTCTGTGATAGAATCGAGAAAAAAGTTAATATTGA
66 TGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGAAAAAAGTTGATATTGA
* * *
1348832 TCCAACTCCTTATGCACTGGATGAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGA
1 TCCAACTCCTTATGCGCTGGATGAAAGTGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGA
* ** * * *
1348897 TGTTGGTGCTGATCTACATTTTTTTATGATAGAATCGAGCAAAAAGTTGATATTGA
66 TGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGAAAAAAGTTGATATTGA
* * * **
1348953 TCCAACTCCTTATGTGCTGGATGAAAGTGTCGATCCACCTCCTTCTATGATGTAATCGATTGAGA
1 TCCAACTCCTTATGCGCTGGATGAAAGTGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGA
* * * * *
1349018 TGTTGGTGCTAATCTACCTCTTTCTGTGATAAAATCGAG-CAAAATTTGATATTGA
66 TGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGAAAAAAGTTGATATTGA
* * *
1349073 TCCAACTCCTTATGCGCTAGATGAAAGTGTCGATCCACCTCATTCTGTGATGGAATCGAATGAGA
1 TCCAACTCCTTATGCGCTGGATGAAAGTGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGA
* * * * **
1349138 TGTCGGTGTTGATCTACCTCCTTCTATGATAGAATCGA-ACAAAACGTTGATGCTGA
66 TGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGA-AAAAAGTTGATATTGA
* * * * * * *
1349194 TCCAACTACTTATGTAATGGATTTGAGCGAAATAAAAATATCGATCCATCTCCTTCTGTGATGGA
1 TCCAACTCCTTATG----CG--CT--G-G--ATGAAAGTGTCGATCCACCTCCTTCTGTGATGGA
* * * *
1349259 ATCGAACGAGATGTTGGTGCTGATTTACCTTCTTATGTGATAGAATCGAGCAAAAAG
55 ATCGAACGAGATGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGAAAAAAG
1349316 CTGAATAATC
Statistics
Matches: 406, Mismatches: 64, Indels: 17
0.83 0.13 0.03
Matches are distributed among these distances:
120 105 0.26
121 222 0.55
125 1 0.00
127 1 0.00
130 1 0.00
132 76 0.19
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (121 bp):
TCCAACTCCTTATGCGCTGGATGAAAGTGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGA
TGTTGGTGCTGATCTACCTCCTTCTGTGATAGAATCGAGAAAAAAGTTGATATTGA
Found at i:1349175 original size:241 final size:242
Alignment explanation
Indices: 1348711--1349208 Score: 712
Period size: 241 Copynumber: 2.1 Consensus size: 242
1348701 TCGGTGATGT
* * *
1348711 TCCAACTCCTTATGCGCTGGATGAAAGTGTCGATCCACCTCCTTCTGTGATAGAATTGAACGAGA
1 TCCAACTCCTTATGTGCTGGATGAAAGTGTCGATCCACCTCCTTCTATGATAGAATCGAACGAGA
* * *
1348776 TGTTGGTGTTGATCTACCTCCTTCTGTGATAGAATCGAGAAAAAAGTTAATATTGATCCAACTCC
66 TGTTGGTGCTAATCTACCTCCTTCTGTGATAAAATCGAGAAAAAAGTTAATATTGATCCAACTCC
* * *
1348841 TTATGCACTGGATGAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACAAGATGTTGGTGC
131 TTATGCACTAGATGAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACAAGATGTCGGTGC
** * * *
1348906 TGATCTACATTTTTTTATGATAGAATCGAGCAAAAAGTTGATATTGA
196 TGATCTACATCCTTCTATGATAGAATCGAACAAAAAGTTGATACTGA
**
1348953 TCCAACTCCTTATGTGCTGGATGAAAGTGTCGATCCACCTCCTTCTATGAT-GTAATCGATTGAG
1 TCCAACTCCTTATGTGCTGGATGAAAGTGTCGATCCACCTCCTTCTATGATAG-AATCGAACGAG
* * * *
1349017 ATGTTGGTGCTAATCTACCTCTTTCTGTGATAAAATCGAG-CAAAATTTGATATTGATCCAACTC
65 ATGTTGGTGCTAATCTACCTCCTTCTGTGATAAAATCGAGAAAAAAGTTAATATTGATCCAACTC
* * **
1349081 CTTATGCGCTAGATGAAAGTGTCGATCCACCTCATTCTGTGATGGAATCGAATGAGATGTCGGTG
130 CTTATGCACTAGATGAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACAAGATGTCGGTG
* * * *
1349146 TTGATCTACCTCCTTCTATGATAGAATCGAACAAAACGTTGATGCTGA
195 CTGATCTACATCCTTCTATGATAGAATCGAACAAAAAGTTGATACTGA
*
1349194 TCCAACTACTTATGT
1 TCCAACTCCTTATGT
1349209 AATGGATTTG
Statistics
Matches: 226, Mismatches: 29, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
241 133 0.59
242 93 0.41
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (242 bp):
TCCAACTCCTTATGTGCTGGATGAAAGTGTCGATCCACCTCCTTCTATGATAGAATCGAACGAGA
TGTTGGTGCTAATCTACCTCCTTCTGTGATAAAATCGAGAAAAAAGTTAATATTGATCCAACTCC
TTATGCACTAGATGAAAATGTCGATCCACCTCATTCTGTGATGGAATCGAACAAGATGTCGGTGC
TGATCTACATCCTTCTATGATAGAATCGAACAAAAAGTTGATACTGA
Found at i:1349842 original size:73 final size:73
Alignment explanation
Indices: 1349711--1349906 Score: 256
Period size: 73 Copynumber: 2.7 Consensus size: 73
1349701 AGAAGCTCTC
* * *
1349711 TCGAGTAAGATAAATTTT-TTTCGAGGGAAAATTATCTCAAGCGAGACAACGTTGGTTTTAAGAA
1 TCGAGTAAGATAAATTTTGTTTCAAGGGAAAATTGTCTCAAGAGAGACAACGTTGGTTTTAAGAA
1349775 AAACCATA
66 AAACCATA
* *
1349783 TCGAGTTAGATAAATTTTGTTTCAAGGGAAAATTGTCTCAAGATAGACGAA-GTTGGTTTTAAGA
1 TCGAGTAAGATAAATTTTGTTTCAAGGGAAAATTGTCTCAAGAGAGAC-AACGTTGGTTTTAAGA
*
1349847 AAAACCATC
65 AAAACCATA
* *
1349856 TCGAGTGAGATAAATTTCTTGTTTCAAGGG-AAACTGTCTCAA-AGGAGACAA
1 TCGAGTAAGATAAA-TT-TTGTTTCAAGGGAAAATTGTCTCAAGA-GAGACAA
1349907 ACTTTGTTTC
Statistics
Matches: 110, Mismatches: 9, Indels: 9
0.86 0.07 0.07
Matches are distributed among these distances:
72 17 0.15
73 62 0.56
74 19 0.17
75 12 0.11
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (73 bp):
TCGAGTAAGATAAATTTTGTTTCAAGGGAAAATTGTCTCAAGAGAGACAACGTTGGTTTTAAGAA
AAACCATA
Found at i:1350143 original size:132 final size:130
Alignment explanation
Indices: 1349874--1350188 Score: 368
Period size: 132 Copynumber: 2.4 Consensus size: 130
1349864 GATAAATTTC
* * * * *
1349874 TTGTTTCAAGGGAAACTGTCTCAAAGGAGACAAACTTTGTTTCAAGGAAAATATATACAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAATAGATACAAAGATT
* * * *
1349939 GGTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAATGATCTCAAAAGT
66 GATGTTTCAAAGAAAACTGTCTCAAGAGAGACAAAATTCGTTTAAAGAGAAATGATCTC-AAAGT
1350004 T
130 T
* *
1350005 TGTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAATAGATACAAAGAT
* *
1350070 TGATGTTTC-AAGAAAAATTGTCTCAAGAGAGACAAAAATTTTGTTTAAAGAGAAATAGA-CTC-
65 TGATGTTTCAAAG-AAAACTGTCTCAAGAGAGAC-AAAA-TTCGTTTAAAGAGAAAT-GATCTCA
*
1350132 ATGCTT
126 AAG-TT
* * * *
1350138 TTGTTTCGAGAGAAATTGTCTCATTA-GAGACAAAATTTGTTTCAAGAGAAA
1 TTGTTTCAAGAGAAACTGTCTCA-AAGGAGACAAAATTTGTTTCAAGGGAAA
1350189 CAATCTCAAA
Statistics
Matches: 158, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
131 4 0.03
132 128 0.81
133 7 0.04
134 17 0.11
135 2 0.01
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (130 bp):
TTGTTTCAAGAGAAACTGTCTCAAAGGAGACAAAATTTGTTTCAAGGGAAATAGATACAAAGATT
GATGTTTCAAAGAAAACTGTCTCAAGAGAGACAAAATTCGTTTAAAGAGAAATGATCTCAAAGTT
Found at i:1350167 original size:68 final size:66
Alignment explanation
Indices: 1349875--1350188 Score: 302
Period size: 66 Copynumber: 4.8 Consensus size: 66
1349865 ATAAATTTCT
* * * * *
1349875 TGTTTCAAGGGAAACTGTCTCAA-AGGAGACAAACTTTGTTTCAAG-GAAAATATA-TACAAATA
1 TGTTTCAAGAGAAATTGTCTCAAGA-GAGACAAAATTTGTTTCAAGAG-AAATAGACT-CAAAGA
*
1349937 TTGG
63 TTGA
* * * *
1349941 TGTTTCAA-AGGAAACTGTCTCAAGAGAGACAAAATTCGTTTCAAGGGAAAT-GATCTCAAAAGT
1 TGTTTCAAGA-GAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAGA-CTC-AAAGA
1350004 TTG-
63 TTGA
* * * *
1350007 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAATAGATTCAAAGATTG
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAGACTCAAAGATTG
1350072 A
66 A
* * * *
1350073 TGTTTCAAGAAAAATTGTCTCAAGAGAGACAAAAATTTTGTTTAAAGAGAAATAGACTC-ATGCT
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGAC-AAAA-TTTGTTTCAAGAGAAATAGACTCAAAGAT
*
1350137 T-T
64 TGA
* **
1350139 TGTTTCGAGAGAAATTGTCTCATTAGAGACAAAATTTGTTTCAAGAGAAA
1 TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAA
1350189 CAATCTCAAA
Statistics
Matches: 213, Mismatches: 24, Indels: 24
0.82 0.09 0.09
Matches are distributed among these distances:
64 15 0.07
65 12 0.06
66 146 0.69
67 20 0.09
68 20 0.09
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.29
Consensus pattern (66 bp):
TGTTTCAAGAGAAATTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAATAGACTCAAAGATTG
A
Found at i:1351562 original size:12 final size:13
Alignment explanation
Indices: 1351541--1351629 Score: 100
Period size: 12 Copynumber: 7.2 Consensus size: 13
1351531 ACTTCTTGTC
1351541 TTTT-TCTTTGCT
1 TTTTCTCTTTGCT
1351553 TTTTCT-TTTGCTT
1 TTTTCTCTTTGC-T
1351566 TTTTCTCTTT-CAT
1 TTTTCTCTTTGC-T
1351579 TTTT-TCTTTG-T
1 TTTTCTCTTTGCT
*
1351590 TTTTTTCTTTGCT
1 TTTTCTCTTTGCT
1351603 TTTTC-CTTTGCT
1 TTTTCTCTTTGCT
*
1351615 TTTTTTCTTTGCT
1 TTTTCTCTTTGCT
1351628 TT
1 TT
1351630 GATTTGACCT
Statistics
Matches: 67, Mismatches: 3, Indels: 13
0.81 0.04 0.16
Matches are distributed among these distances:
11 5 0.07
12 31 0.46
13 28 0.42
14 3 0.04
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (13 bp):
TTTTCTCTTTGCT
Found at i:1351588 original size:38 final size:38
Alignment explanation
Indices: 1351541--1351629 Score: 121
Period size: 37 Copynumber: 2.4 Consensus size: 38
1351531 ACTTCTTGTC
1351541 TTTTTCTTTGCTTTTTCT-TTTGCTTTTTTCTCTTT-CAT
1 TTTTTCTTTGCTTTTTCTCTTTGC-TTTTTC-CTTTGCAT
* *
1351579 TTTTTCTTTG-TTTTTTTCTTTGCTTTTTCCTTTGCTT
1 TTTTTCTTTGCTTTTTCTCTTTGCTTTTTCCTTTGCAT
1351616 TTTTTCTTTGCTTT
1 TTTTTCTTTGCTTT
1351630 GATTTGACCT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
36 4 0.09
37 24 0.52
38 18 0.39
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (38 bp):
TTTTTCTTTGCTTTTTCTCTTTGCTTTTTCCTTTGCAT
Found at i:1351643 original size:30 final size:25
Alignment explanation
Indices: 1351541--1351629 Score: 128
Period size: 25 Copynumber: 3.6 Consensus size: 25
1351531 ACTTCTTGTC
*
1351541 TTTTTCTTTGCTTTTTCTTTTGCTT
1 TTTTTCTTTGCTTTTTCCTTTGCTT
*
1351566 TTTTCTCTTT-CATTTTTTCTTTG-TT
1 TTTT-TCTTTGC-TTTTTCCTTTGCTT
1351591 TTTTTCTTTGCTTTTTCCTTTGCTT
1 TTTTTCTTTGCTTTTTCCTTTGCTT
1351616 TTTTTCTTTGCTTT
1 TTTTTCTTTGCTTT
1351630 GATTTGACCT
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
24 15 0.26
25 28 0.49
26 14 0.25
ACGTcount: A:0.01, C:0.17, G:0.07, T:0.75
Consensus pattern (25 bp):
TTTTTCTTTGCTTTTTCCTTTGCTT
Found at i:1358234 original size:3 final size:3
Alignment explanation
Indices: 1358226--1358254 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1358216 TATCTGAATA
1358226 TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1358255 GTGTAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1358983 original size:22 final size:22
Alignment explanation
Indices: 1358961--1359001 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1358951 TCATAATTAT
1358961 TTAAAAA-ATTAAATAAAAATA
1 TTAAAAATATTAAATAAAAATA
*
1358982 TTAAAAATATTTAATAAAAA
1 TTAAAAATATTAAATAAAAA
1359002 ATAATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAAAATATTAAATAAAAATA
Found at i:1359730 original size:17 final size:18
Alignment explanation
Indices: 1359708--1359741 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1359698 TCAGCCGTTC
1359708 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
1359725 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
1359742 CTAATAGCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Found at i:1361709 original size:22 final size:22
Alignment explanation
Indices: 1361684--1361729 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
1361674 ACGACGTTAT
1361684 AATTATTTAAAAA-ATTAAATAA
1 AATTA-TTAAAAATATTAAATAA
*
1361706 AATTATTAAAAATATTTAATAA
1 AATTATTAAAAATATTAAATAA
1361728 AA
1 AA
1361730 AAAAATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTATTAAAAATATTAAATAA
Found at i:1362740 original size:25 final size:27
Alignment explanation
Indices: 1362693--1362744 Score: 72
Period size: 25 Copynumber: 1.9 Consensus size: 27
1362683 ATTTCAGCCA
1362693 AGCCTTGATAGTTTAGATTAATTAATTTT
1 AGCCTTGATA-TTTAGA-TAATTAATTTT
1362722 AGCCTTGAT-TTTAG-TAATTAATT
1 AGCCTTGATATTTAGATAATTAATT
1362745 ATTTTGGTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.39
27 5 0.22
29 9 0.39
ACGTcount: A:0.31, C:0.08, G:0.13, T:0.48
Consensus pattern (27 bp):
AGCCTTGATATTTAGATAATTAATTTT
Found at i:1362745 original size:29 final size:27
Alignment explanation
Indices: 1362693--1362749 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 27
1362683 ATTTCAGCCA
1362693 AGCCTTGATAGTTTAGATTAATTAATTTT
1 AGCCTTGATA-TTTAGATTAATT-ATTTT
1362722 AGCCTTGAT-TTTAGTAATTAATTATTTT
1 AGCCTTGATATTTAG--ATTAATTATTTT
1362750 GGTGGCACCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
27 5 0.19
28 5 0.19
29 16 0.62
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (27 bp):
AGCCTTGATATTTAGATTAATTATTTT
Found at i:1364102 original size:15 final size:15
Alignment explanation
Indices: 1364067--1364098 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1364057 GAGTTAAAAC
1364067 ATTATT-TTTTAGTT
1 ATTATTATTTTAGTT
1364081 ATTATTATTTTA-TT
1 ATTATTATTTTAGTT
1364095 ATTA
1 ATTA
1364099 ATTAGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
ATTATTATTTTAGTT
Found at i:1364460 original size:59 final size:59
Alignment explanation
Indices: 1364362--1364482 Score: 181
Period size: 59 Copynumber: 2.1 Consensus size: 59
1364352 GGAGGATTGG
* * *
1364362 TTAGAGCCATATTATCGAGTTTGTCTTTATATTGTGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTATATTGCGACTAAGAGGGTTCGATAGGACAC
* *
1364421 TTAGAGCTATATTATCGAGTTTGCCTTT-TCATTGCGACTAAGAGGGTTCGATATGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTAT-ATTGCGACTAAGAGGGTTCGATAGGACAC
1364480 TTA
1 TTA
1364483 TCCATCTATT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
58 1 0.02
59 55 0.98
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCTTTATATTGCGACTAAGAGGGTTCGATAGGACAC
Found at i:1374674 original size:42 final size:41
Alignment explanation
Indices: 1374624--1375048 Score: 290
Period size: 42 Copynumber: 10.3 Consensus size: 41
1374614 AATAATGTAT
*
1374624 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTAAACGTAC
1 TTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACACGTAC
* * * * * *
1374666 TTTAGTGGCATTTTACGCATAAACGTCACTAATTACACGCAC
1 TTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACACGTAC
* * * * * * * *
1374708 TATAGTGGCGTTTTTATATAAAAGTCGATAAATACTA--TAC
1 TTTAGTGGCGTTTTAACACAAACGCCGCTAATTAC-ACGTAC
* * * *
1374748 TTTAGTGGCGTTTTTATACAAACGTCGCTAAAGGT-C-C-TAC
1 TTTAGTGGCGTTTTAACACAAACGCCGCT-AA-TTACACGTAC
* *
1374788 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTACATGTTC
1 TTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACACGTAC
* *
1374830 TTTAGTGGCGTTGTATACACAAACGCCGCTAACTACACGTAC
1 TTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACACGTAC
* * * * * * ** * *
1374872 TCTAGTTGCATTTTTATATAAACGCCGAGAAATAC-TGTAC
1 TTTAGTGGCGTTTTAACACAAACGCCGCTAATTACACGTAC
* * * * ** *
1374912 TTTAGTGGCATTTTTATACAAACGCCGCTAA-CAGTCATAC
1 TTTAGTGGCGTTTTAACACAAACGCCGCTAATTACACGTAC
** * *
1374952 -TTAGTGGCGTTGCAAGCACAAACACCGCTAATTACATGTAC
1 TTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACACGTAC
* * *
1374993 TTTTGTGGCGTTTTACGCACAAACACCGCTAATTACACGTAC
1 TTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACACGTAC
1375035 TTTAGTGGCGTTTT
1 TTTAGTGGCGTTTT
1375049 TAAAAAACTC
Statistics
Matches: 299, Mismatches: 69, Indels: 30
0.75 0.17 0.08
Matches are distributed among these distances:
39 13 0.04
40 94 0.31
41 47 0.16
42 144 0.48
43 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (41 bp):
TTTAGTGGCGTTTTAACACAAACGCCGCTAATTACACGTAC
Found at i:1374756 original size:40 final size:39
Alignment explanation
Indices: 1374710--1374801 Score: 114
Period size: 40 Copynumber: 2.3 Consensus size: 39
1374700 ACACGCACTA
*
1374710 TAGTGGCGTTTTTATATAAAAGTCGATAAA-TACTATACTT
1 TAGTGGCGTTTTTATACAAAAGTCGATAAAGT-C-ATACTT
* * *
1374750 TAGTGGCGTTTTTATACAAACGTCGCTAAAGGTCCTACTT
1 TAGTGGCGTTTTTATACAAAAGTCGATAAA-GTCATACTT
1374790 TAGTGGCGTTTT
1 TAGTGGCGTTTT
1374802 AAGCACAAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 44 0.96
41 1 0.02
42 1 0.02
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (39 bp):
TAGTGGCGTTTTTATACAAAAGTCGATAAAGTCATACTT
Found at i:1375016 original size:163 final size:164
Alignment explanation
Indices: 1374624--1375050 Score: 579
Period size: 164 Copynumber: 2.6 Consensus size: 164
1374614 AATAATGTAT
* * * *
1374624 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTAAACGTACTTTAGTGGCATTTTACGCATAAA
1 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTACATGTACTTTAGTGGCGTTTTACGCACAAA
* * * * *
1374689 CGTCACTAATTACACGCACTATAGTGGCGTTTTTATATAAAAGTCGATAAATACTATACTTTAGT
66 CGCCGCTAATTACACGTACTATAGTGGCGTTTTTATATAAAAGCCGAGAAATACTATACTTTAGT
* * *
1374754 GGCGTTTTTATACAAACGTCGCTAAAGGTCCTAC
131 GGCATTTTTATACAAACGCCGCTAAAGGTCATAC
* * **
1374788 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTACATGTTCTTTAGTGGCGTTGTATACACAAA
1 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTACATGTACTTTAGTGGCGTTTTACGCACAAA
* * * * * *
1374853 CGCCGCTAACTACACGTACTCTAGTTGCATTTTTATATAAACGCCGAGAAATACTGTACTTTAGT
66 CGCCGCTAATTACACGTACTATAGTGGCGTTTTTATATAAAAGCCGAGAAATACTATACTTTAGT
1374918 GGCATTTTTATACAAACGCCGCTAACA-GTCATAC
131 GGCATTTTTATACAAACGCCGCTAA-AGGTCATAC
** * *
1374952 -TTAGTGGCGTTGCAAGCACAAACACCGCTAATTACATGTACTTTTGTGGCGTTTTACGCACAAA
1 TTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTACATGTACTTTAGTGGCGTTTTACGCACAAA
* *
1375016 CACCGCTAATTACACGTACTTTAGTGGCGTTTTTA
66 CGCCGCTAATTACACGTACTATAGTGGCGTTTTTA
1375051 AAAAACTCTG
Statistics
Matches: 227, Mismatches: 35, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
163 86 0.38
164 140 0.62
165 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (164 bp):
TTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTACATGTACTTTAGTGGCGTTTTACGCACAAA
CGCCGCTAATTACACGTACTATAGTGGCGTTTTTATATAAAAGCCGAGAAATACTATACTTTAGT
GGCATTTTTATACAAACGCCGCTAAAGGTCATAC
Found at i:1378105 original size:27 final size:29
Alignment explanation
Indices: 1378039--1378108 Score: 90
Period size: 31 Copynumber: 2.4 Consensus size: 29
1378029 TAACACTAGT
* *
1378039 TATAAAGGAGTTAACACTGGTACTTTCAAAA
1 TATAAAGGAGTTAACACTAGTA-TAT-AAAA
1378070 TATAAAGGAGTTAACACTAGT-TAT-AAA
1 TATAAAGGAGTTAACACTAGTATATAAAA
1378097 TATAAAGGAGTT
1 TATAAAGGAGTT
1378109 CCGTTTGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
27 15 0.41
29 2 0.05
31 20 0.54
ACGTcount: A:0.44, C:0.09, G:0.17, T:0.30
Consensus pattern (29 bp):
TATAAAGGAGTTAACACTAGTATATAAAA
Found at i:1379427 original size:42 final size:42
Alignment explanation
Indices: 1379315--1379692 Score: 398
Period size: 43 Copynumber: 8.8 Consensus size: 42
1379305 TTGTGAATAC
* * *
1379315 AAACGCCGCTATAGATCTGA-CTTTTAGCAGTGTTTGTATCCAAA
1 AAACGCCGCTATAGATATGACCTTTT-GCGGCGTTTGT-TCC-AA
* * * * * *
1379359 AAATGCTGCTATATATCTGACTTTTTGCGGTGTTTGTTCCAA
1 AAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAA
* *
1379401 AACCGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCTAA
1 AAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAA
* * *
1379443 AAGCGCCGCTAAATATATGACCTTTTGCGGCGTTTGTTCCAA
1 AAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAA
* * * * *
1379485 AAGCGCCGCTATAGATCTCAACCTTTTACGGCGTTTGTTCTAA
1 AAACGCCGCTATAGATAT-GACCTTTTGCGGCGTTTGTTCCAA
*
1379528 AAACGCTGCTATAGATAGTGACCTTTTGCGGCGTTTGTTCCAA
1 AAACGCCGCTATAGATA-TGACCTTTTGCGGCGTTTGTTCCAA
* * * *
1379571 AAATGGCGCTATAGATAGCGACCTTTTGCGGCGTTTGTTCTAA
1 AAACGCCGCTATAGATA-TGACCTTTTGCGGCGTTTGTTCCAA
* *
1379614 AAACGCCGCTATAGATAGAGACCTTTTGCGGCATTTGTTCCAA
1 AAACGCCGCTATAGATA-TGACCTTTTGCGGCGTTTGTTCCAA
* * * * *
1379657 AAACGCCGCCATAAATCTTGACCTATTGCGACGTTT
1 AAACGCCGCTATAGAT-ATGACCTTTTGCGGCGTTT
1379693 TTTGTTCTCA
Statistics
Matches: 284, Mismatches: 46, Indels: 9
0.84 0.14 0.03
Matches are distributed among these distances:
42 89 0.31
43 163 0.57
44 28 0.10
45 4 0.01
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.33
Consensus pattern (42 bp):
AAACGCCGCTATAGATATGACCTTTTGCGGCGTTTGTTCCAA
Found at i:1382332 original size:14 final size:14
Alignment explanation
Indices: 1382313--1382344 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1382303 ATATTTTTGA
1382313 AATAAAGTTATGAT
1 AATAAAGTTATGAT
*
1382327 AATAAATTTATGAT
1 AATAAAGTTATGAT
1382341 AATA
1 AATA
1382345 TACTATAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (14 bp):
AATAAAGTTATGAT
Found at i:1385851 original size:215 final size:211
Alignment explanation
Indices: 1385349--1385949 Score: 831
Period size: 215 Copynumber: 2.8 Consensus size: 211
1385339 TTTATTCATA
* *
1385349 TATTGAATAAAAATATTTTTTTATTATTTTGGGTCGGGTCGAT----TTTCTAATTCATATATTC
1 TATTAAATAAAAATA-TTTTTTATTATTTCGGGTCGGGTCGATCGGATTTCTAATTCATATATTC
*
1385410 GGGTCGGGTCGGGTGAAACTTTATTTTAG-TCGGGTAAGATCGGGTTTTTTTAAGTGTGATACTC
65 GGGTCGGGTCGGATGAAACTTTATTTT-GTTCGGGT----T-GGG-TTTTTTAAGTGTGATA-TC
* *
1385474 GAGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCAACACGAAAATATATATAATTCA
122 G-GTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCA
1385539 GGTCGGGTCGGATTAAGTCACTTTTT
186 GGTCGGGTCGGATTAAGTCACTTTTT
* * *
1385565 TATTAAATAAAAATAATTTTTATTATTTCGGGCCGGGTCGGGTCGGATTTCTAATTCATATATTC
1 TATTAAATAAAAATATTTTTTATTATTTCGGGTCGGGTC-GATCGGATTTCTAATTCATATATTC
*
1385630 GGGTCGGGTCGAATGAAACTTTATTTTGTTCGGGTTGGGTTTTTTAAGTGTGATATTCGGGTCGG
65 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTTGGGTTTTTTAAGTGTGATA-TC-GGTCGG
* * * *
1385695 GTCGGGTTCAGGTTTAGGGTGAAAAAAACCGGACTGACCCGAAAATATATATAATTCGGGTTGGG
128 GTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGG
*
1385760 TCGGATTAAGTCATTGTTTT
193 TCGGATTAAGTCACT-TTTT
* *
1385780 TATTAAATAAAAATACTTTTTTATTATTTCGTGTCGGGTCGATCGGATTTCTAATTCATATATTT
1 TATTAAATAAAAATA-TTTTTTATTATTTCGGGTCGGGTCGATCGGATTTCTAATTCATATATTC
* *
1385845 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTTTTTTACGTGTGATAT---TCGGGT
65 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTTGGGTTTTTTAAGTGTGATATCGGTCGGGT
* *
1385907 CAGGTTCGGGTTTAGGGTGAAAAAAATCGGACCGACCCGAAAA
130 CGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAA
1385950 AAAAATATAA
Statistics
Matches: 349, Mismatches: 27, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
210 45 0.13
214 97 0.28
215 119 0.34
216 38 0.11
219 1 0.00
220 49 0.14
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (211 bp):
TATTAAATAAAAATATTTTTTATTATTTCGGGTCGGGTCGATCGGATTTCTAATTCATATATTCG
GGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTTGGGTTTTTTAAGTGTGATATCGGTCGGGTC
GGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGGTCG
GATTAAGTCACTTTTT
Found at i:1386514 original size:16 final size:18
Alignment explanation
Indices: 1386493--1386538 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
1386483 TATGGAATTG
1386493 GATTCCAATTCC-T-ACA
1 GATTCCAATTCCTTCACA
1386509 GATTCCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
*
1386527 GATTTCAATTCC
1 GATTCCAATTCC
1386539 CTCATAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 12 0.44
17 1 0.04
18 14 0.52
ACGTcount: A:0.28, C:0.30, G:0.07, T:0.35
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:1402755 original size:43 final size:43
Alignment explanation
Indices: 1402689--1402869 Score: 175
Period size: 43 Copynumber: 4.2 Consensus size: 43
1402679 AACAAAAAAT
* * *
1402689 GCCGTAATAGGTGAAGAGATATAGCGGTGTTTTTGGAATAAAC
1 GCCGCAATAGGTGAAGAGATATAGCGGCGTTTTTGGAACAAAC
* *
1402732 GCCGCAATAGGTGAAGAGATATAGCGGCGTTTCTGGGACAAAC
1 GCCGCAATAGGTGAAGAGATATAGCGGCGTTTTTGGAACAAAC
** * ***
1402775 GTTGCAATAGGTGAAGAGATATAACAATGTTTTTTGG-ACAAAC
1 GCCGCAATAGGTGAAGAGATATAGCGGCG-TTTTTGGAACAAAC
* * * * * *
1402818 GCCGTAAAAGGTTAAGATATTTAGCGGCGTTTTTCGGATACAAAT
1 GCCGCAATAGGTGAAGAGATATAGCGGCGTTTTT-GGA-ACAAAC
1402863 GCCGCAA
1 GCCGCAA
1402870 AAGTTCTGGT
Statistics
Matches: 109, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
42 5 0.05
43 87 0.80
44 6 0.06
45 11 0.10
ACGTcount: A:0.33, C:0.14, G:0.28, T:0.26
Consensus pattern (43 bp):
GCCGCAATAGGTGAAGAGATATAGCGGCGTTTTTGGAACAAAC
Found at i:1413681 original size:18 final size:19
Alignment explanation
Indices: 1413652--1413700 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
1413642 AGGCCATTTT
*
1413652 AGTATCAGTACTCATGG-G
1 AGTATCAATACTCATGGAG
* *
1413670 AGTATCGATACTGATGGTAG
1 AGTATCAATACTCATGG-AG
1413690 AGTATCAATAC
1 AGTATCAATAC
1413701 GCCAAATAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 14 0.56
20 11 0.44
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (19 bp):
AGTATCAATACTCATGGAG
Found at i:1415054 original size:578 final size:578
Alignment explanation
Indices: 1413959--1415106 Score: 1972
Period size: 578 Copynumber: 2.0 Consensus size: 578
1413949 TTTGGGAAAG
* * * *
1413959 AAACCCAAGGGATTTAGAAATTAAATTGAGGGACCCAATGGCACTAAAACACTATCCAATAAAAC
1 AAACCCAAGGGATTTACAAATGAAATTGAGGGACCCAATGACACTAAAACACCATCCAATAAAAC
*
1414024 TACAAGTGAAAACCTTGCTAATATACAATTACAACTAGAAATAATATCAACTAGGAAGACATAAA
66 TACAAGTGAAAACCTTGCTAATATACAATTACAACTAGAAACAATATCAACTAGGAAGACATAAA
* *
1414089 ACTAGCCTTGGTTGATGCTAGGGAAAACAGTTAGGACACTCGAGTTACTTTAGCAGTTGATGATA
131 ACTAACCTTGGTTGATGCTAGGGAAAACAGTTAGAACACTCGAGTTACTTTAGCAGTTGATGATA
*
1414154 TTTTTTAGGTATAAAATATCCACATATCCTTAACCAAGTGCGCAAGGCACTTTAAGACTAACTAG
196 TTTTTGAGGTATAAAATATCCACATATCCTTAACCAAGTGCGCAAGGCACTTTAAGACTAACTAG
* * ** *
1414219 GGCGCGAAGCCTGAACACTTGTGAGGGGTGGGTTAGTCGGGTGTTTTATCCGATGTTGAGATTAC
261 GACGCGAAGCCTGAACACTCGCAAGGGGTGGGTTAGTCGGGTGTTATATCCGATGTTGAGATTAC
*
1414284 ATACCTCACCCTAGGGGGACTAGAGTGGTGTGTGTCTCAAGATGTGTAAACCTCCAACTAAACCA
326 ATACCTCACCCTAGGGGGACTAGAGTGGAGTGTGTCTCAAGATGTGTAAACCTCCAACTAAACCA
* *
1414349 TGATGTCTACCCTAGAGTAGTGTGCAACATATGAGTATACTTACTTTCTTTATTACAATCGATAG
391 TGATGTCTACCCTAGAGTAGTGAGCAACATATGAGTATACTCACTTTCTTTATTACAATCGATAG
*
1414414 CATGAGCATTTATTGAACACTTTTAGTATGGTTCAATTGTTAGTATGGCACTAGGCTAGTAACCT
456 CATGAGCATTTATTGAACACTTTTAGTATGGTACAATTGTTAGTATGGCACTAGGCTAGTAACCT
* * * *
1414479 AATTGTTCTTAATTTGCATCCATGTGCAAGTCCTTAGGAAAAGCATTCAAGGAGCAAT
521 AAGTGTTCGTAATTTGCATCCATGTGCAAGTACTTAGGAAAAACATTCAAGGAGCAAT
*
1414537 AAACCCAAGGGATTTACAAATGACATTGAGGGACCCAATGACACTAAAACACCATCCAATAAAAC
1 AAACCCAAGGGATTTACAAATGAAATTGAGGGACCCAATGACACTAAAACACCATCCAATAAAAC
* *
1414602 TACAAGTGAAAACCTTGCTAATATACAATTACAGCTAGAAACAATATCAACTAGGACGACATAAA
66 TACAAGTGAAAACCTTGCTAATATACAATTACAACTAGAAACAATATCAACTAGGAAGACATAAA
*
1414667 ACTAACCTTGGTTGATGCTCGGGAAAACAGTTAGAACACTCGAGTTACTTTAGCAGTTGATGATA
131 ACTAACCTTGGTTGATGCTAGGGAAAACAGTTAGAACACTCGAGTTACTTTAGCAGTTGATGATA
* * * *
1414732 TTTTTGAGGTATATAATATCCAGATATCCTTAAGCAAGTGCGCAAGGCACTTTGAGACTAACTAG
196 TTTTTGAGGTATAAAATATCCACATATCCTTAACCAAGTGCGCAAGGCACTTTAAGACTAACTAG
* * *
1414797 GACGCGAAGCTTGAACACTCGCAAGGGGTGGGTTAGTTGGGTGTTATATCCGATGTTGAGATTCC
261 GACGCGAAGCCTGAACACTCGCAAGGGGTGGGTTAGTCGGGTGTTATATCCGATGTTGAGATTAC
* * *
1414862 ATACCTCACCCTAGGGGGACTAGAGTGGAGTGTGTCTCGAGATGTGTAAACCTCCGACTACACCA
326 ATACCTCACCCTAGGGGGACTAGAGTGGAGTGTGTCTCAAGATGTGTAAACCTCCAACTAAACCA
1414927 TGATGTCTACCCTAGAGTAGTGAGCAACATATGAGTATACTCACTTTCTTTATTACAATCGATAG
391 TGATGTCTACCCTAGAGTAGTGAGCAACATATGAGTATACTCACTTTCTTTATTACAATCGATAG
*
1414992 CATGAGCATTTATTGAACACTTTTAGTATGGTACAATTGTTAGTGTGGCACTAGGCTAGTAACCT
456 CATGAGCATTTATTGAACACTTTTAGTATGGTACAATTGTTAGTATGGCACTAGGCTAGTAACCT
1415057 AAGTGTTCGTAATTTGCATCCATGTGCAAGTACTTAGGAAAAACATTCAA
521 AAGTGTTCGTAATTTGCATCCATGTGCAAGTACTTAGGAAAAACATTCAA
1415107 ATAGCAATCA
Statistics
Matches: 534, Mismatches: 36, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
578 534 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.28
Consensus pattern (578 bp):
AAACCCAAGGGATTTACAAATGAAATTGAGGGACCCAATGACACTAAAACACCATCCAATAAAAC
TACAAGTGAAAACCTTGCTAATATACAATTACAACTAGAAACAATATCAACTAGGAAGACATAAA
ACTAACCTTGGTTGATGCTAGGGAAAACAGTTAGAACACTCGAGTTACTTTAGCAGTTGATGATA
TTTTTGAGGTATAAAATATCCACATATCCTTAACCAAGTGCGCAAGGCACTTTAAGACTAACTAG
GACGCGAAGCCTGAACACTCGCAAGGGGTGGGTTAGTCGGGTGTTATATCCGATGTTGAGATTAC
ATACCTCACCCTAGGGGGACTAGAGTGGAGTGTGTCTCAAGATGTGTAAACCTCCAACTAAACCA
TGATGTCTACCCTAGAGTAGTGAGCAACATATGAGTATACTCACTTTCTTTATTACAATCGATAG
CATGAGCATTTATTGAACACTTTTAGTATGGTACAATTGTTAGTATGGCACTAGGCTAGTAACCT
AAGTGTTCGTAATTTGCATCCATGTGCAAGTACTTAGGAAAAACATTCAAGGAGCAAT
Found at i:1416855 original size:17 final size:18
Alignment explanation
Indices: 1416809--1416857 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
1416799 TTGAAGTCTT
* *
1416809 CAACTCATAGAAGATGAG
1 CAACTCAAAGAAGATGAA
*
1416827 CAACTCAAAGAATATGAA
1 CAACTCAAAGAAGATGAA
1416845 CAACT-AAAGAAGA
1 CAACTCAAAGAAGA
1416858 AAAAACAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 7 0.26
18 20 0.74
ACGTcount: A:0.53, C:0.16, G:0.16, T:0.14
Consensus pattern (18 bp):
CAACTCAAAGAAGATGAA
Found at i:1417066 original size:2 final size:2
Alignment explanation
Indices: 1417059--1417087 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1417049 ATACACGCCT
1417059 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1417088 TGAAGTCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1422953 original size:20 final size:19
Alignment explanation
Indices: 1422928--1422992 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
1422918 TTTTCCTTTG
1422928 ATGAACGAGTTCTTCTCATT
1 ATGAAC-AGTTCTTCTCATT
* *
1422948 ATGAAC--TTCTTTTCCTTT
1 ATGAACAGTTCTTCT-CATT
1422966 GATGAACAAGTTCTTCTCATT
1 -ATGAAC-AGTTCTTCTCATT
1422987 ATGAAC
1 ATGAAC
1422993 TTTTTCTTCG
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
17 6 0.17
18 3 0.08
19 6 0.17
20 12 0.33
21 3 0.08
22 6 0.17
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (19 bp):
ATGAACAGTTCTTCTCATT
Found at i:1422970 original size:39 final size:38
Alignment explanation
Indices: 1422897--1422997 Score: 161
Period size: 39 Copynumber: 2.7 Consensus size: 38
1422887 AATGATTAGT
*
1422897 CGAGCTCTTCTCATTATG-A-TTTTTTCCTTTGATGAA
1 CGAGTTCTTCTCATTATGAACTTTTTTCCTTTGATGAA
1422933 CGAGTTCTTCTCATTATGAACTTCTTTTCCTTTGATGAA
1 CGAGTTCTTCTCATTATGAACTT-TTTTCCTTTGATGAA
*
1422972 CAAGTTCTTCTCATTATGAACTTTTT
1 CGAGTTCTTCTCATTATGAACTTTTT
1422998 CTTCGGGGTG
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
36 17 0.28
37 1 0.02
38 5 0.08
39 37 0.62
ACGTcount: A:0.21, C:0.20, G:0.12, T:0.48
Consensus pattern (38 bp):
CGAGTTCTTCTCATTATGAACTTTTTTCCTTTGATGAA
Found at i:1422972 original size:19 final size:20
Alignment explanation
Indices: 1422918--1422972 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 20
1422908 CATTATGATT
1422918 TTTTCCTTTGATGAACGAGTTC
1 TTTTCCTTTGATGAAC--GTTC
* *
1422940 TTCT-CATT-ATGAAC-TTC
1 TTTTCCTTTGATGAACGTTC
1422957 TTTTCCTTTGATGAAC
1 TTTTCCTTTGATGAAC
1422973 AAGTTCTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
17 6 0.22
18 3 0.11
19 6 0.22
20 6 0.22
21 3 0.11
22 3 0.11
ACGTcount: A:0.20, C:0.20, G:0.13, T:0.47
Consensus pattern (20 bp):
TTTTCCTTTGATGAACGTTC
Found at i:1422999 original size:20 final size:20
Alignment explanation
Indices: 1422937--1423001 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 20
1422927 GATGAACGAG
1422937 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAACTTC
* ***
1422957 TT-TTC-CTTTGATGAACAAG
1 TTCTTCTCATT-ATGAACTTC
*
1422976 TTCTTCTCATTATGAACTTT
1 TTCTTCTCATTATGAACTTC
1422996 TTCTTC
1 TTCTTC
1423002 GGGGTGAGTT
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
18 3 0.09
19 11 0.32
20 17 0.50
21 3 0.09
ACGTcount: A:0.20, C:0.22, G:0.08, T:0.51
Consensus pattern (20 bp):
TTCTTCTCATTATGAACTTC
Found at i:1423402 original size:162 final size:163
Alignment explanation
Indices: 1423209--1423509 Score: 451
Period size: 162 Copynumber: 1.9 Consensus size: 163
1423199 AACAAAATAT
* * *
1423209 TGATATTGATCTATCTCTTTCTGTGATAGAATCGAGAAAAAGGTTGAACAAGTTTTTCTCATTAT
1 TGATATTGATCTATCTCCTTCTGTGATAGAATCGAGAAAAAGGGTGAACAAGTTCTTCTCATTAT
*
1423274 GAAATT-TTCTCCTTCTTTGGACGACTTCTTCTCATTATGAACCAATCCATTGGAAATGGTGATC
66 GAAATTCTTCTCCTTCTTTGGACGACTTCTTCTCATTATGAACCAATCCATTGGAAATGGTGAGC
1423338 CACCTCCTTCTGCAATGAATTTGAGCAAAATGG
131 CACCTCCTTCTGCAATGAATTTGAGCAAAATGG
* * * *
1423371 TGATGTTGATCTATCTCCTTCTGTTATAGAATCTAGCAAAAGGGTGAACAAGTTCTTCTCATTAT
1 TGATATTGATCTATCTCCTTCTGTGATAGAATCGAGAAAAAGGGTGAACAAGTTCTTCTCATTAT
* * * * ** * *
1423436 GAACTTCTTCTCTTTCTTTGGATGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGTTGGGC
66 GAAATTCTTCTCCTTCTTTGGACGACTTCTTCTCATTATGAACCAATCCATTGGAAATGGTGAGC
1423501 CACCTCCTT
131 CACCTCCTT
1423510 TTTTGATGGA
Statistics
Matches: 122, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
162 63 0.52
163 59 0.48
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.38
Consensus pattern (163 bp):
TGATATTGATCTATCTCCTTCTGTGATAGAATCGAGAAAAAGGGTGAACAAGTTCTTCTCATTAT
GAAATTCTTCTCCTTCTTTGGACGACTTCTTCTCATTATGAACCAATCCATTGGAAATGGTGAGC
CACCTCCTTCTGCAATGAATTTGAGCAAAATGG
Found at i:1423627 original size:119 final size:119
Alignment explanation
Indices: 1423409--1423638 Score: 325
Period size: 119 Copynumber: 1.9 Consensus size: 119
1423399 GAATCTAGCA
* ** *
1423409 AAAGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTTCTTTGGATGAGTTCTTCTCATTA
1 AAAGGGTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
* * * *
1423474 TGAACCCTTCCATTGGAAATGTTGGGCCACCTCCTTTTTTGATGGATTTGAGCG
66 TGAACCCTTCCATTGGAAATGTTGAGACACCTCCTTCTGTGATGGATTTGAGCG
* * *
1423528 AAAGGTTGAACAAGTTATTCTCATTATGAACTTTTTCTCCCTCATTGGATGAGTTCTTCTCATTG
1 AAAGGGTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
* * * *
1423593 TTAACCCTTCTATTGGAAATGTTGATACATCTCCTTCTGTGATGGA
66 TGAACCCTTCCATTGGAAATGTTGAGACACCTCCTTCTGTGATGGA
1423639 ATCAAACAAA
Statistics
Matches: 96, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
119 96 1.00
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.40
Consensus pattern (119 bp):
AAAGGGTGAACAAGTTATTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATTA
TGAACCCTTCCATTGGAAATGTTGAGACACCTCCTTCTGTGATGGATTTGAGCG
Found at i:1423719 original size:163 final size:163
Alignment explanation
Indices: 1423523--1423941 Score: 558
Period size: 163 Copynumber: 2.6 Consensus size: 163
1423513 TGATGGATTT
* * * * *
1423523 GAGCGAAAGGTTGAACAAGTTATTCTCATTATGAACTTTTTCTCCCTCATT-GGATGAGTTCTTC
1 GAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTC-TTCGGATGAGTTCTTC
* * *
1423587 TCATTGTTAACCCTTCTATTGGAAATGTTGATACATCTCCTTCTGTGATGGAATCAAACAAAATG
65 TCATTATGAACCCTTCCATTGGAAATGTTGATACATCTCCTTCTGTGATGGAATCAAACAAAATG
*
1423652 AC-GATGTTGATTTATCTCCTTCAGCGATAGAGTC
130 -CTGATGTTGATCTATCTCCTTCAGCGATAGAGTC
* * *
1423686 GAGCAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCTTCCTCTTCGGATGAG-TCATTG
1 GAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGATGAGTTC-TTC
* ** * *
1423750 TCATTATGAACCTTTCCATTGGAAATGTTGATTTATCTCCTTCTGTGATGGAATCGAATAAAATG
65 TCATTATGAACCCTTCCATTGGAAATGTTGATACATCTCCTTCTGTGATGGAATCAAACAAAATG
*
1423815 CTGATGTTGATCTATCTCCTTCTGCGATAGAGTC
130 CTGATGTTGATCTATCTCCTTCAGCGATAGAGTC
* ** *
1423849 GAGCAAAAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTTGTTCTTCGGAGGAGTTCTTCT
1 GAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCT
**
1423914 CATTATG-ACTTATTCCATTGGAAATGTT
66 CATTATGAAC-CCTTCCATTGGAAATGTT
1423942 AATCCACTTT
Statistics
Matches: 224, Mismatches: 27, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
162 7 0.03
163 215 0.96
164 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.38
Consensus pattern (163 bp):
GAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCGGATGAGTTCTTCT
CATTATGAACCCTTCCATTGGAAATGTTGATACATCTCCTTCTGTGATGGAATCAAACAAAATGC
TGATGTTGATCTATCTCCTTCAGCGATAGAGTC
Found at i:1423801 original size:282 final size:281
Alignment explanation
Indices: 1423214--1423806 Score: 697
Period size: 282 Copynumber: 2.1 Consensus size: 281
1423204 AATATTGATA
* * *
1423214 TTGATCTATCTCTTTCTGTGATAGAATCGAGAAAAAGGTTGAACAAGTTTTTCTCATTATGAAAT
1 TTGATCTATCTCCTTCTGTGATGGAATCGAGAAAAAGGTTGAACAAGTTATTCTCATTATGAAAT
* * *
1423279 TTTCTCCTTCTTTGGACGACTTCTTCTCATTATGAACCAATCCATTGGAAATGGTGATCCACCTC
66 TTTCTCCCTCATTGGACGACTTCTTCTCATTATGAACCAATCCATTGGAAATGGTGATACACCTC
** * ** * ** *
1423344 CTTCTGCAATGAATTTGAGCAAAATGGTGATGTTGATCTATCTCCTTCTGTTATAGAATCTAGCA
131 CTTCTGCAATGAATTCAAACAAAATGACGATGTTGATCTATCTCCTTCAGCGATAGAATCGAGCA
* * * *
1423409 AAAGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCTCTTTCTTTGGATGAGTTCTTCTCATTA
196 AAAAGGTGAACAAATTCTTCTCATTATGAACTTCTTCTCTCTCTTCGGATGAGTTCTTCTCATTA
1423474 TGAACCCTTCCATTGGAAATG
261 TGAACCCTTCCATTGGAAATG
** * * * * * * ** *
1423495 TTGGGCCACCTCCTTTTTTGATGGATTTGAGCGAAAGGTTGAACAAGTTATTCTCATTATGAACT
1 TTGATCTATCTCCTTCTGTGATGGAATCGAGAAAAAGGTTGAACAAGTTATTCTCATTATGAA-A
* * * * ** * * *
1423560 TTTTCTCCCTCATTGGATGAGTTCTTCTCATTGTTAACCCTTCTATTGGAAATGTTGATACATCT
65 TTTTCTCCCTCATTGGACGACTTCTTCTCATTATGAACCAATCCATTGGAAATGGTGATACACCT
** * *
1423625 CCTTCTGTGATGGAA-TCAAACAAAATGACGATGTTGATTTATCTCCTTCAGCGATAGAGTCGAG
130 CCTTCTGCAAT-GAATTCAAACAAAATGACGATGTTGATCTATCTCCTTCAGCGATAGAATCGAG
* * *
1423689 CAAAAAGTTGAACAAATTCTTCTTATTATGAACTTCTTCT-TCCTCTTCGGATGAG-TCATTGTC
194 CAAAAAGGTGAACAAATTCTTCTCATTATGAACTTCTTCTCT-CTCTTCGGATGAGTTC-TTCTC
*
1423752 ATTATGAACCTTTCCATTGGAAATG
257 ATTATGAACCCTTCCATTGGAAATG
*
1423777 TTGATTTATCTCCTTCTGTGATGGAATCGA
1 TTGATCTATCTCCTTCTGTGATGGAATCGA
1423807 ATAAAATGCT
Statistics
Matches: 252, Mismatches: 56, Indels: 7
0.80 0.18 0.02
Matches are distributed among these distances:
281 53 0.21
282 196 0.78
283 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (281 bp):
TTGATCTATCTCCTTCTGTGATGGAATCGAGAAAAAGGTTGAACAAGTTATTCTCATTATGAAAT
TTTCTCCCTCATTGGACGACTTCTTCTCATTATGAACCAATCCATTGGAAATGGTGATACACCTC
CTTCTGCAATGAATTCAAACAAAATGACGATGTTGATCTATCTCCTTCAGCGATAGAATCGAGCA
AAAAGGTGAACAAATTCTTCTCATTATGAACTTCTTCTCTCTCTTCGGATGAGTTCTTCTCATTA
TGAACCCTTCCATTGGAAATG
Found at i:1424197 original size:103 final size:98
Alignment explanation
Indices: 1424086--1424395 Score: 302
Period size: 101 Copynumber: 3.1 Consensus size: 98
1424076 AGATGGGATA
* * ** *
1424086 AAATTTGTTTAAAGTGAAACAATTCCAAATTTTGTATTTCAAGAGAAAACTGTCTTAAGCGAGAA
1 AAATTTGTTTAAAGTGAAGCAATTCCAAATCTTGTGCTTCAA-AG-AAACTGTCTCAAGCGAGAA
*
1424151 AAATTTGACTTTAAGAAAAAACAATCTCAAGTGATAT
64 AAA-TTGACTTTAAG-AAAAACAATCTCAAGTGAGAT
** * * *
1424188 AAATCTTGTTTTGAGTGAAGCATTTCCAAAACTTGTGCTTCAAATGAAACTATCTCAAGCGA-AA
1 AAAT-TTGTTTAAAGTGAAGCAATTCCAAATCTTGTGCTTCAAA-GAAACTGTCTCAAGCGAGAA
* *
1424252 CGAAATTGATTTTGAGAAAAACAATCTCAAGTGAGAT
64 --AAATTGACTTTAAGAAAAACAATCTCAAGTGAGAT
* * * * * *
1424289 AAATATTGTGTGAAGTGGAGCAATTCC-AATACTTGTGCTTCAACGTAAATTGTCTCAAGTGAGA
1 AAAT-TTGTTTAAAGTGAAGCAATTCCAAAT-CTTGTGCTTCAAAG-AAACTGTCTCAAGCGAGA
*
1424353 TGAAATTG-CTTTTAAGAAAAACAATCTCAAGTGAGAT
63 -AAAATTGAC-TTTAAGAAAAACAATCTCAAGTGAGAT
1424390 AAATTT
1 AAATTT
1424396 TGTCGTATCA
Statistics
Matches: 172, Mismatches: 27, Indels: 20
0.79 0.12 0.09
Matches are distributed among these distances:
100 5 0.03
101 104 0.60
102 29 0.17
103 34 0.20
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (98 bp):
AAATTTGTTTAAAGTGAAGCAATTCCAAATCTTGTGCTTCAAAGAAACTGTCTCAAGCGAGAAAA
ATTGACTTTAAGAAAAACAATCTCAAGTGAGAT
Found at i:1426418 original size:8 final size:9
Alignment explanation
Indices: 1426394--1426420 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
1426384 TAATTTTCTT
1426394 TCCTTTTTC
1 TCCTTTTTC
1426403 TCCTTTTTC
1 TCCTTTTTC
1426412 TCCTTTTTC
1 TCCTTTTTC
1426421 ATTCTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (9 bp):
TCCTTTTTC
Found at i:1426440 original size:14 final size:13
Alignment explanation
Indices: 1426400--1426519 Score: 56
Period size: 12 Copynumber: 9.5 Consensus size: 13
1426390 TCTTTCCTTT
*
1426400 TTCTCCTTT-TTC
1 TTCTTCTTTATTC
*
1426412 TCCTT-TTTCATTC
1 TTCTTCTTT-ATTC
1426425 TTCATTCTTTATTC
1 TTC-TTCTTTATTC
*
1426439 TTCTTC-TTCTTC
1 TTCTTCTTTATTC
* *
1426451 TTCTT-TTCATTT
1 TTCTTCTTTATTC
* *
1426463 TTATTTTTTCATT-
1 TTCTTCTTT-ATTC
* *
1426476 TTTTTCTTTTTTC
1 TTCTTCTTTATTC
*
1426489 TTCTT-TTTCTTC
1 TTCTTCTTTATTC
* *
1426501 TTTTTCCTTATTC
1 TTCTTCTTTATTC
1426514 TT-TTCT
1 TTCTTCT
1426520 GTCATTCTCC
Statistics
Matches: 81, Mismatches: 18, Indels: 18
0.69 0.15 0.15
Matches are distributed among these distances:
11 3 0.04
12 35 0.43
13 28 0.35
14 12 0.15
15 3 0.04
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.72
Consensus pattern (13 bp):
TTCTTCTTTATTC
Found at i:1426477 original size:6 final size:7
Alignment explanation
Indices: 1426418--1426461 Score: 51
Period size: 6 Copynumber: 6.9 Consensus size: 7
1426408 TTTCTCCTTT
1426418 TTCATTC
1 TTCATTC
1426425 TTCATTC
1 TTCATTC
*
1426432 TTTATTC
1 TTCATTC
1426439 TTC-TTC
1 TTCATTC
1426445 TTC-TTC
1 TTCATTC
1426451 TTC-TT-
1 TTCATTC
1426456 TTCATT
1 TTCATT
1426462 TTTATTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 3 0.09
6 16 0.47
7 15 0.44
ACGTcount: A:0.09, C:0.25, G:0.00, T:0.66
Consensus pattern (7 bp):
TTCATTC
Found at i:1426480 original size:9 final size:9
Alignment explanation
Indices: 1426474--1426506 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
1426464 TATTTTTTCA
1426474 TTTTT-TTC
1 TTTTTCTTC
1426482 TTTTTTCTTC
1 -TTTTTCTTC
1426492 TTTTTCTTC
1 TTTTTCTTC
1426501 TTTTTC
1 TTTTTC
1426507 CTTATTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 20 0.87
10 3 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:1428142 original size:21 final size:22
Alignment explanation
Indices: 1428118--1428160 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1428108 TGAATGGAAT
*
1428118 AATAAAAAAATGTAAA-AATGA
1 AATAAAAAAATATAAAGAATGA
*
1428139 AATAAAAGAATATAAAGAATGA
1 AATAAAAAAATATAAAGAATGA
1428161 TAAAGAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.19
Consensus pattern (22 bp):
AATAAAAAAATATAAAGAATGA
Found at i:1428167 original size:19 final size:19
Alignment explanation
Indices: 1428143--1428183 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1428133 AAATGAAATA
1428143 AAAGAATATAAAGAATG-AT
1 AAAGAATATAAA-AATGTAT
*
1428162 AAAGAATATGAAAATGTAT
1 AAAGAATATAAAAATGTAT
1428181 AAA
1 AAA
1428184 ATGATTACCG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (19 bp):
AAAGAATATAAAAATGTAT
Found at i:1428489 original size:155 final size:153
Alignment explanation
Indices: 1428209--1428516 Score: 571
Period size: 155 Copynumber: 2.0 Consensus size: 153
1428199 GAAATCAAGG
1428209 AAAACATCTTTAATTGAAAAAAAAGTAAAATTAACATAGAAGCCATTCACAAAATATCCCTTAAT
1 AAAACATCTTTAATTGAAAAAAAAGTAAAATTAACATAGAAGCCATTCACAAAATATCCCTTAAT
1428274 GCTAGTGGGCAAAAGCATAAGGGTTAATTTCGGGTATTACTCTAAATTTAATCTAAAAAACTACA
66 GCTAGTGGGCAAAAGCATAAGGGTTAATTTCGGGTATTACTCTAAATTTAATCTAAAAAACTACA
1428339 GGAAGATCCTTTGTTCTCCACTT
131 GGAAGATCCTTTGTTCTCCACTT
*
1428362 AAAACATCTTTAATTGAAAAAAAAAAGTAAAATTAACATAGAAGTCATTCACAAAATATCCCTTA
1 AAAACATCTTTAATTG--AAAAAAAAGTAAAATTAACATAGAAGCCATTCACAAAATATCCCTTA
*
1428427 ATGCTAGTGGGCAAAAGCATAAGGGTTAATTTCGGGTATTACTCTAAATTTATTCTAAAAAACTA
64 ATGCTAGTGGGCAAAAGCATAAGGGTTAATTTCGGGTATTACTCTAAATTTAATCTAAAAAACTA
*
1428492 CATGAAGATCCTTTGTTCTCCACTT
129 CAGGAAGATCCTTTGTTCTCCACTT
1428517 GTTAAGTTTC
Statistics
Matches: 150, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
153 16 0.11
155 134 0.89
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (153 bp):
AAAACATCTTTAATTGAAAAAAAAGTAAAATTAACATAGAAGCCATTCACAAAATATCCCTTAAT
GCTAGTGGGCAAAAGCATAAGGGTTAATTTCGGGTATTACTCTAAATTTAATCTAAAAAACTACA
GGAAGATCCTTTGTTCTCCACTT
Found at i:1433147 original size:13 final size:14
Alignment explanation
Indices: 1433114--1433144 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
1433104 TACAACACTC
1433114 AAAAGAAGAAAACA
1 AAAAGAAGAAAACA
*
1433128 AAAAGAAGAAAAGA
1 AAAAGAAGAAAACA
1433142 AAA
1 AAA
1433145 GAAAAGTTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAGAAGAAAACA
Found at i:1439701 original size:17 final size:18
Alignment explanation
Indices: 1439673--1439717 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1439663 AAACAGCATG
1439673 CAAAAT-TAAAATA-AAA
1 CAAAATGTAAAATATAAA
* *
1439689 CAAAATGTAAAATATGAC
1 CAAAATGTAAAATATAAA
1439707 CAAAATGTAAA
1 CAAAATGTAAA
1439718 CAAATAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 6 0.24
17 7 0.28
18 12 0.48
ACGTcount: A:0.64, C:0.09, G:0.07, T:0.20
Consensus pattern (18 bp):
CAAAATGTAAAATATAAA
Found at i:1460410 original size:16 final size:15
Alignment explanation
Indices: 1460375--1460413 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1460365 TCCCCATCTC
*
1460375 TAATTTTTTTTTACA
1 TAATTTTTTTCTACA
*
1460390 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
1460406 TAATTTTT
1 TAATTTTT
1460414 CAATGATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:1461181 original size:24 final size:24
Alignment explanation
Indices: 1461154--1461205 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1461144 GTATTCGAAA
*
1461154 TTTGATATTGGTCAATACCCGGAC
1 TTTGATATTGGCCAATACCCGGAC
* * *
1461178 TTTGATCTTGGCCAATACTCGGAT
1 TTTGATATTGGCCAATACCCGGAC
1461202 TTTG
1 TTTG
1461206 GTGATGTTTC
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:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTGATATTGGCCAATACCCGGAC
Found at i:1463487 original size:18 final size:18
Alignment explanation
Indices: 1463464--1463499 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1463454 AAGAAAAAGG
*
1463464 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
1463482 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
1463500 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:1463961 original size:65 final size:66
Alignment explanation
Indices: 1463820--1463964 Score: 265
Period size: 66 Copynumber: 2.2 Consensus size: 66
1463810 AATTTAAAAT
1463820 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1463885 A
66 A
* *
1463886 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTCCTCATC-AATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1463950 A
66 A
1463951 AACAAATCAACTTT
1 AACAAATCAACTTT
1463965 CAATGTAAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 19 0.25
66 58 0.75
ACGTcount: A:0.51, C:0.18, G:0.01, T:0.30
Consensus pattern (66 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
A
Found at i:1464985 original size:42 final size:44
Alignment explanation
Indices: 1464915--1465002 Score: 162
Period size: 42 Copynumber: 2.0 Consensus size: 44
1464905 ATGCATCAAT
1464915 ATGTTATTTTATATAAAAAAATACATATATTAGTGAATTTATTA
1 ATGTTATTTTATATAAAAAAATACATATATTAGTGAATTTATTA
1464959 ATGTTA-TTT-TATAAAAAAATACATATATTAGTGAATTTATTA
1 ATGTTATTTTATATAAAAAAATACATATATTAGTGAATTTATTA
1465001 AT
1 AT
1465003 AAATTTAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
42 35 0.80
43 3 0.07
44 6 0.14
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (44 bp):
ATGTTATTTTATATAAAAAAATACATATATTAGTGAATTTATTA
Found at i:1465414 original size:21 final size:21
Alignment explanation
Indices: 1465390--1465484 Score: 102
Period size: 21 Copynumber: 4.5 Consensus size: 21
1465380 GAGGGACCCA
* *
1465390 TTGAACAATGACAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
* * *
1465411 TTGAATGGTGGGAGGGGCCTC
1 TTGAACGATGAGAGGGGCCTC
*
1465432 TTGAACGATGAGAGGAGCCTC
1 TTGAACGATGAGAGGGGCCTC
**
1465453 TTGAACGAT-AGGAGGCACCTC
1 TTGAACGATGA-GAGGGGCCTC
1465474 TTGAACGATGA
1 TTGAACGATGA
1465485 CAGGTGAATC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 1 0.02
21 59 0.97
22 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (21 bp):
TTGAACGATGAGAGGGGCCTC
Found at i:1465436 original size:42 final size:42
Alignment explanation
Indices: 1465369--1465488 Score: 152
Period size: 42 Copynumber: 2.9 Consensus size: 42
1465359 AATCGGGCTT
* *
1465369 TTGAACGGTGGGAGGGACC-CATTGAACAATGACAGGGGCCTC
1 TTGAACGGTGGGAGGGACCTC-TTGAACGATGACAGGAGCCTC
* * *
1465411 TTGAATGGTGGGAGGGGCCTCTTGAACGATGAGAGGAGCCTC
1 TTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGAGCCTC
* * *
1465453 TTGAACGATAGGAGGCACCTCTTGAACGATGACAGG
1 TTGAACGGTGGGAGGGACCTCTTGAACGATGACAGG
1465489 TGAATCAGGC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
42 65 0.98
43 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.36, T:0.19
Consensus pattern (42 bp):
TTGAACGGTGGGAGGGACCTCTTGAACGATGACAGGAGCCTC
Found at i:1465660 original size:4 final size:4
Alignment explanation
Indices: 1465628--1465685 Score: 80
Period size: 4 Copynumber: 14.5 Consensus size: 4
1465618 GGGCCACTGA
* * * *
1465628 AAAT AAAT TAAT ACAT AAAT CAGT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1465676 AAAT AAAT AA
1 AAAT AAAT AA
1465686 TGCTGAAAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.69, C:0.03, G:0.02, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:1465806 original size:21 final size:21
Alignment explanation
Indices: 1465782--1465831 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
1465772 TGAAACAATC
*
1465782 TCACGTAGAGCAGCTACCTCA
1 TCACGTAGAGCAGATACCTCA
* *
1465803 TCACGTAAAGTAGATACCTCA
1 TCACGTAGAGCAGATACCTCA
1465824 TCACGTAG
1 TCACGTAG
1465832 CGCACCATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (21 bp):
TCACGTAGAGCAGATACCTCA
Done.