Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008388.1 Hibiscus syriacus cultivar Beakdansim tig00111153_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: 179606
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:9183 original size:20 final size:20
Alignment explanation
Indices: 9158--9203 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
9148 GAGGAGTATT
9158 GATACTGAAAGACCGGCATC
1 GATACTGAAAGACCGGCATC
* *
9178 GATACTGAAAGGCCGGTATC
1 GATACTGAAAGACCGGCATC
9198 GATACT
1 GATACT
9204 CACAGGATAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.20
Consensus pattern (20 bp):
GATACTGAAAGACCGGCATC
Found at i:15943 original size:24 final size:24
Alignment explanation
Indices: 15914--15960 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
15904 AATTTAAAAT
15914 ACTAATATTGCTATCACTTTAAAC
1 ACTAATATTGCTATCACTTTAAAC
15938 ACTAATATTGCTATCACTTTAAA
1 ACTAATATTGCTATCACTTTAAA
15961 AATAAGGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (24 bp):
ACTAATATTGCTATCACTTTAAAC
Found at i:23511 original size:77 final size:76
Alignment explanation
Indices: 23368--23512 Score: 168
Period size: 77 Copynumber: 1.9 Consensus size: 76
23358 CTTATTATTT
* * ** ** *
23368 TTATATATATTTAATTATATATTTTTTATTTATTTACTATATTTCTTTAGTTTTGGTTTTTTTTA
1 TTATATATATTTAATTATATATTTTTTATTTATATACTATATTACTTTAGTTTTCATCATTATTA
23433 TTTATGCTATA
66 TTTATGCTATA
* *
23444 TTATATTATACTTTTATTAT-TATTTTTTATTTATATA-TATATTACTTATATTTTTCATCATTA
1 TTATA-TATA-TTTAATTATATATTTTTTATTTATATACTATATTACTT-TAGTTTTCATCATTA
23507 TTATTT
63 TTATTT
23513 TTTTATATTT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
76 14 0.25
77 35 0.61
78 8 0.14
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (76 bp):
TTATATATATTTAATTATATATTTTTTATTTATATACTATATTACTTTAGTTTTCATCATTATTA
TTTATGCTATA
Found at i:23514 original size:84 final size:83
Alignment explanation
Indices: 23440--23606 Score: 189
Period size: 84 Copynumber: 2.0 Consensus size: 83
23430 TTATTTATGC
*
23440 TATATTATATTATACTTTTATTAT-T-ATTTTTTA-TTTATATATATATTACTTA-TATTTTTCA
1 TATATTATA-TATACTTTTATTATGTAATTTTTTAGTTTATATATATATTAATTATTA-TTTTCA
23501 TCATTATTATTTTTTTATAT
64 TCATTATTATTTTTTTATAT
* * ** * *
23521 TTTTTTATATATTTTTTTGTTGTGTACATTTTTTAGTTTATATATATATTAATTATTATTTTCAT
1 TATATTATATATACTTTTATTATGTA-ATTTTTTAGTTTATATATATATTAATTATTATTTTCAT
* *
23586 TATTATTATTTTATTACTAT
65 CATTATTATTTTTTTA-TAT
23606 T
1 T
23607 TTTACTATTA
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
80 10 0.14
81 8 0.11
83 8 0.11
84 39 0.55
85 6 0.08
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (83 bp):
TATATTATATATACTTTTATTATGTAATTTTTTAGTTTATATATATATTAATTATTATTTTCATC
ATTATTATTTTTTTATAT
Found at i:23523 original size:10 final size:10
Alignment explanation
Indices: 23508--23537 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
23498 TCATCATTAT
23508 TATTTTTTTA
1 TATTTTTTTA
23518 TATTTTTTTA
1 TATTTTTTTA
23528 TATATTTTTT
1 TAT-TTTTTT
23538 TGTTGTGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 13 0.68
11 6 0.32
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (10 bp):
TATTTTTTTA
Found at i:23590 original size:15 final size:14
Alignment explanation
Indices: 23567--23606 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
23557 TTTATATATA
23567 TATTAATTATTATTT
1 TATT-ATTATTATTT
23582 TCATTATTATTATTT
1 T-ATTATTATTATTT
*
23597 TATTACTATT
1 TATTATTATT
23607 TTTACTATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 8 0.35
15 12 0.52
16 3 0.13
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (14 bp):
TATTATTATTATTT
Found at i:23606 original size:26 final size:27
Alignment explanation
Indices: 23570--23635 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 27
23560 ATATATATAT
* * *
23570 TAATTATTATTTTCATTATTATTATT-
1 TAATTACTATTTTCACTATTATCATTA
* *
23596 TTATTACTATTTTTACTATTATCATTA
1 TAATTACTATTTTCACTATTATCATTA
*
23623 TAACTACTATTTT
1 TAATTACTATTTT
23636 TCCCCTTATA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 21 0.66
27 11 0.34
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (27 bp):
TAATTACTATTTTCACTATTATCATTA
Found at i:23667 original size:9 final size:9
Alignment explanation
Indices: 23648--23714 Score: 62
Period size: 10 Copynumber: 6.6 Consensus size: 9
23638 CCCTTATATG
23648 TTTTTACTTT
1 TTTTTA-TTT
23658 TTTTTATTT
1 TTTTTATTT
23667 TTTTTATTT
1 TTTTTATTT
23676 ATCTATTTATGTTT
1 -T-T-TTTA--TTT
23690 TTTATTATTT
1 TTT-TTATTT
23700 TTCTTTATTT
1 TT-TTTATTT
23710 TTTTT
1 TTTTT
23715 CGTTTTTCCC
Statistics
Matches: 50, Mismatches: 0, Indels: 15
0.77 0.00 0.23
Matches are distributed among these distances:
9 15 0.30
10 20 0.40
11 3 0.06
12 8 0.16
13 1 0.02
14 3 0.06
ACGTcount: A:0.13, C:0.04, G:0.01, T:0.81
Consensus pattern (9 bp):
TTTTTATTT
Found at i:23682 original size:17 final size:16
Alignment explanation
Indices: 23661--23709 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
23651 TTACTTTTTT
23661 TTATTTTTTTTATTTA
1 TTATTTTTTTTATTTA
*
23677 TCTATTTATGTTT-TTTA
1 T-TATTT-TTTTTATTTA
23694 TTATTTTTCTTTATTT
1 TTATTTTT-TTTATTT
23710 TTTTTCGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 1 0.04
16 9 0.33
17 13 0.48
18 4 0.15
ACGTcount: A:0.16, C:0.04, G:0.02, T:0.78
Consensus pattern (16 bp):
TTATTTTTTTTATTTA
Found at i:23715 original size:13 final size:13
Alignment explanation
Indices: 23655--23715 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
23645 ATGTTTTTAC
23655 TTTTT-TTTATTT
1 TTTTTCTTTATTT
*
23667 TTTTTATTTATCTAT
1 TTTTTCTTTAT-T-T
* *
23682 TTATGTTTTTTATTA
1 TT-T-TTCTTTATTT
23697 TTTTTCTTTATTT
1 TTTTTCTTTATTT
23710 TTTTTC
1 TTTTTC
23716 GTTTTTCCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
12 5 0.12
13 19 0.47
14 2 0.05
15 5 0.12
16 2 0.05
17 7 0.17
ACGTcount: A:0.13, C:0.05, G:0.02, T:0.80
Consensus pattern (13 bp):
TTTTTCTTTATTT
Found at i:24419 original size:31 final size:31
Alignment explanation
Indices: 24384--24493 Score: 101
Period size: 31 Copynumber: 3.7 Consensus size: 31
24374 AAATATATAT
*
24384 TATATAATATACTAATATTTACTTTCAAAAC
1 TATATAATATACTAATATTTATTTTCAAAAC
24415 TATAT-ATA-A-T-ATA-TTATTTTCAAAAC
1 TATATAATATACTAATATTTATTTTCAAAAC
* * *
24441 TATATTATATAC-ACTATTTTATTTTCGAAAC
1 TATATAATATACTAATA-TTTATTTTCAAAAC
*
24472 TATAT-ATAATA-TAATATATATT
1 TATATAAT-ATACTAATATTTATT
24494 ACTATATATT
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
26 17 0.26
27 6 0.09
28 2 0.03
29 3 0.05
30 10 0.15
31 28 0.42
ACGTcount: A:0.44, C:0.09, G:0.01, T:0.46
Consensus pattern (31 bp):
TATATAATATACTAATATTTATTTTCAAAAC
Found at i:24420 original size:26 final size:26
Alignment explanation
Indices: 24390--24484 Score: 93
Period size: 26 Copynumber: 3.5 Consensus size: 26
24380 ATATTATATA
24390 ATATACTAATAT-TTACTTTCAAAACT
1 ATATA-TAATATATTACTTTCAAAACT
*
24416 ATATATAATATATTATTTTCAAAACTAT
1 ATATATAATATATTACTTTCAAAAC--T
* * *
24444 ATTATATACACTATTTTATTTTCGAAACT
1 A-TATATA-A-TATATTACTTTCAAAACT
24473 ATATATAATATA
1 ATATATAATATA
24485 ATATATATTA
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
25 6 0.10
26 20 0.34
27 1 0.02
28 8 0.14
29 8 0.14
30 1 0.02
31 15 0.25
ACGTcount: A:0.43, C:0.11, G:0.01, T:0.45
Consensus pattern (26 bp):
ATATATAATATATTACTTTCAAAACT
Found at i:24490 original size:40 final size:39
Alignment explanation
Indices: 24441--24532 Score: 96
Period size: 40 Copynumber: 2.3 Consensus size: 39
24431 TTTTCAAAAC
* * *
24441 TATATTATATA-CACTATTTTATTTTCGAAACTATATATAA
1 TATAATATATATCACTA-TATATTTTCAAAACTATATA-AA
* *
24481 TATAATATATATTACTATATATTTTTAAAACTATATAAA
1 TATAATATATATCACTATATATTTTCAAAACTATATAAA
24520 TACTATATATATA
1 TA-TA-ATATATA
24533 ATATATTCTA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
39 4 0.09
40 29 0.66
41 11 0.25
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.47
Consensus pattern (39 bp):
TATAATATATATCACTATATATTTTCAAAACTATATAAA
Found at i:24502 original size:57 final size:57
Alignment explanation
Indices: 24340--24503 Score: 151
Period size: 57 Copynumber: 2.9 Consensus size: 57
24330 ACCTATTATT
** * * *
24340 TAATATTTTATTTTCAAAAGCTATATATGTTTTAAAATATA-TAT-TATATAATATAC
1 TAATATTTTATTTTCAAAA-CTATATATAATATAATATATATTATATATATTATATAC
* * *
24396 TAATA-TTTACTTTCAAAACTATATATAATAT-AT-TATTTTCAAAACTATATTATATAC
1 TAATATTTTATTTTCAAAACTATATATAATATAATATATATT--ATA-TATATTATATAC
* *
24453 -ACTATTTTATTTTCGAAACTATATATAATATAATATATATTACTATATATT
1 TAATATTTTATTTTCAAAACTATATATAATATAATATATATTA-TATATATT
24504 TTTAAAACTA
Statistics
Matches: 86, Mismatches: 13, Indels: 17
0.74 0.11 0.15
Matches are distributed among these distances:
52 3 0.03
53 2 0.02
54 10 0.12
55 13 0.15
56 8 0.09
57 42 0.49
58 3 0.03
59 5 0.06
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.48
Consensus pattern (57 bp):
TAATATTTTATTTTCAAAACTATATATAATATAATATATATTATATATATTATATAC
Found at i:25777 original size:14 final size:14
Alignment explanation
Indices: 25755--25800 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
25745 GAGGACTTAT
* *
25755 TTAATTTAAAAAAA
1 TTAAATTAAAAATA
25769 TTAAATTAAAAATA
1 TTAAATTAAAAATA
25783 -TAAATATAAAAATA
1 TTAAAT-TAAAAATA
25797 TTAA
1 TTAA
25801 GATATTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 5 0.18
14 20 0.71
15 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TTAAATTAAAAATA
Found at i:28588 original size:15 final size:15
Alignment explanation
Indices: 28565--28601 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
28555 AATCTCGTAA
*
28565 ACTCATAAACCAAGC
1 ACTCGTAAACCAAGC
28580 ACTCGTAAACCAAGC
1 ACTCGTAAACCAAGC
28595 ACTCGTA
1 ACTCGTA
28602 CTCATCACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.41, C:0.32, G:0.11, T:0.16
Consensus pattern (15 bp):
ACTCGTAAACCAAGC
Found at i:34205 original size:20 final size:20
Alignment explanation
Indices: 34182--34231 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
34172 TGGTCCCTTA
*
34182 GTATTGATACTAAACTATTG
1 GTATTGATACTAAACTACTG
* * *
34202 GTATCGATACTCACCTACTG
1 GTATTGATACTAAACTACTG
34222 GTATTGATAC
1 GTATTGATAC
34232 CCTGCTGACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (20 bp):
GTATTGATACTAAACTACTG
Found at i:38642 original size:16 final size:17
Alignment explanation
Indices: 38604--38649 Score: 76
Period size: 18 Copynumber: 2.7 Consensus size: 17
38594 TGTTTATGAG
38604 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGT-AA
38622 GGAATTGGAATCTGT-A
1 GGAATTGGAATCTGTAA
38638 GGAATTGGAATC
1 GGAATTGGAATC
38650 CAATTCTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 13 0.46
18 15 0.54
ACGTcount: A:0.33, C:0.07, G:0.33, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:39310 original size:37 final size:38
Alignment explanation
Indices: 39226--39315 Score: 137
Period size: 38 Copynumber: 2.4 Consensus size: 38
39216 CCTAAACCCG
39226 AACCCGACCCGACCCGACCCGAATATCAAACTTAAAAA
1 AACCCGACCCGACCCGACCCGAATATCAAACTTAAAAA
* ** *
39264 AACCGGACCCGACTTGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGACCCGACCCGAATATCAAACTTAAAAA
39301 AACCCGACCCGACCC
1 AACCCGACCCGACCC
39316 AAACAAAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 16 0.36
38 29 0.64
ACGTcount: A:0.38, C:0.39, G:0.12, T:0.11
Consensus pattern (38 bp):
AACCCGACCCGACCCGACCCGAATATCAAACTTAAAAA
Found at i:39860 original size:264 final size:267
Alignment explanation
Indices: 39263--39875 Score: 940
Period size: 263 Copynumber: 2.3 Consensus size: 267
39253 AAACTTAAAA
** *
39263 AAACCGGACCCGACTTGACCCGAATATCACACTTAAAAAACCCGACCCGACCCAAACAAAATAAA
1 AAACC-GACCCGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAA
* * *
39328 GTTTCA-CTCGACCCAACCCGAATATATGAATTAGAAATCCGACCCGACTAGACCCAAAATAATA
65 GTTTCACCT-GACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCAGACCCAAAATAATA
*
39392 AAAATTATTTTTATTTAATAAAAACAGTGACTTAATTGAAAATATATATATATATATAGAGGGGT
129 AAAATTATTTTTATTTAATAAAAACAGTGACTTAATTGAAAATATATATATATATAGAGAGGGGT
* *
39457 ATTATTGTAATTATTCGTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGTCCAATGTT
194 ATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCAGGTCGGTCCAATGTT
39522 TTTCACCCT
259 TTTCACCCT
* * *
39531 -AA---ACCCGAACCAACCCGAATATCACACTTAAAAAACCCGACCCGTCCCGAACAAAATAAAG
1 AAACCGACCCGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAG
* * *
39592 TTTCACCTGACTCGACCCGAATATATGAATTAGAAATCCAACCCGACCCGACCCGAAATAATAAA
66 TTTCACCTGACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCAGACCCAAAATAAT-AA
39657 AAATTATTTTTATTTAATAAAAACAGTGACTTAATTG-AAA-A-A-ATATATATAGAGAGGGGTA
130 AAATTATTTTTATTTAATAAAAACAGTGACTTAATTGAAAATATATATATATATAGAGAGGGGTA
*
39718 TTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTAGGTCGGTCCAAT-TTT
195 TTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCAGGTCGGTCCAATGTTT
*
39782 TTTACCCT
260 TTCACCCT
* *
39790 AAACCGACCCGACCCGACCCGAATATCACACTTAAAAAAACCCGATCCGACCCGACCAAAATAAA
1 AAACCGACCCGACCCGACCCGAATATCACACTT-AAAAAACCCGACCCGACCCGAACAAAATAAA
*
39855 GTTTCACCCGACCCGACCCGA
65 GTTTCACCTGACCCGACCCGA
39876 CCCGAATATA
Statistics
Matches: 314, Mismatches: 24, Indels: 18
0.88 0.07 0.05
Matches are distributed among these distances:
259 10 0.03
260 78 0.25
261 1 0.00
262 1 0.00
263 134 0.43
264 88 0.28
267 2 0.01
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (267 bp):
AAACCGACCCGACCCGACCCGAATATCACACTTAAAAAACCCGACCCGACCCGAACAAAATAAAG
TTTCACCTGACCCGACCCGAATATATGAATTAGAAATCCAACCCGACCAGACCCAAAATAATAAA
AATTATTTTTATTTAATAAAAACAGTGACTTAATTGAAAATATATATATATATAGAGAGGGGTAT
TATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCAGGTCGGTCCAATGTTTT
TCACCCT
Found at i:46829 original size:22 final size:20
Alignment explanation
Indices: 46801--46841 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
46791 AGTTTTATTA
46801 AAGTTTTCTATTTTTACTTTTC
1 AAGTTTTC-ATTTTT-CTTTTC
46823 AAGTTTTCATTTTTCTTTT
1 AAGTTTTCATTTTTCTTTT
46842 ATTTTCAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 6 0.32
22 8 0.42
ACGTcount: A:0.17, C:0.12, G:0.05, T:0.66
Consensus pattern (20 bp):
AAGTTTTCATTTTTCTTTTC
Found at i:51401 original size:15 final size:18
Alignment explanation
Indices: 51375--51411 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
51365 GATCCGAAAT
51375 AATATATTTATT-AA-AA
1 AATATATTTATTCAATAA
51391 AATAT-TTTATTCAATAA
1 AATATATTTATTCAATAA
51408 AATA
1 AATA
51412 GAGTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 7 0.37
17 6 0.32
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATATTTATTCAATAA
Found at i:54217 original size:17 final size:18
Alignment explanation
Indices: 54180--54217 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
54170 TTATTGGATT
*
54180 TTTAAATAAAATTATATA
1 TTTAAATAAAATTATAGA
*
54198 TTTAAATTAAA-TATAGA
1 TTTAAATAAAATTATAGA
54215 TTT
1 TTT
54218 TACCTATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTAAATAAAATTATAGA
Found at i:54595 original size:4 final size:4
Alignment explanation
Indices: 54586--54616 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
54576 GGACGGCAAG
54586 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
1 GAAT GAAT GAAT GAAT GAAT GAAT GAAT GAA
54617 AATGGAGGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.26, T:0.23
Consensus pattern (4 bp):
GAAT
Found at i:56143 original size:60 final size:60
Alignment explanation
Indices: 56019--56143 Score: 130
Period size: 60 Copynumber: 2.1 Consensus size: 60
56009 ATCGAGTGAT
* * * * *
56019 CATTTTATAACTTTTAATAGTCAATGGACTCAATAAAGTAGCACTCTATAGTTAGAGAAT
1 CATTTTATAACTTATAATAGTCAATGGACTCAATAAAGTAGCACTCTATAATCAAAGAAC
* **
56079 CATTTTATAACTTATAATAGTCTAA-GGACTTAATAAAGTATTA-TCCTATAAATCAAAG-AC
1 CATTTTATAACTTATAATAGTC-AATGGACTCAATAAAGTAGCACT-CTAT-AATCAAAGAAC
56139 CATTT
1 CATTT
56144 GTGTACTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
59 1 0.02
60 46 0.85
61 7 0.13
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (60 bp):
CATTTTATAACTTATAATAGTCAATGGACTCAATAAAGTAGCACTCTATAATCAAAGAAC
Found at i:57306 original size:14 final size:13
Alignment explanation
Indices: 57287--57316 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
57277 AATTTTTAAT
57287 AAAAATATATTTTA
1 AAAAATA-ATTTTA
57301 AAAAATAATTTTA
1 AAAAATAATTTTA
57314 AAA
1 AAA
57317 TATGTATCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
AAAAATAATTTTA
Found at i:57918 original size:6 final size:6
Alignment explanation
Indices: 57907--57949 Score: 68
Period size: 6 Copynumber: 6.8 Consensus size: 6
57897 GTTTACTGTT
57907 TATATG TATATG TATATG TATATG TATATG TACATATG TATAT
1 TATATG TATATG TATATG TATATG TATATG T--ATATG TATAT
57950 ATATTGATAG
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
6 29 0.83
8 6 0.17
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (6 bp):
TATATG
Found at i:63857 original size:12 final size:12
Alignment explanation
Indices: 63840--63864 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
63830 GCGAATCCAA
63840 AAATATTTTAAT
1 AAATATTTTAAT
63852 AAATATTTTAAT
1 AAATATTTTAAT
63864 A
1 A
63865 TTATAAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATATTTTAAT
Found at i:64962 original size:2 final size:2
Alignment explanation
Indices: 64957--65004 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
64947 AACTTAAAAT
64957 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
64999 TA TA TA
1 TA TA TA
65005 GAAAAGCCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67103 original size:2 final size:2
Alignment explanation
Indices: 67096--67130 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
67086 TGTCGTAAAT
67096 TA TA TA 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 TA TA TA T
67131 TGTAGATTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:69738 original size:18 final size:18
Alignment explanation
Indices: 69715--69756 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
69705 TTGCAAACAA
69715 CTTGCATCATATAAGAAT
1 CTTGCATCATATAAGAAT
69733 CTTGCATCATATAAGAAT
1 CTTGCATCATATAAGAAT
69751 CTTGCA
1 CTTGCA
69757 GATTTAACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (18 bp):
CTTGCATCATATAAGAAT
Found at i:72328 original size:2 final size:2
Alignment explanation
Indices: 72321--72346 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
72311 GTATAAAAGA
72321 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
72347 GAAGTCTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:72759 original size:25 final size:25
Alignment explanation
Indices: 72716--72791 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 25
72706 AGGATAAAGA
*
72716 TAAAAGATATTTAT-T-TCTTTTAT
1 TAAAAGAGATTTATATCTCTTTTAT
*
72739 TAAAATAGATTTATATCTCTTTTATT
1 TAAAAGAGATTTATATCTCTTTTA-T
*
72765 TAAAAGAGATTTAATAACTCTTTTAT
1 TAAAAGAGATTT-ATATCTCTTTTAT
72791 T
1 T
72792 GTAATTAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
23 12 0.27
24 1 0.02
25 7 0.16
26 14 0.31
27 11 0.24
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (25 bp):
TAAAAGAGATTTATATCTCTTTTAT
Found at i:72774 original size:26 final size:26
Alignment explanation
Indices: 72716--72791 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 26
72706 AGGATAAAGA
*
72716 TAAAAGATATTTAT-T-TCTTTTA-T
1 TAAAAGAGATTTATATCTCTTTTATT
*
72739 TAAAATAGATTTATATCTCTTTTATT
1 TAAAAGAGATTTATATCTCTTTTATT
*
72765 TAAAAGAGATTTAATAACTCTTTTATT
1 TAAAAGAGATTT-ATATCTCTTTTATT
72792 GTAATTAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
23 12 0.27
24 1 0.02
25 7 0.16
26 12 0.27
27 13 0.29
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (26 bp):
TAAAAGAGATTTATATCTCTTTTATT
Found at i:73931 original size:19 final size:20
Alignment explanation
Indices: 73893--73943 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
73883 GAAACCCCTT
73893 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTTAA
73913 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
73932 TGAAGATACATG
1 TGAAAATACATG
73944 CTCTTGGCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:79829 original size:19 final size:19
Alignment explanation
Indices: 79805--79852 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
79795 CAAAGGAGTA
*
79805 AACATCTGATTTCTTAATT
1 AACATCTGATTTCTCAATT
*
79824 AACATCTGATTTCTCAGTT
1 AACATCTGATTTCTCAATT
*
79843 AACTTCTGAT
1 AACATCTGAT
79853 GCTTGTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.29, C:0.19, G:0.08, T:0.44
Consensus pattern (19 bp):
AACATCTGATTTCTCAATT
Found at i:82001 original size:3 final size:3
Alignment explanation
Indices: 81993--82045 Score: 54
Period size: 3 Copynumber: 18.0 Consensus size: 3
81983 GGGTTATAAT
* * * * *
81993 TTA TTA TTA TTA -TA ATA ATA TTA TTA TGA TTA TTA TTA ATA TTA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
82040 TTA TTA
1 TTA TTA
82046 ATTAATTAAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:82035 original size:9 final size:9
Alignment explanation
Indices: 81989--82047 Score: 50
Period size: 9 Copynumber: 6.4 Consensus size: 9
81979 GTCTGGGTTA
81989 TAAT-TTAT
1 TAATATTAT
*
81997 TATTATTAT
1 TAATATTAT
82006 AATAATATTAT
1 --TAATATTAT
82017 T-ATGATTAT
1 TAAT-ATTAT
* *
82026 TATTAATAT
1 TAATATTAT
82035 TAATATTAT
1 TAATATTAT
82044 TAAT
1 TAAT
82048 TAATTAAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
8 5 0.12
9 26 0.65
10 1 0.03
11 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (9 bp):
TAATATTAT
Found at i:88060 original size:6 final size:6
Alignment explanation
Indices: 88049--88084 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
88039 ATAGTTAAAT
88049 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
88085 GGGTGTTACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:88838 original size:3 final size:3
Alignment explanation
Indices: 88830--88857 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
88820 TAATTTTGAC
88830 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
88858 AGGTGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:91512 original size:2 final size:2
Alignment explanation
Indices: 91507--91531 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
91497 TTTTTTAGAT
91507 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 T
91532 TTTTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:91578 original size:4 final size:4
Alignment explanation
Indices: 91547--91689 Score: 59
Period size: 4 Copynumber: 35.8 Consensus size: 4
91537 TATTATCAGT
* * * *
91547 TTTA TTAA TTTA TATATA TATA TATA TTTA TTTA TTTA -CTA TTT- TTTA
1 TTTA TTTA TTTA T-T-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* ** *
91595 TTTTA TATA TACA TTATT TTTA CTTT- TTTA -TTA -TTA TTTTA TTTA
1 -TTTA TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA TTTA -TTTA TTTA
* * *
91640 TTTGT TTTA TTTA TATA TTT- TTTA TTTA --TA TTTA TTTT TTATA TTTA
1 TTT-A TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA
91687 TTT
1 TTT
91690 TACTTACTAT
Statistics
Matches: 106, Mismatches: 18, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
2 2 0.02
3 17 0.16
4 65 0.61
5 19 0.18
6 3 0.03
ACGTcount: A:0.27, C:0.02, G:0.01, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:91599 original size:15 final size:15
Alignment explanation
Indices: 91571--91701 Score: 65
Period size: 13 Copynumber: 9.3 Consensus size: 15
91561 TATATATATA
91571 TATTTATTTATTTAC
1 TATTTATTTATTTAC
91586 TATTT-TTTATTTTA-
1 TATTTATTTA-TTTAC
* * *
91600 TATATACATTATTT-T
1 TATTTA-TTTATTTAC
*
91615 TACTTT-TTTA-TTAT
1 TA-TTTATTTATTTAC
*
91629 TATTTTATTTATTT-G
1 TA-TTTATTTATTTAC
91644 T-TTTATTTA--TA-
1 TATTTATTTATTTAC
91655 TATTT-TTTATTTA-
1 TATTTATTTATTTAC
91668 TATTTATTT-TTTA-
1 TATTTATTTATTTAC
*
91681 TATTTATTTTACTTAC
1 TATTTA-TTTATTTAC
91697 TATTT
1 TATTT
91702 TATCTTTGTT
Statistics
Matches: 93, Mismatches: 7, Indels: 31
0.71 0.05 0.24
Matches are distributed among these distances:
11 6 0.06
12 3 0.03
13 27 0.29
14 23 0.25
15 22 0.24
16 12 0.13
ACGTcount: A:0.24, C:0.04, G:0.01, T:0.71
Consensus pattern (15 bp):
TATTTATTTATTTAC
Found at i:91627 original size:17 final size:16
Alignment explanation
Indices: 91607--91685 Score: 52
Period size: 19 Copynumber: 4.4 Consensus size: 16
91597 TTATATATAC
91607 ATTATTTTTACTTTTTT
1 ATTATTTTTA-TTTTTT
91624 ATTATTATTTTATTTATTTGT
1 ATTA-T-TTTTA-TT-TTT-T
*
91645 TTTATTTATATATTTTTT
1 ATTATTT-T-TATTTTTT
*
91663 ATTTATATTTATTTTTT
1 A-TTATTTTTATTTTTT
91680 A-TATTT
1 ATTATTT
91686 ATTTTACTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
15 4 0.08
17 13 0.26
18 3 0.06
19 17 0.34
20 7 0.14
21 6 0.12
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.75
Consensus pattern (16 bp):
ATTATTTTTATTTTTT
Found at i:91635 original size:41 final size:41
Alignment explanation
Indices: 91511--91638 Score: 125
Period size: 46 Copynumber: 3.0 Consensus size: 41
91501 TTAGATTATA
* * *
91511 TATATATATATATATATATATTTTTTTATTATCAGTTTTATTAATT
1 TATATATACATATATATTTA-TTTTTTATTATTA-TTTTA-T--TT
* *
91557 TATATATATATATATATTTATTTATTTACTATT-TTTTATTT
1 TATATATACATATATATTTATTT-TTTATTATTATTTTATTT
*
91598 TATATATACAT-TATTTTTACTTTTTTATTATTATTTTATTT
1 TATATATACATATATATTTA-TTTTTTATTATTATTTTATTT
91639 ATTTGTTTTA
Statistics
Matches: 73, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
40 15 0.21
41 23 0.32
43 1 0.01
44 5 0.07
45 3 0.04
46 26 0.36
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (41 bp):
TATATATACATATATATTTATTTTTTATTATTATTTTATTT
Found at i:91647 original size:13 final size:15
Alignment explanation
Indices: 91631--91670 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
91621 TTTATTATTA
91631 TTTTATTTAT-T-TG
1 TTTTATTTATATATG
*
91644 TTTTATTTATATATT
1 TTTTATTTATATATG
91659 TTTTATTTATAT
1 TTTTATTTATAT
91671 TTATTTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 13 0.54
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.75
Consensus pattern (15 bp):
TTTTATTTATATATG
Found at i:91680 original size:28 final size:29
Alignment explanation
Indices: 91618--91701 Score: 97
Period size: 28 Copynumber: 3.0 Consensus size: 29
91608 TTATTTTTAC
91618 TTTTTTAT-TATTATTTTATTTAT-TTGT-
1 TTTTTTATATATTATTTTATTTATATT-TA
91645 TTTATTTATATATT-TTTTATTTATATTTA
1 TTT-TTTATATATTATTTTATTTATATTTA
*
91674 TTTTTTATAT-TTATTTTACTTACTATTT
1 TTTTTTATATATTATTTTATTTA-TATTT
91702 TATCTTTGTT
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
27 5 0.10
28 31 0.62
29 14 0.28
ACGTcount: A:0.23, C:0.02, G:0.01, T:0.74
Consensus pattern (29 bp):
TTTTTTATATATTATTTTATTTATATTTA
Found at i:91688 original size:17 final size:17
Alignment explanation
Indices: 91565--91689 Score: 88
Period size: 17 Copynumber: 7.6 Consensus size: 17
91555 TTTATATATA
*
91565 TATATATATTTATTTATT
1 TATATTTATTTATTT-TT
*
91583 TACTATTT-TTTATTTTA
1 TA-TATTTATTTATTTTT
**
91600 TATATACA-TTA-TTTT
1 TATATTTATTTATTTTT
* *
91615 TA-CTTT-TTTA-TTAT
1 TATATTTATTTATTTTT
91629 TAT-TTTATTTATTTGTT
1 TATATTTATTTATTT-TT
*
91646 T-TATTTATATATTTTT
1 TATATTTATTTATTTTT
91662 TAT-TTATATTTATTTTT
1 TATATT-TATTTATTTTT
91679 TATATTTATTT
1 TATATTTATTT
91690 TACTTACTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
14 12 0.14
15 9 0.11
16 14 0.17
17 34 0.40
18 11 0.13
19 4 0.05
ACGTcount: A:0.26, C:0.02, G:0.01, T:0.71
Consensus pattern (17 bp):
TATATTTATTTATTTTT
Found at i:91763 original size:66 final size:66
Alignment explanation
Indices: 91640--91763 Score: 155
Period size: 66 Copynumber: 1.9 Consensus size: 66
91630 ATTTTATTTA
* * *
91640 TTTGTTTTATTTATATATTTTTTATTTATATTTATTTTTTATATTTATTTTACTTACTATTTTAT
1 TTTGTTTTATTTATATATCTTTTATTTATATTTATTTTTTATATTTAATTTAATTACTATTTTAT
91705 C
66 C
* *
91706 TTTGTTTTCTTTATCTTATCTTTTATTTA-ATTT-TTTTCTTCAT-TTTAATTTAATTACT
1 TTTGTTTTATTTAT-ATATCTTTTATTTATATTTATTTT-TT-ATATTTAATTTAATTACT
91764 TTATTTATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
65 4 0.08
66 32 0.64
67 14 0.28
ACGTcount: A:0.21, C:0.07, G:0.02, T:0.70
Consensus pattern (66 bp):
TTTGTTTTATTTATATATCTTTTATTTATATTTATTTTTTATATTTAATTTAATTACTATTTTAT
C
Found at i:91773 original size:23 final size:23
Alignment explanation
Indices: 91714--91773 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
91704 TCTTTGTTTT
* *
91714 CTTTATCTTATCTTTTATTTAATTT
1 CTTTAT-TTAT-TTTAATTTAATTA
* * *
91739 TTTTCTTCATTTTAATTTAATTA
1 CTTTATTTATTTTAATTTAATTA
91762 CTTTATTTATTT
1 CTTTATTTATTT
91774 CTTACTTTTT
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
23 20 0.74
24 3 0.11
25 4 0.15
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (23 bp):
CTTTATTTATTTTAATTTAATTA
Found at i:91780 original size:16 final size:15
Alignment explanation
Indices: 91759--91788 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
91749 TTTAATTTAA
91759 TTACTTTATTTATTTC
1 TTACTTT-TTTATTTC
91775 TTACTTTTTTATTT
1 TTACTTTTTTATTT
91789 AACATGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (15 bp):
TTACTTTTTTATTTC
Found at i:96669 original size:36 final size:36
Alignment explanation
Indices: 96622--96847 Score: 216
Period size: 36 Copynumber: 6.4 Consensus size: 36
96612 ATTGAAAACA
* * *
96622 TTTCCCTTGAAATAAATGTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
*
96658 TTTCCCTTGAAACAAATTTTGTCTCTTTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
* *
96694 TTTCCCTTGAAACAAA-----T-TAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACA-G
*** ** *
96723 TTTTATTTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
** * *
96759 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAG
* *
96796 TTTCTCTTGAAACAAATTTTGTTTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
96832 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
96848 ATCTTTGAAT
Statistics
Matches: 156, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.01
29 18 0.12
30 2 0.01
31 1 0.01
34 1 0.01
35 1 0.01
36 99 0.63
37 32 0.21
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAG
Found at i:96784 original size:138 final size:138
Alignment explanation
Indices: 96642--96901 Score: 394
Period size: 138 Copynumber: 1.9 Consensus size: 138
96632 AATAAATGTC
*
96642 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTTTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * ** *
96707 AAATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC
96772 TAAGTTTT
131 TAAGTTTT
* *
96780 GTCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAAAC
1 GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
* * * **
96845 AAAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCT
96902 CTTGAAACAC
Statistics
Matches: 108, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
138 108 1.00
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.41
Consensus pattern (138 bp):
GTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
AAAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTGAGACAGTTTCTTTTGGAAC
TAAGTTTT
Found at i:96808 original size:102 final size:101
Alignment explanation
Indices: 96546--96813 Score: 277
Period size: 101 Copynumber: 2.6 Consensus size: 101
96536 TTTTGTCTAT
* * * * * * * *
96546 CTTGAGATAGTTTCCCTTGAAACAAAATATTATCTCCCTGGAAACAGTTTCTCTTGAAACATAAA
1 CTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAT
* * ** *** * * *
96611 CA-TTGAAAACATTTCCCTTGAAATAAATGTCGTCTCT
64 TATTTGAATATGTTTTATTTGAAACAAATGTCATCTCC
*
96648 CTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTTTTGAGACAGTTTCCCTTGAAACAAATTA
1 CTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTA
*
96713 TTTGAATATGTTTTATTTGAAACAAATTTCATCTCC
66 TTTGAATATGTTTTATTTGAAACAAATGTCATCTCC
** * * *
96749 CTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAAATT
1 CTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATT
96814 TTGTTTCTCT
Statistics
Matches: 138, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
100 3 0.02
101 75 0.54
102 60 0.43
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (101 bp):
CTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTA
TTTGAATATGTTTTATTTGAAACAAATGTCATCTCC
Found at i:96909 original size:65 final size:67
Alignment explanation
Indices: 96805--96967 Score: 240
Period size: 65 Copynumber: 2.4 Consensus size: 67
96795 GTTTCTCTTG
* **
96805 AAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTTTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
96868 TA
66 TA
* * *
96870 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTTTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
96935 TA
66 TA
*
96937 AAACAAAATTTTGTTTCCCTTGAGACTGTTT
1 AAAC-AAATTTTGTTTCCCTTGAGACAGTTT
96968 TCATAAAACA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
65 33 0.38
66 2 0.02
67 28 0.32
68 24 0.28
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.39
Consensus pattern (67 bp):
AAACAAATTTTGTTTCCCTTGAGACAGTTTCCCTTGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:96977 original size:67 final size:66
Alignment explanation
Indices: 96796--96988 Score: 217
Period size: 67 Copynumber: 2.9 Consensus size: 66
96786 CTTGAGACAG
* * * * * ** **
96796 TTTCTCTTGAAACAAATTTTGTTTCTCTTGAGACAGTTTCCCTTGAA-ACAAAATCTTTGAATTT
1 TTTCCCTTAAAACAAATTTTGTTTCCCTTGAGACAGTTTTCATAAAACACAAAATCTTCAAATTT
96860 A
66 A
* * * *
96861 TTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATT
1 TTTCCCTTAAAACAAATTTTGTTTCCCTTGAGACAGTTT-TCATAAAACACAAAATCTTCAAATT
96926 TA
65 TA
*
96928 TTTCCCTTAAAACAAAATTTTGTTTCCCTTGAGACTGTTTTCATAAAACAACAAATATCTT
1 TTTCCCTTAAAAC-AAATTTTGTTTCCCTTGAGACAGTTTTCATAAAAC-ACAAA-ATCTT
96989 TAAGATCGTT
Statistics
Matches: 107, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
65 34 0.32
66 4 0.04
67 35 0.33
68 29 0.27
69 5 0.05
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.39
Consensus pattern (66 bp):
TTTCCCTTAAAACAAATTTTGTTTCCCTTGAGACAGTTTTCATAAAACACAAAATCTTCAAATTT
A
Found at i:97942 original size:105 final size:108
Alignment explanation
Indices: 97698--97952 Score: 274
Period size: 110 Copynumber: 2.4 Consensus size: 108
97688 TCCCAGTTTT
** * *
97698 AGAGCCAATTTTGACTTCACAGCGAGGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
1 AGAGCCAATTTCAACTTCAAAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
* *
97763 CGAAGGGGCGACTGATTGTCAACAAACAACTATTCAGTTTTATTC
66 CGAAGGGGCGACTGACTGTCAACAAACAACTATTCAG--TTATCC
* * * *
97808 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCGAA-CCAACACAAGCTCAACTTCACA
1 AGAGCCAATTTCAACTTCAAAGCGAAGGATATTGGACTC-AAGACAACACAAGCTCAACTTCACA
* * *
97872 GCG-AGGGGCGGCTGGCTGTCAACAAACAA-T-TTCCCAG-T-TCC
65 ACGAAGGGGCGACTGACTGTCAACAAACAACTATT--CAGTTATCC
97913 AGAGCCAATTTCAACTTCATGAAG-G-AGGATATTGGACTCA
1 AGAGCCAATTTCAACTTCA--AAGCGAAGGATATTGGACTCA
97953 TAACAATAAT
Statistics
Matches: 126, Mismatches: 14, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
104 1 0.01
105 33 0.26
106 2 0.02
107 4 0.03
108 1 0.01
109 26 0.21
110 57 0.45
111 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (108 bp):
AGAGCCAATTTCAACTTCAAAGCGAAGGATATTGGACTCAAGACAACACAAGCTCAACTTCACAA
CGAAGGGGCGACTGACTGTCAACAAACAACTATTCAGTTATCC
Found at i:99240 original size:26 final size:27
Alignment explanation
Indices: 99188--99241 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
99178 TGCATTTTCT
* *
99188 TTTTTTACTTTAGTATATATTTTTATA
1 TTTTTTACTTTAGTATATATATATATA
99215 TTTTTTA-TATTA-TATATATATATATA
1 TTTTTTACT-TTAGTATATATATATATA
99241 T
1 T
99242 ATATTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (27 bp):
TTTTTTACTTTAGTATATATATATATA
Found at i:99286 original size:49 final size:46
Alignment explanation
Indices: 99210--99364 Score: 160
Period size: 49 Copynumber: 3.3 Consensus size: 46
99200 GTATATATTT
99210 TTATATTTT-TTATATTATATATATATATATATATATTATTTTTTTA
1 TTATATTTTATTAT-TTATATATATATATATATATATTATTTTTTTA
* * *
99256 TTATCAGTTTTATTAATTTATATATATATATTTATTTACTATTTTTTTA
1 TTAT-A-TTTTATT-ATTTATATATATATATATATATATTATTTTTTTA
* *
99305 TT-T-TTTTA-T-TTTATATATATATATAT-TATTTTTACTTTTTTA
1 TTATATTTTATTATTTATATATATATATATATA-TATTATTTTTTTA
99347 TTATTATTTTATTTATTT
1 TTA-TATTTTA-TTATTT
99365 GTTTTATTTA
Statistics
Matches: 90, Mismatches: 8, Indels: 20
0.76 0.07 0.17
Matches are distributed among these distances:
41 1 0.01
42 28 0.31
44 2 0.02
45 10 0.11
46 4 0.04
47 2 0.02
48 8 0.09
49 33 0.37
50 2 0.02
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.68
Consensus pattern (46 bp):
TTATATTTTATTATTTATATATATATATATATATATTATTTTTTTA
Found at i:99308 original size:8 final size:8
Alignment explanation
Indices: 99295--99412 Score: 73
Period size: 8 Copynumber: 14.4 Consensus size: 8
99285 ATTTATTTAC
99295 TATTTTTT
1 TATTTTTT
99303 TATTTTTT
1 TATTTTTT
*
99311 TATTTTATA
1 TATTTT-TT
* * *
99320 TATATATA
1 TATTTTTT
99328 TATTATTTT
1 TATT-TTTT
*
99337 TACTTTTT
1 TATTTTTT
*
99345 TA--TTAT
1 TATTTTTT
99351 TATTTTATT
1 TATTTT-TT
99360 TATTTGTTT
1 TATTT-TTT
99369 TATTTATATT
1 TATTT-T-TT
99379 T-TTTTTCT
1 TATTTTT-T
*
99387 T-TTTCTT
1 TATTTTTT
*
99394 TATTTCTT
1 TATTTTTT
99402 TATTTTTT
1 TATTTTTT
99410 TAT
1 TAT
99413 ATTTATTTTA
Statistics
Matches: 89, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
6 5 0.06
7 3 0.03
8 50 0.56
9 27 0.30
10 4 0.04
ACGTcount: A:0.19, C:0.03, G:0.01, T:0.76
Consensus pattern (8 bp):
TATTTTTT
Found at i:99322 original size:91 final size:90
Alignment explanation
Indices: 99207--99435 Score: 245
Period size: 91 Copynumber: 2.5 Consensus size: 90
99197 TTAGTATATA
* *
99207 TTTTTATATTTTTTATATTATATATATATATA-TATATATTATTTTTTTATTATCAGTTTTATTA
1 TTTTTAT-TTTTTTATTTTATATATATATATATTAT-TATTACTTTTTTATTATCA-TTTTATTA
99271 ATTT-ATATATATATATTTATTTACTATT
63 ATTTGATATATATATATTTATTTACT-TT
* * *
99299 TTTTTATTTTTTTATTTTATATATATATATATTATTTTTACTTTTTTATTATTATTTTATTTATT
1 TTTTTATTTTTTTATTTTATATATATATATATTATTATTACTTTTTTATTATCATTTTATTAATT
* * * * *
99364 TGTTTTATTTATATTTTTTTTCTTT
66 TGATATATATATATTTATTTACTTT
* * *
99389 TTCTTTATTTCTTTATTTT-T-T-TATATTTATT-TTAGTTACTATTTTAT
1 TT-TTTATTTTTTTATTTTATATATATATATATTATTA-TTACTTTTTTAT
99436 CTTTGTTTTT
Statistics
Matches: 119, Mismatches: 14, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
87 2 0.02
88 20 0.17
89 1 0.01
90 16 0.13
91 70 0.59
92 10 0.08
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.70
Consensus pattern (90 bp):
TTTTTATTTTTTTATTTTATATATATATATATTATTATTACTTTTTTATTATCATTTTATTAATT
TGATATATATATATTTATTTACTTT
Found at i:99333 original size:28 final size:24
Alignment explanation
Indices: 99300--99397 Score: 83
Period size: 24 Copynumber: 3.8 Consensus size: 24
99290 TTTACTATTT
99300 TTTTATTTTTTTATTTTATATATATA
1 TTTTATTTTTTT-TTTTAT-TATATA
99326 TATATTATTTTTACTTTTTTATTAT-TA
1 T-T-TTATTTTT--TTTTTTATTATATA
*
99353 TTTTATTTATTTGTTTTATT-TATA
1 TTTTATTT-TTTTTTTTATTATATA
*
99377 TTTTTTTTCTTTTTCTTTATT
1 TTTTATTT-TTTTT-TTTATT
99398 TCTTTATTTT
Statistics
Matches: 61, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
23 1 0.02
24 21 0.34
25 12 0.20
26 4 0.07
27 4 0.07
28 11 0.18
29 6 0.10
30 2 0.03
ACGTcount: A:0.20, C:0.03, G:0.01, T:0.76
Consensus pattern (24 bp):
TTTTATTTTTTTTTTTATTATATA
Found at i:99335 original size:36 final size:35
Alignment explanation
Indices: 99272--99353 Score: 87
Period size: 34 Copynumber: 2.3 Consensus size: 35
99262 GTTTTATTAA
* * *
99272 TTTA-TATATATATATTTATTTACTATTTTTTTATTTT
1 TTTATTAT-TATATATATATATACTA--TTTTTACTTT
*
99309 TTTATT-TTATATATATATATATTATTTTTACTTT
1 TTTATTATTATATATATATATACTATTTTTACTTT
99343 TTTATTATTAT
1 TTTATTATTAT
99354 TTTATTTATT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
34 15 0.38
35 4 0.10
36 14 0.36
37 5 0.13
38 1 0.03
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (35 bp):
TTTATTATTATATATATATATACTATTTTTACTTT
Found at i:99390 original size:53 final size:52
Alignment explanation
Indices: 99286--99433 Score: 138
Period size: 53 Copynumber: 2.8 Consensus size: 52
99276 TATATATATA
* * * * *
99286 TTTATTTACTATTTTTTTATTTTTTTATTTTATATATATATATATTATTTTTAC
1 TTTATTTATTA-TTTTTTATTTATTTATTTTATTTATATTTTTATTATTTTT-C
* * *
99340 TTT-TTTATTATTATTTTATTTATTTGTTTTATTTATATTTTTTTTCTTTTTC
1 TTTATTTATTATT-TTTTATTTATTTATTTTATTTATATTTTTATTATTTTTC
* * *
99392 TTTATTTCTTTATTTTTT-TATATTTATTTTAGTTACTATTTT
1 TTTATTT-ATTATTTTTTATTTATTTATTTTATTTA-TATTTT
99434 ATCTTTGTTT
Statistics
Matches: 78, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
52 20 0.26
53 50 0.64
54 8 0.10
ACGTcount: A:0.20, C:0.04, G:0.01, T:0.74
Consensus pattern (52 bp):
TTTATTTATTATTTTTTATTTATTTATTTTATTTATATTTTTATTATTTTTC
Found at i:99450 original size:15 final size:15
Alignment explanation
Indices: 99430--99477 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
99420 TTAGTTACTA
99430 TTTTATCTTTGTTTT
1 TTTTATCTTTGTTTT
*
99445 TTTTATCTTATCTTTT
1 TTTTATCTT-TGTTTT
* *
99461 ATTTA-ATTTGTTTT
1 TTTTATCTTTGTTTT
99475 TTT
1 TTT
99478 CTTCATTTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 7 0.26
15 11 0.41
16 9 0.33
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.77
Consensus pattern (15 bp):
TTTTATCTTTGTTTT
Found at i:99474 original size:27 final size:27
Alignment explanation
Indices: 99444--99495 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
99434 ATCTTTGTTT
*
99444 TTTTTATCTT-ATCTTTTATTTAATTTG
1 TTTTTATCTTCAT-TTTAATTTAATTTG
*
99471 TTTTTTTCTTCATTTTAATTTAATT
1 TTTTTATCTTCATTTTAATTTAATT
99496 AATTTATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (27 bp):
TTTTTATCTTCATTTTAATTTAATTTG
Found at i:99501 original size:36 final size:36
Alignment explanation
Indices: 99461--99529 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
99451 CTTATCTTTT
* *
99461 ATTTAATTTGTTTTTTTCTT-CATTTTAATTTAATTA
1 ATTT-ATTTATTTATTTCTTACATTTTAATTTAATTA
* *
99497 ATTTATTTATTTATTTCTTACCTTTTTATTTAA
1 ATTTATTTATTTATTTCTTACATTTTAATTTAA
99530 CATGGTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 13 0.46
36 15 0.54
ACGTcount: A:0.25, C:0.07, G:0.01, T:0.67
Consensus pattern (36 bp):
ATTTATTTATTTATTTCTTACATTTTAATTTAATTA
Found at i:99512 original size:27 final size:27
Alignment explanation
Indices: 99446--99512 Score: 62
Period size: 27 Copynumber: 2.4 Consensus size: 27
99436 CTTTGTTTTT
* ** *
99446 TTTATCTTATCTTTTATTTAATTTGTTTT
1 TTTAT-TTAT-TTTAATTTAATTAATTTA
* *
99475 TTTCTTCATTTTAATTTAATTAATTTA
1 TTTATTTATTTTAATTTAATTAATTTA
99502 TTTATTTATTT
1 TTTATTTATTT
99513 CTTACCTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
27 23 0.77
28 3 0.10
29 4 0.13
ACGTcount: A:0.22, C:0.06, G:0.01, T:0.70
Consensus pattern (27 bp):
TTTATTTATTTTAATTTAATTAATTTA
Found at i:99866 original size:2 final size:2
Alignment explanation
Indices: 99859--99884 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
99849 TACGGTTACG
99859 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
99885 TATTTTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103276 original size:3 final size:3
Alignment explanation
Indices: 103264--103310 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
103254 TAAATATCAT
* *
103264 TAA T-A TAA TAA TAA TAA TAA TAA TTA TAA TAA TAT TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
103311 AACATGGACG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:104745 original size:122 final size:122
Alignment explanation
Indices: 104183--106063 Score: 1485
Period size: 122 Copynumber: 15.5 Consensus size: 122
104173 AGAGAGTCGG
* * * * *
104183 GTCAATCTAGAAATAATTTGGTGTTGAAGATGACATTGCTCATCCACGTTGAATAG-TCTGGTCA
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGG-CA
* * * * * * *
104247 -TTTTCAAGTAAATTATTT-CATGAGGATGATGTTGTTCATTCTCATTGAGGAAGTCGA
65 GCTTTCAGGTAAATTATTTGC-TGAAGATGATGATGTTCCTTCTTATTGAGGAAGTCAA
* * * * * * * * * *
104304 GTCAATTTAGATACAATTTGGTGTTAAAGATGACATTGCTCATCCACGTTGAAAAGATATGGTCA
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGG-CA
* * * * * **
104369 -CTTTCA-GTTAATTATTTG-TTAGAGATGATGATGTTTCTTCTTGTTGAGAAAGTCGG
65 GCTTTCAGGTAAATTATTTGCTGA-AGATGATGATGTTCCTTCTTATTGAGGAAGTCAA
* * * * *
104425 GTCAATTTGGAGATAATTTAGTGTTGAAGACGACATTGCTCATCCACATTGAAGAGTTCTGGTAG
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGGCAG
** * * * * *
104490 CTTTCAGGTAAATTGGTTACTGAAGATGATGCT-TCTCCTTGTTGTTGAGGAAGTCAG
66 CTTTCAGGTAAATTATTTGCTGAAGATGATGATGT-TCCTTCTTATTGAGGAAGTCAA
* * * * * * * * *
104547 GTC-ATATGGAGATAATTTGGTGTTAAAGACGACCCTGCTCATCTACATTAAAGACTTATAGTC-
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCT-GGCA
* *
104610 GCTTTCAGGTAAATTATTTGCTAAAGATGATGATGCTCCTTCTTATTGAGGAAGTCAA
65 GCTTTCAGGTAAATTATTTGCTGAAGATGATGATGTTCCTTCTTATTGAGGAAGTCAA
* * * * * * *
104668 GTCAATCTGGAGATAATTTGGTGTTGAAGACAACATTTCTCATCCATGTTGAAGTGTTTTGGCAT
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGGCAG
* * * ** *
104733 CTTTTAGGTAAATTGTTTGCTGAAGATGATGCA-ATTCCTTCTCGTTGAGGAAGTCAG
66 CTTTCAGGTAAATTATTTGCTGAAGATGATG-ATGTTCCTTCTTATTGAGGAAGTCAA
* ** *
104790 GTCAATCTAGAGATAATTTGGTGTTGAAGATTACACTGCTAATCCACGTTGAAGAGTTCTGGTC-
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGG-CA
* * * * * * ** * *
104854 GCTTTTC-GATAAA-TAGTTTACTAAAGATGACGTTTTTCCTTCTCGTTGAGTAAGT-TA
65 GC-TTTCAGGTAAATTA-TTTGCTGAAGATGATGATGTTCCTTCTTATTGAGGAAGTCAA
* * * * * * *
104911 GCTCAATTTGGAGATAATTTAGTTTTGAAAACGATAATGCTCATCCACGTTGAAGAGATCTGGTC
1 G-TCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGG-C
* ** * * * *
104976 -GTTTTCAACTAAATTATTTTCT-AGAGATTATGATATTCCTTCTTATTGAGGATGTCAA
64 AGCTTTCAGGTAAATTATTTGCTGA-AGATGATGATGTTCCTTCTTATTGAGGAAGTCAA
* ** ** * * *
105034 GTCAATCTGGACATAATTTAATGTTGAAGATTACACTTCTCAACCACGTTGAAGAGTTCTAGCTA
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGGC-A
* ** * * * **
105099 -CTTTCAAGTAAATCGTTTGCTGAAAATGA-CATTGTTCCTTCTTGTTGAGGAAGTCGG
65 GCTTTCAGGTAAATTATTTGCTGAAGATGATGA-TGTTCCTTCTTATTGAGGAAGTCAA
* * * *
105156 GTCAATCTGGAGATAATTTGGTATTGAAGACGACAATGCTCATCCATGTTGAAGAGTTCTGTCCA
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTG-GCA
* * * * *
105221 -CTTTCAGGTAAATTATTTGATGAAGATGATGTTATTTCTTCTTATTGAGGAAGTCGA
65 GCTTTCAGGTAAATTATTTGCTGAAGATGATGATGTTCCTTCTTATTGAGGAAGTCAA
* ** * * * *
105278 GTCAATCTGGAGGTAATTTGGTGTTGAAGAAAACACTGGTAATCCACGTTGAAGAGTTCTAGCCG
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGGCAG
* * * * * *
105343 CTTTCAGGTAAATTGTTTGCTGAAAATAATGTTGTTCCTTCTCATTGAAGAAGTCAA
66 CTTTCAGGTAAATTATTTGCTGAAGATGATGATGTTCCTTCTTATTGAGGAAGTCAA
* * * * * **
105400 GTTAATCTGGAGATAATTTGATGTTGAAGATGACACTGGTCATCCATGTTGAAGAGTTCTGGTTG
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGGCAG
* * ** * * *
105465 CTTTCAGGAAAATTATCTATTGAAGATGACGTTGTTCCTTGTCT-TTGAGGAAGT-AA
66 CTTTCAGGTAAATTATTTGCTGAAGATGATGATGTTCCTTCT-TATTGAGGAAGTCAA
* * * * * * *
105521 GGTCAATATGGAGATAATTTTGTGGTAAAGACGA-A-TACTCATCCATGTTGAAGAGTTCTGGCC
1 -GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGGCA
* ** * * * * **
105584 GTTTTTGGGTAAATTGTTTACTGAAGATGATGATGTTCCTTCTCATTAAGGAAGTCGG
65 GCTTTCAGGTAAATTATTTGCTGAAGATGATGATGTTCCTTCTTATTGAGGAAGTCAA
* * ** ** * * *
105642 GTCAATCTAGAGATAATTTGATGTTGAAGATAACACTAATCGTCCACGTTGAAGAGTTCTGACCG
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGGCAG
* * * * * * * * *
105707 CTTTTAGGTAAATTGTTTGTTGAAGATGA-CATTATTCATTTTTGTTGAGGAAGTCGA
66 CTTTCAGGTAAATTATTTGCTGAAGATGATGA-TGTTCCTTCTTATTGAGGAAGTCAA
* * * * * *
105764 GTCAATTTGGAGATAATTTGGTGTTGAAGA-GAACACTACTCATCCACATCGAAGAGTTTTGGCC
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACG-ACACTGCTCATCCACGTTGAAGAGTTCTGGCA
* * * * * *
105828 GCTTTCATGTAAATTATTTGATGAAGATGATGTTGTTCCTT-TTCTTTGAGGAATTCAG
65 GCTTTCAGGTAAATTATTTGCTGAAGATGATGATGTTCCTTCTT-ATTGAGGAAGTCAA
* ** * * * * *
105886 GTCAATTTGGAGATAATTTGGCATTAAAGATGACATTGCTCATCCACATTGAAGAGTTCTAGCAG
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGGCAG
* * * * * * **
105951 CTTTCAGGTAAATTATTTGTTGAAGATGAAT-CTATTCTTTCTCATTGAGGAATTCTG
66 CTTTCAGGTAAATTATTTGCTGAAGATG-ATGATGTTCCTTCTTATTGAGGAAGTCAA
* * *
106008 GTCAATCTGGAGATAATTTGGTATTGAAGACGACATTGCTCATCCACATTGAAGAG
1 GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAG
106064 ATCTAGTCAC
Statistics
Matches: 1411, Mismatches: 308, Indels: 81
0.78 0.17 0.05
Matches are distributed among these distances:
120 94 0.07
121 263 0.19
122 1037 0.73
123 17 0.01
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (122 bp):
GTCAATCTGGAGATAATTTGGTGTTGAAGACGACACTGCTCATCCACGTTGAAGAGTTCTGGCAG
CTTTCAGGTAAATTATTTGCTGAAGATGATGATGTTCCTTCTTATTGAGGAAGTCAA
Found at i:108880 original size:14 final size:14
Alignment explanation
Indices: 108861--108908 Score: 64
Period size: 13 Copynumber: 3.6 Consensus size: 14
108851 AAATACTTGA
108861 TTTGTTTTCTTTTT
1 TTTGTTTTCTTTTT
108875 TTTG-TTTCTTTTT
1 TTTGTTTTCTTTTT
* *
108888 TTT-TATTCTCTTT
1 TTTGTTTTCTTTTT
108901 TTTGTTTT
1 TTTGTTTT
108909 TTCTCTTTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 22 0.76
14 7 0.24
ACGTcount: A:0.02, C:0.08, G:0.06, T:0.83
Consensus pattern (14 bp):
TTTGTTTTCTTTTT
Found at i:108891 original size:16 final size:15
Alignment explanation
Indices: 108870--108929 Score: 68
Period size: 16 Copynumber: 3.9 Consensus size: 15
108860 ATTTGTTTTC
*
108870 TTTTTTTTGTT-TCT
1 TTTTTTTTTTTCTCT
*
108884 TTTTTTTTATTCTCT
1 TTTTTTTTTTTCTCT
108899 TTTTTGTTTTTTCTCT
1 TTTTT-TTTTTTCTCT
108915 TTCTTATTTTTTTCT
1 TT-TT-TTTTTTTCT
108930 TTTCTATTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
14 10 0.25
15 8 0.20
16 11 0.28
17 10 0.25
18 1 0.03
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (15 bp):
TTTTTTTTTTTCTCT
Found at i:108933 original size:16 final size:16
Alignment explanation
Indices: 108866--108938 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 16
108856 CTTGATTTGT
* *
108866 TTTCTTTTTTTTGTTTC
1 TTTCTATTTTTT-TCTC
108883 TTT-T-TTTTTATTCTC
1 TTTCTATTTTT-TTCTC
*
108898 TTT-TTTGTTTTTTCTC
1 TTTCTAT-TTTTTTCTC
108914 TTTCTTATTTTTTTCT-
1 TTTC-TATTTTTTTCTC
108930 TTTCTATTT
1 TTTCTATTT
108939 GTTCTGGCTT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
15 17 0.35
16 15 0.31
17 15 0.31
18 2 0.04
ACGTcount: A:0.04, C:0.12, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTCTATTTTTTTCTC
Found at i:108938 original size:15 final size:13
Alignment explanation
Indices: 108865--108932 Score: 64
Period size: 16 Copynumber: 4.7 Consensus size: 13
108855 ACTTGATTTG
108865 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
*
108878 GTTTCTTTTTTTT
1 TTTTCTTTTTTTT
108891 TATTCTCTTTTTTGTTT
1 T-TT-TC-TTTTT-TTT
108908 TTTCTCTTTCTTATTT
1 TTT-TCTTT-TT-TTT
108924 TTTTCTTTT
1 TTTTCTTTT
108933 CTATTTGTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
13 12 0.26
14 3 0.06
15 10 0.21
16 18 0.38
17 4 0.09
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:108940 original size:35 final size:35
Alignment explanation
Indices: 108870--108941 Score: 83
Period size: 35 Copynumber: 2.1 Consensus size: 35
108860 ATTTGTTTTC
* * *
108870 TTTTTTTTGTTTCTTTTTTTTTATTCTCTTTTTTG
1 TTTTTTCTCTTTCTTTTTTTTTATTCTCTTATTTG
* *
108905 TTTTTTCTCTTTCTTATTTTTTTCTTTTC-TATTTG
1 TTTTTTCTCTTTCTT-TTTTTTTATTCTCTTATTTG
108940 TT
1 TT
108942 CTGGCTTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.81
Consensus pattern (35 bp):
TTTTTTCTCTTTCTTTTTTTTTATTCTCTTATTTG
Found at i:110922 original size:22 final size:22
Alignment explanation
Indices: 110894--110964 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
110884 TAAATCACGG
*
110894 AAGTGCCTTAGCACTAATACTA
1 AAGTGCCTTAGCACTAATACAA
* * *
110916 AAGTGCCTCAGTACTGATACAA
1 AAGTGCCTTAGCACTAATACAA
* * * *
110938 AAGTACTTTCGCACTAGTACAA
1 AAGTGCCTTAGCACTAATACAA
110960 AAGTG
1 AAGTG
110965 TAATAACACT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (22 bp):
AAGTGCCTTAGCACTAATACAA
Found at i:114609 original size:24 final size:24
Alignment explanation
Indices: 114577--114625 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
114567 ACTCGACAAG
114577 TCCAAGGAAACTACGCACATTGGA
1 TCCAAGGAAACTACGCACATTGGA
114601 TCCAAGGAAACTACGCACATTGGA
1 TCCAAGGAAACTACGCACATTGGA
114625 T
1 T
114626 ACGTTCTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.18
Consensus pattern (24 bp):
TCCAAGGAAACTACGCACATTGGA
Found at i:117906 original size:22 final size:22
Alignment explanation
Indices: 117878--117962 Score: 91
Period size: 22 Copynumber: 3.9 Consensus size: 22
117868 CCATTCAATC
117878 ACAAAAGTGCCTTAACACTAAT
1 ACAAAAGTGCCTTAACACTAAT
* *
117900 A-ATAAAGTGCCTTAGCACTGAT
1 ACA-AAAGTGCCTTAACACTAAT
* **
117922 ACAAAAGTGCATTCGCACTAAT
1 ACAAAAGTGCCTTAACACTAAT
* *
117944 ACAAAAGTGTCATAACACT
1 ACAAAAGTGCCTTAACACT
117963 GGGAGGAGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
21 1 0.02
22 49 0.96
23 1 0.02
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.24
Consensus pattern (22 bp):
ACAAAAGTGCCTTAACACTAAT
Found at i:117963 original size:44 final size:44
Alignment explanation
Indices: 117878--117963 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
117868 CCATTCAATC
* * *
117878 ACAAAAGTGCCTTAACACTAATAATAAAGTGCCTTAGCACTGAT
1 ACAAAAGTGCATTAACACTAATAATAAAGTGCCATAACACTGAT
** *
117922 ACAAAAGTGCATTCGCACTAATACA-AAAGTGTCATAACACTG
1 ACAAAAGTGCATTAACACTAATA-ATAAAGTGCCATAACACTG
117964 GGAGGAGAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 34 0.97
45 1 0.03
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (44 bp):
ACAAAAGTGCATTAACACTAATAATAAAGTGCCATAACACTGAT
Found at i:120954 original size:2 final size:2
Alignment explanation
Indices: 120947--120979 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
120937 AAATAATAAG
120947 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
120980 CAAAGGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:122968 original size:28 final size:28
Alignment explanation
Indices: 122928--123006 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
122918 GATGCATTCT
122928 TGATTCTGCATGGGCTTAGTCCAT-GTCC
1 TGATTCTGCATGGGCTTAGTCC-TCGTCC
* * *
122956 TGATTCTGCATGGACTTCGACCTCGTCC
1 TGATTCTGCATGGGCTTAGTCCTCGTCC
* *
122984 TGACATCTGTATGGGCTTAGTCC
1 TGA-TTCTGCATGGGCTTAGTCC
123007 CCATCTTGAC
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
27 1 0.02
28 26 0.63
29 14 0.34
ACGTcount: A:0.15, C:0.27, G:0.24, T:0.34
Consensus pattern (28 bp):
TGATTCTGCATGGGCTTAGTCCTCGTCC
Found at i:126479 original size:22 final size:22
Alignment explanation
Indices: 126417--126487 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
126407 TTAAATTTTA
* * *
126417 AAATATTTTATATAAATATTTT
1 AAATATTTTATATTAATCTTTG
*
126439 AAAT-TTATT-TA-TAAACTTTG
1 AAATATT-TTATATTAATCTTTG
126459 AAATATTTTATATTAATCTTTG
1 AAATATTTTATATTAATCTTTG
*
126481 AACTATT
1 AAATATT
126488 AATATCATTA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 11 0.28
21 8 0.21
22 20 0.51
ACGTcount: A:0.41, C:0.04, G:0.03, T:0.52
Consensus pattern (22 bp):
AAATATTTTATATTAATCTTTG
Found at i:134547 original size:22 final size:22
Alignment explanation
Indices: 134521--134570 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
134511 GTTTGTATCT
*
134521 TCTCTGTTTTTTTTTTTCTGTC
1 TCTCTGTCTTTTTTTTTCTGTC
134543 TCTC--TCTTTTTTTTTCTGTC
1 TCTCTGTCTTTTTTTTTCTGTC
134563 TCTCTGTC
1 TCTCTGTC
134571 CCGTTCTCTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 19 0.76
22 6 0.24
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (22 bp):
TCTCTGTCTTTTTTTTTCTGTC
Found at i:134552 original size:20 final size:20
Alignment explanation
Indices: 134529--134567 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
134519 CTTCTCTGTT
134529 TTTTTTTTTCTGTCTCTCTC
1 TTTTTTTTTCTGTCTCTCTC
134549 TTTTTTTTTCTGTCTCTCT
1 TTTTTTTTTCTGTCTCTCT
134568 GTCCCGTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTCTGTCTCTCTC
Found at i:135051 original size:3 final size:3
Alignment explanation
Indices: 135043--135143 Score: 166
Period size: 3 Copynumber: 33.7 Consensus size: 3
135033 AATATATATT
*
135043 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
135091 TAG TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
135139 TAA TA
1 TAA TA
135144 TGGATAAAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:135678 original size:113 final size:113
Alignment explanation
Indices: 135462--136023 Score: 914
Period size: 113 Copynumber: 5.0 Consensus size: 113
135452 AGAATTATGC
* * * *
135462 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCT
* * * * * * *
135527 CATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGC
63 CATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
135578 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
135643 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
135691 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
135756 TATGAACTTTCTCTGGAAAAGCCGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
135804 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
135869 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
66 TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
*
135917 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * *
135982 TATGAAC-TTCTCTGGCAAAA-ATAATCCATCAAATGATAGATT
66 TATGAACTTTCTCTGG-AAAAGCTGATCCATCAAATGATGGATT
136024 TGAATCTTTG
Statistics
Matches: 427, Mismatches: 17, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
112 29 0.07
113 350 0.82
116 48 0.11
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAGGT
Found at i:136925 original size:84 final size:84
Alignment explanation
Indices: 136755--137067 Score: 574
Period size: 84 Copynumber: 3.7 Consensus size: 84
136745 GTAATTTTTA
* * *
136755 CCAAACCAGATTAGATAACTCAAAGAACACTTTCAAAAGATGCTATTG-GCAAATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCAAATTCATCTTCCA
136819 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
*
136838 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCAAATTCATCTTCCA
136903 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
*
136922 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCAAATTCATCTTCCA
136987 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
137006 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCAAATTCATCTT
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCAAATTCATCTT
137068 TCAGTTAATG
Statistics
Matches: 224, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
83 44 0.20
84 180 0.80
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.27
Consensus pattern (84 bp):
CCAAATCAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTATTGAGCAAATTCATCTTCCA
AATTCAATGATTGGTTCTG
Found at i:137857 original size:19 final size:20
Alignment explanation
Indices: 137833--137874 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
137823 AATAGAAAAG
*
137833 AATAAATTGAATTTCCAA-A
1 AATAAATTGAATCTCCAATA
137852 AATAAATTGAATCTCCAATA
1 AATAAATTGAATCTCCAATA
137872 AAT
1 AAT
137875 TGAACTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (20 bp):
AATAAATTGAATCTCCAATA
Found at i:138225 original size:7 final size:7
Alignment explanation
Indices: 138208--138275 Score: 72
Period size: 7 Copynumber: 10.1 Consensus size: 7
138198 TTGACCCCCC
138208 TTTTTCT
1 TTTTTCT
138215 TTTTT-T
1 TTTTTCT
*
138221 CTTTT-T
1 TTTTTCT
138227 TTTTTCT
1 TTTTTCT
*
138234 TTCTTCT
1 TTTTTCT
138241 TTTTT-T
1 TTTTTCT
138247 TTTCTTC-
1 TTT-TTCT
138254 TTTTTCT
1 TTTTTCT
138261 TTTTTCT
1 TTTTTCT
*
138268 TTTCTCT
1 TTTTTCT
138275 T
1 T
138276 CAAGCATAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
6 17 0.33
7 35 0.67
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:138229 original size:18 final size:18
Alignment explanation
Indices: 138208--138265 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 18
138198 TTGACCCCCC
138208 TTTTTCTTTTTTTCTTTT
1 TTTTTCTTTTTTTCTTTT
*
138226 TTTTT-TCTTTCTTCTTTTT
1 TTTTTCT-TTTTTTC-TTTT
138245 TTTTTCTTCTTTTTCTTTT
1 TTTTTCTT-TTTTTCTTTT
138264 TT
1 TT
138266 CTTTTCTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
17 1 0.03
18 11 0.32
19 16 0.47
20 6 0.18
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (18 bp):
TTTTTCTTTTTTTCTTTT
Found at i:138272 original size:18 final size:17
Alignment explanation
Indices: 138216--138275 Score: 77
Period size: 18 Copynumber: 3.5 Consensus size: 17
138206 CCTTTTTCTT
138216 TTTTTCTTTTTTTTTTC
1 TTTTTCTTTTTTTTTTC
138233 TTTCTTCTTTTTTTTTTC
1 TTT-TTCTTTTTTTTTTC
* *
138251 TTCTT-TTTCTTTTTTC
1 TTTTTCTTTTTTTTTTC
138267 TTTTCTCTT
1 TTTT-TCTT
138276 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
16 13 0.35
17 6 0.16
18 18 0.49
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTTTTTTTTC
Found at i:150483 original size:21 final size:21
Alignment explanation
Indices: 150458--150505 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
150448 GTTTGTATCT
* *
150458 TCTCTGTTTTTTTTTTTTGTC
1 TCTCTGTCTTTTTTTTCTGTC
150479 TCTC--TCTTTTTTTTCTGTC
1 TCTCTGTCTTTTTTTTCTGTC
150498 TCTCTGTC
1 TCTCTGTC
150506 CCGTTCTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 17 0.74
21 6 0.26
ACGTcount: A:0.00, C:0.23, G:0.08, T:0.69
Consensus pattern (21 bp):
TCTCTGTCTTTTTTTTCTGTC
Found at i:150490 original size:17 final size:19
Alignment explanation
Indices: 150466--150502 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
150456 CTTCTCTGTT
*
150466 TTTTTTTTTTGTCTCTCTC
1 TTTTTTTTCTGTCTCTCTC
150485 TTTTTTTTCTGTCTCTCT
1 TTTTTTTTCTGTCTCTCT
150503 GTCCCGTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.00, C:0.22, G:0.05, T:0.73
Consensus pattern (19 bp):
TTTTTTTTCTGTCTCTCTC
Found at i:150983 original size:3 final size:3
Alignment explanation
Indices: 150975--151069 Score: 147
Period size: 3 Copynumber: 31.7 Consensus size: 3
150965 TTAATATATT
* *
150975 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
151022 TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
151068 TA
1 TA
151070 TGGATAAAAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
2 2 0.02
3 79 0.94
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:151214 original size:24 final size:22
Alignment explanation
Indices: 151178--151232 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
151168 AAAACACAAG
*
151178 AATTTTCCAA-AAAAAAAT-TT
1 AATTTTCAAATAAAAAAATGTT
151198 AAATTTTCGAAATAAAAAAATGTT
1 -AATTTTC-AAATAAAAAAATGTT
151222 AATTTTCAAAT
1 AATTTTCAAAT
151233 TATTGTGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.23
22 6 0.20
23 15 0.50
24 2 0.07
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (22 bp):
AATTTTCAAATAAAAAAATGTT
Found at i:161486 original size:31 final size:31
Alignment explanation
Indices: 161419--161478 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
161409 CAATTTAAGG
*
161419 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
161450 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
161479 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:166065 original size:12 final size:12
Alignment explanation
Indices: 166026--166065 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
166016 ATCAAATTCT
*
166026 TCCTCAACTTCC
1 TCCTCAGCTTCC
*
166038 TACTCAGCTTCC
1 TCCTCAGCTTCC
*
166050 TCCTCAGCTTCT
1 TCCTCAGCTTCC
166062 TCCT
1 TCCT
166066 GAACATCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.12, C:0.45, G:0.05, T:0.38
Consensus pattern (12 bp):
TCCTCAGCTTCC
Found at i:175758 original size:113 final size:112
Alignment explanation
Indices: 175325--175891 Score: 902
Period size: 112 Copynumber: 5.1 Consensus size: 112
175315 ACTTCGGTTT
* *
175325 GTGTCGATAATTTAT-AAAATGTATTGATCCATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* **
175388 GGTCTATAAATGACAAAACAGGTAAAACGCTACTAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
175435 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
175500 GGTCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
175547 GTGTCAATACTTTATAAAAATGTA---ATCCATAACAATAT-A-AGGTAAAAAAATGACAAAAGC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
175607 GGTCTATAAATGGACAAAACAAGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAAT-GACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
175655 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAAAATGACAAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGAC-AAAAC
*
175720 CGGTCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
175768 GTGTCGATACTTTATAAAAATGTATCAATCTATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
175832 GGT-TATAAATGATAAAACAGGTAAAGCGCTA-CGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
175877 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
175892 TATAAGTATC
Statistics
Matches: 426, Mismatches: 22, Indels: 19
0.91 0.05 0.04
Matches are distributed among these distances:
107 31 0.07
108 58 0.14
109 41 0.10
110 40 0.09
111 54 0.13
112 93 0.22
113 93 0.22
114 16 0.04
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:175996 original size:66 final size:67
Alignment explanation
Indices: 175878--176021 Score: 227
Period size: 66 Copynumber: 2.2 Consensus size: 67
175868 ATGTTGATAG
* *
175878 TGTCGATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGTTATAGCGCTAGTAA
1 TGTCAATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGTTATAGCGCTAATAA
175943 AA
66 AA
* *
175945 TGTCAATATTTTATTATAAGTATCGACA-TTTTGGAATTTAAAAGAGAAGTTATAGCGCTAATAA
1 TGTCAATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGTTATAGCGCTAATAA
*
176009 AG
66 AA
*
176011 TGTCGATACTT
1 TGTCAATACTT
176022 ATAAAAAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
66 44 0.63
67 26 0.37
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.36
Consensus pattern (67 bp):
TGTCAATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGTTATAGCGCTAATAA
AA
Done.