Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001607.1 Hibiscus syriacus cultivar Beakdansim tig00003191_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: 136664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:713 original size:31 final size:29
Alignment explanation
Indices: 671--767 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 29
661 TTTATGAGTT
* *
671 AAATTGGTATTTTAACTAAAGTTTAAGGATC
1 AAATTGATATTTTATCTAAA-TTTAA-GATC
* *
702 AAATTGATATTTTATCTTAAAATTATATATC
1 AAATTGATATTTTATC-TAAATTTA-AGATC
* *
733 AAATTAATATTTTATCTAAAATCTAATGATC
1 AAATTGATATTTTATCT-AAATTTAA-GATC
764 AAAT
1 AAAT
768 ATAAAATTAA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
30 2 0.04
31 47 0.87
32 5 0.09
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.42
Consensus pattern (29 bp):
AAATTGATATTTTATCTAAATTTAAGATC
Found at i:1182 original size:24 final size:22
Alignment explanation
Indices: 1155--1208 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 22
1145 TGTTGTTGGT
1155 GATCAAGCTACCGATAACACAACC
1 GATCAAGCTACCGATAAC-CAA-C
1179 GATC-A---ACCGATAACCAAC
1 GATCAAGCTACCGATAACCAAC
1197 GATCAAGCTACC
1 GATCAAGCTACC
1209 AATCAAGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
18 5 0.19
19 4 0.15
20 9 0.35
22 3 0.12
23 1 0.04
24 4 0.15
ACGTcount: A:0.41, C:0.33, G:0.13, T:0.13
Consensus pattern (22 bp):
GATCAAGCTACCGATAACCAAC
Found at i:1201 original size:18 final size:20
Alignment explanation
Indices: 1164--1202 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1154 TGATCAAGCT
1164 ACCGATAACACAACCGATCA
1 ACCGATAACACAACCGATCA
1184 ACCGATAAC-CAA-CGATCA
1 ACCGATAACACAACCGATCA
1202 A
1 A
1203 GCTACCAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.46, C:0.33, G:0.10, T:0.10
Consensus pattern (20 bp):
ACCGATAACACAACCGATCA
Found at i:4413 original size:23 final size:23
Alignment explanation
Indices: 4369--4412 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
4359 TATATTTCGA
4369 TTTTATTTATTTTTCATTTTTTG
1 TTTTATTTATTTTTCATTTTTTG
4392 TTTTA-TTATTTTTCATTTTTT
1 TTTTATTTATTTTTCATTTTTT
4413 TTTATTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.80
Consensus pattern (23 bp):
TTTTATTTATTTTTCATTTTTTG
Found at i:7502 original size:15 final size:15
Alignment explanation
Indices: 7477--7516 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
7467 AAAAAGAGAA
7477 AAAGAGAAAAAAAAGC
1 AAAGAGAAAAAAAA-C
7493 AAAGAGAAAAAAAAC
1 AAAGAGAAAAAAAAC
7508 AAAG-GAAAA
1 AAAGAGAAAA
7517 TTGAAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 5 0.21
15 5 0.21
16 14 0.58
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAGAGAAAAAAAAC
Found at i:7707 original size:69 final size:69
Alignment explanation
Indices: 7589--7726 Score: 224
Period size: 69 Copynumber: 2.0 Consensus size: 69
7579 GGTTCAAACT
* *
7589 ATGAGATTGATCAAGCACAATCATTTCCGAATCACTGAACTACTTCACTCAAAGATCATAGAGCA
1 ATGAGACTGATCAAGCACAATCATTTCCGAATCACTGAACTACTCCACTCAAAGATCATAGAGCA
7654 TCAA
66 TCAA
* *
7658 ATGAGACTGATCAAGCACAATCATTTCTGAATCACTGAA-TCACTCCACTCGAAGATCATAGAGC
1 ATGAGACTGATCAAGCACAATCATTTCCGAATCACTGAACT-ACTCCACTCAAAGATCATAGAGC
7722 ATCAA
65 ATCAA
7727 GAGAGAGAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
68 1 0.02
69 63 0.98
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (69 bp):
ATGAGACTGATCAAGCACAATCATTTCCGAATCACTGAACTACTCCACTCAAAGATCATAGAGCA
TCAA
Found at i:9319 original size:36 final size:36
Alignment explanation
Indices: 9272--9361 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
9262 ATTGAAAACA
*
9272 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* *
9308 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
9344 TTTCCCTTGAAACAAATT
1 TTTCCCTTGAAACAAATT
9362 ATTTGAAACA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:9357 original size:86 final size:86
Alignment explanation
Indices: 9277--9445 Score: 214
Period size: 86 Copynumber: 2.0 Consensus size: 86
9267 AAACATTTCC
* * * *
9277 CTTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACTAAATCTTGTCTCTCTTGAGA
*
9341 TAGTTTCCCTTGAAACAAATTA
66 CAGTTTCCCTTGAAAC-AATTA
* * ** * *
9363 TTTGAAACAAATTTCATCTCCCTTGAGACATTTTCTTTTGGAACTAAGTCTTGTCTCTCTTGAGA
1 CTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACTAAATCTTGTCTCTCTTGAGA
*
9428 CAGTTTCTCTTGAAACAA
66 CAGTTTCCCTTGAAACAA
9446 ATTTCATCTC
Statistics
Matches: 70, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
86 38 0.54
87 32 0.46
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (86 bp):
CTTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACTAAATCTTGTCTCTCTTGAGA
CAGTTTCCCTTGAAACAATTA
Found at i:9434 original size:87 final size:86
Alignment explanation
Indices: 9278--9448 Score: 234
Period size: 87 Copynumber: 2.0 Consensus size: 86
9268 AACATTTCCC
* * * * *
9278 TTGAAATAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATA
1 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAATCTTGTCTCTCTTGAGACA
9343 GTTTCCCTTGAAACAAATTAT
66 GTTTCCCTTGAAACAAATTAT
* ** * *
9364 TTGAAACAAATTTCATCTCCCTTGAGACATTTTCTTTTGGAACTAAGTCTTGTCTCTCTTGAGAC
1 TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAAC-AAATCTTGTCTCTCTTGAGAC
*
9429 AGTTTCTCTTGAAACAAATT
65 AGTTTCCCTTGAAACAAATT
9449 TCATCTCTCT
Statistics
Matches: 73, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
86 36 0.49
87 37 0.51
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (86 bp):
TTGAAACAAATTTCATCTCCCTTGAGACAGTTTCCCTTGAAACAAATCTTGTCTCTCTTGAGACA
GTTTCCCTTGAAACAAATTAT
Found at i:9463 original size:36 final size:36
Alignment explanation
Indices: 9364--9478 Score: 142
Period size: 36 Copynumber: 3.2 Consensus size: 36
9354 AACAAATTAT
* * *
9364 TTGAAACAAATTTCATCTCCCTTGAGACATTTTCTT
1 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTC
* * *
9400 TTGGAACTAAGTCTT-GTCTCTCTTGAGACAGTTTCTC
1 TTGAAAC-AAAT-TTCATCTCTCTTGAGACAGTTTCTC
*
9437 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCCC
1 TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTC
9473 TTGAAA
1 TTGAAA
9479 AAAAATCTTT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
35 2 0.03
36 35 0.53
37 27 0.41
38 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (36 bp):
TTGAAACAAATTTCATCTCTCTTGAGACAGTTTCTC
Found at i:9610 original size:67 final size:67
Alignment explanation
Indices: 9440--9612 Score: 210
Period size: 65 Copynumber: 2.6 Consensus size: 67
9430 GTTTCTCTTG
** * * * **
9440 AAACAAATTTCATCTCTCTTGAGACAGTTTCCCTTGAAA-A-AAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
9503 TA
66 TA
* *
9505 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
9570 TA
66 TA
*
9572 AAACAAAATTTTGTTTCCCTTGAGACCA-TTT-TCATGAAACA
1 AAAC-AAATTTTGTCTCCCTTGAGA-CAGTTTCTCATGAAACA
9613 ACATATGTCT
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
65 35 0.37
66 1 0.01
67 35 0.37
68 22 0.23
69 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.36
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCATGAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:10598 original size:110 final size:109
Alignment explanation
Indices: 10332--10698 Score: 485
Period size: 110 Copynumber: 3.4 Consensus size: 109
10322 GCTTCCCAGT
* * *
10332 TTCAGAGCCAATTTCAACTTCACAGCGAGGGATATTGGACTCAATACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
*
10397 CAACGAAGGGGCAACTGATTGTCAACAAACAACTTTCAGTTTCA
66 CAACGAAGGGGCGACTGATTGTCAACAAACAACTTTCAGTTTCA
*
10441 TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * *
10506 CAACGAAGCGGCGATTGATTGTCAACAAACAACTTTTCAGTTTTA
66 CAACGAAGGGGCGACTGATTGTCAACAAACAAC-TTTCAGTTTCA
* ** *
10551 TTCAGAGCCAATTTCAACTTCATATTGAAGGATATTGAACTCGAGACAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
* * **
10616 CACCGAAGGGGCGGCTGGCTGTCAACAAACAA-TTTCCCAG-TTC-
66 CAACGAAGGGGCGACTGATTGTCAACAAACAACTTT--CAGTTTCA
* * *
10659 --CAGATCCAATTTCAACTTCAC-GACGGAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGAACTC
10699 GGAACAATAC
Statistics
Matches: 228, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
106 33 0.14
108 3 0.01
109 93 0.41
110 99 0.43
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (109 bp):
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGAACTCAAGACAACACAAGCTCAACTTCA
CAACGAAGGGGCGACTGATTGTCAACAAACAACTTTCAGTTTCA
Found at i:12021 original size:18 final size:18
Alignment explanation
Indices: 12000--12043 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
11990 TTTCATCCCC
12000 TATATATATATATTTAAT
1 TATATATATATATTTAAT
* * *
12018 TATATTTATTTATTTATT
1 TATATATATATATTTAAT
12036 TACTATAT
1 TA-TATAT
12044 TCCTTTTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATATATATATTTAAT
Found at i:12035 original size:22 final size:23
Alignment explanation
Indices: 12010--12072 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 23
12000 TATATATATA
12010 TATTTAATTATATTTATTTAT-T
1 TATTTAATTATATTTATTTATGT
* ** *
12032 TATTT-ACTATATTCCTTTTTGT
1 TATTTAATTATATTTATTTATGT
12054 TATTTATATTATA-TTATTT
1 TATTTA-ATTATATTTATTT
12073 TTATTATATA
Statistics
Matches: 31, Mismatches: 7, Indels: 5
0.72 0.16 0.12
Matches are distributed among these distances:
21 11 0.35
22 11 0.35
23 4 0.13
24 5 0.16
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.67
Consensus pattern (23 bp):
TATTTAATTATATTTATTTATGT
Found at i:12072 original size:14 final size:14
Alignment explanation
Indices: 12053--12092 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
12043 TTCCTTTTTG
12053 TTATTTATATTATA
1 TTATTTATATTATA
*
12067 TTATTTTTATTATA
1 TTATTTATATTATA
12081 TATATCTTATAT
1 T-TAT-TTATAT
12093 CATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 14 0.64
15 3 0.14
16 5 0.23
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (14 bp):
TTATTTATATTATA
Found at i:12438 original size:18 final size:17
Alignment explanation
Indices: 12415--12448 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
12405 ATTTTTATTC
12415 ATTTTTAATTTCTTTTAT
1 ATTTTTAATTT-TTTTAT
*
12433 ATTTTTTATTTTTTTA
1 ATTTTTAATTTTTTTA
12449 CTTCATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTAATTTTTTTAT
Found at i:12445 original size:26 final size:26
Alignment explanation
Indices: 12416--12465 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
12406 TTTTTATTCA
* * *
12416 TTTTTAATTTCTTTTATATTTTTTAT
1 TTTTTAACTTCATTAATATTTTTTAT
*
12442 TTTTTTACTTCATTAATATTTTTT
1 TTTTTAACTTCATTAATATTTTTT
12466 TCCAATTCTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.74
Consensus pattern (26 bp):
TTTTTAACTTCATTAATATTTTTTAT
Found at i:17371 original size:28 final size:28
Alignment explanation
Indices: 17339--17431 Score: 82
Period size: 28 Copynumber: 3.2 Consensus size: 28
17329 TTAGGTAATT
17339 ATAATTTTTTGTTATACTGTTAGATAAA
1 ATAATTTTTTGTTATACTGTTAGATAAA
* * * *
17367 ATAATCATTTT-TAATCAAT-TTAGACTGTAATT
1 ATAAT-TTTTTGTTAT-ACTGTTAGA---TAA-A
17399 ATAATTTTTTGTTATACTGTTAGATAAA
1 ATAATTTTTTGTTATACTGTTAGATAAA
17427 ATAAT
1 ATAAT
17432 CATTTTAATC
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
28 18 0.37
29 9 0.18
31 9 0.18
32 13 0.27
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (28 bp):
ATAATTTTTTGTTATACTGTTAGATAAA
Found at i:17422 original size:32 final size:31
Alignment explanation
Indices: 17333--17423 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 31
17323 AATTATTTAG
17333 GTAATTATAATTTTTTGTTATACTGTTAGAT
1 GTAATTATAATTTTTTGTTATACTGTTAGAT
** * * ** *
17364 AAAATAATCATTTTTAATCA-A-T-TTAGACT
1 GTAATTATAATTTTTTGTTATACTGTTAGA-T
17393 GTAATTATAATTTTTTGTTATACTGTTAGAT
1 GTAATTATAATTTTTTGTTATACTGTTAGAT
17424 AAAATAATCA
Statistics
Matches: 42, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
28 5 0.12
29 15 0.36
30 2 0.05
31 15 0.36
32 5 0.12
ACGTcount: A:0.34, C:0.05, G:0.10, T:0.51
Consensus pattern (31 bp):
GTAATTATAATTTTTTGTTATACTGTTAGAT
Found at i:17447 original size:59 final size:60
Alignment explanation
Indices: 17333--17459 Score: 238
Period size: 60 Copynumber: 2.1 Consensus size: 60
17323 AATTATTTAG
17333 GTAATTATAATTTTTTGTTATACTGTTAGATAAAATAATCATTTTTAATCAATTTAGACT
1 GTAATTATAATTTTTTGTTATACTGTTAGATAAAATAATCATTTTTAATCAATTTAGACT
17393 GTAATTATAATTTTTTGTTATACTGTTAGATAAAATAATCA-TTTTAATCAATTTAGACT
1 GTAATTATAATTTTTTGTTATACTGTTAGATAAAATAATCATTTTTAATCAATTTAGACT
*
17452 TTAATTAT
1 GTAATTAT
17460 TTGATAATTA
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
59 25 0.38
60 41 0.62
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.49
Consensus pattern (60 bp):
GTAATTATAATTTTTTGTTATACTGTTAGATAAAATAATCATTTTTAATCAATTTAGACT
Found at i:19839 original size:29 final size:29
Alignment explanation
Indices: 19784--19840 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
19774 TGAGAGTCAT
* * *
19784 AGTTTGGGGATGAATTTGAAATGTTTAAG
1 AGTTTGAGGATGAATTAGAAATATTTAAG
19813 AGTTTGAGGATGAAATTAG-AATATTTAA
1 AGTTTGAGGATG-AATTAGAAATATTTAA
19841 ATGCTTAGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.37, C:0.00, G:0.26, T:0.37
Consensus pattern (29 bp):
AGTTTGAGGATGAATTAGAAATATTTAAG
Found at i:21502 original size:59 final size:59
Alignment explanation
Indices: 21374--21510 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
21364 AAAGTTGGGT
* * * * *
21374 GACCATTTTGTAACTTTAATAGTCGAGGGACTCAACAAAGCAACTCCTTATAGTCGAGG
1 GACCATTTTGTAACTTTAATAATCGAGGGACTCAACAAAACAACACCATATAGTCAAGG
* *
21433 GACCATTTTGTAACTTTTAATAATCTG-GGGATTCAACAAAACTACACCATATAGTCAAGG
1 GACCATTTTGTAAC-TTTAATAATC-GAGGGACTCAACAAAACAACACCATATAGTCAAGG
*
21493 GATCATTTGTGT-ACTTTA
1 GACCATTT-TGTAACTTTA
21511 TCCATTTTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
59 18 0.27
60 45 0.67
61 4 0.06
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (59 bp):
GACCATTTTGTAACTTTAATAATCGAGGGACTCAACAAAACAACACCATATAGTCAAGG
Found at i:21562 original size:22 final size:22
Alignment explanation
Indices: 21537--21586 Score: 91
Period size: 22 Copynumber: 2.3 Consensus size: 22
21527 TTTGAATTTT
21537 ATCTCTTAAATTTTATTACTTC
1 ATCTCTTAAATTTTATTACTTC
*
21559 ATCTCTTAAATTTTATTAGTTC
1 ATCTCTTAAATTTTATTACTTC
21581 ATCTCT
1 ATCTCT
21587 AACGTAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.02, T:0.54
Consensus pattern (22 bp):
ATCTCTTAAATTTTATTACTTC
Found at i:22199 original size:6 final size:6
Alignment explanation
Indices: 22190--22227 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
22180 AAAAGAGGAC
*
22190 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGG GAGGGA GA
1 GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GAGGGA GA
22228 ATTTTACTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGGGA
Found at i:26261 original size:60 final size:60
Alignment explanation
Indices: 26195--26359 Score: 190
Period size: 60 Copynumber: 2.8 Consensus size: 60
26185 AGTTTTATTT
* * * *
26195 TAAATTAGACTTTAAAGTTTTGCATATTTTAATTTTATCCCTAAACTATGAC-TCTCATTC
1 TAAATTAGACCTTAAACTTTTGAATATTATAATTTTATCCCTAAACTATGACAT-TCATTC
* * * *
26255 TAAATTA-ATCCTTAAACTTTTGAATATTCTGATTTCATCCCTAAACTATGACATTCTTTC
1 TAAATTAGA-CCTTAAACTTTTGAATATTATAATTTTATCCCTAAACTATGACATTCATTC
* * * *
26315 TAAATTAGTCCTCAAACTTTTGAACATTATACTTTTATCCCTAAA
1 TAAATTAGACCTTAAACTTTTGAATATTATAATTTTATCCCTAAA
26360 TTCATCCAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
59 1 0.01
60 86 0.98
61 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.43
Consensus pattern (60 bp):
TAAATTAGACCTTAAACTTTTGAATATTATAATTTTATCCCTAAACTATGACATTCATTC
Found at i:26557 original size:59 final size:60
Alignment explanation
Indices: 26490--26625 Score: 163
Period size: 60 Copynumber: 2.3 Consensus size: 60
26480 TTATAGATTG
*
26490 GGATGAAATTGAAATGTTGAAAAATTAG-GGACTAATTTAGAATGA-ATGTCATAGTTT-A
1 GGATGAAATTGAAATATTGAAAAATTAGAGGACTAATTTAGAATGATA-GTCATAGTTTAA
* * * * *
26548 GAGATGAAATTGAAATATTTAAAAGTTTGATGACTAATTTAGAATGCTAGTCATAGTTTAA
1 G-GATGAAATTGAAATATTGAAAAATTAGAGGACTAATTTAGAATGATAGTCATAGTTTAA
26609 GGAT-AAAGTTGAAATAT
1 GGATGAAA-TTGAAATAT
26626 ATATAAAAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
58 1 0.01
59 26 0.39
60 37 0.55
61 3 0.04
ACGTcount: A:0.42, C:0.04, G:0.21, T:0.34
Consensus pattern (60 bp):
GGATGAAATTGAAATATTGAAAAATTAGAGGACTAATTTAGAATGATAGTCATAGTTTAA
Found at i:38571 original size:296 final size:296
Alignment explanation
Indices: 38028--38614 Score: 790
Period size: 296 Copynumber: 2.0 Consensus size: 296
38018 AAGAAAAAAA
* * * *
38028 CTATTGTTTTAAATAAATATAAAAAAAGGTTGTAGTAAAATAAAAATGATTAAGTTATTTTAACA
1 CTATTGTTTTAAATAAACATAAAAAAAGGTTGCAGTAAAATAAAAATAATTAAGCTATTTTAACA
* *
38093 TTAACCATAGAATTAGAATAGAATGACGGGATGTAGCTCAAATGGTAGAGCGCTCGCTTTGCATG
66 TTAACCATAGAATTAGAATAGAATGACGGGATGTAGCACAAATGATAGAGCGCTCGCTTTGCATG
** * ** * * * * * *
38158 CAAGAAGTACGGTGGTTGATACCCCGCATCTTGACATTGGAAGTACATGGACTCATATTATTTCT
131 CAAGAAGTACGGTGGTCAATACCCCACATCTCCACATTAGAAATACAAGGACTCACAGTATTACT
* * *
38223 AGCAAAACACGTGAATTCAATTTAATATAAACTATTAAAAGTGATCTATTAGTATCTTAATTTAA
196 AGCAAAACACGTGAATTAAATTTAATATAAACTATTAAAAGCGATCTATTAGTATCTTAATTAAA
*
38288 ATTGTTTTGTGGCGATAACTATTCTTTTAAAAATAT
261 ATTGTTTTGTGGCGATAACTATTATTTTAAAAATAT
38324 CTATTGTTTTAAATAAACAT-AAAAAAGTGTTGCAGTAAAATAAAAATAATTAAGCTATTTTAAC
1 CTATTGTTTTAAATAAACATAAAAAAAG-GTTGCAGTAAAATAAAAATAATTAAGCTATTTTAAC
* * * * * *
38388 GA-TAACCATAGACTTATAATAGAATGA-GGGTATGTAGCACAAATTATTGAGTGCTCGGTTTGC
65 -ATTAACCATAGAATTAGAATAGAATGACGGG-ATGTAGCACAAATGATAGAGCGCTCGCTTTGC
*
38451 ATGCGAA-AAGTACGG-GGATCAATACCCCACATCTCCACATTAGAAATGCAAGGACTCACAGTA
128 ATGC-AAGAAGTACGGTGG-TCAATACCCCACATCTCCACATTAGAAATACAAGGACTCACAGTA
* * * *
38514 TTACTAGCAAAACAAC-TTATTTAAATTTAATATACACTATTAAAAGCGATTTATTAGTATCTTA
191 TTACTAGCAAAAC-ACGTGAATTAAATTTAATATAAACTATTAAAAGCGATCTATTAGTATCTTA
38578 ATTAAAATTGTTTTGTGGCGATAACTATTATTTTAAA
255 ATTAAAATTGTTTTGTGGCGATAACTATTATTTTAAA
38615 TAATGATAAA
Statistics
Matches: 253, Mismatches: 32, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
295 12 0.05
296 236 0.93
297 5 0.02
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.33
Consensus pattern (296 bp):
CTATTGTTTTAAATAAACATAAAAAAAGGTTGCAGTAAAATAAAAATAATTAAGCTATTTTAACA
TTAACCATAGAATTAGAATAGAATGACGGGATGTAGCACAAATGATAGAGCGCTCGCTTTGCATG
CAAGAAGTACGGTGGTCAATACCCCACATCTCCACATTAGAAATACAAGGACTCACAGTATTACT
AGCAAAACACGTGAATTAAATTTAATATAAACTATTAAAAGCGATCTATTAGTATCTTAATTAAA
ATTGTTTTGTGGCGATAACTATTATTTTAAAAATAT
Found at i:41656 original size:139 final size:139
Alignment explanation
Indices: 41401--41678 Score: 380
Period size: 139 Copynumber: 2.0 Consensus size: 139
41391 AATATAATAA
* *
41401 AAATGATTAAGCTATTTTAACGTTAATCATGATCTTAGAATAAAATGAGGGAATGCAGCTCAAAT
1 AAATGATTAAGCTATTTTAACGTTAATCATGATATTAGAATAAAATGAAGGAATGCAGCTCAAAT
* ** * * * *
41466 GGTAGAGCGATTGCTTTGCATGTGAGATGTACATGATTGATACCTGACATCTCTACATTACAAAT
66 GGTAGAGCGATCGCTTTGCATGCAAGAAGTACAGGATCGATACCTGACATCTCCACATTACAAAT
*
41531 GTAAGGATT
131 GCAAGGATT
* *
41540 AAATGATTAAGCTATTTTAACTTTAATCATGATATTAGAATAAAATGAAGGAATGTAGCTCAAAT
1 AAATGATTAAGCTATTTTAACGTTAATCATGATATTAGAATAAAATGAAGGAATGCAGCTCAAAT
* * * *
41605 GGTAGAGCG-TCCGCTTTGTATGCAAGAAGTACGGGATCGATATCTCG-CATCTCCATATTACAA
66 GGTAGAGCGAT-CGCTTTGCATGCAAGAAGTACAGGATCGATACCT-GACATCTCCACATTACAA
41668 ATGCAAGGATT
129 ATGCAAGGATT
41679 CATAATATTT
Statistics
Matches: 121, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
138 1 0.01
139 119 0.98
140 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.31
Consensus pattern (139 bp):
AAATGATTAAGCTATTTTAACGTTAATCATGATATTAGAATAAAATGAAGGAATGCAGCTCAAAT
GGTAGAGCGATCGCTTTGCATGCAAGAAGTACAGGATCGATACCTGACATCTCCACATTACAAAT
GCAAGGATT
Found at i:53732 original size:20 final size:19
Alignment explanation
Indices: 53709--53753 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
53699 ATGATACTTG
53709 ATTTGGAAAGAGAATACAAC
1 ATTTGG-AAGAGAATACAAC
53729 ATTTGG-AGAGAATACAAC
1 ATTTGGAAGAGAATACAAC
53747 ATTTGGA
1 ATTTGGA
53754 TTGACTAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 18 0.75
20 6 0.25
ACGTcount: A:0.44, C:0.09, G:0.22, T:0.24
Consensus pattern (19 bp):
ATTTGGAAGAGAATACAAC
Found at i:55111 original size:3 final size:3
Alignment explanation
Indices: 55099--55156 Score: 73
Period size: 3 Copynumber: 19.7 Consensus size: 3
55089 AAAAAACCTT
* * *
55099 TTA TTA -TA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA ATA TTT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
55146 TTA TTT TTA TT
1 TTA TTA TTA TT
55157 TTTTGGTAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:56110 original size:23 final size:23
Alignment explanation
Indices: 56084--56129 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
56074 AAGAACCAAC
*
56084 ATAAA-CTTAAATATACCATTAAA
1 ATAAAGCTTAAACAT-CCATTAAA
*
56107 ATAAAGTTTAAACATCCATTAAA
1 ATAAAGCTTAAACATCCATTAAA
56130 CTAACCACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.30
Consensus pattern (23 bp):
ATAAAGCTTAAACATCCATTAAA
Found at i:63973 original size:21 final size:21
Alignment explanation
Indices: 63929--63973 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
63919 AGACGAGCTA
* * *
63929 TGACTTTGAAGTAAGGCGCCT
1 TGACTATGAAGTAAAGCGCAT
*
63950 TGACTATGAAGTAAAGCTCAT
1 TGACTATGAAGTAAAGCGCAT
63971 TGA
1 TGA
63974 TTCTTATCTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (21 bp):
TGACTATGAAGTAAAGCGCAT
Found at i:66796 original size:18 final size:17
Alignment explanation
Indices: 66742--66790 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
66732 TTGGACTCCT
* *
66742 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
66760 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
66778 AGTGCATTCGATG
1 AGTGCA-TCGATG
66791 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:66811 original size:64 final size:60
Alignment explanation
Indices: 66742--66921 Score: 157
Period size: 64 Copynumber: 2.8 Consensus size: 60
66732 TTGGACTCCT
*
66742 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATGAAGTGCATTCGATGTTTGAA-AAAT-AG
1 AGTGCATCGATGCA-T-AGAGTGCATCGATGCATGAA-TGCATTCGATGTTTGAATAAATCAG
* * * * * *
66803 CCTGGTGCATCGATGCATGGATTGTGCATCGATGCATCAAATTCATTTGATGTTTTAATTAAATC
1 ---AGTGCATCGATGCATAGA--GTGCATCGATGCAT-GAATGCATTCGATGTTTGAA-TAAATC
66868 AG
59 AG
*
66870 AGTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCGATGTTT
1 AGTGCATCGATGCAT--AGAGTGCATCGATGCAT-GAATGCATTCGATGTTT
66922 CAATTTATTC
Statistics
Matches: 94, Mismatches: 14, Indels: 16
0.76 0.11 0.13
Matches are distributed among these distances:
62 2 0.02
63 1 0.01
64 81 0.86
65 2 0.02
66 6 0.06
67 2 0.02
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (60 bp):
AGTGCATCGATGCATAGAGTGCATCGATGCATGAATGCATTCGATGTTTGAATAAATCAG
Found at i:66892 original size:19 final size:19
Alignment explanation
Indices: 66868--66918 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
66858 TAATTAAATC
66868 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
66887 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
66906 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
66919 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:66956 original size:21 final size:21
Alignment explanation
Indices: 66932--66971 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
66922 CAATTTATTC
66932 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
66953 ATTGATGCATCGATGCATG
1 ATTGATGCATCGATGCATG
66972 CCTTTGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:69590 original size:24 final size:23
Alignment explanation
Indices: 69519--69598 Score: 85
Period size: 24 Copynumber: 3.5 Consensus size: 23
69509 CATGGTCTTG
* *
69519 TGCATCGATGCACATTCAATGCA
1 TGCATCGATGCACATTCAAGGGA
* *
69542 TGCATCGGTG--CA-TCATGCGGA
1 TGCATCGATGCACATTCAAG-GGA
69563 TGCATCGATGCACATTCAAAGGGA
1 TGCATCGATGCACATTC-AAGGGA
69587 TGCATCGATGCA
1 TGCATCGATGCA
69599 TTGTTAAGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 3 0.07
21 13 0.28
23 11 0.24
24 17 0.37
25 2 0.04
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGGA
Found at i:69611 original size:44 final size:42
Alignment explanation
Indices: 69496--69618 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 42
69486 AAAACTCGAC
* * *
69496 GGATGCATCGATGCATGGTCTTGTGCATCGATGCACATTCAAT
1 GGATGCATCGATGCATTGT-TAGTGCATCGATGCACATTCAAG
* * **
69539 GCATGCATCGGTGCATCATG-CGGATGCATCGATGCACATTCAAAG
1 GGATGCATCGATGCAT--TGTTAG-TGCATCGATGCACATTC-AAG
*
69584 GGATGCATCGATGCATTGTTAAGTGCATCGGTGCA
1 GGATGCATCGATGCATTGTT-AGTGCATCGATGCA
69619 TTAAGCACAA
Statistics
Matches: 63, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
43 17 0.27
44 28 0.44
45 18 0.29
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (42 bp):
GGATGCATCGATGCATTGTTAGTGCATCGATGCACATTCAAG
Found at i:73471 original size:20 final size:21
Alignment explanation
Indices: 73427--73471 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
73417 GTTTGTTTTC
* *
73427 ATTTTTAAATTTTGAAACATC
1 ATTTTTAAATTTTGAAAAATA
*
73448 ATTTTTATATTTT-AAAAATA
1 ATTTTTAAATTTTGAAAAATA
73468 ATTT
1 ATTT
73472 CTCATAATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTTAAATTTTGAAAAATA
Found at i:75521 original size:64 final size:64
Alignment explanation
Indices: 75408--75617 Score: 221
Period size: 64 Copynumber: 3.2 Consensus size: 64
75398 TGCACTAAGA
* * *
75408 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAA--AAAT-AGCCTGGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAG---AGTGCATCGATGCATGGA
75470 TT
63 TT
* * **
75472 GTGCATCGATGCATCAAATGCATTCGATGTTTTAATTAAATCAGAGTGCATCGATGCATGGAGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
* * * *
75536 GTGCATCGGTGCATGGAATGCATTCGATGTTTCAATTTATTCATTGA-TGCATCGATGCATGGTA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCA--GAGTGCATCGATGCATGG-A
75600 TT
63 TT
*
75602 GATGCATCGGTGCATG
1 G-TGCATCGATGCATG
75618 CCTTTGAAAA
Statistics
Matches: 125, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
64 86 0.69
65 15 0.12
66 8 0.06
67 16 0.13
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAAATCAGAGTGCATCGATGCATGGATT
Found at i:75538 original size:19 final size:19
Alignment explanation
Indices: 75514--75564 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
75504 TAATTAAATC
75514 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
75533 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
75552 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
75565 TTTCAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:75602 original size:21 final size:21
Alignment explanation
Indices: 75578--75617 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
75568 CAATTTATTC
75578 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
75599 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
75618 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:76098 original size:23 final size:23
Alignment explanation
Indices: 76072--76120 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
76062 ATAAAAAACC
*
76072 AAAATAAA-CTTAAATATACCATT
1 AAAATAAAGCTTAAACAT-CCATT
*
76095 AAAATAAAGTTTAAACATCCATT
1 AAAATAAAGCTTAAACATCCATT
76118 AAA
1 AAA
76121 CTAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.57, C:0.12, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAAGCTTAAACATCCATT
Found at i:77763 original size:11 final size:11
Alignment explanation
Indices: 77715--77804 Score: 69
Period size: 11 Copynumber: 7.8 Consensus size: 11
77705 ATTCAATTTA
*
77715 TTATTATTATT
1 TTATTTTTATT
77726 ATTATTTTT-TT
1 -TTATTTTTATT
*
77737 CTATTTTTTATCT
1 TTA-TTTTTAT-T
77750 TT-TATTTTATT
1 TTAT-TTTTATT
*
77761 TT-TTTATATGAT
1 TTATTTTTAT--T
77773 TTATTTTTTATT
1 TTA-TTTTTATT
77785 TTATTTTTATT
1 TTATTTTTATT
77796 TTATTTTTA
1 TTATTTTTA
77805 ATTCGATTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
10 7 0.11
11 29 0.45
12 21 0.32
13 2 0.03
14 6 0.09
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.77
Consensus pattern (11 bp):
TTATTTTTATT
Found at i:77792 original size:6 final size:6
Alignment explanation
Indices: 77711--77804 Score: 59
Period size: 6 Copynumber: 14.7 Consensus size: 6
77701 ATTTATTCAA
* * *
77711 TTTATT ATTATT ATTATT ATTT-TT TTCTATTT TTTATCT TTTATT TTATTTT
1 TTTATT TTTATT TTTATT -TTTATT TT-TA-TT TTTAT-T TTTATT TT-TATT
77763 TTTATAT GATTTATT TTT-TAT TTTATT TTTA-T TTTATT TTTA
1 TTTAT-T --TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTA
77805 ATTCGATTTA
Statistics
Matches: 72, Mismatches: 4, Indels: 24
0.72 0.04 0.24
Matches are distributed among these distances:
5 8 0.11
6 37 0.51
7 17 0.24
8 5 0.07
9 5 0.07
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:77804 original size:29 final size:28
Alignment explanation
Indices: 77711--77804 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 28
77701 ATTTATTCAA
*
77711 TTTATTATTATTATTATTATTTTTTTCTATTT
1 TTTATT-TT-TTATT-TTATTTTTTTATA-TT
* *
77743 TTTATCTTTTATTTTATTTTTTTATATGA
1 TTTATTTTTTATTTTATTTTTTTATAT-T
*
77772 TTTATTTTTTATTTTATTTTTATTTTATT
1 TTTATTTTTTATTTTATTTTT-TTATATT
77801 TTTA
1 TTTA
77805 ATTCGATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 1 0.02
29 36 0.67
30 10 0.19
31 2 0.04
32 5 0.09
ACGTcount: A:0.20, C:0.02, G:0.01, T:0.77
Consensus pattern (28 bp):
TTTATTTTTTATTTTATTTTTTTATATT
Found at i:82342 original size:12 final size:11
Alignment explanation
Indices: 82325--82372 Score: 60
Period size: 12 Copynumber: 4.1 Consensus size: 11
82315 CATATTGAAT
82325 TTTCTTTTAAA
1 TTTCTTTTAAA
82336 CTTTCTTTTTAAA
1 -TTTC-TTTTAAA
*
82349 TTTCTTTTTAA
1 TTTCTTTTAAA
82360 TCTTCTTTTAAA
1 T-TTCTTTTAAA
82372 T
1 T
82373 CTTTTTATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 7 0.22
12 18 0.56
13 7 0.22
ACGTcount: A:0.23, C:0.12, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTCTTTTAAA
Found at i:82375 original size:21 final size:22
Alignment explanation
Indices: 82342--82388 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
82332 TAAACTTTCT
82342 TTTTAAATTTCTTTTTAATCTTC
1 TTTTAAA-TTCTTTTTAATCTTC
* *
82365 TTTTAAA-TCTTTTTATTTTTC
1 TTTTAAATTCTTTTTAATCTTC
82386 TTT
1 TTT
82389 CTTCTATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 15 0.68
23 7 0.32
ACGTcount: A:0.19, C:0.11, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTAAATTCTTTTTAATCTTC
Found at i:85408 original size:13 final size:12
Alignment explanation
Indices: 85381--85417 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
85371 TCAAAGAATA
85381 TTAAAAATAAAT
1 TTAAAAATAAAT
85393 TTAAAAATAAAGT
1 TTAAAAATAAA-T
85406 TTAAAAA-AAAT
1 TTAAAAATAAAT
85417 T
1 T
85418 CAATATGGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 2 0.08
12 14 0.58
13 8 0.33
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (12 bp):
TTAAAAATAAAT
Found at i:89301 original size:15 final size:15
Alignment explanation
Indices: 89283--89317 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
89273 CGAGGGTATT
89283 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
89298 GTAGTCCTTCGGGAC
1 GTAGTCCTTCGGGAC
*
89313 CTAGT
1 GTAGT
89318 GGTCCTACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCGGGAC
Found at i:109706 original size:20 final size:21
Alignment explanation
Indices: 109681--109729 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
109671 TAATTTCTAT
109681 TAATAATAATATAAAT-AAAA
1 TAATAATAATATAAATGAAAA
* * *
109701 TAATAAAAATATGAATGAAAT
1 TAATAATAATATAAATGAAAA
109722 TAATAATA
1 TAATAATA
109730 GCAATAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 14 0.58
21 10 0.42
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (21 bp):
TAATAATAATATAAATGAAAA
Found at i:121023 original size:58 final size:57
Alignment explanation
Indices: 120920--121066 Score: 163
Period size: 58 Copynumber: 2.6 Consensus size: 57
120910 TCAGGTAACT
* * *
120920 ATTTTATAACTTTTAATAGTCAGAAGACTCAATAATATAGATTATAGTCGAGAT-ATC
1 ATTTTGTAACTTTTAATAGTCAGAAGACTCAATAAAATAGATTATAATCGAG-TGATC
* ** *
120977 ATTTTTGTAACTTTTAATAGTCA-ATGAACTCAATAAAATATCTTATAATTGAGTGATC
1 A-TTTTGTAACTTTTAATAGTCAGAAG-ACTCAATAAAATAGATTATAATCGAGTGATC
* * *
121035 ATTTTGTAAATTTTAATAGTCAGTAGATTCAA
1 ATTTTGTAACTTTTAATAGTCAGAAGACTCAA
121067 CAAAGAAACA
Statistics
Matches: 75, Mismatches: 11, Indels: 8
0.80 0.12 0.09
Matches are distributed among these distances:
57 29 0.39
58 46 0.61
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.40
Consensus pattern (57 bp):
ATTTTGTAACTTTTAATAGTCAGAAGACTCAATAAAATAGATTATAATCGAGTGATC
Found at i:121487 original size:16 final size:16
Alignment explanation
Indices: 121468--121498 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
121458 TTATTAATAA
*
121468 TTTACTTATTTAAAAT
1 TTTAATTATTTAAAAT
121484 TTTAATTATTTAAAA
1 TTTAATTATTTAAAA
121499 ATAATAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAATTATTTAAAAT
Found at i:125239 original size:18 final size:18
Alignment explanation
Indices: 125216--125256 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
125206 AGTTTAGGTG
125216 TTGGGCTAGGGTTTGGGT
1 TTGGGCTAGGGTTTGGGT
*
125234 TTGGGCTCGGGTTTGGGT
1 TTGGGCTAGGGTTTGGGT
125252 TTGGG
1 TTGGG
125257 TTTGGATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.02, C:0.07, G:0.51, T:0.39
Consensus pattern (18 bp):
TTGGGCTAGGGTTTGGGT
Found at i:125275 original size:7 final size:6
Alignment explanation
Indices: 125224--125280 Score: 69
Period size: 6 Copynumber: 9.2 Consensus size: 6
125214 TGTTGGGCTA
* * *
125224 GGGTTT GGGTTT GGGCTC GGGTTT GGGTTT GGGTTT GGATGTT GGGTATT
1 GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGTTT GGGT-TT GGGT-TT
125274 GGGTTT G
1 GGGTTT G
125281 TAATAAATAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
6 32 0.74
7 11 0.26
ACGTcount: A:0.04, C:0.04, G:0.49, T:0.44
Consensus pattern (6 bp):
GGGTTT
Found at i:125294 original size:3 final size:3
Alignment explanation
Indices: 125281--125342 Score: 81
Period size: 3 Copynumber: 20.3 Consensus size: 3
125271 ATTGGGTTTG
* *
125281 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TTTA TTA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
125328 TAA TAA TAA T-A TAA T
1 TAA TAA TAA TAA TAA T
125343 GGTTGAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 2 0.04
3 47 0.87
4 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:126185 original size:21 final size:21
Alignment explanation
Indices: 126161--126202 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
126151 AAAAGTTATT
126161 CTCATT-ATGAAGTTCTTCTCC
1 CTCATTGATG-AGTTCTTCTCC
126182 CTCATTGGATGAGTTCTTCTC
1 CTCATT-GATGAGTTCTTCTC
126203 ATTATGAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 10 0.53
23 3 0.16
ACGTcount: A:0.17, C:0.26, G:0.14, T:0.43
Consensus pattern (21 bp):
CTCATTGATGAGTTCTTCTCC
Found at i:127327 original size:14 final size:15
Alignment explanation
Indices: 127297--127333 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
127287 TTGAACCCTG
127297 TTTTT-TCTTTTCAC
1 TTTTTCTCTTTTCAC
*
127311 TTTTTCTCTTTT-TC
1 TTTTTCTCTTTTCAC
127325 TTTTTCTCT
1 TTTTTCTCT
127334 CCTTCATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTCTCTTTTCAC
Found at i:127352 original size:24 final size:23
Alignment explanation
Indices: 127319--127373 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 23
127309 ACTTTTTCTC
127319 TTTTTCTTTT-TCTCTCCTTCATTCA
1 TTTTT-TTTTATCT-TCCTTCA-TCA
**
127344 TTTTTTTTTATCTTTTTTCATCA
1 TTTTTTTTTATCTTCCTTCATCA
127367 TTTTTTT
1 TTTTTTT
127374 GAAGCATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 10 0.37
24 9 0.33
25 8 0.30
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (23 bp):
TTTTTTTTTATCTTCCTTCATCA
Found at i:135991 original size:19 final size:19
Alignment explanation
Indices: 135951--135992 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
135941 TAAATTAGCT
**
135951 ATTCTTTCTTCAAGGCCTA
1 ATTCTTTCTTCAAGGCAAA
135970 ATTCTTTCTTCGAAGG-AAA
1 ATTCTTTCTTC-AAGGCAAA
135989 ATTC
1 ATTC
135993 CATTACGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (19 bp):
ATTCTTTCTTCAAGGCAAA
Done.