Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006369.1 Hibiscus syriacus cultivar Beakdansim tig00015318_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: 121726
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1046 original size:21 final size:22
Alignment explanation
Indices: 1017--1061 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
1007 GAGTTAGTTA
* *
1017 AAGATAGTAAAAT-ATATAAAT
1 AAGAAAGTAAAATAAAATAAAT
1038 AAGAAAGTAAAATAAAATAAAT
1 AAGAAAGTAAAATAAAATAAAT
1060 AA
1 AA
1062 AAACATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.69, C:0.00, G:0.09, T:0.22
Consensus pattern (22 bp):
AAGAAAGTAAAATAAAATAAAT
Found at i:1070 original size:22 final size:22
Alignment explanation
Indices: 1024--1076 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
1014 TTAAAGATAG
* *
1024 TAAAAT-ATATAAATAAGAAAG
1 TAAAATAAAATAAATAAGAAAA
1045 TAAAATAAAATAAATAA-AAACA
1 TAAAATAAAATAAATAAGAAA-A
1067 TAAAAATAAA
1 T-AAAATAAA
1077 GACGATGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 9 0.33
22 10 0.37
23 8 0.30
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.21
Consensus pattern (22 bp):
TAAAATAAAATAAATAAGAAAA
Found at i:1262 original size:18 final size:19
Alignment explanation
Indices: 1241--1288 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
1231 AAATTAAAAT
1241 AAAATAAAAATAG-ATATA
1 AAAATAAAAATAGTATATA
1259 AAAAT-AAAAT-GTATATA
1 AAAATAAAAATAGTATATA
*
1276 AATAATAATAATA
1 AA-AATAAAAATA
1289 ATAAAAGACT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 1 0.04
17 12 0.48
18 8 0.32
19 4 0.16
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (19 bp):
AAAATAAAAATAGTATATA
Found at i:1332 original size:5 final size:6
Alignment explanation
Indices: 1229--1335 Score: 58
Period size: 6 Copynumber: 17.2 Consensus size: 6
1219 CAAAATAATG
* * * *
1229 AAAAAT TAAAAT -AAAAT AAAAAT AGATAT AAAAAT AAAATGTAT ATAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA---AT AAAAAT
* * * *
1279 AATAAT AATAAT AAAAGACT AAAGAAT AATAAAT --ATAG AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAA-A-T AAA-AAT AA-AAAT AAAAAT AAAAAT AAAAAT
1329 AAAAAT A
1 AAAAAT A
1336 GTATAATGTA
Statistics
Matches: 78, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
4 2 0.03
5 5 0.06
6 52 0.67
7 7 0.09
8 6 0.08
9 6 0.08
ACGTcount: A:0.71, C:0.01, G:0.05, T:0.23
Consensus pattern (6 bp):
AAAAAT
Found at i:1403 original size:2 final size:2
Alignment explanation
Indices: 1396--1448 Score: 58
Period size: 2 Copynumber: 28.0 Consensus size: 2
1386 ATAAAATAAA
*
1396 AT AT AT AT AT AT A- AT AT CT AT AT AT AT AT A- AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
1435 AT AA AT AT AA AT AT
1 AT AT AT AT AT AT AT
1449 GATAAAAGGA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1998 original size:17 final size:17
Alignment explanation
Indices: 1972--2007 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1962 CAAAAAACGC
*
1972 CTCGTGGGGGTATGGAT
1 CTCGTAGGGGTATGGAT
1989 CTCGTAGGGGTATGGAT
1 CTCGTAGGGGTATGGAT
2006 CT
1 CT
2008 AGAAAAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.42, T:0.31
Consensus pattern (17 bp):
CTCGTAGGGGTATGGAT
Found at i:2692 original size:2 final size:2
Alignment explanation
Indices: 2685--2719 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
2675 ATAAACATAA
*
2685 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2720 GTAATATGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3083 original size:34 final size:35
Alignment explanation
Indices: 3040--3107 Score: 93
Period size: 35 Copynumber: 2.0 Consensus size: 35
3030 GTGGCATATG
*
3040 CACATTGCTCAAACTGT-GTTTATGTAAACAAAAC
1 CACATTGCTCAAACTGTGGTTAATGTAAACAAAAC
* **
3074 CACATTGCTCCATGTGTGGTTAATGTAAACAAAA
1 CACATTGCTCAAACTGTGGTTAATGTAAACAAAA
3108 ACACTCCTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 14 0.48
35 15 0.52
ACGTcount: A:0.37, C:0.19, G:0.15, T:0.29
Consensus pattern (35 bp):
CACATTGCTCAAACTGTGGTTAATGTAAACAAAAC
Found at i:7860 original size:16 final size:18
Alignment explanation
Indices: 7824--7861 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
7814 TTTAATTATT
*
7824 TTTTTATTTTGTTATATA
1 TTTTTATTTTGTTAAATA
7842 TTTTTA-TTT-TTAAATA
1 TTTTTATTTTGTTAAATA
7858 TTTT
1 TTTT
7862 AGATGGCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 3 0.16
18 6 0.32
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTATTTTGTTAAATA
Found at i:11237 original size:31 final size:31
Alignment explanation
Indices: 11184--11249 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
11174 AAATTACGTA
* * *
11184 TTTAGTATCTAAACAATCAGTTTTGTTCTGT
1 TTTAATATCTAAACAATCAGTTTTGGTATGT
* * *
11215 TTTAATATCTGAACATTTAGTTTTGGTATGT
1 TTTAATATCTAAACAATCAGTTTTGGTATGT
11246 TTTA
1 TTTA
11250 GCACTTAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.52
Consensus pattern (31 bp):
TTTAATATCTAAACAATCAGTTTTGGTATGT
Found at i:18458 original size:34 final size:35
Alignment explanation
Indices: 18415--18497 Score: 105
Period size: 36 Copynumber: 2.4 Consensus size: 35
18405 TAAAAGTTAG
*
18415 TTTCAAAGTTTGGCAACCA-ACTTTGAAAAATATT
1 TTTCAAAGTTTGGCAAACATACTTTGAAAAATATT
* * * *
18449 TTTCAAAGTTTGGTAAATATTTCTTTGAAAAATCTT
1 TTTCAAAGTTTGGCAAACA-TACTTTGAAAAATATT
18485 TTTCAAAGTTTGG
1 TTTCAAAGTTTGG
18498 TAAAATTTGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
34 16 0.38
36 26 0.62
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (35 bp):
TTTCAAAGTTTGGCAAACATACTTTGAAAAATATT
Found at i:18487 original size:36 final size:35
Alignment explanation
Indices: 18435--18505 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 35
18425 TGGCAACCAA
18435 CTTTGAAAAATATTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAA-ATTT
*
18471 CTTTGAAAAATCTTTTTCAAAGTTTGGTAAAATTT
1 CTTTGAAAAATATTTTTCAAAGTTTGGTAAAATTT
18506 GGTAGATGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 4 0.12
36 30 0.88
ACGTcount: A:0.35, C:0.07, G:0.11, T:0.46
Consensus pattern (35 bp):
CTTTGAAAAATATTTTTCAAAGTTTGGTAAAATTT
Found at i:21962 original size:194 final size:193
Alignment explanation
Indices: 21687--22119 Score: 650
Period size: 194 Copynumber: 2.2 Consensus size: 193
21677 ATTGAAATTT
* * * *
21687 GTATCGATACTTTTCTAAGTATATGCACCAAATTATCGATACTTTAGGAATTTAAAAAAATTGCA
1 GTATCGATAC-TTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAAAATTGCA
* * * * * *
21752 ATAATAGCGACTATAAAGTATCGATACTTTATAAACATTTATCGATACATGACAATATAATAGGT
65 AGAATAGCCACTATAAAGTATCGATACTTTAGAAACATGTATCGATACATGACAATATAACAAGT
21817 AAAAATATCACAAAACCGGTTTCAATATGACAAAACCGGTAAAGAGAAACCAGATATGTTGAAG
130 AAAAATATCACAAAACCGGTTTCAATATGACAAAACCGGTAAAGAGAAACCAGATATGTTGAAG
* *
21881 GTATCAATACATTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAGAATTGCA
1 GTATCGATAC-TTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAAAATTGCA
*
21946 AGAATAGCCCCTATAAAGTATCGATACTTTAGAAACATGTATCGATACATGACAATATAACAAGT
65 AGAATAGCCACTATAAAGTATCGATACTTTAGAAACATGTATCGATACATGACAATATAACAAGT
* ** * * **
22011 TAAAATATGGCAAAACCGGTTTCAGTATGACAAAACCGGTAAAGGGCTACCAGATATGTTGAAG
130 AAAAATATCACAAAACCGGTTTCAATATGACAAAACCGGTAAAGAGAAACCAGATATGTTGAAG
*
22075 GTATCGATACTTTAATAATTATATGTATCATATTATCGATACTTT
1 GTATCGATACTTT-ATAAGTATATGTATCATATTATCGATACTTT
22120 TAAAAGAAAA
Statistics
Matches: 215, Mismatches: 23, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
193 3 0.01
194 212 0.99
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.31
Consensus pattern (193 bp):
GTATCGATACTTTATAAGTATATGTATCATATTATCGATACTTTAGGAATTTAAAAAAATTGCAA
GAATAGCCACTATAAAGTATCGATACTTTAGAAACATGTATCGATACATGACAATATAACAAGTA
AAAATATCACAAAACCGGTTTCAATATGACAAAACCGGTAAAGAGAAACCAGATATGTTGAAG
Found at i:22741 original size:20 final size:19
Alignment explanation
Indices: 22699--22765 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
22689 TTTGAGACTG
* * *
22699 ATTATAGTTAGAAAGTGAT
1 ATTATAGGTAGAAAATAAT
*
22718 ATTATATGTAGAAAATAAAT
1 ATTATAGGTAGAAAAT-AAT
22738 ATTATAGGTAGAAAATAAT
1 ATTATAGGTAGAAAATAAT
*
22757 ATTGTAGGT
1 ATTATAGGT
22766 TGTATAAATG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.46, C:0.00, G:0.18, T:0.36
Consensus pattern (19 bp):
ATTATAGGTAGAAAATAAT
Found at i:22764 original size:19 final size:20
Alignment explanation
Indices: 22716--22765 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
22706 TTAGAAAGTG
*
22716 ATATTATATGTAGAAAATAA
1 ATATTATAGGTAGAAAATAA
22736 ATATTATAGGTAGAAAAT-A
1 ATATTATAGGTAGAAAATAA
*
22755 ATATTGTAGGT
1 ATATTATAGGT
22766 TGTATAAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (20 bp):
ATATTATAGGTAGAAAATAA
Found at i:24388 original size:12 final size:12
Alignment explanation
Indices: 24373--24434 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
24363 AAAGGAGGTA
24373 GAGGAGGAAGAG
1 GAGGAGGAAGAG
* *
24385 GAGGAAGAGGAG
1 GAGGAGGAAGAG
24397 GAAGATGAGGAAGAG
1 G-AG--GAGGAAGAG
*
24412 GAGAAGGAAGAG
1 GAGGAGGAAGAG
* *
24424 AAGGAAGAAGA
1 GAGGAGGAAGA
24435 AAAGGTAGTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
12 27 0.69
13 2 0.05
14 2 0.05
15 8 0.21
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (12 bp):
GAGGAGGAAGAG
Found at i:24397 original size:21 final size:20
Alignment explanation
Indices: 24372--24431 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 20
24362 GAAAGGAGGT
24372 AGAGGAGGAAGAGGAGG-A-
1 AGAGGAGGAAGAGGAGGAAG
*
24390 AGAGGAGGAAGATGAGGAAG
1 AGAGGAGGAAGAGGAGGAAG
* *
24410 AGGAGAAGGAAGAGAAGGAAG
1 A-GAGGAGGAAGAGGAGGAAG
24431 A
1 A
24432 AGAAAAGGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.46
19 1 0.03
20 1 0.03
21 17 0.49
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (20 bp):
AGAGGAGGAAGAGGAGGAAG
Found at i:24431 original size:9 final size:9
Alignment explanation
Indices: 24361--24414 Score: 83
Period size: 9 Copynumber: 6.1 Consensus size: 9
24351 GAAGGTTATT
24361 GGAA-AGGA
1 GGAAGAGGA
*
24369 GGTAGAGGA
1 GGAAGAGGA
24378 GGAAGAGGA
1 GGAAGAGGA
24387 GGAAGAGGA
1 GGAAGAGGA
*
24396 GGAAGATGA
1 GGAAGAGGA
24405 GGAAGAGGA
1 GGAAGAGGA
24414 G
1 G
24415 AAGGAAGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
8 3 0.07
9 38 0.93
ACGTcount: A:0.43, C:0.00, G:0.54, T:0.04
Consensus pattern (9 bp):
GGAAGAGGA
Found at i:24439 original size:21 final size:21
Alignment explanation
Indices: 24395--24439 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24385 GAGGAAGAGG
* *
24395 AGGAAGATGAGGAAGAGGAGA
1 AGGAAGATGAGGAAGAAGAAA
24416 AGGAAGA-GAAGGAAGAAGAAA
1 AGGAAGATG-AGGAAGAAGAAA
24437 AGG
1 AGG
24440 TAGTAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.02
Consensus pattern (21 bp):
AGGAAGATGAGGAAGAAGAAA
Found at i:28336 original size:181 final size:179
Alignment explanation
Indices: 28136--28504 Score: 528
Period size: 181 Copynumber: 2.1 Consensus size: 179
28126 ATACAATTAT
28136 GAAAGTATCGATTCTTAAAACTTTGAAACCGATTAACTTAAAGTAATAGGTAAATTTAAAATGAT
1 GAAAGTATCGATTCTTAAAACTTTGAAACCGATTAACTTAAAGTAATAGGTAAATTTAAAATGAT
* * * *
28201 AGCTGTAAAAAGATACTAGTTTATGATAAAATA-TGTTAACATAAAGTAGCAATACTTTTTTTAT
66 AGCGGTAAAAAGATACCAGTTTATGATAAAATACT-TTAACATAAAGTAGAAATA-ATTTTTTAT
* * ** *
28265 GTGTATCAATAATTTTTGT-TCAGTATGC-TTCGTAATCTTAAGTAAGTAAAAA
129 GTGTATCAATACTTTTT-TCT-AGTATGCTTTC-CAAAATTAAGTAAGCAAAAA
* * * *
28317 GAAAGTATCGATTCTTAAAACTTTGAAACTGATTAACTTAAAGTAATAGGTCAATTTACAATGTT
1 GAAAGTATCGATTCTTAAAACTTTGAAACCGATTAACTTAAAGTAATAGGTAAATTTAAAATGAT
* *
28382 AGCGGTAAAAAGATACCAGTTTATTATAAAATACTTTAACATAAAGTATAAATAATTTTTTATGT
66 AGCGGTAAAAAGATACCAGTTTATGATAAAATACTTTAACATAAAGTAGAAATAATTTTTTATGT
*
28447 GTATCGATACTTTTTTCTAGTATGCTTTCCAAAATTAAGTAAGCAAAAA
131 GTATCAATACTTTTTTCTAGTATGCTTTCCAAAATTAAGTAAGCAAAAA
28496 GAAAGTATC
1 GAAAGTATC
28505 AATACACATA
Statistics
Matches: 169, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
179 33 0.20
180 27 0.16
181 108 0.64
182 1 0.01
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (179 bp):
GAAAGTATCGATTCTTAAAACTTTGAAACCGATTAACTTAAAGTAATAGGTAAATTTAAAATGAT
AGCGGTAAAAAGATACCAGTTTATGATAAAATACTTTAACATAAAGTAGAAATAATTTTTTATGT
GTATCAATACTTTTTTCTAGTATGCTTTCCAAAATTAAGTAAGCAAAAA
Found at i:28703 original size:200 final size:197
Alignment explanation
Indices: 28318--29649 Score: 1161
Period size: 200 Copynumber: 6.8 Consensus size: 197
28308 AAGTAAAAAG
* *
28318 AAAGTATCGATTCTTAAAACTTTGAAACTGATTA-ACTTAAAGTAATAGGTCAATTTACAATGTT
1 AAAGTATCGATTCTTAAAACTTTGAAAC-GATTATA--TAAAGTAATAGGTAAATTTACAATGTA
* * * * * ** * *
28382 AGCGGTAAAAAGATACCAGTTT-ATTATAAAATACTTTAACATAAAGTATAAATAATTTTT-TAT
63 AGCGGTAAAAATATACCAGTTTAATGAAAAAATACGTAAACATAAAGTATCGATACTTTTTGTAA
* * * * ** * *** *
28445 GTGTATCGATACTTTTT-TCTAGTATGCTTTCCAAAATTAAGTAAGCAAAAAGAAAGTATCAATA
128 GAGTATCGATACTTTTTGTCCAGTATGC-ATCCCAAA-CGAG-ATGCATGCAGAAAGTATCGATA
28509 CACATATGA
190 CA-ATATGA
** * * * * *
28518 AAAGTATCGATTCACAAAACTTTAAAATCGATTATTTGAAGGTAATAGGTAACTTTACAATGTTA
1 AAAGTATCGATTCTTAAAACTTTGAAA-CGATTATAT-AAAGTAATAGGTAAATTTACAATGTAA
* * * **
28583 GCGGTAAAAATATACCAGTTTAATGACAAGATACGTAAACATAAAGTATCGATCCTTTTTGTATT
64 GCGGTAAAAATATACCAGTTTAATGAAAAAATACGTAAACATAAAGTATCGATACTTTTTGTAAG
* * * * *
28648 TGTGTCGATACTTTTTGTCCAGTATGCATCCCAATCGAGATGCACGCATAAAGTATCGATACAAG
129 AGTATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGATGCATGCAGAAAGTATCGATACAA-
28713 TATGA
193 TATGA
* ** * * *
28718 AAAGTATCGATTCTTAAAACATCAAAACTGATTATTTAATGGTAATAGGTAAATTGACAATGTAA
1 AAAGTATCGATTCTTAAAACTTTGAAAC-GATTATATAA-AGTAATAGGTAAATTTACAATGTAA
* * * *
28783 GCAGTAAAAATATATCAGTTTAATG-AGAAATACGTAAACATAAAGTATCGATACATTTTGTAAG
64 GCGGTAAAAATATACCAGTTTAATGAAAAAATACGTAAACATAAAGTATCGATACTTTTTGTAAG
* * * * * * *
28847 AGTATCGATACTTTTTGTCTAATATGCATCCCAAACGAGGTGAACGCTGAAAGCATCGATACAAG
129 AGTATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGATGCATGCAGAAAGTATCGATACAA-
*
28912 TACGA
193 TATGA
* * * ** *
28917 GAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAAGTAATAGAAAAATTTACAATGTCA
1 AAAGTATCGATTCTTAAAACTTTGAAA-CGATTA-TATAAAGTAATAGGTAAATTTACAATGTAA
* *
28982 GCAGTAAAAA-ATACC-GATTTAATGAAAACAATACATAAACATAAAGTATCGATACTTTTTGTC
64 GCGGTAAAAATATACCAG-TTTAATGAAAA-AATACGTAAACATAAAGTATCGATACTTTTTGT-
* ***** * **
29045 CA-A-TAT-GCAT-C--CCAAACGAG-ATGCA-CGTAGAA--A-AT--AT-C-G--A-TA-C-AT
126 AAGAGTATCG-ATACTTTTTGTCCAGTATGCATCCCA-AACGAGATGCATGCAGAAAGTATCGAT
*
29090 ---GTATGA
189 ACAATATGA
* * * * *
29096 GAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAAGTAATAGGTAAATTGACAATGAAA
1 AAAGTATCGATTCTTAAAACTTTGAAA-CGATTA-TATAAAGTAATAGGTAAATTTACAATGTAA
* * * * *
29161 GCGGTAAAAATATATCGGTTTAATGAGAAAATACGTAAACATAAAGTATCGATAGTTTTTGTAAT
64 GCGGTAAAAATATACCAGTTTAATGAAAAAATACGTAAACATAAAGTATCGATACTTTTTGTAAG
* * * * *
29226 ACTATCGATACTTTTTGTCCAGTATGCATTCCAAACGAGATGCATGTAGAAAATATCAATACATA
129 AGTATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGATGCATGCAGAAAGTATCGATACA-A
29291 TAT-A
193 TATGA
* *
29295 AGAAGTATCGATTCTTAAAACTTTGATACCGACTAGTATAAAGTAATAGGTAAATTTACAATGTA
1 A-AAGTATCGATTCTTAAAACTTTGA-AACGATTA-TATAAAGTAATAGGTAAATTTACAATGTA
* * *
29360 AGCGGTAAAAATATATCAGTTTAATGAAAAAATACGTATACATAAAGTATCGATAC-TTCTGTAA
63 AGCGGTAAAAATATACCAGTTTAATGAAAAAATACGTAAACATAAAGTATCGATACTTTTTGTAA
* * *
29424 GAGTATCGATACTTTTTGTCTAGTATGCATCCCAAACGAGATGCATACAGAAAGTATTGATACAT
128 GAGTATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGATGCATGCAGAAAGTATCGATACA-
*
29489 GTATGA
192 ATATGA
*
29495 GAAGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATTCTTAAAACTTTGAAA-CGATTA-TATAAAGTAATAGGTAAATTTACAATGTAA
* * * * *
29560 GCGGTAGAAATATA-CTGATTTAATGACAAAATATGTAAA-AGTAGAA-TATCGATACTTTTTGA
64 GCGGTAAAAATATACCAG-TTTAATGAAAAAATACGTAAACA-TA-AAGTATCGATACTTTTTGT
* *
29622 AAGAGTATTGATACTTTTT-TCTAGTATG
126 AAGAGTATCGATACTTTTTGTCCAGTATG
29650 AAAACACCGA
Statistics
Matches: 939, Mismatches: 142, Indels: 103
0.79 0.12 0.09
Matches are distributed among these distances:
178 1 0.00
179 105 0.11
180 19 0.02
181 3 0.00
183 5 0.01
184 8 0.01
185 2 0.00
186 2 0.00
187 2 0.00
188 1 0.00
189 3 0.00
190 1 0.00
191 1 0.00
192 1 0.00
193 2 0.00
194 4 0.00
195 8 0.01
196 4 0.00
197 1 0.00
198 17 0.02
199 339 0.36
200 344 0.37
201 34 0.04
202 23 0.02
203 9 0.01
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (197 bp):
AAAGTATCGATTCTTAAAACTTTGAAACGATTATATAAAGTAATAGGTAAATTTACAATGTAAGC
GGTAAAAATATACCAGTTTAATGAAAAAATACGTAAACATAAAGTATCGATACTTTTTGTAAGAG
TATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGATGCATGCAGAAAGTATCGATACAATAT
GA
Found at i:28910 original size:199 final size:199
Alignment explanation
Indices: 28318--29649 Score: 1130
Period size: 199 Copynumber: 6.8 Consensus size: 199
28308 AAGTAAAAAG
* * * *
28318 AAAGTATCGATTCTTAAAACTTTGAAACTGATTAACT-TAAAGTAATAGGTCAATTTACAATGTT
1 AAAGTATCGATTCTTAAAACTTTGAAACCGATT-AGTATAAAGTAATAGGTAAATTTACAATGTA
* * * * * ** * *
28382 AGCGGTAAAAAGATACCAGTTT-ATTATAAAATACTTTAACATAAAGTATAAATAATTTTT-TAT
65 AGCGGTAAAAATATATCAGTTTAATGA-AAAATACGTAAACATAAAGTATCGATACTTTTTGTAA
* * * ** * *** *
28445 GTGTATCGATACTTTTT-TCTAGTATGCTTTCCAAAATTAAGTAAGCAAAAAGAAAGTATCAATA
129 GAGTATCGATACTTTTTGTCTAGTATGC-ATCCCAAA-CGAG-ATGCACGCAGAAAGTATCGATA
28509 CACA-TATGA
191 CA-AGTATGA
** * * * * * *
28518 AAAGTATCGATTCACAAAACTTTAAAATCGATTA-TTTGAAGGTAATAGGTAACTTTACAATGTT
1 AAAGTATCGATTCTTAAAACTTTGAAACCGATTAGTAT-AAAGTAATAGGTAAATTTACAATGTA
* * * *
28582 AGCGGTAAAAATATACCAGTTTAATGACAAGATACGTAAACATAAAGTATCGATCCTTTTTGTAT
65 AGCGGTAAAAATATATCAGTTTAATGA-AAAATACGTAAACATAAAGTATCGATACTTTTTGTAA
** * * * *
28647 TTGTGTCGATACTTTTTGTCCAGTATGCATCCCAATCGAGATGCACGCATAAAGTATCGATACAA
129 GAGTATCGATACTTTTTGTCTAGTATGCATCCCAAACGAGATGCACGCAGAAAGTATCGATACAA
28712 GTATGA
194 GTATGA
* ** * * * *
28718 AAAGTATCGATTCTTAAAACATCAAAACTGATTA-TTTAATGGTAATAGGTAAATTGACAATGTA
1 AAAGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAA-AGTAATAGGTAAATTTACAATGTA
* * *
28782 AGCAGTAAAAATATATCAGTTTAATGAGAAATACGTAAACATAAAGTATCGATACATTTTGTAAG
65 AGCGGTAAAAATATATCAGTTTAATGAAAAATACGTAAACATAAAGTATCGATACTTTTTGTAAG
* * * * *
28847 AGTATCGATACTTTTTGTCTAATATGCATCCCAAACGAGGTGAACGCTGAAAGCATCGATACAAG
130 AGTATCGATACTTTTTGTCTAGTATGCATCCCAAACGAGATGCACGCAGAAAGTATCGATACAAG
*
28912 TACGA
195 TATGA
* * * ** *
28917 GAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAAGTAATAGAAAAATTTACAATGTCA
1 AAAGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAA
* * *
28982 GCAGTAAAAA-ATA-CCGATTTAATGAAAACAATACATAAACATAAAGTATCGATACTTTTTGTC
66 GCGGTAAAAATATATCAG-TTTAATG-AAA-AATACGTAAACATAAAGTATCGATACTTTTTGT-
* ***** * ** * *
29045 CA-A-TAT-GCAT-C--CCAAACGAG-ATGCA-CGTAGAA--A-AT--ATCG-ATACATGTAT-G
127 AAGAGTATCG-ATACTTTTTGTCTAGTATGCATCCCA-AACGAGATGCA-CGCAGA-AAGTATCG
*
29095 --AGAAGTATCG-
188 ATACAAGTAT-GA
* ** *** * * *
29105 --A-T-TC---T-TAAAACTTCGAA-ACCAATTAGTATAAAGTAATAGGTAAATTGACAATGAAA
1 AAAGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAA
* * *
29161 GCGGTAAAAATATATCGGTTTAATGAGAAAATACGTAAACATAAAGTATCGATAGTTTTTGTAAT
66 GCGGTAAAAATATATCAGTTTAATGA-AAAATACGTAAACATAAAGTATCGATACTTTTTGTAAG
* * * * * * *
29226 ACTATCGATACTTTTTGTCCAGTATGCATTCCAAACGAGATGCATGTAGAAAATATCAATACATA
130 AGTATCGATACTTTTTGTCTAGTATGCATCCCAAACGAGATGCACGCAGAAAGTATCGATACA-A
29291 -TAT-A
194 GTATGA
* *
29295 AGAAGTATCGATTCTTAAAACTTTGATACCGACTAGTATAAAGTAATAGGTAAATTTACAATGTA
1 A-AAGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTA
* *
29360 AGCGGTAAAAATATATCAGTTTAATGAAAAAATACGTATACATAAAGTATCGATAC-TTCTGTAA
65 AGCGGTAAAAATATATCAGTTTAATG-AAAAATACGTAAACATAAAGTATCGATACTTTTTGTAA
** * *
29424 GAGTATCGATACTTTTTGTCTAGTATGCATCCCAAACGAGATGCATACAGAAAGTATTGATACAT
129 GAGTATCGATACTTTTTGTCTAGTATGCATCCCAAACGAGATGCACGCAGAAAGTATCGATACAA
29489 GTATGA
194 GTATGA
*
29495 GAAGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAA
* * * *
29560 GCGGTAGAAATATA-CTGATTTAATGACAAAATATGTAAA-AGTAGAA-TATCGATACTTTTTGA
66 GCGGTAAAAATATATCAG-TTTAATGA-AAAATACGTAAACA-TA-AAGTATCGATACTTTTTGT
*
29622 AAGAGTATTGATACTTTTT-TCTAGTATG
127 AAGAGTATCGATACTTTTTGTCTAGTATG
29650 AAAACACCGA
Statistics
Matches: 918, Mismatches: 157, Indels: 115
0.77 0.13 0.10
Matches are distributed among these distances:
178 1 0.00
179 76 0.08
180 23 0.03
181 5 0.01
183 3 0.00
184 9 0.01
185 2 0.00
186 2 0.00
187 2 0.00
188 11 0.01
189 4 0.00
190 3 0.00
191 11 0.01
192 2 0.00
193 2 0.00
194 3 0.00
195 9 0.01
196 2 0.00
197 2 0.00
198 18 0.02
199 345 0.38
200 318 0.35
201 33 0.04
202 23 0.03
203 9 0.01
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (199 bp):
AAAGTATCGATTCTTAAAACTTTGAAACCGATTAGTATAAAGTAATAGGTAAATTTACAATGTAA
GCGGTAAAAATATATCAGTTTAATGAAAAATACGTAAACATAAAGTATCGATACTTTTTGTAAGA
GTATCGATACTTTTTGTCTAGTATGCATCCCAAACGAGATGCACGCAGAAAGTATCGATACAAGT
ATGA
Found at i:29170 original size:179 final size:179
Alignment explanation
Indices: 28847--29222 Score: 558
Period size: 179 Copynumber: 2.1 Consensus size: 179
28837 ATTTTGTAAG
* * *
28847 AGTATCGATACTTTTTGTCTAATATGCATCCCAAACGAGGTGAACGCTGAAAGCATCGATACAAG
1 AGTATCGATACTTTTTGTCCAATATGCATCCCAAACGAGATGAACGCTGAAAACATCGATACAAG
*
28912 TACGAGAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAAGTAATAGAAAAATTTACAA
66 TACGAGAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAAGTAATAGAAAAATTGACAA
**
28977 TGTCAGCAGTAAAAA-ATACCGATTTAATGAAAACAATACATAAACATAA
131 TGAAAGCAGTAAAAATATACCGATTTAATGAAAA-AATACATAAACATAA
* * *
29026 AGTATCGATACTTTTTGTCCAATATGCATCCCAAACGAGATGCACG-TAGAAAATATCGATACAT
1 AGTATCGATACTTTTTGTCCAATATGCATCCCAAACGAGATGAACGCT-GAAAACATCGATACAA
* **
29090 GTATGAGAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAAGTAATAGGTAAATTGACA
65 GTACGAGAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAAGTAATAGAAAAATTGACA
* * * * *
29155 ATGAAAGCGGTAAAAATATATCGGTTTAATGAGAAAATACGTAAACATAA
130 ATGAAAGCAGTAAAAATATACCGATTTAATGAAAAAATACATAAACATAA
*
29205 AGTATCGATAGTTTTTGT
1 AGTATCGATACTTTTTGT
29223 AATACTATCG
Statistics
Matches: 177, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
178 1 0.01
179 161 0.91
180 15 0.08
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (179 bp):
AGTATCGATACTTTTTGTCCAATATGCATCCCAAACGAGATGAACGCTGAAAACATCGATACAAG
TACGAGAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAAGTAATAGAAAAATTGACAA
TGAAAGCAGTAAAAATATACCGATTTAATGAAAAAATACATAAACATAA
Found at i:29236 original size:578 final size:578
Alignment explanation
Indices: 28559--29620 Score: 1517
Period size: 578 Copynumber: 1.8 Consensus size: 578
28549 TTATTTGAAG
* * ** *
28559 GTAATAGGTAACTTTACAATGTTAGCGGTAAAAATATACCAGTTTAATGACAAGATACGTAAACA
1 GTAATAGGTAAATTGACAATGAAAGCGGTAAAAATATACCAGTTTAATGACAAAATACGTAAACA
* * ** * *
28624 TAAAGTATCGATCCTTTTTGTATTTGTGTCGATACTTTTTGTCCAGTATGCATCCCAATCGAGAT
66 TAAAGTATCGATACTTTTTGTAATACTATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGAT
* * * * *
28689 GCACGCATAAAGTATCGATACA-AGTATGAA-AAGTATCGATTCTTAAAACATCAAAACTGATTA
131 GCACGCAGAAAATATCAATACATA-TAT-AAGAAGTATCGATTCTTAAAACATCAAAACCGACTA
* * *
28752 -TTTAATGGTAATAGGTAAATTGACAATGTAAGCAGTAAAAATATATCAGTTTAATG-AGAAATA
194 GTATAA-AGTAATAGGTAAATTGACAATGTAAGCAGTAAAAATATATCAGTTTAATGAAAAAATA
*
28815 CGTAAACATAAAGTATCGATACATTTTGTAAGAGTATCGATACTTTTTGTCTAATATGCATCCCA
258 CGTAAACATAAAGTATCGATAC-TTCTGTAAGAGTATCGATACTTTTTGTCTAATATGCATCCCA
* * *
28880 AACGAGGTGAACGCTGAAAGCATCGATACAAGTACGAGAAGTATCGATTCTTAAAACTTCGAAAC
322 AACGAGATGAACACAGAAAGCATCGATACAAGTACGAGAAGTATCGATTCTTAAAACTTCGAAAC
*
28945 CAATTAGTATAAAGTAATAGAAAAATTTACAATGTCAGCAGTA-AAAAATACCGATTTAATGAAA
387 CAATTAGTATAAAGTAATAGAAAAATTTACAATGTAAGCAGTAGAAAAATACCGATTTAATGAAA
29009 ACAATACATAAACA-TA-AAGTATCGATACTTTTTGTCCAATATGCATCCCAAACGAGATGCACG
452 A-AATACATAAA-AGTAGAA-TATCGATACTTTTTGTCCAATATGCATCCCAAACGAGATGCACG
29072 TAGAAAATATCGATACATGTATGAGAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAA
514 TAGAAAATATCGATACATGTATGAGAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAA
* * *
29137 GTAATAGGTAAATTGACAATGAAAGCGGTAAAAATATATCGGTTTAATGAGAAAATACGTAAACA
1 GTAATAGGTAAATTGACAATGAAAGCGGTAAAAATATACCAGTTTAATGACAAAATACGTAAACA
* *
29202 TAAAGTATCGATAGTTTTTGTAATACTATCGATACTTTTTGTCCAGTATGCATTCCAAACGAGAT
66 TAAAGTATCGATACTTTTTGTAATACTATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGAT
* * * ** *
29267 GCATGTAGAAAATATCAATACATATATAAGAAGTATCGATTCTTAAAACTTTGATACCGACTAGT
131 GCACGCAGAAAATATCAATACATATATAAGAAGTATCGATTCTTAAAACATCAAAACCGACTAGT
* *
29332 ATAAAGTAATAGGTAAATTTACAATGTAAGCGGTAAAAATATATCAGTTTAATGAAAAAATACGT
196 ATAAAGTAATAGGTAAATTGACAATGTAAGCAGTAAAAATATATCAGTTTAATGAAAAAATACGT
* *
29397 ATACATAAAGTATCGATACTTCTGTAAGAGTATCGATACTTTTTGTCTAGTATGCATCCCAAACG
261 AAACATAAAGTATCGATACTTCTGTAAGAGTATCGATACTTTTTGTCTAATATGCATCCCAAACG
* * * * * * * *
29462 AGATGCATACAGAAAGTATTGATACATGTATGAGAAGTATCGATTCTTAAAACTTTGAAACCGAT
326 AGATGAACACAGAAAGCATCGATACAAGTACGAGAAGTATCGATTCTTAAAACTTCGAAACCAAT
** * * * *
29527 TAGTATAAAGTAATAGGTAAATTTACAATGTAAGCGGTAGAAATATACTGATTTAATGACAAAAT
391 TAGTATAAAGTAATAGAAAAATTTACAATGTAAGCAGTAGAAAAATACCGATTTAATGAAAAAAT
**
29592 ATGTAAAAGTAGAATATCGATACTTTTTG
456 ACATAAAAGTAGAATATCGATACTTTTTG
29621 AAAGAGTATT
Statistics
Matches: 422, Mismatches: 55, Indels: 14
0.86 0.11 0.03
Matches are distributed among these distances:
577 3 0.01
578 366 0.87
579 53 0.13
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (578 bp):
GTAATAGGTAAATTGACAATGAAAGCGGTAAAAATATACCAGTTTAATGACAAAATACGTAAACA
TAAAGTATCGATACTTTTTGTAATACTATCGATACTTTTTGTCCAGTATGCATCCCAAACGAGAT
GCACGCAGAAAATATCAATACATATATAAGAAGTATCGATTCTTAAAACATCAAAACCGACTAGT
ATAAAGTAATAGGTAAATTGACAATGTAAGCAGTAAAAATATATCAGTTTAATGAAAAAATACGT
AAACATAAAGTATCGATACTTCTGTAAGAGTATCGATACTTTTTGTCTAATATGCATCCCAAACG
AGATGAACACAGAAAGCATCGATACAAGTACGAGAAGTATCGATTCTTAAAACTTCGAAACCAAT
TAGTATAAAGTAATAGAAAAATTTACAATGTAAGCAGTAGAAAAATACCGATTTAATGAAAAAAT
ACATAAAAGTAGAATATCGATACTTTTTGTCCAATATGCATCCCAAACGAGATGCACGTAGAAAA
TATCGATACATGTATGAGAAGTATCGATTCTTAAAACTTCGAAACCAATTAGTATAAA
Found at i:30078 original size:18 final size:18
Alignment explanation
Indices: 30055--30100 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
30045 GAGGGGTCCG
30055 TCTTCTCAACAAAAAC-CT
1 TCTTCTCAAC-AAAACTCT
* *
30073 TCTTCTCAACCAAGCTCT
1 TCTTCTCAACAAAACTCT
30091 TCTTCTCAAC
1 TCTTCTCAAC
30101 TAAGGGATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 22 0.88
ACGTcount: A:0.28, C:0.37, G:0.02, T:0.33
Consensus pattern (18 bp):
TCTTCTCAACAAAACTCT
Found at i:30566 original size:19 final size:19
Alignment explanation
Indices: 30539--30584 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
30529 TTTTGTGTAC
*
30539 CGATTCACAAGCCATGCAT
1 CGATGCACAAGCCATGCAT
30558 CGATGCACAAGCCATGCAT
1 CGATGCACAAGCCATGCAT
30577 CGATGCAC
1 CGATGCAC
30585 TCTTGAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (19 bp):
CGATGCACAAGCCATGCAT
Found at i:30686 original size:65 final size:65
Alignment explanation
Indices: 30559--30686 Score: 154
Period size: 65 Copynumber: 2.0 Consensus size: 65
30549 GCCATGCATC
** *
30559 GATGCACAAGCCATGCATCGATGCACTCTTGAATATTTTGAAACATAGAATGTATTTTGTGTATT
1 GATGCACAAGCCATGCATCGATGCACTCCAGAATATTTTGAAACATAGAATGTATTTAGTGTATT
** *
30624 GATGCAC-AGACCATGCATCGATGCACTCCAGGCTCA-TTTGAAACATCGAATGT-TATTAGTGT
1 GATGCACAAG-CCATGCATCGATGCACTCCAGAAT-ATTTTGAAACATAGAATGTAT-TTAGTGT
30686 A
63 A
30687 CGGATGAACC
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
64 3 0.06
65 50 0.93
66 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (65 bp):
GATGCACAAGCCATGCATCGATGCACTCCAGAATATTTTGAAACATAGAATGTATTTAGTGTATT
Found at i:36216 original size:44 final size:43
Alignment explanation
Indices: 36132--36229 Score: 144
Period size: 44 Copynumber: 2.3 Consensus size: 43
36122 TTTTGTGCTC
* *
36132 TGTGCATCGATACACTAGACAGTGTACCGATGCATCCCTTGAA
1 TGTGCATCGATACACCAGACAGTGCACCGATGCATCCCTTGAA
*
36175 TGTGCATCGATACACCATGA-AGGTGCACCGATGCATTCCTTGAA
1 TGTGCATCGATACACCA-GACA-GTGCACCGATGCATCCCTTGAA
36219 TGTGCATCGAT
1 TGTGCATCGAT
36230 GCACTTTGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
43 17 0.34
44 33 0.66
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.27
Consensus pattern (43 bp):
TGTGCATCGATACACCAGACAGTGCACCGATGCATCCCTTGAA
Found at i:36223 original size:23 final size:22
Alignment explanation
Indices: 36157--36232 Score: 82
Period size: 23 Copynumber: 3.4 Consensus size: 22
36147 TAGACAGTGT
36157 ACCGATGCATCCCTTGAATGTGC
1 ACCGATGCAT-CCTTGAATGTGC
* * * *
36180 ATCGATACA-CCATGAAGGTGC
1 ACCGATGCATCCTTGAATGTGC
36201 ACCGATGCATTCCTTGAATGTGC
1 ACCGATGCA-TCCTTGAATGTGC
*
36224 ATCGATGCA
1 ACCGATGCA
36233 CTTTGCTGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
21 17 0.40
23 25 0.60
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (22 bp):
ACCGATGCATCCTTGAATGTGC
Found at i:38218 original size:22 final size:21
Alignment explanation
Indices: 38192--38232 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
38182 GTTTTCGGAT
*
38192 TGTTTGAATTTGATGATTTGGA
1 TGTTTGAATTGGATG-TTTGGA
38214 TGTTTGAATTGGATGTTTG
1 TGTTTGAATTGGATGTTTG
38233 AACTTAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (21 bp):
TGTTTGAATTGGATGTTTGGA
Found at i:38227 original size:13 final size:13
Alignment explanation
Indices: 38209--38234 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38199 ATTTGATGAT
38209 TTGGATGTTTGAA
1 TTGGATGTTTGAA
38222 TTGGATGTTTGAA
1 TTGGATGTTTGAA
38235 CTTAAATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (13 bp):
TTGGATGTTTGAA
Found at i:38959 original size:65 final size:65
Alignment explanation
Indices: 38889--39045 Score: 183
Period size: 65 Copynumber: 2.4 Consensus size: 65
38879 GCACTCCATT
* * **
38889 TCGAATGCATTTTGTGTACCGATGCACA-AGCCATGCATCGATGCACTCTTGAAT-ATTTTGAAA
1 TCGAATGTATTTTGTGTACCGATGCACAGA-CCATGCATCGAAGCACTCCAGAATCA-TTTGAAA
38952 CA
64 CA
* * * **
38954 TCGAATGTATTTTTTATATCGATGCACAGACCATGCATCGAAGCACTCCAGGCTCATTTGAAACA
1 TCGAATGTATTTTGTGTACCGATGCACAGACCATGCATCGAAGCACTCCAGAATCATTTGAAACA
* *
39019 TCGAATGTAATTAGTGTACCGATGCAC
1 TCGAATGTATTTTGTGTACCGATGCAC
39046 CCCTAGTGTA
Statistics
Matches: 76, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
65 74 0.97
66 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (65 bp):
TCGAATGTATTTTGTGTACCGATGCACAGACCATGCATCGAAGCACTCCAGAATCATTTGAAACA
Found at i:42151 original size:6 final size:6
Alignment explanation
Indices: 42142--42204 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
42132 GCATTTCATG
* * * * * *
42142 TTCAAT TTCAAT TTTAAT TTGAGT TTGAAT TTCAAT TTCAAT TTGAGT
1 TTCAAT TTCAAT TTCAAT TTCAAT TTCAAT TTCAAT TTCAAT TTCAAT
*
42190 TTGAAT TTCAAT TTC
1 TTCAAT TTCAAT TTC
42205 GGCTCCACTA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (6 bp):
TTCAAT
Found at i:42161 original size:24 final size:24
Alignment explanation
Indices: 42145--42204 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
42135 TTTCATGTTC
*
42145 AATTTCAATTTTAATTTGAGTTTG
1 AATTTCAATTTCAATTTGAGTTTG
42169 AATTTCAATTTCAATTTGAGTTTG
1 AATTTCAATTTCAATTTGAGTTTG
42193 AATTTCAATTTC
1 AATTTCAATTTC
42205 GGCTCCACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.30, C:0.08, G:0.10, T:0.52
Consensus pattern (24 bp):
AATTTCAATTTCAATTTGAGTTTG
Found at i:42186 original size:18 final size:18
Alignment explanation
Indices: 42142--42203 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
42132 GCATTTCATG
* *
42142 TTCAATTTCAATTTTAAT
1 TTCAATTTGAATTTCAAT
* *
42160 TTGAGTTTGAATTTCAAT
1 TTCAATTTGAATTTCAAT
* *
42178 TTCAATTTGAGTTTGAAT
1 TTCAATTTGAATTTCAAT
42196 TTCAATTT
1 TTCAATTT
42204 CGGCTCCACT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (18 bp):
TTCAATTTGAATTTCAAT
Found at i:43980 original size:19 final size:20
Alignment explanation
Indices: 43937--43980 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
43927 GTTAAAATAA
**
43937 AGTATCGATACTTTTTTATT
1 AGTATCGATACTTTTTTACC
*
43957 TGTATCGATACTTTTTT-CC
1 AGTATCGATACTTTTTTACC
43976 AGTAT
1 AGTAT
43981 GCTTCCCAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.23, C:0.14, G:0.11, T:0.52
Consensus pattern (20 bp):
AGTATCGATACTTTTTTACC
Found at i:46808 original size:108 final size:108
Alignment explanation
Indices: 46648--47254 Score: 434
Period size: 108 Copynumber: 5.5 Consensus size: 108
46638 AAATGTTTCC
* * * * *
46648 AGTAATTAGCCGGTTATGTTATCGTCGGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGATTTTGTTATCGTCGGATTTCTAAAGCTCCATCAGCTTAAACTTTGGTAACAT
46713 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTA
66 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTA
* * * ***
46756 AGTAATTAACCTATTTTGTTATCTTCGGATTTCTAAAGC-CCATCAGCTTTAAAAGGGCGCTACC
1 AGTAATTAACCGATTTTGTTATCGTCGGATTTCTAAAGCTCCATCAGC-TT-AAA---C-TTTGG
* * * * * *** *
46820 TATTACGTTATATAAGCGCTACCTAATATGTT-ATTAA-GCTTGATAA-TGTTTCC
60 TA--ACATT-T-TAGGCGTTACCTAATATGTTCA-TAATAC-TAATAACAAATT-A
* * * * * *
46873 AGTAATTAATCGATTATGTTATCGTCAGATTTCTAAGGCTCTATCAACTTAAACTTTGGTAACAT
1 AGTAATTAACCGATTTTGTTATCGTCGGATTTCTAAAGCTCCATCAGCTTAAACTTTGGTAACAT
46938 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTA
66 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTA
* ** * * * * ***
46981 AGTAATTATCTTATTTTGTTATCATCGGATTTCCAAAGCCCCATCAGCTTAAAAAGGCGCTACAT
1 AGTAATTAACCGATTTTGTTATCGTCGGATTTCTAAAGCTCCATCAGCTT--AAA--C-TTTGGT
* * * * * * **** *
47046 ATTACGTTATATAAGCGCTACCTAATATGTT-ATTATGCTTGATAATGTTTTC
61 A--ACATT-T-TAGGCGTTACCTAATATGTTCATAATAC-TAATAACAAATTA
* * * ** * * *
47098 AGTAATTAACCGGTTATGTTATCATCATATTTCTAATGCTCTATCATCTTAAACTTTGGTAACAT
1 AGTAATTAACCGATTTTGTTATCGTCGGATTTCTAAAGCTCCATCAGCTTAAACTTTGGTAACAT
*
47163 TTTAGGCATTACCTAATATGTTCATAATACTAATAACAAATTA
66 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTA
* * *
47206 AGTAATTAACCCATTTT-TTATCGTCGGATTTCCAAAGCCCCATCAGCTT
1 AGTAATTAACCGATTTTGTTATCGTCGGATTTCTAAAGCTCCATCAGCTT
47255 TAAAAAGGCA
Statistics
Matches: 364, Mismatches: 107, Indels: 57
0.69 0.20 0.11
Matches are distributed among these distances:
107 31 0.09
108 137 0.38
109 14 0.04
110 11 0.03
112 8 0.02
113 8 0.02
115 11 0.03
116 14 0.04
117 124 0.34
118 6 0.02
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (108 bp):
AGTAATTAACCGATTTTGTTATCGTCGGATTTCTAAAGCTCCATCAGCTTAAACTTTGGTAACAT
TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTA
Found at i:46842 original size:23 final size:22
Alignment explanation
Indices: 46812--46858 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
46802 CTTTAAAAGG
*
46812 GCGCTACCTATTACGTTATATAA
1 GCGCTACCTAATACGTTAT-TAA
*
46835 GCGCTACCTAATATGTTATTAA
1 GCGCTACCTAATACGTTATTAA
46857 GC
1 GC
46859 TTGATAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (22 bp):
GCGCTACCTAATACGTTATTAA
Found at i:46936 original size:225 final size:226
Alignment explanation
Indices: 46422--47348 Score: 1527
Period size: 225 Copynumber: 4.1 Consensus size: 226
46412 TAACAAATCA
* * *
46422 AGTAATTAACCAGTTATGTTATCATTAGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
* *
46487 TTTAGGTGTTACCTAATATATTCATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * *
46552 CGTCGGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTTCCTATTATGTTATATAAGTGCTAC
131 CGTCGGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTATATAAGCGCTAC
*
46617 CTAATATGTTATTATGCTTGAAAATGTTTCC
196 CTAATATGTTATTATGCTTGATAATGTTTCC
* *
46648 AGTAATTAGCCGGTTATGTTATCGTCGGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
46713 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * *
46778 CTTCGGATTTCTAAAG-CCCATCAGCTTTAAAAGGGCGCTACCTATTACGTTATATAAGCGCTAC
131 CGTCGGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTATATAAGCGCTAC
*
46842 CTAATATGTTATTAAGCTTGATAATGTTTCC
196 CTAATATGTTATTATGCTTGATAATGTTTCC
* * *
46873 AGTAATTAATCGATTATGTTATCGTCAGATTTCTAAGGCTCTATCAACTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
* *
46938 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTAAGTAATTATCTTATTTTGTTAT
66 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
* *
47003 CATCGGATTTCCAAAGCCCCATCAGC-TTAAAAAGGCGCTACATATTACGTTATATAAGCGCTAC
131 CGTCGGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTATATAAGCGCTAC
*
47067 CTAATATGTTATTATGCTTGATAATGTTTTC
196 CTAATATGTTATTATGCTTGATAATGTTTCC
* * * *
47098 AGTAATTAACCGGTTATGTTATCATCATATTTCTAATGCTCTATCATCTTAAACTTTGGTAACAT
1 AGTAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
* *
47163 TTTAGGCATTACCTAATATGTTCATAATACTAATAACAAATTAAGTAATTAACCCATTTT-TTAT
66 TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
* * *
47227 CGTCGGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCACTACCCATTATGTTATATAAGCGCTAC
131 CGTCGGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTATATAAGCGCTAC
* *
47292 CTAATATGTTATTATGTTTGATAATGTTTCT
196 CTAATATGTTATTATGCTTGATAATGTTTCC
47323 AGTAATTAACCGGTTATGTTATCGTC
1 AGTAATTAACCGGTTATGTTATCGTC
47349 TATATTTTTT
Statistics
Matches: 652, Mismatches: 47, Indels: 5
0.93 0.07 0.01
Matches are distributed among these distances:
224 29 0.04
225 477 0.73
226 146 0.22
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (226 bp):
AGTAATTAACCGGTTATGTTATCGTCAGATTTCTAAGGCTCTATCAGCTTAAACTTTGGTAACAT
TTTAGGCGTTACCTAATATGTTCATAATACTAATAACAAATTAAGTAATTAACCTATTTTGTTAT
CGTCGGATTTCCAAAGCCCCATCAGCTTTAAAAAGGCGCTACCTATTACGTTATATAAGCGCTAC
CTAATATGTTATTATGCTTGATAATGTTTCC
Found at i:47745 original size:29 final size:28
Alignment explanation
Indices: 47712--47801 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
47702 AAATTTTGAC
47712 TAGTGACCAAAATATAAGTTTTGAAAGTT
1 TAGTGACCAAAATATAA-TTTTGAAAGTT
* ** *
47741 TAGTGGCCAATGTATAAATTTGGAAAAGTT
1 TAGTGACCAAAATAT-AATTTTG-AAAGTT
* *
47771 TA-TGAACCAAAAATATAATTTTTAAAATT
1 TAGTG-ACC-AAAATATAATTTTGAAAGTT
47800 TA
1 TA
47802 TATATTTTGG
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
29 25 0.53
30 17 0.36
31 5 0.11
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (28 bp):
TAGTGACCAAAATATAATTTTGAAAGTT
Found at i:48421 original size:21 final size:22
Alignment explanation
Indices: 48397--48437 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
48387 CTAGGACAGG
48397 GAGTATTGGTAC-TCCTTTAAT
1 GAGTATTGGTACTTCCTTTAAT
*
48418 GAGTATTTGTACTTCCTTTA
1 GAGTATTGGTACTTCCTTTA
48438 TAATTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.46
Consensus pattern (22 bp):
GAGTATTGGTACTTCCTTTAAT
Found at i:50552 original size:323 final size:322
Alignment explanation
Indices: 49946--50595 Score: 1081
Period size: 323 Copynumber: 2.0 Consensus size: 322
49936 TAGAAATTAA
49946 TTCTTTTTCTTTCGTTAAGCTTTCAAGCTTAACTTTCAAATCAATTTTTTTCTCTAAATCATTGA
1 TTCTTTTTCTTTCGTTAAGCTTTCAAGCTTAACTTTCAAATCAATTTTTTTCTCTAAATCATTGA
*
50011 TTTTGATTTTTGAAAGCTCTAAATCATTTTTCAAAGTTTATTTTGTTTTTCAAAATCTAATATTG
66 TTTTGATTTTTGAAAGCTCTAAATCATTTTTCAAAGTTTATTATGTTTTTCAAAATCTAATATTG
*
50076 CTTTCAAAAGAAAATCATTTTCAACTTTGAATTTTGAAATCAATTTCTTATATTTGGAATTAATA
131 CTTTAAAAAGAAAATCATTTTCAACTTTGAATTTTGAAATCAATTTCTTATATTTGGAATTAATA
* * *
50141 GTCTTAAATTCCAAATACGACTTATCATAGGTATCTTGTAACTCTTTAAATGAATAAGAATTTGA
196 GTCTCAAATTCCAAATACGACTCATCATAGGCATCTTGTAACTCTTTAAATGAATAAGAATTTGA
* * *
50206 ATCACAAGAGTTAGAGGATACCTCGGGCTTTTCAAGAGCCATTAAGGACATCGCCTTTGTTGG
261 ATCACAAGAGTTAGAGCATACCTCGGGCTTTT-AAGAGCCATTAAGGACACCACCTTTGTTGG
*
50269 TTCTTCTTT-TTTTGTTAAGCTTTCAAGCTTAACTTTCAAATCAATTTTTTTC-CTAAATCATTG
1 TTCTT-TTTCTTTCGTTAAGCTTTCAAGCTTAACTTTCAAATCAATTTTTTTCTCTAAATCATTG
* * *
50332 ATTTTGATTTTTTAAATCTCTAAATCATTTTTCAAAGTTTCATTATGTTTTTCAAAATCTAATTT
65 ATTTTGATTTTTGAAAGCTCTAAATCATTTTTCAAAGTTT-ATTATGTTTTTCAAAATCTAATAT
* *
50397 TGCTTTAAAAAGAAAATCATTTTTAACTTTGAATTTTGAAATCAATTTCTTATATTTGGAATTCA
129 TGCTTTAAAAAGAAAATCATTTTCAACTTTGAATTTTGAAATCAATTTCTTATATTTGGAATTAA
* *
50462 TGGTCTCAAATTCCAAATA-GAACTCATTATAGGCATCTTGTAACTCTTTAAATGAATAAGAATT
194 TAGTCTCAAATTCCAAATACG-ACTCATCATAGGCATCTTGTAACTCTTTAAATGAATAAGAATT
* *
50526 TGAATCATAAGAGTTAGAGCATACCTCGGGCTTTTAGGAGCCATTAAGGACACCACCTTTGTTGG
258 TGAATCACAAGAGTTAGAGCATACCTCGGGCTTTTAAGAGCCATTAAGGACACCACCTTTGTTGG
50591 TTCTT
1 TTCTT
50596 ATTTATTGTT
Statistics
Matches: 306, Mismatches: 18, Indels: 7
0.92 0.05 0.02
Matches are distributed among these distances:
322 82 0.27
323 221 0.72
324 3 0.01
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (322 bp):
TTCTTTTTCTTTCGTTAAGCTTTCAAGCTTAACTTTCAAATCAATTTTTTTCTCTAAATCATTGA
TTTTGATTTTTGAAAGCTCTAAATCATTTTTCAAAGTTTATTATGTTTTTCAAAATCTAATATTG
CTTTAAAAAGAAAATCATTTTCAACTTTGAATTTTGAAATCAATTTCTTATATTTGGAATTAATA
GTCTCAAATTCCAAATACGACTCATCATAGGCATCTTGTAACTCTTTAAATGAATAAGAATTTGA
ATCACAAGAGTTAGAGCATACCTCGGGCTTTTAAGAGCCATTAAGGACACCACCTTTGTTGG
Found at i:56284 original size:18 final size:18
Alignment explanation
Indices: 56261--56316 Score: 112
Period size: 18 Copynumber: 3.1 Consensus size: 18
56251 TCATATATAA
56261 GAGTTCTAAGATAGAAAG
1 GAGTTCTAAGATAGAAAG
56279 GAGTTCTAAGATAGAAAG
1 GAGTTCTAAGATAGAAAG
56297 GAGTTCTAAGATAGAAAG
1 GAGTTCTAAGATAGAAAG
56315 GA
1 GA
56317 AGTAGAAATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 38 1.00
ACGTcount: A:0.45, C:0.05, G:0.29, T:0.21
Consensus pattern (18 bp):
GAGTTCTAAGATAGAAAG
Found at i:58398 original size:22 final size:24
Alignment explanation
Indices: 58373--58422 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
58363 ATCTAGAAAT
58373 TAAAAAT-AAA-AATAAAAATATA
1 TAAAAATAAAACAATAAAAATATA
*
58395 TAAAAATGAAAACAATAATAATATA
1 TAAAAAT-AAAACAATAAAAATATA
58420 TAA
1 TAA
58423 TCAAAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
24 3 0.12
25 14 0.58
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (24 bp):
TAAAAATAAAACAATAAAAATATA
Found at i:58490 original size:38 final size:40
Alignment explanation
Indices: 58425--58523 Score: 105
Period size: 40 Copynumber: 2.5 Consensus size: 40
58415 ATATATAATC
*
58425 AAAATATATAATATAT-TTTCAGTAAAACCATATATATTTT-
1 AAAATATATAATATATATTTCA--AAAACCACATATATTTTA
* * *
58465 AAAATATATAATTTATATTTC-AAAACTACATATGTTTTCA
1 AAAATATATAATATATATTTCAAAAACCACATATATTTT-A
58505 AAAATATATATATATATAT
1 AAAATATATA-ATATATAT
58524 ATATTTAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
38 14 0.28
40 25 0.50
41 11 0.22
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.42
Consensus pattern (40 bp):
AAAATATATAATATATATTTCAAAAACCACATATATTTTA
Found at i:58581 original size:15 final size:16
Alignment explanation
Indices: 58542--58584 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
58532 AATATATATC
*
58542 TCAAAACTATATGTTT
1 TCAAAACAATATGTTT
58558 TCAAAACAATATGTTT
1 TCAAAACAATATGTTT
58574 TC-AAACAATAT
1 TCAAAACAATAT
58585 ATATATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 9 0.35
16 17 0.65
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.37
Consensus pattern (16 bp):
TCAAAACAATATGTTT
Found at i:58643 original size:2 final size:2
Alignment explanation
Indices: 58581--58624 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
58571 TTTTCAAACA
58581 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58623 AT
1 AT
58625 GAAAACCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67202 original size:17 final size:18
Alignment explanation
Indices: 67180--67217 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
67170 TTTGGTAAGA
*
67180 AAATAA-TAAAAGCGATT
1 AAATAAGTAAAAGCAATT
67197 AAATAAGTAAAAGCAATT
1 AAATAAGTAAAAGCAATT
67215 AAA
1 AAA
67218 GTAAAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.63, C:0.05, G:0.11, T:0.21
Consensus pattern (18 bp):
AAATAAGTAAAAGCAATT
Found at i:72031 original size:14 final size:14
Alignment explanation
Indices: 72012--72039 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
72002 ATATCCCTAC
72012 GGCTTGAGTCAGTT
1 GGCTTGAGTCAGTT
72026 GGCTTGAGTCAGTT
1 GGCTTGAGTCAGTT
72040 CGAGTCTGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.36, T:0.36
Consensus pattern (14 bp):
GGCTTGAGTCAGTT
Found at i:80645 original size:2 final size:2
Alignment explanation
Indices: 80638--80737 Score: 104
Period size: 2 Copynumber: 52.5 Consensus size: 2
80628 GTGTCTACAG
80638 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
* * *
80680 TA TA AA CA TA -A TA TA T- TA -A TA -A TA -A CCA 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
* *
80718 TA TA TA -A TA TG TA CA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
80738 TTAGTAATAA
Statistics
Matches: 83, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
1 6 0.07
2 76 0.92
3 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (2 bp):
TA
Found at i:80783 original size:3 final size:3
Alignment explanation
Indices: 80768--80824 Score: 98
Period size: 3 Copynumber: 19.0 Consensus size: 3
80758 ATATTATTAC
80768 TAA TAA -AA TTAA TAA TAA 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
80813 TAA TAA TAA TAA
1 TAA TAA TAA TAA
80825 AACTTGGAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 48 0.92
4 2 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:80983 original size:2 final size:2
Alignment explanation
Indices: 80976--81005 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
80966 CCAATTATGC
80976 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
81006 GCAACTTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:88772 original size:125 final size:125
Alignment explanation
Indices: 88550--88793 Score: 409
Period size: 125 Copynumber: 2.0 Consensus size: 125
88540 AGGTCAGATC
* * * *
88550 TAGAGAGATTTTTAACGAGGCTCTTAATCTAGGTCTTGATTAATAAAACTTATTTTACCGAGAAA
1 TAGAGAGATTTTTAACAAGGATCTTAATCTAAGTCTTGACTAATAAAACTTATTTTACCGAGAAA
*
88615 AAAAAAAAGAATAGTTGCTGAGATTGCATGTCGGCATAGCTTAGCTATAGTTTTTTTTAT
66 AAAAAAAAGAATAGTTGATGAGATTGCATGTCGGCATAGCTTAGCTATAGTTTTTTTTAT
* *
88675 TAGAGAGGTTTTTAACAAGGATCTTAATCTAAGTCTTGACTAATAAAACTTATTTTACGGAGAAA
1 TAGAGAGATTTTTAACAAGGATCTTAATCTAAGTCTTGACTAATAAAACTTATTTTACCGAGAAA
88740 AAAAAAAAGAATAGCTT-ATGAGATTGCATGTCGGCATAGCTTAGCTATAGTTTT
66 AAAAAAAAGAATAG-TTGATGAGATTGCATGTCGGCATAGCTTAGCTATAGTTTT
88794 GTAATTGATG
Statistics
Matches: 111, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
125 109 0.98
126 2 0.02
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.34
Consensus pattern (125 bp):
TAGAGAGATTTTTAACAAGGATCTTAATCTAAGTCTTGACTAATAAAACTTATTTTACCGAGAAA
AAAAAAAAGAATAGTTGATGAGATTGCATGTCGGCATAGCTTAGCTATAGTTTTTTTTAT
Found at i:93103 original size:46 final size:47
Alignment explanation
Indices: 93008--93107 Score: 116
Period size: 49 Copynumber: 2.1 Consensus size: 47
92998 AGGATTATAT
*
93008 TTATTATTTTATTAGGAATTAAGGTTAAGTTAAAATATTTTTTTAGTTA
1 TTATTATTTTATTAGGAATTAAGGTTAAG-T-AAATATTTGTTTAGTTA
* *
93057 TTATTATTTTATTAGGAATT-AGAGTTAAG-ACATGTTTAGTTT-GTTA
1 TTATTATTTTATTAGGAATTAAG-GTTAAGTAAATATTT-GTTTAGTTA
93103 TTATT
1 TTATT
93108 TTATTCATTA
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
46 15 0.33
47 3 0.07
48 2 0.04
49 26 0.57
ACGTcount: A:0.32, C:0.01, G:0.14, T:0.53
Consensus pattern (47 bp):
TTATTATTTTATTAGGAATTAAGGTTAAGTAAATATTTGTTTAGTTA
Found at i:101698 original size:59 final size:59
Alignment explanation
Indices: 101625--101749 Score: 250
Period size: 59 Copynumber: 2.1 Consensus size: 59
101615 GATTTCAGAG
101625 GAACACCAGCTGTCCCTCCATGTTTCAGAAGCTTCCGGTAGCTCCACCCGTGGTCTCTC
1 GAACACCAGCTGTCCCTCCATGTTTCAGAAGCTTCCGGTAGCTCCACCCGTGGTCTCTC
101684 GAACACCAGCTGTCCCTCCATGTTTCAGAAGCTTCCGGTAGCTCCACCCGTGGTCTCTC
1 GAACACCAGCTGTCCCTCCATGTTTCAGAAGCTTCCGGTAGCTCCACCCGTGGTCTCTC
101743 GAACACC
1 GAACACC
101750 GTCCACGTTC
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 66 1.00
ACGTcount: A:0.18, C:0.38, G:0.20, T:0.24
Consensus pattern (59 bp):
GAACACCAGCTGTCCCTCCATGTTTCAGAAGCTTCCGGTAGCTCCACCCGTGGTCTCTC
Found at i:102872 original size:30 final size:31
Alignment explanation
Indices: 102838--102898 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
102828 GATCTACTTT
*
102838 TTATTTATTTAATTT-CATTACTTTAATTTC
1 TTATTTATTTAATTTACAATACTTTAATTTC
* *
102868 TTATTTTTTTATTTTCACAATACTTTAATTT
1 TTATTTATTTAATTT-ACAATACTTTAATTT
102899 TAGTTCTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 13 0.50
32 13 0.50
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (31 bp):
TTATTTATTTAATTTACAATACTTTAATTTC
Found at i:103234 original size:2 final size:2
Alignment explanation
Indices: 103227--103277 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
103217 ACCTTACTTA
103227 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
103269 AT AT AT AT A
1 AT AT AT AT A
103278 CTTTAATTAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:107094 original size:17 final size:16
Alignment explanation
Indices: 107055--107128 Score: 55
Period size: 14 Copynumber: 4.7 Consensus size: 16
107045 TATTCATCAG
* *
107055 AAAAAAGAAAAGAGAG
1 AAAAAAAAAAAGAGAA
** *
107071 ATGAAAAACAAGA-AA
1 AAAAAAAAAAAGAGAA
*
107086 AAGAAAAAAAAGAG--
1 AAAAAAAAAAAGAGAA
107100 AAAAAAAAAAAGAGAA
1 AAAAAAAAAAAGAGAA
107116 AAGGAAAAAAAAA
1 AA--AAAAAAAAA
107129 AAATTGAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
14 13 0.29
15 12 0.27
16 11 0.24
18 9 0.20
ACGTcount: A:0.80, C:0.01, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAAAAAAAAAGAGAA
Found at i:107124 original size:14 final size:14
Alignment explanation
Indices: 107053--107117 Score: 67
Period size: 14 Copynumber: 4.4 Consensus size: 14
107043 CTTATTCATC
107053 AGAAAAAAGAAAAGAG
1 AGAAAAAA-AAAA-AG
** *
107069 AGATGAAAAACAAG
1 AGAAAAAAAAAAAG
*
107083 AAAAAGAAAAAAAAG
1 AGAAA-AAAAAAAAG
107098 AGAAAAAAAAAAAG
1 AGAAAAAAAAAAAG
107112 AGAAAA
1 AGAAAA
107118 GGAAAAAAAA
Statistics
Matches: 40, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
14 19 0.47
15 15 0.38
16 6 0.15
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (14 bp):
AGAAAAAAAAAAAG
Found at i:107131 original size:14 final size:15
Alignment explanation
Indices: 107053--107126 Score: 73
Period size: 16 Copynumber: 4.9 Consensus size: 15
107043 CTTATTCATC
*
107053 AGAAAA-AAGAAAAG
1 AGAAAAGAAAAAAAG
* *
107067 AGAGATGAAAAACAAG
1 AGAAAAGAAAAA-AAG
107083 A-AAAAGAAAAAAAAG
1 AGAAAAG-AAAAAAAG
107098 AGAAAA-AAAAAAAG
1 AGAAAAGAAAAAAAG
107112 AGAAAAGGAAAAAAA
1 AGAAAA-GAAAAAAA
107127 AAAAATTGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
14 18 0.37
15 11 0.22
16 20 0.41
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (15 bp):
AGAAAAGAAAAAAAG
Found at i:110018 original size:74 final size:72
Alignment explanation
Indices: 109813--110146 Score: 449
Period size: 74 Copynumber: 4.5 Consensus size: 72
109803 GGATGTTTTA
* * *
109813 AAATAGCAATTTTATCTCACTTGAGATTGTTTTTCTT-AAAGAAATTGTTTCTCTCTTGAGAAAA
1 AAATA-CAA-TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAAG
*
109877 TTTCACTCG
64 TTTCACTTG
* *
109886 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTCAAAAC-AATATGTTTCTCACTTGAGAAAG
1 AAATA-CAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAT-TGTTTCTCGCTTGAGAAAG
*
109950 TTTCACTTA
64 TTTCACTTG
109959 AAATA-AATTTTATCTCACTTGAGATTGTTTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAA
1 AAATACAA-TTTATCTCACTTGAGATTG--TTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAA
*
110023 GGTTCACTTG
63 GTTTCACTTG
* * *
110033 AAATAGCAATTTATCTCACTTGAGATGTTTTTTTCTTAAAATAAATTGTTTCTTGCTTGAGAAAG
1 AAATA-CAATTTATCTCACTTGAGAT-TGTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAAG
*
110098 TTTCACTCG
64 TTTCACTTG
110107 AAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 AAATA-CAATTTATCTCACTTGAGATTGTTTTTCTTAAAA
110147 TATTTCCAGA
Statistics
Matches: 236, Mismatches: 16, Indels: 18
0.87 0.06 0.07
Matches are distributed among these distances:
71 2 0.01
72 48 0.20
73 54 0.23
74 109 0.46
75 20 0.08
76 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (72 bp):
AAATACAATTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAAGTT
TCACTTG
Found at i:110057 original size:37 final size:36
Alignment explanation
Indices: 109813--110131 Score: 152
Period size: 37 Copynumber: 8.7 Consensus size: 36
109803 GGATGTTTTA
** **
109813 AAATAGCAATTTTATCTCACTTGAGATTGTTTTTCTT-
1 AAATA-CAA-TTTATCTCACTTGAGAAAGTTTCACTTG
* * * * *
109850 AAAGA-AATTGTTTCTCTCTTGAGAAAATTTCACTCG
1 AAATACAATT-TATCTCACTTGAGAAAGTTTCACTTG
** ** *
109886 AAATAGCAATTTATCTCACTTGAGATTGTTTTTC-TC
1 AAATA-CAATTTATCTCACTTGAGAAAGTTTCACTTG
* *
109922 AAA-ACAATATGTTTCTCACTTGAGAAAGTTTCACTTA
1 AAATACAAT-T-TATCTCACTTGAGAAAGTTTCACTTG
** **
109959 AAATA-AATTTTATCTCACTTGAGATTGTTTTTTTCTT-
1 AAATACAA-TTTATCTCACTTGAGAAAG--TTTCACTTG
* * *
109996 AAA-ACAAATTGTTTCTCGCTTGAGAAAGGTTCACTTG
1 AAATAC-AATT-TATCTCACTTGAGAAAGTTTCACTTG
* ** *
110033 AAATAGCAATTTATCTCACTTGAG-ATGTTTTTTTCTTA
1 AAATA-CAATTTATCTCACTTGAGAAAG--TTTCACTTG
* ** *
110071 AAATA-AATTGTTTCTTGCTTGAGAAAGTTTCACTCG
1 AAATACAATT-TATCTCACTTGAGAAAGTTTCACTTG
110107 AAATAGCAATTTATCTCACTTGAGA
1 AAATA-CAATTTATCTCACTTGAGA
110132 TTGTTTTTCT
Statistics
Matches: 204, Mismatches: 55, Indels: 46
0.67 0.18 0.15
Matches are distributed among these distances:
34 6 0.03
35 21 0.10
36 61 0.30
37 67 0.33
38 48 0.24
39 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.13, T:0.41
Consensus pattern (36 bp):
AAATACAATTTATCTCACTTGAGAAAGTTTCACTTG
Found at i:110139 original size:147 final size:147
Alignment explanation
Indices: 109812--110146 Score: 491
Period size: 147 Copynumber: 2.3 Consensus size: 147
109802 AGGATGTTTT
* *
109812 AAAATAGCAATTTTATCTCACTTGAGATTGTTTTTCTT-AAAGAAATTGTTTCTCTCTTGAGAAA
1 AAAATAGCAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAA
* *
109876 ATTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTCAAAACAATATGTTTCTCAC
66 AGTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTCAAAAAAATATGTTTCTCAC
*
109941 TTGAGAAAGTTTCACTT
131 TTGAGAAAGTTTCACTC
109958 AAAATA--AATTTTATCTCACTTGAGATTGTTTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGA
1 AAAATAGCAATTTTATCTCACTTGAGATTG--TTTTTCTTAAAACAAATTGTTTCTCGCTTGAGA
* * * *
110021 AAGGTTCACTTGAAATAGCAATTTATCTCACTTGAGATGTTTTTTTCTTAAAATAAAT-TGTTTC
64 AAAGTTCACTCGAAATAGCAATTTATCTCACTTGAGAT-TGTTTTTCTCAAAA-AAATATGTTTC
**
110085 TTGCTTGAGAAAGTTTCACTC
127 TCACTTGAGAAAGTTTCACTC
*
110106 GAAATAGCAA-TTTATCTCACTTGAGATTGTTTTTCTTAAAA
1 AAAATAGCAATTTTATCTCACTTGAGATTGTTTTTCTTAAAA
110147 TATTTCCAGA
Statistics
Matches: 170, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
144 22 0.13
146 14 0.08
147 69 0.41
148 41 0.24
149 22 0.13
150 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (147 bp):
AAAATAGCAATTTTATCTCACTTGAGATTGTTTTTCTTAAAACAAATTGTTTCTCGCTTGAGAAA
AGTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTCAAAAAAATATGTTTCTCAC
TTGAGAAAGTTTCACTC
Found at i:110264 original size:90 final size:91
Alignment explanation
Indices: 110153--110344 Score: 300
Period size: 91 Copynumber: 2.1 Consensus size: 91
110143 AAAATATTTC
110153 CAGAAGAAGATTGTAATAAGAAGAACTCATCTGAAGAGAA-A-TAAGTTCATAATCTGAAGAACG
1 CAGAAGAAGATTGTAATAAGAAGAACTCATCTGAAG-GAATATTAAGTTCATAATCTGAAGAACG
110216 TATTCAACCTTTTGCTCGACTCTATCG
65 TATTCAACCTTTTGCTCGACTCTATCG
* *
110243 CAGAAGAAG-TTCGTAATAAGAAGAGCTCATCTGAAGGAATATTAAGTTCATAATCTGAAGAACT
1 CAGAAGAAGATT-GTAATAAGAAGAACTCATCTGAAGGAATATTAAGTTCATAATCTGAAGAACG
* *
110307 TTTTCAACCTTTTGGTCGACTCTATCG
65 TATTCAACCTTTTGCTCGACTCTATCG
*
110334 CAGAAGGAGAT
1 CAGAAGAAGAT
110345 AGAGCAGCAT
Statistics
Matches: 93, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
89 5 0.05
90 33 0.35
91 54 0.58
92 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (91 bp):
CAGAAGAAGATTGTAATAAGAAGAACTCATCTGAAGGAATATTAAGTTCATAATCTGAAGAACGT
ATTCAACCTTTTGCTCGACTCTATCG
Found at i:114728 original size:36 final size:36
Alignment explanation
Indices: 114540--114729 Score: 258
Period size: 36 Copynumber: 5.3 Consensus size: 36
114530 GTAAATAAGA
* * *
114540 GAACGAAAGAAAGAATCG-CACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
*
114575 GAACAGAAGGAAGCATCGACACTTCCGATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
*
114611 GAACGGAAGGAAGCATC-AGCACTTCCGATTCATGTC
1 GAACGGAAGGAAGCATCGA-CACTTCCGATTCAAGTC
* *
114647 GAACGGAAGGAATCATCGACACTTCCTATTCAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
* * *
114683 GAACAGAAGGAAGCATCGACACTTCTGATTTAAGTC
1 GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
*
114719 GAATGGAAGGA
1 GAACGGAAGGA
114730 TGTATCGCAC
Statistics
Matches: 136, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
35 15 0.11
36 120 0.88
37 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.23, T:0.19
Consensus pattern (36 bp):
GAACGGAAGGAAGCATCGACACTTCCGATTCAAGTC
Found at i:117842 original size:2 final size:2
Alignment explanation
Indices: 117835--117860 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
117825 TTTCCCCTAA
117835 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
117861 TCGAATAAAA
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:118611 original size:5 final size:5
Alignment explanation
Indices: 118601--118625 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
118591 TTTTAGTCAT
118601 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
118626 AGTTAGCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:118644 original size:24 final size:24
Alignment explanation
Indices: 118615--118660 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
118605 ATTTTATTTT
*
118615 ATTTTATTTTAAGTTAGCCCTTAC
1 ATTTTACTTTAAGTTAGCCCTTAC
* *
118639 ATTTTACTTTAATTTATCCCTT
1 ATTTTACTTTAAGTTAGCCCTT
118661 TGCATGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.04, T:0.54
Consensus pattern (24 bp):
ATTTTACTTTAAGTTAGCCCTTAC
Found at i:118733 original size:16 final size:15
Alignment explanation
Indices: 118712--118766 Score: 51
Period size: 16 Copynumber: 3.5 Consensus size: 15
118702 TAGGTCCTCA
118712 TATTTTATGTTATTTT
1 TATTTTATG-TATTTT
118728 TATTTTACTGT-TTTT
1 TATTTTA-TGTATTTT
*
118743 TATCATT-TGATATTTT
1 TAT-TTTATG-TATTTT
118759 TATTTTAT
1 TATTTTAT
118767 TTTTATTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
14 2 0.06
15 10 0.31
16 18 0.56
17 2 0.06
ACGTcount: A:0.20, C:0.04, G:0.05, T:0.71
Consensus pattern (15 bp):
TATTTTATGTATTTT
Done.