Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004862.1 Hibiscus syriacus cultivar Beakdansim tig00010968_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: 2846896
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 13
Found at i:2629855 original size:13 final size:13
Alignment explanation
Indices: 2629804--2629851 Score: 51
Period size: 13 Copynumber: 3.7 Consensus size: 13
2629794 GTCATAAATC
2629804 TATGACGCGCATT
1 TATGACGCGCATT
* *
2629817 GATGACACGCATT
1 TATGACGCGCATT
* **
2629830 TATGACTCATATT
1 TATGACGCGCATT
2629843 TATGACGCG
1 TATGACGCG
2629852 TATTGAACAT
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:2642827 original size:37 final size:38
Alignment explanation
Indices: 2642741--2642849 Score: 102
Period size: 37 Copynumber: 2.9 Consensus size: 38
2642731 TATGTGTGTG
*
2642741 TGTTTTCAAAAATTATAT-TATATATGTTTTCAAAAAACCA
1 TGTTTTCAAAAACTATATAT-TATATG-TTT-AAAAAACCA
* *
2642781 --TTTTAAAAAACTATATATTATATGTTTAAAAAA-TA
1 TGTTTTCAAAAACTATATATTATATGTTTAAAAAACCA
* *
2642816 TGTTTTCAAAAACTATACTA-TATATCTTCAAAAA
1 TGTTTTCAAAAACTATA-TATTATATGTTTAAAAA
2642850 CTATATATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
35 1 0.02
36 6 0.10
37 29 0.49
38 22 0.37
39 1 0.02
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (38 bp):
TGTTTTCAAAAACTATATATTATATGTTTAAAAAACCA
Found at i:2642858 original size:19 final size:21
Alignment explanation
Indices: 2642820--2642859 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2642810 AAAATATGTT
2642820 TTCAAAAACTATACTATATATC
1 TTCAAAAAC-ATACTATATATC
2642842 TTCAAAAAC-TA-TATATAT
1 TTCAAAAACATACTATATAT
2642860 TATATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
22 9 0.50
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (21 bp):
TTCAAAAACATACTATATATC
Found at i:2642918 original size:2 final size:2
Alignment explanation
Indices: 2642879--2642907 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2642869 TTGAAATTAT
2642879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2642908 TACCATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2643268 original size:32 final size:31
Alignment explanation
Indices: 2643202--2643269 Score: 75
Period size: 32 Copynumber: 2.2 Consensus size: 31
2643192 TAAAATATGA
* *
2643202 CATGTCATCATTTGGGTGAAGTTACACATGT
1 CATGTCATCATTTGAGTGAAGTGACACATGT
* *
2643233 CATGTCATCAATTTGAGTGATA-TGACATATTT
1 CATGTCATC-ATTTGAGTGA-AGTGACACATGT
2643265 CATGT
1 CATGT
2643270 TACTATTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
31 9 0.29
32 21 0.68
33 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (31 bp):
CATGTCATCATTTGAGTGAAGTGACACATGT
Found at i:2648199 original size:16 final size:16
Alignment explanation
Indices: 2648178--2648211 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
2648168 TTAATCTCAA
2648178 TTAATTGAGA-ATTATT
1 TTAATT-AGATATTATT
2648194 TTAATTAGATATTATT
1 TTAATTAGATATTATT
2648210 TT
1 TT
2648212 TTATTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.18
16 14 0.82
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (16 bp):
TTAATTAGATATTATT
Found at i:2648379 original size:31 final size:32
Alignment explanation
Indices: 2648336--2648424 Score: 105
Period size: 31 Copynumber: 2.8 Consensus size: 32
2648326 ATTTTTAAAA
* *
2648336 ATTATAAGATAATTATT-TTATTTATTAAATT-
1 ATTATAAAATAATTATTATT-TTTAATAAATTC
2648367 ATTATAAAATAATTATTATTTTTAATAAATTC
1 ATTATAAAATAATTATTATTTTTAATAAATTC
2648399 A--ATAAAATTAATTATTATTTTATAAT
1 ATTATAAAA-TAATTATTATTTT-TAAT
2648425 TTTTAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
30 6 0.12
31 39 0.75
32 7 0.13
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (32 bp):
ATTATAAAATAATTATTATTTTTAATAAATTC
Found at i:2648391 original size:28 final size:28
Alignment explanation
Indices: 2648326--2648419 Score: 93
Period size: 31 Copynumber: 3.2 Consensus size: 28
2648316 TAATCATTAA
*
2648326 ATTTTTAAA-AATTATAAGATAATTATTTT
1 ATTTTTAAATAATTATAAAATAATTA--TT
*
2648355 ATTTATTAAATTATTATAAAATAATTATT
1 ATTT-TTAAATAATTATAAAATAATTATT
2648384 ATTTTT-AATAAATTCAATAAAATTAATTATT
1 ATTTTTAAAT-AATT--ATAAAA-TAATTATT
2648415 ATTTT
1 ATTTT
2648420 ATAATTTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
27 3 0.05
28 5 0.09
29 10 0.18
30 11 0.20
31 27 0.48
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (28 bp):
ATTTTTAAATAATTATAAAATAATTATT
Found at i:2650316 original size:26 final size:27
Alignment explanation
Indices: 2650261--2650312 Score: 81
Period size: 25 Copynumber: 2.0 Consensus size: 27
2650251 CCTAATAATA
2650261 AAATATTACTTGATATATATATTTTTT
1 AAATATTACTTGATATATATATTTTTT
*
2650288 AAATATTA-TTGATCTA-ATATTTTTT
1 AAATATTACTTGATATATATATTTTTT
2650313 TAAAATAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
26 7 0.29
27 8 0.33
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (27 bp):
AAATATTACTTGATATATATATTTTTT
Found at i:2650318 original size:27 final size:28
Alignment explanation
Indices: 2650259--2650319 Score: 83
Period size: 26 Copynumber: 2.2 Consensus size: 28
2650249 CACCTAATAA
2650259 TAAAATATTACTTGATATATATATTTTT
1 TAAAATATTACTTGATATATATATTTTT
*
2650287 T-AAATATTA-TTGATCTA-ATATTTTTT
1 TAAAATATTACTTGATATATATA-TTTTT
2650313 TAAAATA
1 TAAAATA
2650320 AGGATAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 3 0.10
26 13 0.43
27 13 0.43
28 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (28 bp):
TAAAATATTACTTGATATATATATTTTT
Found at i:2650523 original size:14 final size:15
Alignment explanation
Indices: 2650501--2650540 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2650491 TAAGACGTGT
2650501 CTTCCATTATTCT-C
1 CTTCCATTATTCTCC
* *
2650515 CTTCAATTATTGTCC
1 CTTCCATTATTCTCC
2650530 CTTCCATTATT
1 CTTCCATTATT
2650541 ACCCTAGTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 11 0.50
15 11 0.50
ACGTcount: A:0.17, C:0.30, G:0.03, T:0.50
Consensus pattern (15 bp):
CTTCCATTATTCTCC
Found at i:2657936 original size:24 final size:24
Alignment explanation
Indices: 2657867--2657928 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
2657857 TACATACATG
*
2657867 AGTTTATGCATCCTTAGTAACCCA
1 AGTTGATGCATCCTTAGTAACCCA
2657891 AGTTGATGCATCCTTAGTAACCCA
1 AGTTGATGCATCCTTAGTAACCCA
2657915 AGTTGATGCATCCT
1 AGTTGATGCATCCT
2657929 CAGGAACCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.27, C:0.24, G:0.16, T:0.32
Consensus pattern (24 bp):
AGTTGATGCATCCTTAGTAACCCA
Found at i:2658218 original size:178 final size:181
Alignment explanation
Indices: 2657919--2658279 Score: 674
Period size: 178 Copynumber: 2.0 Consensus size: 181
2657909 AACCCAAGTT
2657919 GATGCATCCTCAGGAACCTATATACTTTTCCATGTTTGAATCAACATATGATTTTGAGGACATGA
1 GATGCATCCTCAGGAACCTATATACTTTTCCATGTTTGAATCAACATATGATTTTGAGGACATGA
2657984 CATCTATGATGTCAAATATGACTACTTGTCATTCTACATTTCCATCAGAGATGCAAGAGCAAAGT
66 CATCTATGATGTCAAATATGACTACTTGTCATTCTACATTTCCATCAGAGATGCAAGAGCAAAGT
2658049 GGTGGGC-ATATTTACAACACCAAATC-ATGCCCTTA-TGAATAAGGAGAA
131 GGTGGGCAATATTTACAACACCAAATCAATGCCCTTAGTGAATAAGGAGAA
2658097 GATGCATCCTCAGGAACCTATATACTTTTCCATGTTTGAATCAACATATGATTTTGAGGACATGA
1 GATGCATCCTCAGGAACCTATATACTTTTCCATGTTTGAATCAACATATGATTTTGAGGACATGA
*
2658162 CATCTATGATGTCAAATATGACTATTTGTCATTCTACATTTCCATCAGAGATGCAAGAGCAAAGT
66 CATCTATGATGTCAAATATGACTACTTGTCATTCTACATTTCCATCAGAGATGCAAGAGCAAAGT
2658227 GGTGGGCATATATTTACAACACCAAATCATATGCCCTTAGTGAATAAGGAGAA
131 GGTGGGCA-ATATTTACAACACCAAATCA-ATGCCCTTAGTGAATAAGGAGAA
2658280 TGGCTACCAG
Statistics
Matches: 177, Mismatches: 1, Indels: 5
0.97 0.01 0.03
Matches are distributed among these distances:
178 136 0.77
180 19 0.11
182 9 0.05
183 13 0.07
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (181 bp):
GATGCATCCTCAGGAACCTATATACTTTTCCATGTTTGAATCAACATATGATTTTGAGGACATGA
CATCTATGATGTCAAATATGACTACTTGTCATTCTACATTTCCATCAGAGATGCAAGAGCAAAGT
GGTGGGCAATATTTACAACACCAAATCAATGCCCTTAGTGAATAAGGAGAA
Found at i:2658498 original size:60 final size:60
Alignment explanation
Indices: 2658404--2658519 Score: 157
Period size: 60 Copynumber: 1.9 Consensus size: 60
2658394 TATCATACTC
* *
2658404 ATTCAAATAAAATGTGGAAATCAATCACACTCATTCAAAAAATATAAATAGG-CAAACATTT
1 ATTCAAATAAAATATGGAAATCAATCAAACTCATTC-AAAAA-ATAAATAGGACAAACATTT
*
2658465 ATTCATATAAAA-ATGGAAAT-ACATCAAACTCATTCAAAAAATAAATAGGACAAAC
1 ATTCAAATAAAATATGGAAATCA-ATCAAACTCATTCAAAAAATAAATAGGACAAAC
2658520 TAAACATTCA
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
58 9 0.18
59 11 0.22
60 19 0.38
61 11 0.22
ACGTcount: A:0.53, C:0.15, G:0.08, T:0.24
Consensus pattern (60 bp):
ATTCAAATAAAATATGGAAATCAATCAAACTCATTCAAAAAATAAATAGGACAAACATTT
Found at i:2662407 original size:23 final size:25
Alignment explanation
Indices: 2662381--2662427 Score: 62
Period size: 23 Copynumber: 1.9 Consensus size: 25
2662371 GCATTTTTAG
*
2662381 AAAACGAAAG-AAA-AACTTTAAGT
1 AAAAAGAAAGAAAAGAACTTTAAGT
2662404 AAAAAGAAAGTAAAAGAACTTTAA
1 AAAAAGAAAG-AAAAGAACTTTAA
2662428 AAACCCAAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
25 3 0.15
26 8 0.40
ACGTcount: A:0.64, C:0.06, G:0.13, T:0.17
Consensus pattern (25 bp):
AAAAAGAAAGAAAAGAACTTTAAGT
Found at i:2663458 original size:10 final size:9
Alignment explanation
Indices: 2663440--2663473 Score: 52
Period size: 8 Copynumber: 3.8 Consensus size: 9
2663430 TTCTCTGAAC
2663440 TCTTTTTTT
1 TCTTTTTTT
2663449 TCTCTTTTTT
1 TCT-TTTTTT
2663459 TC-TTTTTT
1 TCTTTTTTT
2663467 TCTTTTT
1 TCTTTTT
2663474 CTCCGAACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
8 8 0.35
9 7 0.30
10 8 0.35
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:2667285 original size:23 final size:23
Alignment explanation
Indices: 2667256--2667302 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2667246 GCACCAAAGT
2667256 ACCACATAGAAATGTCCCGAAGG
1 ACCACATAGAAATGTCCCGAAGG
* *
2667279 ACCACATAGTATTGTCCCGAAGG
1 ACCACATAGAAATGTCCCGAAGG
2667302 A
1 A
2667303 GAGTGTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (23 bp):
ACCACATAGAAATGTCCCGAAGG
Found at i:2667333 original size:23 final size:23
Alignment explanation
Indices: 2667262--2667335 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
2667252 AAGTACCACA
* *
2667262 TAGAAATGTCCCGAAGGACCACA
1 TAGAAATGTCCCGAAGGACCGCG
* * ** *
2667285 TAGTATTGTCCCGAAGGAGAGTG
1 TAGAAATGTCCCGAAGGACCGCG
*
2667308 TAGAAATGTCCCGAAAGACCGCG
1 TAGAAATGTCCCGAAGGACCGCG
2667331 TAGAA
1 TAGAA
2667336 CCCTTGACTC
Statistics
Matches: 38, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.20, G:0.27, T:0.18
Consensus pattern (23 bp):
TAGAAATGTCCCGAAGGACCGCG
Found at i:2669378 original size:73 final size:73
Alignment explanation
Indices: 2669259--2669401 Score: 286
Period size: 73 Copynumber: 2.0 Consensus size: 73
2669249 TCACAATAAT
2669259 TTTCCTCAGAACCGGAAGAAAGAGGTCTATGAGATCATCTTCTTCATCACGGACAATCTCAATTT
1 TTTCCTCAGAACCGGAAGAAAGAGGTCTATGAGATCATCTTCTTCATCACGGACAATCTCAATTT
2669324 GAGACTAA
66 GAGACTAA
2669332 TTTCCTCAGAACCGGAAGAAAGAGGTCTATGAGATCATCTTCTTCATCACGGACAATCTCAATTT
1 TTTCCTCAGAACCGGAAGAAAGAGGTCTATGAGATCATCTTCTTCATCACGGACAATCTCAATTT
2669397 GAGAC
66 GAGAC
2669402 GATGACGACA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (73 bp):
TTTCCTCAGAACCGGAAGAAAGAGGTCTATGAGATCATCTTCTTCATCACGGACAATCTCAATTT
GAGACTAA
Found at i:2670501 original size:36 final size:36
Alignment explanation
Indices: 2670456--2670529 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
2670446 GCCAATATGG
2670456 TTTTTGGCAGGTACTTGAACTCCCAACTATAAATGT
1 TTTTTGGCAGGTACTTGAACTCCCAACTATAAATGT
2670492 TTTTTGGCAGGTACTTGAACTCCCAACTATAAATGT
1 TTTTTGGCAGGTACTTGAACTCCCAACTATAAATGT
2670528 TT
1 TT
2670530 CACATAGTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.38
Consensus pattern (36 bp):
TTTTTGGCAGGTACTTGAACTCCCAACTATAAATGT
Found at i:2677018 original size:11 final size:11
Alignment explanation
Indices: 2676987--2677024 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
2676977 GCATTTTTAG
2676987 AAAATAAAGTA
1 AAAATAAAGTA
2676998 AAAACTTAAAGTA
1 AAAA--TAAAGTA
2677011 AAAATAAAGTA
1 AAAATAAAGTA
2677022 AAA
1 AAA
2677025 GAACTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 14 0.56
13 11 0.44
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (11 bp):
AAAATAAAGTA
Found at i:2677827 original size:21 final size:22
Alignment explanation
Indices: 2677796--2677836 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
2677786 TTTAAAAATA
* *
2677796 TAAAGGAAGTATTGTTACTCAT
1 TAAAGGAAGTACTGATACTCAT
2677818 TAAAGG-AGTACTGATACTC
1 TAAAGGAAGTACTGATACTC
2677837 CCTGTCTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.32
Consensus pattern (22 bp):
TAAAGGAAGTACTGATACTCAT
Found at i:2683153 original size:20 final size:21
Alignment explanation
Indices: 2683128--2683167 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
2683118 CTTTGTATAG
2683128 TAGTATCGATACCA-AAGGCA
1 TAGTATCGATACCATAAGGCA
2683148 TAGTATCGATACCATAAGGC
1 TAGTATCGATACCATAAGGC
2683168 TCCAACGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (21 bp):
TAGTATCGATACCATAAGGCA
Found at i:2686798 original size:18 final size:17
Alignment explanation
Indices: 2686760--2686823 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
2686750 TTTTATTCAA
* *
2686760 TAAAGCTAGTTTACTAAT
1 TAAA-CTAGTTCATTAAT
*
2686778 TAAACTAGTTCATTCATT
1 TAAACTAGTTCATT-AAT
*
2686796 TAAACTGGTTCATTAAT
1 TAAACTAGTTCATTAAT
*
2686813 TATACTAGTTC
1 TAAACTAGTTC
2686824 TTTATATGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 19 0.50
18 19 0.50
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (17 bp):
TAAACTAGTTCATTAAT
Found at i:2687280 original size:24 final size:24
Alignment explanation
Indices: 2687235--2687283 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
2687225 CATTCATGGA
**
2687235 TGATTTAATCATCCAATTCAAGGT
1 TGATTTAATCATCCAAACCAAGGT
* *
2687259 TGATTTAATTATTCAAACCAAGGT
1 TGATTTAATCATCCAAACCAAGGT
2687283 T
1 T
2687284 TGTTCATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (24 bp):
TGATTTAATCATCCAAACCAAGGT
Found at i:2696355 original size:46 final size:46
Alignment explanation
Indices: 2696305--2696423 Score: 166
Period size: 46 Copynumber: 2.6 Consensus size: 46
2696295 TTATTCATTA
*
2696305 ATTTCATTTATGACATCCTTTCATGCCTTAATGCATCATTTCATGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* * *
2696351 ATTTCATTTATGGCATTCTTTCATGCCTTAATGCATCCTTTCTTGC
1 ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
* * *
2696397 ATTTTTAGTTATGGCATCCTTTTATGC
1 A-TTTCATTTATGGCATCCTTTCATGC
2696424 ATTTTAATTA
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 43 0.67
47 21 0.33
ACGTcount: A:0.20, C:0.22, G:0.11, T:0.47
Consensus pattern (46 bp):
ATTTCATTTATGGCATCCTTTCATGCCTTAATGCATCATTTCATGC
Found at i:2696391 original size:20 final size:20
Alignment explanation
Indices: 2696318--2696392 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
2696308 TCATTTATGA
2696318 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
2696338 CATCATTTCATGCATTTCATTTATGG
1 CATCCTTTCATGC----C-TTAAT-G
*
2696364 CATTCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
2696384 CATCCTTTC
1 CATCCTTTC
2696393 TTGCATTTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 21 0.49
21 4 0.09
22 1 0.02
24 1 0.02
25 4 0.09
26 12 0.28
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.44
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:2696424 original size:73 final size:72
Alignment explanation
Indices: 2696337--2696495 Score: 210
Period size: 73 Copynumber: 2.2 Consensus size: 72
2696327 ATGCCTTAAT
* * * * * *
2696337 GCATCATTTCATGCATTTCATTTATGGCATTCTTTCATGCCTTAATGCATCCTTTCTTGCATTTT
1 GCATCCTTTCATGCATTTCAATTACGGCATCCTTTCATGCCTTAATACATCCTTTCATGCA-TTT
*
2696402 TAGTTATG
65 TAATTATG
* * * *
2696410 GCATCCTTTTATGCATTTTAATTACGGTATCCTTTCATGCCTTAATATATCCTTTCATGCATTTT
1 GCATCCTTTCATGCATTTCAATTACGGCATCCTTTCATGCCTTAATACATCCTTTCATGCATTTT
2696475 AATTATG
66 AATTATG
2696482 GCATCCTTTCATGC
1 GCATCCTTTCATGC
2696496 CTTAATGCAT
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
72 23 0.31
73 51 0.69
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (72 bp):
GCATCCTTTCATGCATTTCAATTACGGCATCCTTTCATGCCTTAATACATCCTTTCATGCATTTT
AATTATG
Found at i:2696441 original size:26 final size:26
Alignment explanation
Indices: 2696337--2696495 Score: 126
Period size: 26 Copynumber: 6.5 Consensus size: 26
2696327 ATGCCTTAAT
* * *
2696337 GCATCATTTCATGCATTTCATTTATG
1 GCATCCTTTCATGCATTTTAATTATG
* *
2696363 GCATTCTTTCATGC--CTT-A--AT-
1 GCATCCTTTCATGCATTTTAATTATG
* *
2696383 GCATCCTTTCTTGCATTTTTAGTTATG
1 GCATCCTTTCATGCA-TTTTAATTATG
* *
2696410 GCATCCTTTTATGCATTTTAATTACG
1 GCATCCTTTCATGCATTTTAATTATG
* *
2696436 GTATCCTTTCATGC--CTTAA-TAT-
1 GCATCCTTTCATGCATTTTAATTATG
2696458 --ATCCTTTCATGCATTTTAATTATG
1 GCATCCTTTCATGCATTTTAATTATG
2696482 GCATCCTTTCATGC
1 GCATCCTTTCATGC
2696496 CTTAATGCAT
Statistics
Matches: 102, Mismatches: 18, Indels: 26
0.70 0.12 0.18
Matches are distributed among these distances:
20 24 0.24
21 2 0.02
22 4 0.04
23 7 0.07
24 5 0.05
26 47 0.46
27 13 0.13
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (26 bp):
GCATCCTTTCATGCATTTTAATTATG
Found at i:2696462 original size:20 final size:20
Alignment explanation
Indices: 2696437--2696515 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 20
2696427 TTAATTACGG
2696437 TATCCTTTCATGCCTTAATA
1 TATCCTTTCATGCCTTAATA
*
2696457 TATCCTTTCATGCATTTTAATTA
1 TATCCTTTCATGC--CTTAA-TA
*
2696480 TGGCATCCTTTCATGCCTTAATG
1 T---ATCCTTTCATGCCTTAATA
* *
2696503 CATCCTTTTATGC
1 TATCCTTTCATGC
2696516 ATTTTAGTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 24 0.50
22 4 0.08
23 4 0.08
24 4 0.08
26 12 0.25
ACGTcount: A:0.22, C:0.24, G:0.09, T:0.46
Consensus pattern (20 bp):
TATCCTTTCATGCCTTAATA
Found at i:2696470 original size:46 final size:46
Alignment explanation
Indices: 2696411--2696521 Score: 177
Period size: 46 Copynumber: 2.4 Consensus size: 46
2696401 TTAGTTATGG
*
2696411 CATCCTTTTATGCATTTTAATTACGGTATCCTTTCATGCCTTAATA
1 CATCCTTTTATGCATTTTAATTACGGCATCCTTTCATGCCTTAATA
* * * *
2696457 TATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
1 CATCCTTTTATGCATTTTAATTACGGCATCCTTTCATGCCTTAATA
2696503 CATCCTTTTATGCATTTTA
1 CATCCTTTTATGCATTTTA
2696522 GTTATAAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 58 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.47
Consensus pattern (46 bp):
CATCCTTTTATGCATTTTAATTACGGCATCCTTTCATGCCTTAATA
Found at i:2710888 original size:39 final size:39
Alignment explanation
Indices: 2710834--2710913 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
2710824 ATCTGTGTCT
2710834 AAATCTGAGGGAGAGGTTAATGCTGCAACCAATTCTTCA
1 AAATCTGAGGGAGAGGTTAATGCTGCAACCAATTCTTCA
* **
2710873 AAATCTGAGGGAGAGGTTAATGTTGCAACTGATTCTTCA
1 AAATCTGAGGGAGAGGTTAATGCTGCAACCAATTCTTCA
2710912 AA
1 AA
2710914 GGCTGCTGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.34, C:0.15, G:0.24, T:0.28
Consensus pattern (39 bp):
AAATCTGAGGGAGAGGTTAATGCTGCAACCAATTCTTCA
Found at i:2723001 original size:16 final size:16
Alignment explanation
Indices: 2722980--2723013 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2722970 ACTCTATAGT
2722980 TTACCCTATTATTAAA
1 TTACCCTATTATTAAA
2722996 TTACCCTATTATTAAA
1 TTACCCTATTATTAAA
2723012 TT
1 TT
2723014 CTTTCATTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACCCTATTATTAAA
Found at i:2724257 original size:2 final size:2
Alignment explanation
Indices: 2724250--2724301 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
2724240 TCAAACCATG
2724250 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
2724292 AT AT AT AT AT
1 AT AT AT AT AT
2724302 GCCGAACCAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2728504 original size:13 final size:13
Alignment explanation
Indices: 2728488--2728514 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2728478 ATGTACTTAA
2728488 GGATGATACTTTT
1 GGATGATACTTTT
2728501 GGATGATACTTTT
1 GGATGATACTTTT
2728514 G
1 G
2728515 CCACACCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.26, T:0.44
Consensus pattern (13 bp):
GGATGATACTTTT
Found at i:2734863 original size:13 final size:13
Alignment explanation
Indices: 2734845--2734869 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2734835 AATTTTGGCT
2734845 TTTTTGTTTTTTG
1 TTTTTGTTTTTTG
2734858 TTTTTGTTTTTT
1 TTTTTGTTTTTT
2734870 TGCCCTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (13 bp):
TTTTTGTTTTTTG
Found at i:2740671 original size:46 final size:46
Alignment explanation
Indices: 2740619--2741011 Score: 563
Period size: 46 Copynumber: 8.5 Consensus size: 46
2740609 TCAGTTATGT
* * *
2740619 CGTTCATGCACGTTAATGATGGCATCCTTTCATGCCTTAATG-AAC
1 CGTTCATGCACGTTAATTATGGCATCCTTTCATGCCTTAGTGCATC
** *
2740664 TCGTTCATGCATTTTAATTATGGCATCCTTTCGTGCCTTAGTGCATC
1 -CGTTCATGCACGTTAATTATGGCATCCTTTCATGCCTTAGTGCATC
*
2740711 CGTTCATGCACGTTAATTATGGCATCCTTTCATGCATTAGTGCATC
1 CGTTCATGCACGTTAATTATGGCATCCTTTCATGCCTTAGTGCATC
* * *
2740757 CGTTCATGCATGTTAAATATGGCATCCTTTCATGCCTTAATGCATC
1 CGTTCATGCACGTTAATTATGGCATCCTTTCATGCCTTAGTGCATC
* ** *
2740803 TGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAGTGAATC
1 CGTTCATGCACGTTAATTATGGCATCCTTTCATGCCTTAGTGCATC
*
2740849 CGTTCATGCACGTTAATTATGGTATCCTTTCATGCCTTAGTGCATC
1 CGTTCATGCACGTTAATTATGGCATCCTTTCATGCCTTAGTGCATC
* *
2740895 TGTTCATGCACGTTAATTATGGCATCCTTTCATTCCTTAGTGCATC
1 CGTTCATGCACGTTAATTATGGCATCCTTTCATGCCTTAGTGCATC
* * * *
2740941 CGTTCATGCACATGAATTATGGCATCATTTCATGCCTTAATGCATC
1 CGTTCATGCACGTTAATTATGGCATCCTTTCATGCCTTAGTGCATC
**
2740987 CGTTCATGCATTTTAATTATGGCAT
1 CGTTCATGCACGTTAATTATGGCAT
2741012 TGTTTAATGC
Statistics
Matches: 310, Mismatches: 36, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
46 308 0.99
47 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.39
Consensus pattern (46 bp):
CGTTCATGCACGTTAATTATGGCATCCTTTCATGCCTTAGTGCATC
Found at i:2746241 original size:8 final size:8
Alignment explanation
Indices: 2746213--2746258 Score: 58
Period size: 8 Copynumber: 5.6 Consensus size: 8
2746203 GTCTGAGTCT
2746213 TATTATTA
1 TATTATTA
*
2746221 TATAATGTA
1 TATTAT-TA
2746230 TATTATTA
1 TATTATTA
2746238 TATTATTA
1 TATTATTA
2746246 T-TATATTA
1 TAT-TATTA
2746254 TATTA
1 TATTA
2746259 CAAATATTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
7 1 0.03
8 24 0.73
9 8 0.24
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TATTATTA
Found at i:2746246 original size:11 final size:11
Alignment explanation
Indices: 2746230--2746258 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
2746220 ATATAATGTA
2746230 TATTATTATAT
1 TATTATTATAT
2746241 TATTATTATAT
1 TATTATTATAT
2746252 TA-TATTA
1 TATTATTA
2746259 CAAATATTAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTATTATAT
Found at i:2747897 original size:20 final size:20
Alignment explanation
Indices: 2747872--2747913 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
2747862 AAACAGACAC
2747872 CTATTTAGAAATGGGGAAAG
1 CTATTTAGAAATGGGGAAAG
2747892 CTATTTAGAAATGGGGAAAG
1 CTATTTAGAAATGGGGAAAG
2747912 CT
1 CT
2747914 TTGAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.07, G:0.29, T:0.26
Consensus pattern (20 bp):
CTATTTAGAAATGGGGAAAG
Found at i:2747923 original size:20 final size:20
Alignment explanation
Indices: 2747880--2747923 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
2747870 ACCTATTTAG
* *
2747880 AAATGGGGAAAGCTATTTAG
1 AAATGGGGAAAGCTATTAAA
2747900 AAATGGGGAAAGCT-TTGAAA
1 AAATGGGGAAAGCTATT-AAA
2747920 AAAT
1 AAAT
2747924 AGCATTGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.45, C:0.05, G:0.27, T:0.23
Consensus pattern (20 bp):
AAATGGGGAAAGCTATTAAA
Found at i:2749279 original size:19 final size:19
Alignment explanation
Indices: 2749241--2749279 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2749231 CCCACTCTCA
2749241 AAACCTCATCGATCACTTG
1 AAACCTCATCGATCACTTG
*
2749260 AAACCATCATTGATCA-TTG
1 AAACC-TCATCGATCACTTG
2749279 A
1 A
2749280 CCTCACCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.36, C:0.26, G:0.10, T:0.28
Consensus pattern (19 bp):
AAACCTCATCGATCACTTG
Found at i:2749914 original size:143 final size:143
Alignment explanation
Indices: 2749656--2749941 Score: 493
Period size: 143 Copynumber: 2.0 Consensus size: 143
2749646 CAGGGGACAA
* *
2749656 GTAAACCATATTTTTATTACAGTGTATGAATAATCATGCTCGAGATTGATATCATATATATGCAT
1 GTAAACCATATTTTTATTACAATGTATGAATAATCATGCTCGAGATTGATATCATATATATACAT
*
2749721 CATGCAAAAGATATAAATAATCGTCATGTCATACTTACATATCATAAATGAAGTAATTATCACAA
66 CATGCAAAAGATATAAATAATCGTCAAGTCATACTTACATATCATAAATGAAGTAATTATCACAA
2749786 AAGTGAT-TGAAGT
131 AAGTG-TCTGAAGT
*
2749799 GTAAATCATATTTTTATTACAATGTATGAATAATCATGCTCGAGATTGATATCATATATATACAT
1 GTAAACCATATTTTTATTACAATGTATGAATAATCATGCTCGAGATTGATATCATATATATACAT
* * *
2749864 CATGCATAAGATATAAATAATCTTCAAGTTATACTTACATATCATAAATGAAGTAATTATCACAA
66 CATGCAAAAGATATAAATAATCGTCAAGTCATACTTACATATCATAAATGAAGTAATTATCACAA
2749929 AAGTGTCTGAAGT
131 AAGTGTCTGAAGT
2749942 AACGTAGAAG
Statistics
Matches: 135, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
142 1 0.01
143 134 0.99
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (143 bp):
GTAAACCATATTTTTATTACAATGTATGAATAATCATGCTCGAGATTGATATCATATATATACAT
CATGCAAAAGATATAAATAATCGTCAAGTCATACTTACATATCATAAATGAAGTAATTATCACAA
AAGTGTCTGAAGT
Found at i:2751937 original size:23 final size:23
Alignment explanation
Indices: 2751907--2751957 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
2751897 CAGCTCCCCC
* *
2751907 TTTTTCATTGATAAATTTAATTT
1 TTTTTCATTGAGAAATTGAATTT
2751930 TTTTTCATTGAGAAATTGAATTT
1 TTTTTCATTGAGAAATTGAATTT
2751953 TTTTT
1 TTTTT
2751958 AACCCATACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.04, G:0.08, T:0.61
Consensus pattern (23 bp):
TTTTTCATTGAGAAATTGAATTT
Found at i:2752147 original size:16 final size:16
Alignment explanation
Indices: 2752103--2752151 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
2752093 TTCCAAACAA
2752103 AAAATTGAC-TTTAA-
1 AAAATTGACATTTAAC
**
2752117 AAGCTTGACATTTAAAC
1 AAAATTGACATTT-AAC
2752134 AAAATTGA-ATTTAAC
1 AAAATTGACATTTAAC
2752149 AAA
1 AAA
2752152 GAATAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 7 0.25
15 9 0.32
16 6 0.21
17 6 0.21
ACGTcount: A:0.51, C:0.10, G:0.08, T:0.31
Consensus pattern (16 bp):
AAAATTGACATTTAAC
Found at i:2752870 original size:24 final size:23
Alignment explanation
Indices: 2752820--2752871 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
2752810 AACTTCCATA
* *
2752820 TAGAATTGCACCGAAGTGCCGCT
1 TAGAATTGCACCGAAGTGCCACG
2752843 TAGAATATGCACCGAAGTGCCACG
1 TAGAAT-TGCACCGAAGTGCCACG
2752867 TAGAA
1 TAGAA
2752872 AAGTCCCGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 6 0.23
24 20 0.77
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (23 bp):
TAGAATTGCACCGAAGTGCCACG
Found at i:2752941 original size:24 final size:23
Alignment explanation
Indices: 2752854--2752965 Score: 95
Period size: 23 Copynumber: 4.8 Consensus size: 23
2752844 AGAATATGCA
*
2752854 CCGAAGTG-CCACGTAGAA-AAGTC
1 CCGAAG-GACCACGTAGAATTA-TC
*
2752877 CCGAAGAACCACGTAGAAATTATC
1 CCGAAGGACCACGTAG-AATTATC
*
2752901 CCGAAGGA-CAGTGTAGAATTTATC
1 CCGAAGGACCA-CGTAGAA-TTATC
*
2752925 CCGAAGGACCACATAGAATTATC
1 CCGAAGGACCACGTAGAATTATC
* * *
2752948 CTGAAAGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
2752966 CCCTCGACTC
Statistics
Matches: 73, Mismatches: 10, Indels: 12
0.77 0.11 0.13
Matches are distributed among these distances:
23 37 0.51
24 33 0.45
25 3 0.04
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAATTATC
Found at i:2752964 original size:23 final size:23
Alignment explanation
Indices: 2752875--2752965 Score: 92
Period size: 24 Copynumber: 3.9 Consensus size: 23
2752865 CGTAGAAAAG
* *
2752875 TCCCGAAGAACCACGTAGAAATTA
1 TCCCGAAGGACCGCGTAG-AATTA
* *
2752899 TCCCGAAGGACAGTGTAGAATTTA
1 TCCCGAAGGACCGCGTAGAA-TTA
* *
2752923 TCCCGAAGGACCACATAGAATTA
1 TCCCGAAGGACCGCGTAGAATTA
* *
2752946 TCCTGAAAGACCGCGTAGAA
1 TCCCGAAGGACCGCGTAGAA
2752966 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 12, Indels: 3
0.78 0.17 0.04
Matches are distributed among these distances:
23 21 0.39
24 33 0.61
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.19
Consensus pattern (23 bp):
TCCCGAAGGACCGCGTAGAATTA
Found at i:2757896 original size:20 final size:21
Alignment explanation
Indices: 2757850--2757910 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
2757840 CCCTATGGGG
2757850 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
2757873 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
* *
2757893 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
2757911 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 18 0.50
21 2 0.06
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.34, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:2766815 original size:80 final size:79
Alignment explanation
Indices: 2766679--2766843 Score: 271
Period size: 80 Copynumber: 2.1 Consensus size: 79
2766669 AAAACTCGAC
*
2766679 CTCTCTGTCTGAAGGTAATCCAGACAATCAGAGAAATACATCTGGAAATTCTTATACCGTC-AAA
1 CTCTCCGTCTGAAGGTAATCCAGACAATCAGAGAAATACATCTGGAAATTCTTATACCGTCAAAA
*
2766743 TGT-CTCTATTTCT
66 TGTCCTCTAGTTCT
2766756 CTCTCCGTCTGAAGGTAATCCAGACAACTCAGCTAGAAATACATCTGGAAATTCTTATACCGTCA
1 CTCTCCGTCTGAAGGTAATCCAGACAA-TCAG--AGAAATACATCTGGAAATTCTTATACCGTCA
2766821 AAATGTCCTCTAGTTCT
63 AAATGTCCTCTAGTTCT
2766838 CTCTCC
1 CTCTCC
2766844 TTGACTCGAG
Statistics
Matches: 81, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
77 26 0.32
78 4 0.05
80 30 0.37
81 6 0.07
82 15 0.19
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (79 bp):
CTCTCCGTCTGAAGGTAATCCAGACAATCAGAGAAATACATCTGGAAATTCTTATACCGTCAAAA
TGTCCTCTAGTTCT
Found at i:2767694 original size:147 final size:147
Alignment explanation
Indices: 2767427--2767712 Score: 545
Period size: 147 Copynumber: 1.9 Consensus size: 147
2767417 CCTCTTCATC
2767427 TACCTCACTGAGGTACAATAGAAAATCGCTCTGTTTGTACAGGATCTCCAGTCATCAATGGGTAA
1 TACCTCACTGAGGTACAATAGAAAATCGCTCTGTTTGTACAGGATCTCCAGTCATCAATGGGTAA
* *
2767492 TCCCGTATAAAATGTCCAATGTCCCTACATCAGAAATATTCTTCGGATACCACTCGACATACTCC
66 TCCCGTATAAAATGTCCAATGTCCCTACATCAGAAATATGCTCCGGATACCACTCGACATACTCC
2767557 GATATGATTTTCTATTG
131 GATATGATTTTCTATTG
*
2767574 TACCTCACTGAGGTACAATAGAAAATCGCTCTGTTTGTACAGGATCTCCGGTCATCAATGGGTAA
1 TACCTCACTGAGGTACAATAGAAAATCGCTCTGTTTGTACAGGATCTCCAGTCATCAATGGGTAA
2767639 TCCCGTATAAAATGTCCAATGTCCCTACATCAGAAATATGCTCCGGATACCACTCGACATACTCC
66 TCCCGTATAAAATGTCCAATGTCCCTACATCAGAAATATGCTCCGGATACCACTCGACATACTCC
2767704 GATATGATT
131 GATATGATT
2767713 CTTCCCACAA
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
147 136 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (147 bp):
TACCTCACTGAGGTACAATAGAAAATCGCTCTGTTTGTACAGGATCTCCAGTCATCAATGGGTAA
TCCCGTATAAAATGTCCAATGTCCCTACATCAGAAATATGCTCCGGATACCACTCGACATACTCC
GATATGATTTTCTATTG
Found at i:2769477 original size:23 final size:24
Alignment explanation
Indices: 2769450--2769501 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2769440 AACAGCCACA
** *
2769450 TAGAAT-TGCACTGAAGTGTCACG
1 TAGAATATGCACCAAAGTGACACG
2769473 TAGAATATGCACCAAAGTGACACG
1 TAGAATATGCACCAAAGTGACACG
2769497 TAGAA
1 TAGAA
2769502 ATGTCCCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (24 bp):
TAGAATATGCACCAAAGTGACACG
Found at i:2769536 original size:24 final size:24
Alignment explanation
Indices: 2769493--2769595 Score: 102
Period size: 24 Copynumber: 4.4 Consensus size: 24
2769483 ACCAAAGTGA
2769493 CACGTAGAAA-TGTCCCGAAGGAC
1 CACGTAGAAATTGTCCCGAAGGAC
** *
2769516 CACGTAGAAATTGTCTTGAAGAAC
1 CACGTAGAAATTGTCCCGAAGGAC
* * *
2769540 CGCGTAGAATTTGTCCCGAATGAC
1 CACGTAGAAATTGTCCCGAAGGAC
* * *
2769564 CACATAG-AATTGTCCTGAAAGAC
1 CACGTAGAAATTGTCCCGAAGGAC
*
2769587 CGCGTAGAA
1 CACGTAGAA
2769596 CCCTCGACTC
Statistics
Matches: 62, Mismatches: 16, Indels: 3
0.77 0.20 0.04
Matches are distributed among these distances:
23 28 0.45
24 34 0.55
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.20
Consensus pattern (24 bp):
CACGTAGAAATTGTCCCGAAGGAC
Found at i:2769546 original size:47 final size:47
Alignment explanation
Indices: 2769495--2769595 Score: 134
Period size: 47 Copynumber: 2.1 Consensus size: 47
2769485 CAAAGTGACA
* *
2769495 CGTAGAA-ATGTCCCGAAGGACCACGTAGAAATTGTCTTG-AAGAACCG
1 CGTAGAATATGTCCCGAAGGACCACATAG-AATTGTCCTGAAAG-ACCG
* *
2769542 CGTAGAATTTGTCCCGAATGACCACATAGAATTGTCCTGAAAGACCG
1 CGTAGAATATGTCCCGAAGGACCACATAGAATTGTCCTGAAAGACCG
2769589 CGTAGAA
1 CGTAGAA
2769596 CCCTCGACTC
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 27 0.56
48 21 0.44
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.21
Consensus pattern (47 bp):
CGTAGAATATGTCCCGAAGGACCACATAGAATTGTCCTGAAAGACCG
Found at i:2778736 original size:2 final size:2
Alignment explanation
Indices: 2778729--2778757 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2778719 AATGTATTGT
2778729 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2778758 GATCATAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2779634 original size:7 final size:7
Alignment explanation
Indices: 2779622--2779646 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2779612 CACCATTGGG
2779622 ATCCGCC
1 ATCCGCC
2779629 ATCCGCC
1 ATCCGCC
2779636 ATCCGCC
1 ATCCGCC
2779643 ATCC
1 ATCC
2779647 AGATTGTCGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.56, G:0.12, T:0.16
Consensus pattern (7 bp):
ATCCGCC
Found at i:2780133 original size:5 final size:6
Alignment explanation
Indices: 2780118--2780142 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2780108 TCAAAATTCT
2780118 TTTTTA TTTTTA TTTTTA TTTTTA T
1 TTTTTA TTTTTA TTTTTA TTTTTA T
2780143 GATCAATCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTA
Found at i:2783989 original size:20 final size:20
Alignment explanation
Indices: 2783964--2784053 Score: 119
Period size: 20 Copynumber: 4.5 Consensus size: 20
2783954 CACTGTTCAT
* * *
2783964 TACTGTTCACACAGTATTGG
1 TACTATTCATACAGTATCGG
*
2783984 TACTGTTCATACAGTATCGG
1 TACTATTCATACAGTATCGG
*
2784004 TACTATTCATACAGTATCGA
1 TACTATTCATACAGTATCGG
*
2784024 TACTATTCATACAGTA-CAG
1 TACTATTCATACAGTATCGG
2784043 TACTATTCATA
1 TACTATTCATA
2784054 AAAAAATTTG
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
19 12 0.19
20 52 0.81
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAGTATCGG
Found at i:2785190 original size:2 final size:2
Alignment explanation
Indices: 2785183--2785221 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2785173 GCAAAGTCTC
2785183 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2785222 TCGAGTCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2789126 original size:12 final size:12
Alignment explanation
Indices: 2789109--2789133 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2789099 AAGTTATTTT
2789109 CTTCTTCTTCTC
1 CTTCTTCTTCTC
2789121 CTTCTTCTTCTC
1 CTTCTTCTTCTC
2789133 C
1 C
2789134 GTTGCACGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (12 bp):
CTTCTTCTTCTC
Found at i:2790918 original size:15 final size:14
Alignment explanation
Indices: 2790900--2790942 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
2790890 TAATATTAAA
2790900 TTAAAATTTAAATTT
1 TTAAAATTTAAA-TT
2790915 TTAAAATTTTAAATT
1 TTAAAA-TTTAAATT
2790930 TTAAAGATTTAAA
1 TTAAA-ATTTAAA
2790943 CTTAGAGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 19 0.73
16 7 0.27
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (14 bp):
TTAAAATTTAAATT
Found at i:2790939 original size:16 final size:16
Alignment explanation
Indices: 2790900--2790931 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2790890 TAATATTAAA
2790900 TTAAAA-TTTAAATTT
1 TTAAAATTTTAAATTT
2790915 TTAAAATTTTAAATTT
1 TTAAAATTTTAAATTT
2790931 T
1 T
2790932 AAAGATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAAAATTTTAAATTT
Found at i:2793821 original size:419 final size:412
Alignment explanation
Indices: 2793044--2793829 Score: 1150
Period size: 419 Copynumber: 1.9 Consensus size: 412
2793034 ATAAATCTTT
2793044 TAGTATAATTTTTCATAATGATTAAAATATATAACTACAAAAATAATTGATTAAAAAAACTTGAA
1 TAGTATAATTTTTCATAATGATTAAAATATATAACTACAAAAATAATTGATTAAAAAAACTTGAA
* *
2793109 TTTTATTATCTGATGGGGTAATTTTTTCTATAACAATAACTATAAATTATAATTACAAAATTTAT
66 TTTTATTATCTGATGGGATAATTTTTTCTATAACAATAACTATAAATTATAATTACAAAAATTAT
* * *
2793174 CAATATAGCTTTTTGAAGAAAAAAAAAAGTGAAAAGATATTTATCACAATATATGCTATCACTAT
131 CAATATAACTTTTT--AGAAAAAAAAAAGTGAAAAAATAGTTATCACAATATATGCTATCACTAT
*
2793239 AATTAAAATTTATAACTACAAGTATAATTTCTCACAAAAATGTGAATATCATTATTTTTATGACA
194 AATTAAAATTTATAACTACAAATATAATTTCTCACAAAAATGTGAATATCATTATTTTTATGACA
* * *
2793304 ATGTTTTTTGTAATAATTATAAACACTTATAGTTACAAAAATTATTACTATATGATTTTTTTATG
259 ATATTTTTTGTAATAATTATAAACACTTAAAGTTACAAAAATTATCACTATATGATTTTTTTATG
*
2793369 CAAACAAATATGGAGAAAAATCTTTATGACAATATATTTTGTTACTATATAATATTTTTGACATT
324 CAAAAAAATATGGAGAAAAATCTTTATGACAATATATTTTGTTACTATATAATATTTTTGACATT
2793434 AAAAAATAGGAAAAATGGTTCTAA
389 AAAAAATAGGAAAAATGGTTCTAA
* *
2793458 TAGTATAATTTTTCATAATGATTAAAATATATAAGTACAAAAATAATTTATTATAAAAAAACTTG
1 TAGTATAATTTTTCATAATGATTAAAATATATAACTACAAAAATAATTGA-T-TAAAAAAACTTG
* * *
2793523 AATTTTATTATTTGATGTGATAATTTTTTCTATAACAATAACTATAAATTATAATTATAAAAATT
64 AATTTTATTATCTGATGGGATAATTTTTTCTATAACAATAACTATAAATTATAATTACAAAAATT
* * *
2793588 GTCAATATAAC-TTTT-GAAACAAAAAAGTGGAGAAAAATAGTTATGACAATTAATATATGCTAT
129 ATCAATATAACTTTTTAGAAAAAAAAAAGT-GA-AAAAATAGTTAT--C-A-CAATATATGCTAT
** * *
2793651 CACTATTGTTAAAATTTATAACTACAAATATAATTTGTCACAAAAATGTGAATATCGTTATTTTT
188 CACTATAATTAAAATTTATAACTACAAATATAATTTCTCACAAAAATGTGAATATCATTA-TTTT
* * * **
2793716 TGTGACAATATTTTTTGTAATAATTATTAACACTTAAAGTTATAAACTTTATCACTATATGA-TT
252 TATGACAATATTTTTTGTAATAATTATAAACACTTAAAGTTACAAAAATTATCACTATATGATTT
* *
2793780 TTTTA-GCGTAAAAAAATATGGA-AGGAAATCTTTGTGACAATATATTTTGT
317 TTTTATGC--AAAAAAATATGGAGA-AAAATCTTTATGACAATATATTTTGT
2793830 CATTATAATT
Statistics
Matches: 331, Mismatches: 29, Indels: 19
0.87 0.08 0.05
Matches are distributed among these distances:
412 12 0.04
413 2 0.01
414 58 0.18
415 5 0.02
416 82 0.25
417 3 0.01
418 75 0.23
419 94 0.28
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.40
Consensus pattern (412 bp):
TAGTATAATTTTTCATAATGATTAAAATATATAACTACAAAAATAATTGATTAAAAAAACTTGAA
TTTTATTATCTGATGGGATAATTTTTTCTATAACAATAACTATAAATTATAATTACAAAAATTAT
CAATATAACTTTTTAGAAAAAAAAAAGTGAAAAAATAGTTATCACAATATATGCTATCACTATAA
TTAAAATTTATAACTACAAATATAATTTCTCACAAAAATGTGAATATCATTATTTTTATGACAAT
ATTTTTTGTAATAATTATAAACACTTAAAGTTACAAAAATTATCACTATATGATTTTTTTATGCA
AAAAAATATGGAGAAAAATCTTTATGACAATATATTTTGTTACTATATAATATTTTTGACATTAA
AAAATAGGAAAAATGGTTCTAA
Found at i:2794066 original size:179 final size:177
Alignment explanation
Indices: 2793650--2794088 Score: 422
Period size: 179 Copynumber: 2.5 Consensus size: 177
2793640 ATATATGCTA
** * * * * *
2793650 TCACTATTGTTAAAATTTATAACTACAAATATAATTTGTCACAAAAATGTGAATATCGTTATTTT
1 TCACTATAATTAAAATATATAACTACAAATATAATTTGTCACAAAAATCTGAATCTCATTATTTG
* * * * *
2793715 TTGTGACAATATTTTTTGTAATAATTATTAACACTTAAAGTTATAAACTTTATCACTATATGATT
66 TTGTGAC-AT-TTTTTTGTAACAATAATGAACACTTAAAGTTAAAAACATTATCACTATATGATT
*
2793780 TTTTAGCGTAAAAAAATATGGAAGGAAATCTTTGTGACAATATATTTTG
129 TTTTAGCGTAAAAAAATATGGAAGGAAATCTTTGTGACAATACATTTTG
* * * * ** * *
2793829 TCATTATAATTAAAACATATAACGACAAACATTGTTTTTTACTAAAAA-CTTGAATCTCATTATT
1 TCACTATAATTAAAATATATAACTACAAATATAATTTGTCAC-AAAAATC-TGAATCTCATTATT
* *
2793893 TGTTGTGACATTTTTTTGTAACAATAATGATA-GCTTATAGTTACAAAACATT-TCACTATATGA
64 TGTTGTGACATTTTTTTGTAACAATAATGA-ACACTTAAAGTTA-AAAACATTATCACTATATGA
**** * *
2793956 TTTTGTTTTTTTACCAAAAAT-TGG-A-GATAATCATTTGTGACTATACATTTTG
127 TTTT-TTAGCGTA-AAAAAATATGGAAGGA-AATC-TTTGTGACAATACATTTTG
* * * *
2794008 TCACTATAATTAAAATATATAATTACAAATAAAATTTGTCACAACAAATCTAAATCTCATTACTT
1 TCACTATAATTAAAATATATAACTACAAATATAATTTGTCACAA-AAATCTGAATCTCATTATTT
* *
2794073 GTTGTGATAATTTTTT
65 GTTGTGACATTTTTTT
2794089 CTGTCATAGT
Statistics
Matches: 207, Mismatches: 43, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
177 2 0.01
178 47 0.23
179 126 0.61
180 32 0.15
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (177 bp):
TCACTATAATTAAAATATATAACTACAAATATAATTTGTCACAAAAATCTGAATCTCATTATTTG
TTGTGACATTTTTTTGTAACAATAATGAACACTTAAAGTTAAAAACATTATCACTATATGATTTT
TTAGCGTAAAAAAATATGGAAGGAAATCTTTGTGACAATACATTTTG
Found at i:2798847 original size:31 final size:30
Alignment explanation
Indices: 2798795--2798856 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 30
2798785 ATCTTTATAC
* *
2798795 TTTTATTTTTTAAAATCTATTTTTCATTAA
1 TTTTATTTTTTAAAATCTATTTATCAATAA
* * *
2798825 TTTTATTTTTTCTATATTTATTTATCAATAA
1 TTTTATTTTTT-AAAATCTATTTATCAATAA
2798856 T
1 T
2798857 GCAGACTGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (30 bp):
TTTTATTTTTTAAAATCTATTTATCAATAA
Found at i:2799367 original size:118 final size:118
Alignment explanation
Indices: 2799138--2799383 Score: 336
Period size: 118 Copynumber: 2.1 Consensus size: 118
2799128 AAAATATATA
* * * * *
2799138 GACGATAACATAACCGGTTAATTATTCGAAACATTATCAAGCACAATAACATATTAGGTAACATT
1 GACGATAACATAACCAGTTAATTACTCGAAACATTATCAAACACAATAACATATTAGATAACACT
* *
2799203 TATATAACGTAATAGGTAGCGCCTTGTTAAAGCTGATGGAGCTTTGGAAATCT
66 TATATAACGTAATAGGTAGCGCCTTGTTAAAGCTGATAGAGCTTTGGAAATCC
* * *
2799256 GACGATAACATAACCAGTTAATTACTGGAAACATTATCAAACATAATAACATATTAGATAGCACT
1 GACGATAACATAACCAGTTAATTACTCGAAACATTATCAAACACAATAACATATTAGATAACACT
* *
2799321 TATATAACGTAATATAGGTAG-TCCTT-TTTAAGC-GATAGAGCTTTTGGAAATCC
66 TATATAACGT-A-ATAGGTAGCGCCTTGTTAAAGCTGATAGAGC-TTTGGAAATCC
2799374 GACGATAACA
1 GACGATAACA
2799384 AAATAGGTTA
Statistics
Matches: 113, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
117 7 0.06
118 93 0.82
119 5 0.04
120 8 0.07
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.29
Consensus pattern (118 bp):
GACGATAACATAACCAGTTAATTACTCGAAACATTATCAAACACAATAACATATTAGATAACACT
TATATAACGTAATAGGTAGCGCCTTGTTAAAGCTGATAGAGCTTTGGAAATCC
Found at i:2801582 original size:183 final size:183
Alignment explanation
Indices: 2801351--2801998 Score: 1064
Period size: 183 Copynumber: 3.5 Consensus size: 183
2801341 TTATTAAAGT
* * *
2801351 ATCGATACCTTCAACATATCCGATAGCGCTTTATCGGTTTCGTCATAATGAAACC-AGTTTTGTC
1 ATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGA-TTTTGTC
2801415 ATATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGC
65 ATATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGC
* *
2801480 GCTATTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGAA
130 GCTATTATTGCTTTTCTTTAAAATTCCATAAGTATCGATACTTATTTGAATGAA
* * * * *
2801534 ATTGATACCTTCAACATATCTGGTAACGATTTACCGGTTTTGTCATAATGAAACCGATTTTTTCA
1 ATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCA
* * *
2801599 TATTTTTACATGTTATATTGTTATGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGAG
66 TATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGCG
* *
2801664 CTATTATTGTTTTTCTTTAAAATTCCATAAGTATCGATACTTATTTGAATGGA
131 CTATTATTGCTTTTCTTTAAAATTCCATAAGTATCGATACTTATTTGAATGAA
**
2801717 ATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGGCTTTGTCA
1 ATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCA
* * *
2801782 TATTTTTACCTGTTATATTGTTACGTACCGATACATGTTTGTAAAATATCGATACTTTATAGGCG
66 TATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGCG
2801847 CTATTATTGCTTTTCTTTAAAATTCCATAAGTATCGATACTTATTTGAATGAA
131 CTATTATTGCTTTTCTTTAAAATTCCATAAGTATCGATACTTATTTGAATGAA
* * * *
2801900 ATCGACACCTTCAACATATTCGGTAGCGCTTTACCGATTTTGTCATAATGAAATCGATTTTGTCA
1 ATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCA
2801965 TATTTTTACCTGTTATATTGTTACGTATCGATAC
66 TATTTTTACCTGTTATATTGTTACGTATCGATAC
2801999 TTTATAGGCG
Statistics
Matches: 427, Mismatches: 37, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
183 426 1.00
184 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (183 bp):
ATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTGTCA
TATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAGTATCGATACTTTATAGGCG
CTATTATTGCTTTTCTTTAAAATTCCATAAGTATCGATACTTATTTGAATGAA
Found at i:2801629 original size:162 final size:165
Alignment explanation
Indices: 2801461--2802342 Score: 760
Period size: 183 Copynumber: 5.1 Consensus size: 165
2801451 TGTTTATAAA
* *
2801461 GTATCGATAC-TTTATAGGCGCTA-TTAT-TGCTTTTCTTTTAAATTCCAAAAGTATCGATACTT
1 GTATCGATACTTTTATAGGCGATACTTATGCGCTTTTCTTTTAAATTCCAAAAGTATCGATACTT
* *
2801523 ATTTGAATGAAATTGATACCTTCAACATATCTGGTAACGATTTACCGGTTTTGTCATAATGAAAC
66 ATTTGAATGAAATCGATACCTTCAACATATCTGGTAGCGATTTACCGGTTTTGTCATAATGAAAC
* *
2801588 CGATTTTTTCATATTTTTACATGTTATATTGTTAT
131 CGATTTTGTCATATTTTTACATGTTATATTGTTAC
* * *
2801623 GTATCGATACATGTTTATAAAGTATCGATACTTTATAGGAGCTATTATTGTTTTTCTTTAAAATT
1 GTATCGATAC-T-TTTAT--AG--GCGATAC-TTAT----GC-------GCTTTTCTTTTAAATT
* * * *
2801688 CCATAAGTATCGATACTTATTTGAATGGAATCGATACCTTCAACATATCCGGTAGCGCTTTACCG
48 CCAAAAGTATCGATACTTATTTGAATGAAATCGATACCTTCAACATATCTGGTAGCGATTTACCG
** *
2801753 GTTTTGTCATAATGAAACCGGCTTTGTCATATTTTTACCTGTTATATTGTTAC
113 GTTTTGTCATAATGAAACCGATTTTGTCATATTTTTACATGTTATATTGTTAC
* *
2801806 GTACCGATACATGTTTGTAAAATA-TCGATACTTTATAGGCGCTATTATTGCTTTTCTTTAAAAT
1 GTATCGATAC---TTT-T---ATAGGCGATAC-TTAT--GCGC--TT-TT-C---T-TTT-AAAT
* * *
2801870 TCCATAAGTATCGATACTTATTTGAATGAAATCGACACCTTCAACATAT-TCGGTAGCGCTTTAC
47 TCCAAAAGTATCGATACTTATTTGAATGAAATCGATACCTTCAACATATCT-GGTAGCGATTTAC
* * *
2801934 CGATTTTGTCATAATGAAATCGATTTTGTCATATTTTTACCTGTTATATTGTTAC
111 CGGTTTTGTCATAATGAAACCGATTTTGTCATATTTTTACATGTTATATTGTTAC
* * *
2801989 GTATCGATAC-TTTATAGGCGCTA-TTAT-CACTTTTCTTTAAAATT-CAATAAGTA-CTGATAC
1 GTATCGATACTTTTATAGGCGATACTTATGCGCTTTTCTTTTAAATTCCAA-AAGTATC-GATAC
* * *
2802049 TTATTTAAATGGAATCGATACCTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAA
64 TTATTTGAATGAAATCGATACCTTCAACATATCTGGTAGCGATTTACCGGTTTTGTCATAATGAA
* *
2802114 ACCGGTTTTGTCATATTTTTACATTTTATATTGTTAC
129 ACCGATTTTGTCATATTTTTACATGTTATATTGTTAC
** * * *
2802151 GTATCGATACATGTTTATAAAATATCGATACTTTATAGGCACTATTATTGTTTTTTTTTAAATTT
1 GTATCGATAC-T-TTTAT---A-GGCGATAC-TTAT--GCGC--------TTTTCTTTTAAATTC
* * * *
2802216 CATAAGTATCGATACTTATTTGAATGGAATCGATACCTTCAACATATCTGGTAGCGCTTTATCGG
49 CAAAAGTATCGATACTTATTTGAATGAAATCGATACCTTCAACATATCTGGTAGCGATTTACCGG
* * * *
2802281 TTTTGTCATATTG-AACCTGATTTTATCATATTTTTACCTGTTATATTGTTAT
114 TTTTGTCATAATGAAACC-GATTTTGTCATATTTTTACATGTTATATTGTTAC
2802333 GTATCGATAC
1 GTATCGATAC
2802343 ATATTTGAAT
Statistics
Matches: 599, Mismatches: 57, Indels: 108
0.78 0.07 0.14
Matches are distributed among these distances:
161 3 0.01
162 127 0.21
163 3 0.01
164 1 0.00
165 10 0.02
167 3 0.01
168 3 0.01
169 10 0.02
171 10 0.02
174 8 0.01
175 3 0.01
176 6 0.01
177 2 0.00
178 2 0.00
179 2 0.00
181 7 0.01
182 123 0.21
183 269 0.45
184 2 0.00
185 2 0.00
186 1 0.00
188 2 0.00
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.43
Consensus pattern (165 bp):
GTATCGATACTTTTATAGGCGATACTTATGCGCTTTTCTTTTAAATTCCAAAAGTATCGATACTT
ATTTGAATGAAATCGATACCTTCAACATATCTGGTAGCGATTTACCGGTTTTGTCATAATGAAAC
CGATTTTGTCATATTTTTACATGTTATATTGTTAC
Found at i:2802068 original size:366 final size:342
Alignment explanation
Indices: 2801705--2802344 Score: 918
Period size: 345 Copynumber: 1.9 Consensus size: 342
2801695 TATCGATACT
*
2801705 TATTTGAATGGAATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAA
1 TATTTAAATGGAATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAA
* * *
2801770 CCGGCTTTGTCATATTTTTACCTGTTATATTGTTACGTACCGATACATGTTTGTAAAATATCGAT
66 CCGGTTTTGTCATATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAATATCGAT
*
2801835 ACTTTATAGGCGCTATTATTGCTTTTCTTTAAAATTCCATAAGTATCGATACTTATTTGAATGAA
131 ACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCATAAGTATCGATACTTATTTGAATGAA
* * * *
2801900 ATCGACACCTTCAACATAT-TCGGTAGCGCTTTACCGATTTTGTCATAATGAAATCGATTTTGTC
196 ATCGATACCTTCAACATATCT-GGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTATC
* ** * *
2801964 ATATTTTTACCTGTTATATTGTTACGTATCGATAC-TTTATAGGCGCTAT-TATCACTTTTCTTT
260 ATATTTTTACCTGTTATATTGTTATGTATCGATACATTTATA-AAG-TATCGAT-AC--TT-TAT
*
2802027 AAAATTCAATAAGTACTGATAC--T-
319 AAAA-GCAATAA-TACTGATACTATA
*
2802050 TATTTAAATGGAATCGATACCTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAAA
1 TATTTAAATGGAATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAA
* *
2802115 CCGGTTTTGTCATATTTTTACATTTTATATTGTTACGTATCGATACATGTTTATAAAATATCGAT
66 CCGGTTTTGTCATATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAATATCGAT
* * * *
2802180 ACTTTATAGGCACTATTATTG-TTTTTTTTTAAATTTCATAAGTATCGATACTTATTTGAATGGA
131 ACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCATAAGTATCGATACTTATTTGAATGAA
* *
2802244 ATCGATACCTTCAACATATCTGGTAGCGCTTTATCGGTTTTGTCATATTG-AACCTGATTTTATC
196 ATCGATACCTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAAACC-GATTTTATC
2802308 ATATTTTTACCTGTTATATTGTTATGTATCGATACAT
260 ATATTTTTACCTGTTATATTGTTATGTATCGATACAT
2802345 ATTTGAATGA
Statistics
Matches: 273, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
343 3 0.01
344 125 0.46
345 145 0.53
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (342 bp):
TATTTAAATGGAATCGATACCTTCAACATATCCGGTAGCGCTTTACCGGTTTTGTCATAATGAAA
CCGGTTTTGTCATATTTTTACCTGTTATATTGTTACGTATCGATACATGTTTATAAAATATCGAT
ACTTTATAGGCGCTATTATTGCTTTTCTTTTAAATTCCATAAGTATCGATACTTATTTGAATGAA
ATCGATACCTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAAACCGATTTTATCA
TATTTTTACCTGTTATATTGTTATGTATCGATACATTTATAAAGTATCGATACTTTATAAAAGCA
ATAATACTGATACTATA
Found at i:2802244 original size:182 final size:183
Alignment explanation
Indices: 2801990--2802344 Score: 545
Period size: 182 Copynumber: 1.9 Consensus size: 183
2801980 TATTGTTACG
*
2801990 TATCGATACTTTATAGGCGCTATTATCACTTTTCTTTAAAATTCAATAAGTACTGATACTTATTT
1 TATCGATACTTTATAGGCACTATTATCACTTTTCTTTAAAATTCAATAAGTACTGATACTTATTT
*
2802055 AAATGGAATCGATACCTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAAACC-GG
66 AAATGGAATCGATACCTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATG-AACCTGA
* *
2802119 TTTTGTCATATTTTTACATTTTATATTGTTACGTATCGATACATGTTTATAAAA
130 TTTTATCATATTTTTACATGTTATATTGTTACGTATCGATACATGTTTATAAAA
*** * *
2802173 TATCGATACTTTATAGGCACTATTATTGTTTTTTTTTAAATTTC-ATAAGTA-TCGATACTTATT
1 TATCGATACTTTATAGGCACTATTATCACTTTTCTTTAAAATTCAATAAGTACT-GATACTTATT
* * *
2802236 TGAATGGAATCGATACCTTCAACATATCTGGTAGCGCTTTATCGGTTTTGTCATATTGAACCTGA
65 TAAATGGAATCGATACCTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAACCTGA
* *
2802301 TTTTATCATATTTTTACCTGTTATATTGTTATGTATCGATACAT
130 TTTTATCATATTTTTACATGTTATATTGTTACGTATCGATACAT
2802345 ATTTGAATGA
Statistics
Matches: 156, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
181 5 0.03
182 113 0.72
183 38 0.24
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (183 bp):
TATCGATACTTTATAGGCACTATTATCACTTTTCTTTAAAATTCAATAAGTACTGATACTTATTT
AAATGGAATCGATACCTTCAACATATCTGGTAGCGCTTTACCGGTTTTGTCATAATGAACCTGAT
TTTATCATATTTTTACATGTTATATTGTTACGTATCGATACATGTTTATAAAA
Found at i:2810398 original size:3 final size:3
Alignment explanation
Indices: 2810392--2810507 Score: 178
Period size: 3 Copynumber: 38.7 Consensus size: 3
2810382 TTAATATATT
*
2810392 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * **
2810440 TAA TAA TAA TAA TGA TAA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
2810488 TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
2810508 TGGGTAAAAA
Statistics
Matches: 101, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 101 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2810957 original size:113 final size:113
Alignment explanation
Indices: 2810759--2811411 Score: 1024
Period size: 113 Copynumber: 5.8 Consensus size: 113
2810749 TCTTGATGAG
*
2810759 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
* * * *
2810823 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGCAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
2810872 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
* * * *
2810936 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGCAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
2810985 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
2811050 GAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GCAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
* *
2811098 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
2811163 GCAAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAA
66 GCAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
* *
2811211 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
2811276 GCAAAAATAATCCATCAAGTGATGAATTCAGGTAAAAGGTTGAACAAA
66 GCAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
*
2811324 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
2811388 GAAAAGCTGCTCCATCAAGTGATG
66 GCAAAGATGATCCATCAAATGATG
2811412 GATTTGAATC
Statistics
Matches: 518, Mismatches: 21, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
112 27 0.05
113 491 0.95
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GCAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
Found at i:2812169 original size:82 final size:82
Alignment explanation
Indices: 2812032--2812460 Score: 680
Period size: 82 Copynumber: 5.2 Consensus size: 82
2812022 TTTACTATGA
* **
2812032 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCCAACCAAATCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCAAACCAGGTCAGATAACTCAAAGAACACT
2812097 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
*
2812114 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCCAACCAGGTCAGATAACTCAAAGAACACT
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCAAACCAGGTCAGATAACTCAAAGAACACT
2812179 TCCAGAAGATGCTATTG
66 TCCAGAAGATGCTATTG
* * ** * * *
2812196 GTAAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAAATTAGATCAAATAACTCAACGAACA
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTG-TCAAACCAGGTCAGATAACTCAAAGAACA
2812261 CTTCCAGAAGATGCTATTG
64 CTTCCAGAAGATGCTATTG
*
2812280 GCAAATTCATCTTCTAAATTCAATGATTGTTCTG-CTAAACCAGGTCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTC-AAACCAGGTCAGATAACTCAAAGAACAC
2812344 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
* *
2812362 GTAAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATT-GTTCTGTCAAACCAGGTCAGATAACTCAAAGAACAC
2812427 TTCCAGAAGATGCTATTG
65 TTCCAGAAGATGCTATTG
*
2812445 GTAAATTCATCTTCCA
1 GCAAATTCATCTTCCA
2812461 TTTAATGTTT
Statistics
Matches: 321, Mismatches: 21, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
82 174 0.54
83 80 0.25
84 67 0.21
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (82 bp):
GCAAATTCATCTTCCAAATTCAATGATTGTTCTGTCAAACCAGGTCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTG
Found at i:2812306 original size:166 final size:165
Alignment explanation
Indices: 2812034--2812460 Score: 723
Period size: 166 Copynumber: 2.6 Consensus size: 165
2812024 TACTATGAGC
** *
2812034 AAATTCATCTTCCAAATTCAATGATT-GTTCTGTCCAACCAAATCAGATAACTCAAAGAACACTT
1 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGATCAGATAACTCAAAGAACACTT
*
2812098 CCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGTTCTG-TCCAACCAGGTCAG
66 CCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGTTCTGCT-AAACCAGGTCAG
2812162 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGT
130 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGT
** * *
2812198 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAAATTAGATCAAATAACTCAACGAACACT
1 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTT-AAACCAGATCAGATAACTCAAAGAACACT
*
2812263 TCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAG
65 TCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGGTCAG
2812328 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGT
130 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGT
*
2812364 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACACTT
1 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGATCAGATAACTCAAAGAACACTT
*
2812429 CCAGAAGATGCTATTGGTAAATTCATCTTCCA
66 CCAGAAGATGCTATTGGCAAATTCATCTTCCA
2812461 TTTAATGTTT
Statistics
Matches: 244, Mismatches: 16, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
164 26 0.11
165 62 0.25
166 155 0.64
167 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.30
Consensus pattern (165 bp):
AAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGATCAGATAACTCAAAGAACACTT
CCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGGTCAGA
TAACTCAAAGAACACTTCCAGAAGATGCTATTGGT
Found at i:2813605 original size:8 final size:7
Alignment explanation
Indices: 2813589--2813663 Score: 59
Period size: 6 Copynumber: 10.7 Consensus size: 7
2813579 CTTAACCCCC
2813589 TTTTTCT
1 TTTTTCT
2813596 TTTTTCCTT
1 TTTTT-C-T
2813605 TTTTTCT
1 TTTTTCT
*
2813612 TCTTT-T
1 TTTTTCT
2813618 TTTTTC-
1 TTTTTCT
2813624 TTTTTC-
1 TTTTTCT
*
2813630 ATTTTCT
1 TTTTTCT
2813637 ATTTTT-T
1 -TTTTTCT
*
2813644 TTTCTCT
1 TTTTTCT
2813651 TTTTTCT
1 TTTTTCT
2813658 TCTTTT
1 T-TTTT
2813664 TTCTCTTCAA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
6 20 0.36
7 19 0.35
8 10 0.18
9 6 0.11
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:2813620 original size:12 final size:11
Alignment explanation
Indices: 2813590--2813665 Score: 73
Period size: 12 Copynumber: 6.5 Consensus size: 11
2813580 TTAACCCCCT
2813590 TTTTCTTTTTTCC
1 TTTT-TTTTTT-C
*
2813603 TTTTTTTCTTC
1 TTTTTTTTTTC
2813614 -TTTTTTTTTC
1 TTTTTTTTTTC
*
2813624 TTTTTCATTTTC
1 TTTTT-TTTTTC
2813636 TATTTTTTTTTC
1 T-TTTTTTTTTC
*
2813648 TCTTTTTTCTTC
1 T-TTTTTTTTTC
2813660 TTTTTT
1 TTTTTT
2813666 CTCTTCAAGC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.17
11 10 0.19
12 27 0.50
13 8 0.15
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:2813634 original size:26 final size:26
Alignment explanation
Indices: 2813606--2813654 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
2813596 TTTTTCCTTT
2813606 TTTTCT-TCTTTTTTTT-TCTTTTTCA
1 TTTTCTAT-TTTTTTTTCTCTTTTTCA
2813631 TTTTCTATTTTTTTTTCTCTTTTT
1 TTTTCTATTTTTTTTTCTCTTTTT
2813655 TCTTCTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (26 bp):
TTTTCTATTTTTTTTTCTCTTTTTCA
Found at i:2813665 original size:19 final size:19
Alignment explanation
Indices: 2813589--2813670 Score: 73
Period size: 19 Copynumber: 4.5 Consensus size: 19
2813579 CTTAACCCCC
*
2813589 TTTT-TCTTTTTTCCT-TT
1 TTTTCTCTTTTTTCTTCTT
*
2813606 TTTTCTTCTTTTTTTTTC-T
1 TTTTC-TCTTTTTTCTTCTT
* * * *
2813625 TTTTC-ATTTTCTATTTTT
1 TTTTCTCTTTTTTCTTCTT
2813643 TTTTCTCTTTTTTCTTCTT
1 TTTTCTCTTTTTTCTTCTT
2813662 TTTTCTCTT
1 TTTTCTCTT
2813671 CAAGCATAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
17 11 0.22
18 6 0.12
19 33 0.66
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTTCTCTTTTTTCTTCTT
Found at i:2813670 original size:9 final size:9
Alignment explanation
Indices: 2813641--2813670 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2813631 TTTTCTATTT
2813641 TTTTTTCTC
1 TTTTTTCTC
2813650 TTTTTTCTTC
1 TTTTTTC-TC
2813660 TTTTTTCTC
1 TTTTTTCTC
2813669 TT
1 TT
2813671 CAAGCATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:2825118 original size:13 final size:13
Alignment explanation
Indices: 2825100--2825126 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2825090 ATTCGGATTT
2825100 ATAAAATAAATTA
1 ATAAAATAAATTA
2825113 ATAAAATAAATTA
1 ATAAAATAAATTA
2825126 A
1 A
2825127 AAATAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
ATAAAATAAATTA
Found at i:2826303 original size:3 final size:3
Alignment explanation
Indices: 2826297--2826385 Score: 124
Period size: 3 Copynumber: 29.7 Consensus size: 3
2826287 TTAATATATT
* * *
2826297 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
** *
2826345 TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2826386 TGGGTAAAAA
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:2826306 original size:15 final size:16
Alignment explanation
Indices: 2826288--2826386 Score: 102
Period size: 15 Copynumber: 6.6 Consensus size: 16
2826278 TATTATTTTT
*
2826288 TAAT-ATATTTAATAA
1 TAATAATATATAATAA
*
2826303 TAATGATA-ATAATAA
1 TAATAATATATAATAA
*
2826318 TAATAATA-ATAATGA
1 TAATAATATATAATAA
*
2826333 TAATAATA-ATATTAA
1 TAATAATATATAATAA
**
2826348 TAATAATA-AGGATAA
1 TAATAATATATAATAA
2826363 TAATAATAT-TAATAA
1 TAATAATATATAATAA
2826378 TAATAATAT
1 TAATAATAT
2826387 GGGTAAAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
15 69 0.96
16 3 0.04
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (16 bp):
TAATAATATATAATAA
Found at i:2827596 original size:13 final size:13
Alignment explanation
Indices: 2827578--2827605 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2827568 TCCTCACAAT
2827578 TTATCATTTGATC
1 TTATCATTTGATC
2827591 TTATCATTTGATC
1 TTATCATTTGATC
2827604 TT
1 TT
2827606 TAGGGGTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (13 bp):
TTATCATTTGATC
Found at i:2829408 original size:17 final size:17
Alignment explanation
Indices: 2829355--2829410 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
2829345 TTTTGCGACT
2829355 TTTTTTTGG-CTTTTTGA
1 TTTTTTTGGCCTTTTT-A
*
2829372 TTTTTTTGGCC-TTTGA
1 TTTTTTTGGCCTTTTTA
*
2829388 TTTTTTTGGCCTTTTTC
1 TTTTTTTGGCCTTTTTA
2829405 TTTTTT
1 TTTTTT
2829411 GAAAAAATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 12 0.35
17 21 0.62
18 1 0.03
ACGTcount: A:0.04, C:0.11, G:0.14, T:0.71
Consensus pattern (17 bp):
TTTTTTTGGCCTTTTTA
Found at i:2829411 original size:16 final size:16
Alignment explanation
Indices: 2829355--2829401 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
2829345 TTTTGCGACT
*
2829355 TTTTTTTGGCTTTTTGA
1 TTTTTTTGGC-CTTTGA
2829372 TTTTTTTGGCCTTTGA
1 TTTTTTTGGCCTTTGA
2829388 TTTTTTTGGCCTTT
1 TTTTTTTGGCCTTT
2829402 TTCTTTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 19 0.66
17 10 0.34
ACGTcount: A:0.04, C:0.11, G:0.17, T:0.68
Consensus pattern (16 bp):
TTTTTTTGGCCTTTGA
Found at i:2830075 original size:43 final size:42
Alignment explanation
Indices: 2830002--2830359 Score: 491
Period size: 42 Copynumber: 8.4 Consensus size: 42
2829992 ATAGGTTAAG
*
2830002 ATCTATAGCGGCGTTTTTTGAAACAAACGCCGCAAAAGGTCGAT
1 ATCTATAGCGGCG-TTTTTGGAACAAACGCCGCAAAAGGTC-AT
* * *
2830046 ATATATAGTGGCATTTTTGGAACAAACGCCGCAAAAGGTCGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-AT
* *
2830089 ATCTATAGCGGCGTTTTTAGAACAAACTCCGCAAAAGGTCGAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTC-AT
2830132 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
* * * * * *
2830174 ATTTATAACGTCATTTTTGAAACAAACGTCGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
* * * *
2830216 ATCTTTAGCGGCGTTTTTAGAACAAACACCGCAAAAGGTCAA
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
* * *
2830258 ATCTATAGCGGCGTTTTTGTAACAAACACCGCAAAAGGTCAG
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
**
2830300 ATCTATAGCGGCGTTTTTATAACAAACGCCGCAAAAGGTCAT
1 ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
2830342 ATCTATAGCGGCGTTTTT
1 ATCTATAGCGGCGTTTTT
2830360 TTTATACAAA
Statistics
Matches: 280, Mismatches: 34, Indels: 2
0.89 0.11 0.01
Matches are distributed among these distances:
42 165 0.59
43 105 0.38
44 10 0.04
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (42 bp):
ATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAT
Found at i:2832991 original size:2 final size:2
Alignment explanation
Indices: 2832984--2833022 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2832974 GTGTATTCCT
2832984 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2833023 TCAGATAGAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2833638 original size:42 final size:41
Alignment explanation
Indices: 2833333--2833683 Score: 247
Period size: 41 Copynumber: 8.4 Consensus size: 41
2833323 CATTTATTCA
* *
2833333 AAAAATGCCACTATAGTA-TGAGTATTTAGCGGCGTTTGT-T
1 AAAAACGCCACTAAAGTACTGA-TATTTAGCGGCGTTTGTCT
* * *
2833373 GGAAAACGCCACTAAAGTA-TGGGTATTTAGCGGCGTTTTTTTGCT
1 -AAAAACGCCACTAAAGTACT-GATATTTAGCGGCG--TTTGT-CT
* * * *
2833418 TAAAACGCCATTAAAGTA-TTATGTTTTAGCGGCGTTTGT-T
1 AAAAACGCCACTAAAGTACTGAT-ATTTAGCGGCGTTTGTCT
* *
2833458 GAAAAATGCCACTAAAGTACATGGT-TTTAGCGGCGTTTGTCT
1 -AAAAACGCCACTAAAGTAC-TGATATTTAGCGGCGTTTGTCT
* ** *
2833500 AAAAACGCCACGATATATGTAC-CCTA-TT-GCGGCGTTTGTTT
1 AAAAACGCCAC--TA-AAGTACTGATATTTAGCGGCGTTTGTCT
* * * * *
2833541 AAAAACACCACTAAAGAAC-GACTATAT-GACGGCATTTGTTT
1 AAAAACGCCACTAAAGTACTGA-TATTTAG-CGGCGTTTGTCT
* * *
2833582 ACAAATGCCACTAAAGTACTGATATTTAGCGGCGTTTGTCA
1 AAAAACGCCACTAAAGTACTGATATTTAGCGGCGTTTGTCT
* *
2833623 AATAAACGCCACTAAAGTACTTATATTTAGCGGCGTTTGTCA
1 AA-AAACGCCACTAAAGTACTGATATTTAGCGGCGTTTGTCT
*
2833665 AATAAACACCACTAAAGTA
1 AA-AAACGCCACTAAAGTA
2833684 TGAGTTTTAG
Statistics
Matches: 250, Mismatches: 40, Indels: 39
0.76 0.12 0.12
Matches are distributed among these distances:
38 4 0.02
39 4 0.02
40 3 0.01
41 130 0.52
42 67 0.27
43 9 0.04
44 32 0.13
45 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (41 bp):
AAAAACGCCACTAAAGTACTGATATTTAGCGGCGTTTGTCT
Found at i:2843611 original size:30 final size:32
Alignment explanation
Indices: 2843571--2843631 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
2843561 AGAAAAGGAC
2843571 TTGGACACTGGAAAG-GAGTTTG-TATGATTTT
1 TTGGACACTGGAAAGTGA-TTTGTTATGATTTT
2843602 TTGGA-ACTGGAAAGTGATTTGTTATGATTT
1 TTGGACACTGGAAAGTGATTTGTTATGATTT
2843632 ATGTTGCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 13 0.46
31 15 0.54
ACGTcount: A:0.26, C:0.05, G:0.28, T:0.41
Consensus pattern (32 bp):
TTGGACACTGGAAAGTGATTTGTTATGATTTT
Found at i:2846061 original size:19 final size:20
Alignment explanation
Indices: 2846023--2846061 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
2846013 TGTAAGAATT
*
2846023 ACACTTTAATCCTCAAATCA
1 ACACTTTAATCCTAAAATCA
*
2846043 ACACTTTAA-CTTAAAATCA
1 ACACTTTAATCCTAAAATCA
2846062 GCATTCCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.31
Consensus pattern (20 bp):
ACACTTTAATCCTAAAATCA
Done.