Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000913.1 Hibiscus syriacus cultivar Beakdansim tig00001818_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: 1610646
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:498353 original size:83 final size:83
Alignment explanation
Indices: 498209--498462 Score: 456
Period size: 83 Copynumber: 3.1 Consensus size: 83
498199 CTTATTTCTA
*
498209 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAA
*
498273 AGAACACTTCCAGAATATG
65 AGAACACTTCCAGAAGATG
*
498292 CTATTAGCAAATTCATCTTCCAAATTTAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
498357 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
*
498375 CTATTAGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGTCCAACCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
498440 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
498458 CTATT
1 CTATT
498463 GAGTCTCCTT
Statistics
Matches: 165, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
83 163 0.99
84 2 0.01
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:498360 original size:271 final size:271
Alignment explanation
Indices: 497877--498518 Score: 1257
Period size: 271 Copynumber: 2.4 Consensus size: 271
497867 GTTCCTACCA
*
497877 AACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTAT
497942 GAGTAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAAC
66 GAGTAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAAC
498007 ACTTCCAGAATATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGA
131 ACTTCCAGAATATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGA
498072 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT
196 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT
498137 TAGTTCTGTCC
261 TAGTTCTGTCC
498148 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTAT
*
498213 GAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAAC
66 GAGTAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAAC
*
498278 ACTTCCAGAATATGCTATTAGCAAATTCATCTTCCAAATTTAATGATTGGTTCTGTCCAACCAGA
131 ACTTCCAGAATATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGA
498343 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT
196 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT
498408 TAGTTCTGTCC
261 TAGTTCTGTCC
498419 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTAT
498484 GAGTAAATTCATCTTCCAAATTCAATGATTGGTTC
66 GAGTAAATTCATCTTCCAAATTCAATGATTGGTTC
498519 GGGTGGTGGC
Statistics
Matches: 367, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
271 367 1.00
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.30
Consensus pattern (271 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGTCTCCTTATTTCTACTAT
GAGTAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAAC
ACTTCCAGAATATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGA
TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGAT
TAGTTCTGTCC
Found at i:510927 original size:11 final size:11
Alignment explanation
Indices: 510904--510935 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
510894 CTGTAATTAT
510904 TATTTATATATA
1 TATTTA-ATATA
510916 TATTTAATATA
1 TATTTAATATA
510927 TATTTAATA
1 TATTTAATA
510936 ATAATAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAATATA
Found at i:510939 original size:3 final size:3
Alignment explanation
Indices: 510931--510994 Score: 101
Period size: 3 Copynumber: 20.7 Consensus size: 3
510921 AATATATATT
*
510931 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
510979 TAGGA TAA TAA TAA TA
1 TA--A TAA TAA TAA TA
510995 TGGATAAAAA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
3 54 0.95
5 3 0.05
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:512142 original size:20 final size:21
Alignment explanation
Indices: 512117--512168 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
512107 TTTTCCCAAT
*
512117 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
512137 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
512158 TCGCAATGCGA
1 TCGCAATGCGA
512169 TACTTACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:512182 original size:20 final size:20
Alignment explanation
Indices: 512157--512251 Score: 75
Period size: 20 Copynumber: 4.7 Consensus size: 20
512147 AATTGGGAAA
*
512157 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTTACT
* * *
512177 ATCGCAATGCGATA-ATACAAA
1 ATCGCAACGCGATACTTAC--T
* *
512198 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTTACT
* * *
512218 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTTACT
*
512238 TTCGCAACGCGATA
1 ATCGCAACGCGATA
512252 ATACATAATC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.05
20 44 0.72
21 12 0.20
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTTACT
Found at i:512801 original size:19 final size:20
Alignment explanation
Indices: 512746--512803 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
512736 GCGATTCTCT
**
512746 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
512766 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* *
512786 TGTTGCGAT-TTCATTTTC
1 CGTTGCGATAGTCATTTTC
512804 AGAAACTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 8 0.24
20 26 0.76
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.41
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:512994 original size:25 final size:24
Alignment explanation
Indices: 512940--512994 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
512930 TGTTTATTAT
* *
512940 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
512964 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
512990 TGTTT
1 TGTTT
512995 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:514144 original size:18 final size:18
Alignment explanation
Indices: 514123--514167 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
514113 TCCACTTCGG
*
514123 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
514141 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
514159 GAGCCATCA
1 GAGCCATCA
514168 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:514703 original size:19 final size:20
Alignment explanation
Indices: 514649--514715 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
514639 TAGTTTACTT
* *
514649 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
514669 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
514689 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
514708 TCGCAACG
1 TCGCAACG
514716 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:514723 original size:14 final size:14
Alignment explanation
Indices: 514704--514762 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
514694 ATGCGAAATG
514704 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
514718 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
514737 AAAATCGCAACGAC
1 AAAATCGCAACGAC
514751 AAAATCGCAACG
1 AAAATCGCAACG
514763 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:514730 original size:33 final size:33
Alignment explanation
Indices: 514688--514779 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
514678 GGAAATGGCT
514688 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
514721 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
514754 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
514780 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:514742 original size:19 final size:19
Alignment explanation
Indices: 514688--514784 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
514678 GGAAATGGCT
514688 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
514707 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
514721 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
514740 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
514754 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
514773 ATCGCAATGCGA
1 ATCGCAATGCGA
514785 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:514846 original size:33 final size:33
Alignment explanation
Indices: 514796--514921 Score: 209
Period size: 33 Copynumber: 3.8 Consensus size: 33
514786 TTGTGTTTCA
514796 CGTTGCGA-TTTCATTTCGCATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
* *
514828 CGTTGTGATTTTCATTTCGCATTGTGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
*
514861 CGTTGCGATTTTCATTTCGTATTGCGATTTTGT
1 CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
*
514894 CGTTGCGATTTGCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
514922 AGCCATTTCC
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
32 7 0.08
33 79 0.92
ACGTcount: A:0.13, C:0.17, G:0.22, T:0.48
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTTTGT
Found at i:514920 original size:19 final size:18
Alignment explanation
Indices: 514798--514921 Score: 83
Period size: 14 Copynumber: 7.4 Consensus size: 18
514788 GTGTTTCACG
514798 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
*
514816 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
*
514830 TTGTGATTTTCATTTCGCA
1 TTGCGA-TTTCATTTCGCA
* *
514849 TTGTGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
*
514863 TTGCGATTTTCATTTCGTA
1 TTGCGA-TTTCATTTCGCA
*
514882 TTGCGATTT--TGTCG--
1 TTGCGATTTCATTTCGCA
514896 TTGCGATTTGCATTTCGCA
1 TTGCGATTT-CATTTCGCA
514915 TTGCGAT
1 TTGCGAT
514922 AGCCATTTCC
Statistics
Matches: 83, Mismatches: 8, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.23
15 6 0.07
16 12 0.14
17 12 0.14
18 15 0.18
19 19 0.23
ACGTcount: A:0.13, C:0.16, G:0.22, T:0.49
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:514940 original size:20 final size:19
Alignment explanation
Indices: 514906--514958 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
514896 TTGCGATTTG
*
514906 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
514925 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
514945 CATTTTCGCGTTGC
1 CA-TTTCGCGTTGC
514959 AATTTTAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 5 0.17
20 22 0.73
21 3 0.10
ACGTcount: A:0.15, C:0.26, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:516852 original size:14 final size:14
Alignment explanation
Indices: 516818--516856 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
516808 TTGATTGTTT
516818 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
516832 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
516846 TGTTGATTTGT
1 AATTGATTTGT
516857 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:517017 original size:19 final size:19
Alignment explanation
Indices: 516993--517079 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
516983 ATCACAACGA
516993 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
517012 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
517031 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
517050 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
517064 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
517080 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 49 0.75
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:517123 original size:20 final size:20
Alignment explanation
Indices: 517098--517153 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
517088 TCGCATTGCG
*
517098 ATTTTCTAGTTGCGATAGCC
1 ATTTTCCAGTTGCGATAGCC
517118 ATTTTCGCA-TTGCGATAGCC
1 ATTTTC-CAGTTGCGATAGCC
517138 ATTTTCGC-GTTGCGAT
1 ATTTTC-CAGTTGCGAT
517154 TTCCCCGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 32 0.97
21 1 0.03
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTTTCCAGTTGCGATAGCC
Found at i:517392 original size:20 final size:20
Alignment explanation
Indices: 517367--517479 Score: 77
Period size: 20 Copynumber: 5.5 Consensus size: 20
517357 TTGAAGATGA
517367 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
517387 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
* **
517407 TTGCGATTTTGTATTATCTCG
1 TTGCGATTTT-CAGAATCTCG
** * * *
517428 TTGCGATAGTCAGTATCGCA
1 TTGCGATTTTCAGAATCTCG
517448 TTGCGATTTTCCA-AAT-TCG
1 TTGCGATTTT-CAGAATCTCG
517467 CATTGCGATTTTC
1 --TTGCGATTTTC
517480 CAAATTCGCA
Statistics
Matches: 69, Mismatches: 20, Indels: 8
0.71 0.21 0.08
Matches are distributed among these distances:
19 1 0.01
20 41 0.59
21 27 0.39
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:517514 original size:22 final size:21
Alignment explanation
Indices: 517443--517498 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
517433 ATAGTCAGTA
517443 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
517464 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
517485 TCGCATTGCGATTT
1 TCGCATTGCGATTT
517499 ACTTATATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:520849 original size:33 final size:33
Alignment explanation
Indices: 520812--520919 Score: 146
Period size: 33 Copynumber: 3.3 Consensus size: 33
520802 GGAAATTACT
*
520812 ATCGCAACGAGAAAATCGCAATACGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
**
520845 ATCGCAAC-ACGAATTTCGCAATGCGAAATGAAA
1 ATCGCAACGA-GAAAATCGCAATGCGAAATGAAA
* **
520878 AGCGCAACGAGGGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
520911 ATCGCAACG
1 ATCGCAACG
520920 CGAATTTAAT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 1 0.02
33 62 0.97
34 1 0.02
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:520915 original size:19 final size:19
Alignment explanation
Indices: 520822--520923 Score: 62
Period size: 19 Copynumber: 5.9 Consensus size: 19
520812 ATCGCAACGA
*
520822 GAAAATCGCAATACGAAAT
1 GAAAATCGCAATGCGAAAT
*
520841 GAAAATCGCAA--C---AC
1 GAAAATCGCAATGCGAAAT
**
520855 GAATTTCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
520874 GAAAAGCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
**
520888 GGGAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
520907 GAAAATCGCAACGCGAA
1 GAAAATCGCAATGCGAA
520924 TTTAATTTCA
Statistics
Matches: 60, Mismatches: 13, Indels: 20
0.65 0.14 0.22
Matches are distributed among these distances:
14 18 0.30
15 1 0.02
16 3 0.05
17 3 0.05
18 1 0.02
19 34 0.57
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:520972 original size:19 final size:19
Alignment explanation
Indices: 520948--520994 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
520938 GCGATTCTCT
*
520948 CGTTGCGATTTTCATTTCG
1 CGTTGCGATCTTCATTTCG
520967 CGTTGCGATCTTCATTTCG
1 CGTTGCGATCTTCATTTCG
*
520986 CATTGCGAT
1 CGTTGCGAT
520995 AGTACTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.13, C:0.23, G:0.21, T:0.43
Consensus pattern (19 bp):
CGTTGCGATCTTCATTTCG
Found at i:521116 original size:14 final size:14
Alignment explanation
Indices: 521097--521133 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
521087 CATCAATTAA
521097 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
521111 ACAAATCACCTTTT
1 ACAAATCAACTTTT
521125 ACAAATCAA
1 ACAAATCAA
521134 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:522533 original size:21 final size:21
Alignment explanation
Indices: 522467--522536 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
522457 GTGAATCGGG
*
522467 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
522487 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
522509 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
522530 CTCTTGA
1 CTCTTGA
522537 GGAATGATAG
Statistics
Matches: 35, Mismatches: 13, Indels: 2
0.70 0.26 0.04
Matches are distributed among these distances:
21 33 0.94
22 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:522552 original size:42 final size:41
Alignment explanation
Indices: 522467--522589 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 41
522457 GTGAATCGGG
* * * *
522467 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTT-GAGGATGACAGGGGC
*
522509 CTCTTGAACGGTGGGAGGGGACTCTTGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTGAGG-ATGACAGGGGC
* * * *
522551 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTTGA-GGATGACAGG
522590 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 2 0.03
42 60 0.88
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTTGAGGATGACAGGGGC
Found at i:522985 original size:91 final size:90
Alignment explanation
Indices: 522807--522991 Score: 291
Period size: 91 Copynumber: 2.0 Consensus size: 90
522797 ATTTCAAACT
* *
522807 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGT
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
522872 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
522900 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
522964 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
522991 T
1 T
522992 AAGCAATCTA
Statistics
Matches: 87, Mismatches: 3, Indels: 6
0.91 0.03 0.06
Matches are distributed among these distances:
91 41 0.47
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:524762 original size:19 final size:19
Alignment explanation
Indices: 524738--524812 Score: 106
Period size: 19 Copynumber: 4.2 Consensus size: 19
524728 GCAACGAGAG
524738 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
524757 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
524776 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
524790 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
524809 AATC
1 AATC
524813 ACAATACGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
14 10 0.20
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 33 0.67
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:524786 original size:52 final size:53
Alignment explanation
Indices: 524684--524816 Score: 187
Period size: 52 Copynumber: 2.5 Consensus size: 53
524674 TTGAAATGAA
* * * ** *
524684 AATCGCAACGAGATAATGAGAATCACAACGCGGAAATTACTATTGCAACGAGAG
1 AATCGCAACGCGA-AATGAAAATCACAACGCGGAAATGAAAATCGCAACGAGAG
*
524738 AATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCACAACGCGGAAATGAAAATCGCAACGAGAG
524790 AATCGCAACGCGAAATGAAAATCACAA
1 AATCGCAACGCGAAATGAAAATCACAA
524817 TACGATTTTG
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
52 44 0.62
53 15 0.21
54 12 0.17
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (53 bp):
AATCGCAACGCGAAATGAAAATCACAACGCGGAAATGAAAATCGCAACGAGAG
Found at i:525424 original size:20 final size:20
Alignment explanation
Indices: 525401--525558 Score: 264
Period size: 20 Copynumber: 7.8 Consensus size: 20
525391 CAATAGTAAG
*
525401 ATTCGCATTGCGATTTACGT-
1 ATTCGCGTTGCGATTTAC-TA
* *
525421 ATTCGCATTGCGATTTTCCTA
1 ATTCGCGTTGCGA-TTTACTA
525442 ATTCGCGTTGCGATTTACTA
1 ATTCGCGTTGCGATTTACTA
525462 ATTCGCGTTGCGATTTACTA
1 ATTCGCGTTGCGATTTACTA
525482 ATTCGCGTTGCGATTTACTA
1 ATTCGCGTTGCGATTTACTA
525502 ATTCGCGTTGCGATTTACTA
1 ATTCGCGTTGCGATTTACTA
525522 ATTCGCGTTGCGATTTACTA
1 ATTCGCGTTGCGATTTACTA
525542 ATTCGCGTTGCGATTTA
1 ATTCGCGTTGCGATTTA
525559 TGAAAATCGC
Statistics
Matches: 133, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
20 117 0.88
21 16 0.12
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTA
Found at i:525453 original size:41 final size:42
Alignment explanation
Indices: 525401--525718 Score: 234
Period size: 41 Copynumber: 7.8 Consensus size: 42
525391 CAATAGTAAG
*
525401 ATTCGCATTGCGATTTACGT-ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCAA
* * * *
525442 ATTCGCGTTGCGATTTAC-TAATTCGCGTTGCGA-TTTACTA
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCAA
* * * *
525482 ATTCGCGTTGCGATTTAC-TAATTCGCGTTGCGA-TTTACTA
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCAA
* * *
525522 ATTCGCGTTGCGATTTAC-TAATTCGCGTTGCGATTTAT-GAA
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTT-TCCAA
* ** * * * * ***
525563 AATCGCAACGCGA-ATACGTAAATCGCAATGCGAATTAGGAA
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCAA
* * *
525604 AATCGCATTGCGA--TA-GTCAGTATCCCATTGCGATTTTCCAA
1 ATTCGCATTGCGATTTACGT-AAT-TCGCATTGCGATTTTCCAA
* *
525645 ATTCGCATTGC-A-ATA-GTCAGTATCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGATTTACGT-AAT-TCGCATTGCGATTTTCCAA
*
525686 ATTCGCATTGCGATTTAC-TTATTCGCATTGCGA
1 ATTCGCATTGCGATTTACGTAATTCGCATTGCGA
525719 ATTGGGAAAA
Statistics
Matches: 236, Mismatches: 30, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
39 2 0.01
40 87 0.37
41 141 0.60
42 3 0.01
43 3 0.01
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (42 bp):
ATTCGCATTGCGATTTACGTAATTCGCATTGCGATTTTCCAA
Found at i:525615 original size:21 final size:21
Alignment explanation
Indices: 525550--525616 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
525540 TAATTCGCGT
* *
525550 TGCGATTTATGAAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* *
525571 CGCGAA-TACGTAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* *
525591 TGCGAATTAGGAAAATCGCAT
1 TGCGAATTACGAAAATCGCAA
525612 TGCGA
1 TGCGA
525617 TAGTCAGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCGAATTACGAAAATCGCAA
Found at i:525711 original size:20 final size:21
Alignment explanation
Indices: 525401--525718 Score: 148
Period size: 20 Copynumber: 15.6 Consensus size: 21
525391 CAATAGTAAG
**
525401 ATTCGCATTGCGA-TTTACGT
1 ATTCGCATTGCGATTTTACAA
* *
525421 ATTCGCATTGCGATTTTCCTA
1 ATTCGCATTGCGATTTTACAA
* *
525442 ATTCGCGTTGCGA-TTTACTA
1 ATTCGCATTGCGATTTTACAA
* *
525462 ATTCGCGTTGCGA-TTTACTA
1 ATTCGCATTGCGATTTTACAA
* *
525482 ATTCGCGTTGCGA-TTTACTA
1 ATTCGCATTGCGATTTTACAA
* *
525502 ATTCGCGTTGCGA-TTTACTA
1 ATTCGCATTGCGATTTTACAA
* *
525522 ATTCGCGTTGCGA-TTTACTA
1 ATTCGCATTGCGATTTTACAA
*
525542 ATTCGCGTTGCGATTTATGA-AA
1 ATTCGCATTGCGATTT-T-ACAA
** *
525564 A-TCGCAACGCGA--ATACGTAA
1 ATTCGCATTGCGATTTTAC--AA
* * *
525584 A-TCGCAATGCGA-ATTAGGAA
1 ATTCGCATTGCGATTTTA-CAA
* **
525604 AATCGCATTGCGATAGT-C-A
1 ATTCGCATTGCGATTTTACAA
* * *
525623 GTATCCCATTGCGATTTTCCAA
1 AT-TCGCATTGCGATTTTACAA
* **
525645 ATTCGCATTGCAATAGT-C-A
1 ATTCGCATTGCGATTTTACAA
* *
525664 GTATCGCATTGCGATTTTCCAA
1 AT-TCGCATTGCGATTTTACAA
**
525686 ATTCGCATTGCGA-TTTACTT
1 ATTCGCATTGCGATTTTACAA
525706 ATTCGCATTGCGA
1 ATTCGCATTGCGA
525719 ATTGGGAAAA
Statistics
Matches: 247, Mismatches: 34, Indels: 34
0.78 0.11 0.11
Matches are distributed among these distances:
17 1 0.00
18 1 0.00
19 3 0.01
20 170 0.69
21 62 0.25
22 9 0.04
23 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (21 bp):
ATTCGCATTGCGATTTTACAA
Found at i:525760 original size:21 final size:22
Alignment explanation
Indices: 525708--525760 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
525698 ATTTACTTAT
525708 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
525729 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
525750 TCGCATTGCGA
1 TCGCATTGCGA
525761 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:525995 original size:24 final size:23
Alignment explanation
Indices: 525963--526008 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
525953 AGGGACAAAT
* *
525963 TTATGAAATTTTAACGGGGTGAAC
1 TTATAAAATTTTAA-GAGGTGAAC
525987 TTATAAAATTTTAAGAGGTGAA
1 TTATAAAATTTTAAGAGGTGAA
526009 AATAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (23 bp):
TTATAAAATTTTAAGAGGTGAAC
Found at i:528952 original size:2 final size:2
Alignment explanation
Indices: 528945--528983 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
528935 CTTGGTGATC
528945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
528984 GGATTTGATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:531004 original size:23 final size:23
Alignment explanation
Indices: 530978--531047 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
530968 TATAAACAAG
*
530978 CATGTTCACAATCGTTAAATGAA
1 CATGTTCAGAATCGTTAAATGAA
* *
531001 CATGTTCTTGAAT-GTTAAACGAA
1 CATGTTC-AGAATCGTTAAATGAA
*
531024 CAAGTTCATGAA-CGTTAAATGAA
1 CATGTTCA-GAATCGTTAAATGAA
531047 C
1 C
531048 CAACGCCTTG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
23 35 0.92
24 3 0.08
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (23 bp):
CATGTTCAGAATCGTTAAATGAA
Found at i:531899 original size:21 final size:20
Alignment explanation
Indices: 531865--531903 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
531855 CATAGCTATA
*
531865 GTTATAGCCTATGACTATGG
1 GTTATAGACTATGACTATGG
531885 GTTATAAGACTATGACTAT
1 GTTAT-AGACTATGACTAT
531904 AAGCATATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTATAGACTATGACTATGG
Found at i:546434 original size:11 final size:11
Alignment explanation
Indices: 546404--546437 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
546394 TATACACTTA
*
546404 TAAAATATATT
1 TAAAATATTTT
546415 TAAAATATTTT
1 TAAAATATTTT
546426 TAAAATATTTT
1 TAAAATATTTT
546437 T
1 T
546438 TTGATGATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TAAAATATTTT
Found at i:554459 original size:15 final size:17
Alignment explanation
Indices: 554441--554477 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
554431 CGTGTCTTTT
554441 AAAA-CAATTTTAAGA-
1 AAAATCAATTTTAAGAC
*
554456 AAAATCATTTTTAAGAC
1 AAAATCAATTTTAAGAC
554473 AAAAT
1 AAAAT
554478 TTAGTCTGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 10 0.53
17 5 0.26
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (17 bp):
AAAATCAATTTTAAGAC
Found at i:555170 original size:2 final size:2
Alignment explanation
Indices: 555163--555205 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
555153 ATAATATGGC
555163 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
555205 T
1 T
555206 GTTTAGTATA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:556092 original size:166 final size:166
Alignment explanation
Indices: 555818--556149 Score: 664
Period size: 166 Copynumber: 2.0 Consensus size: 166
555808 ACCACCCATG
555818 GTTTTTCGAACAACCAACACTCTCTCTAAAACAAACACACAACAACATCCTTTCACTCCTTGGAA
1 GTTTTTCGAACAACCAACACTCTCTCTAAAACAAACACACAACAACATCCTTTCACTCCTTGGAA
555883 TCTAATTGAGACCCTAAATCAAACTAAAACCCGACCCCATAGACGACCGACGTAGCCTTAGACGC
66 TCTAATTGAGACCCTAAATCAAACTAAAACCCGACCCCATAGACGACCGACGTAGCCTTAGACGC
555948 GACCACCTTCTCCGGCAAGGATCACTCCTAAAGTAA
131 GACCACCTTCTCCGGCAAGGATCACTCCTAAAGTAA
555984 GTTTTTCGAACAACCAACACTCTCTCTAAAACAAACACACAACAACATCCTTTCACTCCTTGGAA
1 GTTTTTCGAACAACCAACACTCTCTCTAAAACAAACACACAACAACATCCTTTCACTCCTTGGAA
556049 TCTAATTGAGACCCTAAATCAAACTAAAACCCGACCCCATAGACGACCGACGTAGCCTTAGACGC
66 TCTAATTGAGACCCTAAATCAAACTAAAACCCGACCCCATAGACGACCGACGTAGCCTTAGACGC
556114 GACCACCTTCTCCGGCAAGGATCACTCCTAAAGTAA
131 GACCACCTTCTCCGGCAAGGATCACTCCTAAAGTAA
556150 ATGTATTATT
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
166 166 1.00
ACGTcount: A:0.35, C:0.33, G:0.12, T:0.20
Consensus pattern (166 bp):
GTTTTTCGAACAACCAACACTCTCTCTAAAACAAACACACAACAACATCCTTTCACTCCTTGGAA
TCTAATTGAGACCCTAAATCAAACTAAAACCCGACCCCATAGACGACCGACGTAGCCTTAGACGC
GACCACCTTCTCCGGCAAGGATCACTCCTAAAGTAA
Found at i:559861 original size:134 final size:135
Alignment explanation
Indices: 559615--559888 Score: 525
Period size: 134 Copynumber: 2.0 Consensus size: 135
559605 TCTTGTATTC
559615 CATCAATTTAGAGTCTCAACCTCTTAGTAGTCCATACTAAGGCACAACATAACTTTTCAATCGAG
1 CATCAATTTAGAGTCTCAACCTCTTAGTAGTCCATACTAAGGCACAACATAACTTTTCAATCGAG
559680 GAATATCGAGTCTCACAGTAAGTGAATTTCTTACTGAGATAGTAAATAGCTCTTTCTC-TCTTCC
66 GAATATCGAGTCTCACAGTAAGTGAATTTCTTACTGAGATAGTAAATAGCTCTTTCTCTTCTTCC
559744 AGTTT
131 AGTTT
559749 -ATCAATTTTAGAGTCTCAACCTCTTAGTAGTCCATACTAAGGCACAACATAACTTTTCAATCGA
1 CATCAA-TTTAGAGTCTCAACCTCTTAGTAGTCCATACTAAGGCACAACATAACTTTTCAATCGA
559813 GGAATATCGAGTCTCACAGTAAGTGAATTTCTTACTGAGATAGTAAATAGCTCTTTCTCTTCTTC
65 GGAATATCGAGTCTCACAGTAAGTGAATTTCTTACTGAGATAGTAAATAGCTCTTTCTCTTCTTC
559878 CAGTTT
130 CAGTTT
559884 CATCA
1 CATCA
559889 TGCTGTGCCA
Statistics
Matches: 137, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
133 5 0.04
134 117 0.85
135 11 0.08
136 4 0.03
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.34
Consensus pattern (135 bp):
CATCAATTTAGAGTCTCAACCTCTTAGTAGTCCATACTAAGGCACAACATAACTTTTCAATCGAG
GAATATCGAGTCTCACAGTAAGTGAATTTCTTACTGAGATAGTAAATAGCTCTTTCTCTTCTTCC
AGTTT
Found at i:568019 original size:92 final size:92
Alignment explanation
Indices: 567862--568045 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
567852 CGGAAAGAGT
567862 TCAATTCGAGGGGATTCACTACCTTATACCCATACGAGGAATAAATCCCTACGAAGGTACAAAGT
1 TCAATTCGAGGGGATTCACTACCTTATACCCATACGAGGAATAAATCCCTACGAAGGTACAAAGT
567927 ATGTATCCCGTGGGTTATTTGCTAAAA
66 ATGTATCCCGTGGGTTATTTGCTAAAA
567954 TCAATTCGAGGGGATTCACTACCTTATACCCATACGAGGAATAAATCCCTACGAAGGTACAAAGT
1 TCAATTCGAGGGGATTCACTACCTTATACCCATACGAGGAATAAATCCCTACGAAGGTACAAAGT
568019 ATGTATCCCGTGGGTTATTTGCTAAAA
66 ATGTATCCCGTGGGTTATTTGCTAAAA
568046 CTCATAAGAA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (92 bp):
TCAATTCGAGGGGATTCACTACCTTATACCCATACGAGGAATAAATCCCTACGAAGGTACAAAGT
ATGTATCCCGTGGGTTATTTGCTAAAA
Found at i:568456 original size:15 final size:17
Alignment explanation
Indices: 568438--568474 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
568428 CATTTCTTTT
568438 AAAA-CAATTTTAAGA-
1 AAAATCAATTTTAAGAC
*
568453 AAAATCATTTTTAAGAC
1 AAAATCAATTTTAAGAC
568470 AAAAT
1 AAAAT
568475 TCGGTATGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 4 0.21
16 10 0.53
17 5 0.26
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (17 bp):
AAAATCAATTTTAAGAC
Found at i:579054 original size:17 final size:17
Alignment explanation
Indices: 579034--579072 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
579024 GGTGATGTGT
*
579034 TATTAAATGATGAATTC
1 TATTAAATAATGAATTC
* *
579051 TATTAAATAATGCATTT
1 TATTAAATAATGAATTC
579068 TATTA
1 TATTA
579073 TGCATAATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (17 bp):
TATTAAATAATGAATTC
Found at i:583543 original size:2 final size:2
Alignment explanation
Indices: 583536--583560 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
583526 ATAATATGGC
583536 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
583561 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:587038 original size:15 final size:15
Alignment explanation
Indices: 587018--587048 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
587008 TGCATACAAA
587018 GCATTTCAATAACAT
1 GCATTTCAATAACAT
587033 GCATTTCAATAACAT
1 GCATTTCAATAACAT
587048 G
1 G
587049 TTAAACATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (15 bp):
GCATTTCAATAACAT
Found at i:589927 original size:10 final size:10
Alignment explanation
Indices: 589912--589949 Score: 58
Period size: 10 Copynumber: 3.8 Consensus size: 10
589902 ATCACACCAT
589912 ATTCTCTCAA
1 ATTCTCTCAA
589922 ATTCTCTCAA
1 ATTCTCTCAA
*
589932 ATTCTTTCAA
1 ATTCTCTCAA
*
589942 ATACTCTC
1 ATTCTCTC
589950 TCTATTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (10 bp):
ATTCTCTCAA
Found at i:590027 original size:17 final size:18
Alignment explanation
Indices: 589991--590031 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
589981 ATATTATGTA
*
589991 TTTAATTTATTTAAGCAT
1 TTTACTTTATTTAAGCAT
*
590009 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGCAT
590026 TTTACT
1 TTTACT
590032 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.29, C:0.07, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAGCAT
Found at i:594493 original size:22 final size:22
Alignment explanation
Indices: 594449--594493 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
594439 CACCGGAAAA
*
594449 TTAAGAATGAGAGAAATATTTT
1 TTAAGAATGAGAGAAACATTTT
*
594471 TTAAGAATGAGATAGAACATTTT
1 TTAAGAATGAGAGA-AACATTTT
594494 GTTTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.44, C:0.02, G:0.18, T:0.36
Consensus pattern (22 bp):
TTAAGAATGAGAGAAACATTTT
Found at i:599422 original size:53 final size:53
Alignment explanation
Indices: 599355--599557 Score: 255
Period size: 53 Copynumber: 3.8 Consensus size: 53
599345 AAGACTCAAC
* * ** * *
599355 TTTTCCTAATTTCTTGTCCGTATACATTATTATCCATAAATGAAACACTCACA
1 TTTTCCTAAATTCTTGCCCACATACATCATCATCCATAAATGAAACACTCACA
** * *
599408 TTTTCCTAAATTCTTGTGCACATACATCATCATCCATAAATGAAAGACTCATA
1 TTTTCCTAAATTCTTGCCCACATACATCATCATCCATAAATGAAACACTCACA
**
599461 TTTTCCTAGTTTCTTGCCCACATACATCATCATCCATAAATGAAACACTCACA
1 TTTTCCTAAATTCTTGCCCACATACATCATCATCCATAAATGAAACACTCACA
* * *
599514 TTTTCAT-AATTGCTTGCCCGCATATATCATCATCCATAAATGAA
1 TTTTCCTAAATT-CTTGCCCACATACATCATCATCCATAAATGAA
599558 TTTCAACCTT
Statistics
Matches: 130, Mismatches: 19, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
52 2 0.02
53 128 0.98
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (53 bp):
TTTTCCTAAATTCTTGCCCACATACATCATCATCCATAAATGAAACACTCACA
Found at i:599543 original size:106 final size:106
Alignment explanation
Indices: 599345--599557 Score: 295
Period size: 106 Copynumber: 2.0 Consensus size: 106
599335 AATGAGGGGG
* ** * *
599345 AAGACTCAACTTTTCCTAATTTCTTGTCCGTATACATTATTATCCATAAATGAAACACTCACATT
1 AAGACTCAACTTTTCCTAATTTCTTGCCCACATACATCATCATCCATAAATGAAACACTCACATT
* **
599410 TTCCTAAATTCTTGTGCACATACATCATCATCCATAAATGA
66 TTCATAAATTCTTGCCCACATACATCATCATCCATAAATGA
*
599451 AAGACTCATA-TTTTCCTAGTTTCTTGCCCACATACATCATCATCCATAAATGAAACACTCACAT
1 AAGACTCA-ACTTTTCCTAATTTCTTGCCCACATACATCATCATCCATAAATGAAACACTCACAT
* *
599515 TTTCAT-AATTGCTTGCCCGCATATATCATCATCCATAAATGA
65 TTTCATAAATT-CTTGCCCACATACATCATCATCCATAAATGA
599557 A
1 A
599558 TTTCAACCTT
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
105 4 0.04
106 89 0.95
107 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.34
Consensus pattern (106 bp):
AAGACTCAACTTTTCCTAATTTCTTGCCCACATACATCATCATCCATAAATGAAACACTCACATT
TTCATAAATTCTTGCCCACATACATCATCATCCATAAATGA
Found at i:614360 original size:18 final size:18
Alignment explanation
Indices: 614337--614401 Score: 82
Period size: 18 Copynumber: 3.7 Consensus size: 18
614327 TTAAACAAAT
614337 TAATAATTTAAATGTAAA
1 TAATAATTTAAATGTAAA
614355 TAATAATTT-AAT-TAAA
1 TAATAATTTAAATGTAAA
*
614371 TTAATAATTTAAA-GTTAAC
1 -TAATAATTTAAATG-TAAA
614390 TAATAATTTAAA
1 TAATAATTTAAA
614402 CTATTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
16 4 0.10
17 12 0.29
18 23 0.55
19 3 0.07
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.42
Consensus pattern (18 bp):
TAATAATTTAAATGTAAA
Found at i:614377 original size:35 final size:35
Alignment explanation
Indices: 614333--614400 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
614323 ATCCTTAAAC
614333 AAATTAATAATTTAAA-TGTAAATAATAATTTAATT
1 AAATTAATAATTTAAAGT-TAAATAATAATTTAATT
*
614368 AAATTAATAATTTAAAGTTAACTAATAATTTAA
1 AAATTAATAATTTAAAGTTAAATAATAATTTAA
614401 ACTATTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 30 0.97
36 1 0.03
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (35 bp):
AAATTAATAATTTAAAGTTAAATAATAATTTAATT
Found at i:618613 original size:34 final size:34
Alignment explanation
Indices: 618565--618678 Score: 147
Period size: 34 Copynumber: 3.3 Consensus size: 34
618555 AGATGATTTT
* **
618565 CAGTTATTAGATATTTACAGATAACATATTATTA
1 CAGTTATCAGATATTTACAGATATTATATTATTA
* * * *
618599 CAGTTATCAAATATTTACATATATTAGATGATTA
1 CAGTTATCAGATATTTACAGATATTATATTATTA
*
618633 CAGTTATCAGATATTTACAGATATTATATGTTTTA
1 CAGTTATCAGATATTTACAGATATTATAT-TATTA
618668 CAGTTATCAGA
1 CAGTTATCAGA
618679 CACATATTAA
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
34 53 0.79
35 14 0.21
ACGTcount: A:0.39, C:0.10, G:0.11, T:0.41
Consensus pattern (34 bp):
CAGTTATCAGATATTTACAGATATTATATTATTA
Found at i:618616 original size:17 final size:17
Alignment explanation
Indices: 618543--618678 Score: 98
Period size: 17 Copynumber: 7.9 Consensus size: 17
618533 ATTCTAAATG
*
618543 TTTATAGTTATCAGATGA
1 TTTACAGTTATCAGAT-A
* *
618561 TTTTCAGTTATTAGATA
1 TTTACAGTTATCAGATA
* * *
618578 TTTACAGATAACATAT-
1 TTTACAGTTATCAGATA
*
618594 TATTACAGTTATCAAATA
1 T-TTACAGTTATCAGATA
*
618612 TTTACA-TATATTAGATGA
1 TTTACAGT-TATCAGAT-A
618630 -TTACAGTTATCAGATA
1 TTTACAGTTATCAGATA
* * * *
618646 TTTACAGATATTATATGT
1 TTTACAGTTATCAGAT-A
618664 TTTACAGTTATCAGA
1 TTTACAGTTATCAGA
618679 CACATATTAA
Statistics
Matches: 90, Mismatches: 21, Indels: 14
0.72 0.17 0.11
Matches are distributed among these distances:
16 3 0.03
17 59 0.66
18 28 0.31
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (17 bp):
TTTACAGTTATCAGATA
Found at i:619561 original size:4 final size:4
Alignment explanation
Indices: 619552--619588 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
619542 CAGTATTTAG
619552 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
619589 TATATATATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:620802 original size:4 final size:4
Alignment explanation
Indices: 620793--620870 Score: 68
Period size: 4 Copynumber: 18.8 Consensus size: 4
620783 ATTTCCCTTC
** * *
620793 AAAT AAAT AAAT AAAT TCA- AAAT AAAT AAAT AAAT TATT CAAAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT --AAAT AAAT
*
620842 AAAT AATT CAAAGT AAAT AAAT AAAT AAA
1 AAAT AAAT -AAA-T AAAT AAAT AAAT AAA
620871 AATTACCTAT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
3 1 0.02
4 50 0.85
5 5 0.08
6 3 0.05
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (4 bp):
AAAT
Found at i:620811 original size:18 final size:19
Alignment explanation
Indices: 620793--620867 Score: 107
Period size: 22 Copynumber: 3.8 Consensus size: 19
620783 ATTTCCCTTC
620793 AAATAAATAAATAAATTCA
1 AAATAAATAAATAAATTCA
620812 AAATAAATAAATAAATTATTCA
1 AAATAAATAAAT-AA--ATTCA
620834 AAATAAATAAAT-AATTCA
1 AAATAAATAAATAAATTCA
*
620852 AAGTAAATAAATAAAT
1 AAATAAATAAATAAAT
620868 AAAAATTACC
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
18 16 0.31
19 15 0.29
20 3 0.06
22 17 0.33
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (19 bp):
AAATAAATAAATAAATTCA
Found at i:621597 original size:31 final size:31
Alignment explanation
Indices: 621562--621629 Score: 109
Period size: 31 Copynumber: 2.2 Consensus size: 31
621552 TCAAAATACA
*
621562 TAAGATATGATCACCTTCATTTTTATTTAAT
1 TAAGATATGATCACCTTCAATTTTATTTAAT
* *
621593 TAAGATATGATCACTTTTAATTTTATTTAAT
1 TAAGATATGATCACCTTCAATTTTATTTAAT
621624 TAAGAT
1 TAAGAT
621630 GTGGTCATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (31 bp):
TAAGATATGATCACCTTCAATTTTATTTAAT
Found at i:622252 original size:28 final size:28
Alignment explanation
Indices: 622214--622289 Score: 143
Period size: 28 Copynumber: 2.7 Consensus size: 28
622204 ACCATAAGTG
622214 TTCTTGCATGGATCCAATCCTCTCCATC
1 TTCTTGCATGGATCCAATCCTCTCCATC
*
622242 TTCTTGCATGGATCCAATGCTCTCCATC
1 TTCTTGCATGGATCCAATCCTCTCCATC
622270 TTCTTGCATGGATCCAATCC
1 TTCTTGCATGGATCCAATCC
622290 CGTTGCTGCT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 46 1.00
ACGTcount: A:0.18, C:0.33, G:0.13, T:0.36
Consensus pattern (28 bp):
TTCTTGCATGGATCCAATCCTCTCCATC
Found at i:624111 original size:2 final size:2
Alignment explanation
Indices: 624098--624128 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
624088 AACCTGATAA
*
624098 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
624129 AGTAAATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:626533 original size:32 final size:31
Alignment explanation
Indices: 626460--626537 Score: 95
Period size: 32 Copynumber: 2.5 Consensus size: 31
626450 AGTCAAATTT
* * *
626460 GCATTCAGATAATGCACAGTATGTCAGGTTT
1 GCATTCAGATAATGCACAGAATATCAGGTTC
626491 GCATTCAGATAATGCACAGGAATATCA-GTGTC
1 GCATTCAGATAATGCACA-GAATATCAGGT-TC
*
626523 GCATTTAGATAATGC
1 GCATTCAGATAATGC
626538 GTAGCATGTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
31 20 0.49
32 21 0.51
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (31 bp):
GCATTCAGATAATGCACAGAATATCAGGTTC
Found at i:627698 original size:40 final size:40
Alignment explanation
Indices: 627634--627771 Score: 120
Period size: 40 Copynumber: 3.5 Consensus size: 40
627624 ACTTTTGACT
** *
627634 TTTTTAACAAACGTCGCAACAAACTATACTTTAGTGGCAG
1 TTTTTAACAAACACCGTAACAAACTATACTTTAGTGGCAG
* * * *
627674 TTTTTAACAAACACCGTAAAAAACTCTACTCTAGT-GCCG
1 TTTTTAACAAACACCGTAACAAACTATACTTTAGTGGCAG
** * * *
627713 TTTAAAAAAAAACACCG--ACAAACTCATACTTTAGTGACAT
1 TTT-TTAACAAACACCGTAACAAACT-ATACTTTAGTGGCAG
*
627753 TTTTTAACAAACGCCGTAA
1 TTTTTAACAAACACCGTAA
627772 TAAGATACAT
Statistics
Matches: 73, Mismatches: 20, Indels: 9
0.72 0.20 0.09
Matches are distributed among these distances:
38 6 0.08
39 23 0.32
40 43 0.59
41 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (40 bp):
TTTTTAACAAACACCGTAACAAACTATACTTTAGTGGCAG
Found at i:635826 original size:21 final size:21
Alignment explanation
Indices: 635782--635827 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
635772 GGAAGTACCG
* **
635782 CATATATGTTCCAAATGATTA
1 CATATATGTCCCAAATGACCA
*
635803 CATATATGTCCCGAATGACCA
1 CATATATGTCCCAAATGACCA
635824 CATA
1 CATA
635828 GAACCCTCGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (21 bp):
CATATATGTCCCAAATGACCA
Found at i:638777 original size:27 final size:27
Alignment explanation
Indices: 638747--638810 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
638737 AATAAATTAT
*
638747 ATATTTTTGAATGAAAATAAAAATAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
* * * *
638774 ATATTTTTAAATTAAGATAATAGTAAA
1 ATATTTTTAAATGAAAATAAAAATAAA
*
638801 ATATATTTAA
1 ATATTTTTAA
638811 TTAGTTTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (27 bp):
ATATTTTTAAATGAAAATAAAAATAAA
Found at i:639133 original size:39 final size:39
Alignment explanation
Indices: 639087--639192 Score: 142
Period size: 39 Copynumber: 2.7 Consensus size: 39
639077 TTTTAAAAAT
639087 AATTTAGAATGTTAAAGTGAAATAATTTAAGAAATTAAG
1 AATTTAGAATGTTAAAGTGAAATAATTTAAGAAATTAAG
* ** *
639126 AATTTAGAACGTTATTGTGTAAA-AATTTAAGAAATTAGG
1 AATTTAGAATGTTAAAGTG-AAATAATTTAAGAAATTAAG
* *
639165 ATTTTAGAATGTTAGAGTGAAATAATTT
1 AATTTAGAATGTTAAAGTGAAATAATTT
639193 GAGGATTATG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
38 3 0.05
39 51 0.89
40 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.17, T:0.37
Consensus pattern (39 bp):
AATTTAGAATGTTAAAGTGAAATAATTTAAGAAATTAAG
Found at i:642978 original size:20 final size:21
Alignment explanation
Indices: 642940--642980 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
642930 AAAATTAAAC
642940 AAATTATTATTTAAATTAATTGT
1 AAATTATTATTT--ATTAATTGT
642963 AAATTATTATTT-TTAATT
1 AAATTATTATTTATTAATT
642981 AAAAATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
23 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
AAATTATTATTTATTAATTGT
Found at i:642986 original size:20 final size:21
Alignment explanation
Indices: 642940--642986 Score: 51
Period size: 23 Copynumber: 2.2 Consensus size: 21
642930 AAAATTAAAC
**
642940 AAATTATTATTTAAATTAATTGT
1 AAATTATTATTT--ATTAATTAA
642963 AAATTATTATTT-TTAATTAA
1 AAATTATTATTTATTAATTAA
642983 AAAT
1 AAAT
642987 ATTCAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 10 0.45
23 12 0.55
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
AAATTATTATTTATTAATTAA
Found at i:643161 original size:29 final size:29
Alignment explanation
Indices: 643127--643184 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
643117 AAAAAATCGG
643127 TTAATTC-AGTTCGGTTAATAATTTTCAAA
1 TTAATTCGA-TTCGGTTAATAATTTTCAAA
643156 TTAATTCGATTCGGTTAATAATTTTCAAA
1 TTAATTCGATTCGGTTAATAATTTTCAAA
643185 CAAATTTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (29 bp):
TTAATTCGATTCGGTTAATAATTTTCAAA
Found at i:643300 original size:29 final size:29
Alignment explanation
Indices: 643266--643327 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
643256 TAAAAATCAG
643266 TTAATTAGGTTCGGTTAATAATTTTCAAA
1 TTAATTAGGTTCGGTTAATAATTTTCAAA
* *
643295 TTAATTCGGTTTGGTTAATAATTTTCAAA
1 TTAATTAGGTTCGGTTAATAATTTTCAAA
643324 TTAA
1 TTAA
643328 CCGAATCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (29 bp):
TTAATTAGGTTCGGTTAATAATTTTCAAA
Found at i:643338 original size:124 final size:124
Alignment explanation
Indices: 643199--643448 Score: 376
Period size: 124 Copynumber: 2.0 Consensus size: 124
643189 TTTTTGTTCG
* * **
643199 ATTAACTGAACCGAATTAA-TCAAATTTTTTCTTAGATTAATTCGAATAATAATTTTTTAAAAAT
1 ATTAACCGAACCGAATTAACT-AAATTTTTGCTTAGATTAATTCGAATAATAATTTTAAAAAAAT
* * *
643263 CAGTTAATTAGGTTCGGTTAATAATTTTCAAATTAATTCGGTTTGGTTAATAATTTTCAA
65 CAGTTAATTAGGTTCGATTAATAATTTTCAAATTAATTCGGTTCGATTAATAATTTTCAA
* * **
643323 ATTAACCGAATCGAATTAACTAAATTTTTGCTTCGATTAATTCGGTTAATAATTTTAAAAAAATC
1 ATTAACCGAACCGAATTAACTAAATTTTTGCTTAGATTAATTCGAATAATAATTTTAAAAAAATC
*
643388 AGTTAATTCGGTTCGATTAATAATTTTCAAATTAATTCGGTTCGATTAATAATTTTCAA
66 AGTTAATTAGGTTCGATTAATAATTTTCAAATTAATTCGGTTCGATTAATAATTTTCAA
643447 AT
1 AT
643449 AAATTTTGGT
Statistics
Matches: 113, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
124 112 0.99
125 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.10, T:0.42
Consensus pattern (124 bp):
ATTAACCGAACCGAATTAACTAAATTTTTGCTTAGATTAATTCGAATAATAATTTTAAAAAAATC
AGTTAATTAGGTTCGATTAATAATTTTCAAATTAATTCGGTTCGATTAATAATTTTCAA
Found at i:643429 original size:29 final size:29
Alignment explanation
Indices: 643390--643466 Score: 127
Period size: 29 Copynumber: 2.6 Consensus size: 29
643380 AAAAAATCAG
643390 TTAATTCGGTTCGATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
643419 TTAATTCGGTTCGATTAATAATTTTCAAA
1 TTAATTCGGTTCGATTAATAATTTTCAAA
* *
643448 TAAATTTTGGTTCGATTAA
1 TTAA-TTCGGTTCGATTAA
643467 CCGAACCAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 32 0.71
30 13 0.29
ACGTcount: A:0.34, C:0.09, G:0.12, T:0.45
Consensus pattern (29 bp):
TTAATTCGGTTCGATTAATAATTTTCAAA
Found at i:643514 original size:105 final size:106
Alignment explanation
Indices: 643404--643602 Score: 337
Period size: 105 Copynumber: 1.9 Consensus size: 106
643394 TTCGGTTCGA
643404 TTAATAATTTTCAAATTAATTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACC
1 TTAATAATTTTCAAATTAATTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACC
643469 GAACCAAATCAACCGATTTTTTT-TTTAAAATTTGGTTTGG
66 GAACCAAATCAACCGATTTTTTTCTTTAAAATTTGGTTTGG
** *
643509 TTAATAATTTTCAAATTAATTTTGTTCGGTTAATAATTTTCAAATAAATTTTGGTTCGATTAACC
1 TTAATAATTTTCAAATTAATTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACC
** *
643574 GAACTGAATTAACCGATTTTTTTCTTTAA
66 GAACCAAATCAACCGATTTTTTTCTTTAA
643603 GCGTTAATCA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
105 82 0.94
106 5 0.06
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (106 bp):
TTAATAATTTTCAAATTAATTCGGTTCGATTAATAATTTTCAAATAAATTTTGGTTCGATTAACC
GAACCAAATCAACCGATTTTTTTCTTTAAAATTTGGTTTGG
Found at i:643529 original size:29 final size:29
Alignment explanation
Indices: 643496--643571 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
643486 TTTTTTTTTA
*
643496 AAATTTGGTTTGGTTAATAATTTTCAAAT
1 AAATTTGGTTCGGTTAATAATTTTCAAAT
* *
643525 TAATTTTGTTCGGTTAATAATTTTCAAAT
1 AAATTTGGTTCGGTTAATAATTTTCAAAT
*
643554 AAATTTTGGTTCGATTAA
1 AAA-TTTGGTTCGGTTAA
643572 CCGAACTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 28 0.70
30 12 0.30
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (29 bp):
AAATTTGGTTCGGTTAATAATTTTCAAAT
Found at i:646622 original size:3 final size:3
Alignment explanation
Indices: 646614--646656 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
646604 TTTGTCCCAT
646614 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
646657 AAAAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:646740 original size:21 final size:21
Alignment explanation
Indices: 646714--646768 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
646704 GTCCAACAGT
*
646714 AGATCCAGAACCCGGAGGCCC
1 AGATCCAGAACCCGGAAGCCC
* *
646735 AGATCCAAAACCCGGAAGCTC
1 AGATCCAGAACCCGGAAGCCC
646756 AGATCCAG-ACCCG
1 AGATCCAGAACCCG
646769 ACCCAACATC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 5 0.17
21 25 0.83
ACGTcount: A:0.33, C:0.36, G:0.24, T:0.07
Consensus pattern (21 bp):
AGATCCAGAACCCGGAAGCCC
Found at i:650944 original size:32 final size:32
Alignment explanation
Indices: 650908--650998 Score: 80
Period size: 32 Copynumber: 2.9 Consensus size: 32
650898 CAATTTTTTC
650908 AATTTTCAAAAAAGAACATATTTTTAAATACA
1 AATTTTCAAAAAAGAACATATTTTTAAATACA
* ** * * *
650940 AATTTTGAAAATTG-GCATATTCTTTAATTCCA
1 AATTTTCAAAAAAGAACATATT-TTTAAATACA
*
650972 AA-TTTCAAAAAAATAACAT-TTTTTAAA
1 AATTTTC-AAAAAAGAACATATTTTTAAA
650999 ATTTTATAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
31 14 0.32
32 27 0.61
33 3 0.07
ACGTcount: A:0.47, C:0.10, G:0.04, T:0.38
Consensus pattern (32 bp):
AATTTTCAAAAAAGAACATATTTTTAAATACA
Found at i:651160 original size:16 final size:16
Alignment explanation
Indices: 651137--651190 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 16
651127 ATGAATGAAT
651137 TTTTTTAATTAAATT-
1 TTTTTTAATTAAATTA
651152 TTATTTTAATTAAAAGTTA
1 TT-TTTTAATT-AAA-TTA
651171 TTTTTTAATTAAATATA
1 TTTTTTAATTAAAT-TA
651188 TTT
1 TTT
651191 CATTTTTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.06
16 9 0.26
17 11 0.32
18 10 0.29
19 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TTTTTTAATTAAATTA
Found at i:651176 original size:18 final size:16
Alignment explanation
Indices: 651136--651183 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 16
651126 TATGAATGAA
651136 TTTTTTTAATT-AAAT
1 TTTTTTTAATTAAAAT
651151 TTTATTTTAATTAAAAGT
1 TTT-TTTTAATTAAAA-T
651169 TATTTTTTAATTAAA
1 T-TTTTTTAATTAAA
651184 TATATTTCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 3 0.10
16 8 0.28
17 3 0.10
18 13 0.45
19 2 0.07
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTTTTAATTAAAAT
Found at i:654003 original size:32 final size:32
Alignment explanation
Indices: 653966--654027 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
653956 TTCATTTAAA
* *
653966 TTTTTAA-TATTGTGTTCGTGTTCGTTTATTTT
1 TTTTTAATTATTATGTTCG-ATTCGTTTATTTT
*
653998 TTTTTAATTCTTATGTTCGATTCGTTTATT
1 TTTTTAATTATTATGTTCGATTCGTTTATT
654028 GTTTGTGAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 17 0.65
33 9 0.35
ACGTcount: A:0.15, C:0.08, G:0.13, T:0.65
Consensus pattern (32 bp):
TTTTTAATTATTATGTTCGATTCGTTTATTTT
Found at i:656329 original size:6 final size:6
Alignment explanation
Indices: 655432--656326 Score: 1694
Period size: 6 Copynumber: 149.8 Consensus size: 6
655422 TAATATTTTT
* * *
655432 CATATT CATATT CATATT CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655480 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655528 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655576 C--ATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655622 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655670 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655718 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655766 CATATC CATATC CATATC CATCCATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CAT--ATC CATATC CATATC CATATC CATATC
655816 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655864 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655912 CATATC CATATC C--ATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
655958 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
656006 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
656054 CATATC CATATC CATATC CATATC CATATC CATATC C--ATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
656100 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
656148 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
656196 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
656244 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
1 CATATC CATATC CATATC CATATC CATATC CATATC CATATC CATATC
*
656292 CATATC CATATC CATATC CATATC CATATT CATAT
1 CATATC CATATC CATATC CATATC CATATC CATAT
656327 TCACAAAGAT
Statistics
Matches: 879, Mismatches: 2, Indels: 16
0.98 0.00 0.02
Matches are distributed among these distances:
4 12 0.01
6 861 0.98
8 6 0.01
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.34
Consensus pattern (6 bp):
CATATC
Found at i:656756 original size:42 final size:42
Alignment explanation
Indices: 656694--656786 Score: 159
Period size: 42 Copynumber: 2.2 Consensus size: 42
656684 ACTTAGTAAG
*
656694 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
656736 TCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
*
656778 TCTTTCGGG
1 TCCTTCGGG
656787 TAATTTGTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.32
Consensus pattern (42 bp):
TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:656781 original size:22 final size:21
Alignment explanation
Indices: 656714--656784 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
656704 CATCAATAAG
656714 TCTTTCGAGCATGATGCTTAAA
1 TCTTTCGAGCATGATG-TTAAA
* * * *
656736 TCCTTCGGGCCATCA-G-TAAG
1 TCTTTCGAG-CATGATGTTAAA
656756 TCTTTCGAGCATGATGATTAAA
1 TCTTTCGAGCATGATG-TTAAA
656778 TCTTTCG
1 TCTTTCG
656785 GGTAATTTGT
Statistics
Matches: 37, Mismatches: 8, Indels: 8
0.70 0.15 0.15
Matches are distributed among these distances:
19 4 0.11
20 11 0.30
22 18 0.49
23 4 0.11
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (21 bp):
TCTTTCGAGCATGATGTTAAA
Found at i:657117 original size:53 final size:52
Alignment explanation
Indices: 656951--657104 Score: 272
Period size: 53 Copynumber: 2.9 Consensus size: 52
656941 GAATCACACT
656951 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGTGAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAG-GAACCCGTAGGC
*
657004 AGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGGAAACCCGTAGGC
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGG-AACCCGTAGGC
657057 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCG
1 AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAG-GAACCCG
657105 CTGGTCGAAG
Statistics
Matches: 97, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
52 1 0.01
53 95 0.98
54 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.19
Consensus pattern (52 bp):
AGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGGAACCCGTAGGC
Found at i:657289 original size:14 final size:15
Alignment explanation
Indices: 657270--657303 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
657260 TTTCTCCGGG
657270 TTATAAATATT-ATA
1 TTATAAATATTAATA
*
657284 TTATAATTATTAATA
1 TTATAAATATTAATA
657299 TTATA
1 TTATA
657304 TTATAACTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAAATATTAATA
Found at i:657352 original size:3 final size:3
Alignment explanation
Indices: 657277--657335 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
657267 GGGTTATAAA
* * * *
657277 TAT TA- TAT TAT AAT TAT TAA TAT TA- TAT TAT AAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
657323 TAT TAT TAT TAT T
1 TAT TAT TAT TAT T
657336 CTAACAAATA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:667408 original size:41 final size:42
Alignment explanation
Indices: 667326--667417 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
667316 AGGCCATCAG
* * * *
667326 TAAGTCTTTCGAGCATGATGATGAAATCCTTCGGATCATCTA
1 TAAGCCTTTAGAGCAAGATGATGAAATCATTCGGATCATCTA
*
667368 TAAGCCTTTAGAGCAAGATGAT-AAGTCATTCGG-TCCATCTA
1 TAAGCCTTTAGAGCAAGATGATGAAATCATTCGGAT-CATCTA
667409 TAAGACCTT
1 TAAG-CCTT
667418 CGGGTAGGAT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
40 1 0.02
41 19 0.44
42 23 0.53
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (42 bp):
TAAGCCTTTAGAGCAAGATGATGAAATCATTCGGATCATCTA
Found at i:667585 original size:42 final size:42
Alignment explanation
Indices: 667526--667610 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
667516 ACTTAGTAAG
* *
667526 TCCTTCGGGCCATCAATAAGTCTTTTGAGCATGATGTTTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
667568 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
667610 T
1 T
667611 TTTTCGAGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (42 bp):
TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGATTAAA
Found at i:667846 original size:53 final size:53
Alignment explanation
Indices: 667782--667935 Score: 272
Period size: 53 Copynumber: 2.9 Consensus size: 53
667772 AGAATCACAC
667782 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
1 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
667835 TAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGAAGCGAACTCGTAGG
1 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
*
667888 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
1 CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
667936 TCTGGTTGAA
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 94 1.00
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (53 bp):
CAGAAGATTATTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:668130 original size:20 final size:20
Alignment explanation
Indices: 668102--668152 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
668092 TTTGTCTGGG
*
668102 TTATAAATATTATATTATAA
1 TTATTAATATTATATTATAA
668122 TTATTAATATTATATTATAA
1 TTATTAATATTATATTATAA
* *
668142 CTATTATTATT
1 TTATTAATATT
668153 CTAACAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATTAATATTATATTATAA
Found at i:668138 original size:14 final size:15
Alignment explanation
Indices: 668102--668148 Score: 55
Period size: 14 Copynumber: 3.3 Consensus size: 15
668092 TTTGTCTGGG
*
668102 TTATAAATATT-ATA
1 TTATAATTATTAATA
668116 TTATAATTATTAATA
1 TTATAATTATTAATA
668131 TTAT-ATTA-TAACTA
1 TTATAATTATTAA-TA
668145 TTAT
1 TTAT
668149 TATTCTAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 3 0.10
14 20 0.67
15 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATAATTATTAATA
Found at i:677381 original size:13 final size:13
Alignment explanation
Indices: 677347--677373 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
677337 GGTACATCAC
677347 ATACAATTTCAAA
1 ATACAATTTCAAA
677360 ATACAATTTCAAA
1 ATACAATTTCAAA
677373 A
1 A
677374 AGCCATTTAC
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:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (13 bp):
ATACAATTTCAAA
Found at i:691352 original size:12 final size:12
Alignment explanation
Indices: 691335--691370 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
691325 TTACAAATAT
691335 GATAAATTAAAA
1 GATAAATTAAAA
691347 GATAAATTAAAA
1 GATAAATTAAAA
* *
691359 CACAAATTAAAA
1 GATAAATTAAAA
691371 TTAGACATGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (12 bp):
GATAAATTAAAA
Found at i:691497 original size:30 final size:30
Alignment explanation
Indices: 691390--691497 Score: 91
Period size: 29 Copynumber: 3.7 Consensus size: 30
691380 CTTAGTAAAA
* *
691390 TAAAGGACTAAATAGC--AAAAATAGAAATT
1 TAAAGGACTAAA-AACATAAAAACAGAAATT
* *
691419 TACAGGACT-AAAACA-ACAAAACAAAAATT
1 TAAAGGACTAAAAACATA-AAAACAGAAATT
* * *
691448 TCAAGGATTAAAAAAATAAAAACAGAAA-T
1 TAAAGGACTAAAAACATAAAAACAGAAATT
691477 TAAAGGGACTAAAAACATAAA
1 TAAA-GGACTAAAAACATAAA
691498 TATCACAAAC
Statistics
Matches: 62, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
27 2 0.03
28 3 0.05
29 28 0.45
30 28 0.45
31 1 0.02
ACGTcount: A:0.62, C:0.10, G:0.11, T:0.17
Consensus pattern (30 bp):
TAAAGGACTAAAAACATAAAAACAGAAATT
Found at i:693084 original size:3 final size:3
Alignment explanation
Indices: 693051--693142 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
693041 TAAAATTTAT
* * * *
693051 TAA TAA AAA TAA TAA CAA TAG TAA TAG TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
693099 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
693143 TTTTTATAGA
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:693455 original size:43 final size:43
Alignment explanation
Indices: 693406--693874 Score: 215
Period size: 43 Copynumber: 10.6 Consensus size: 43
693396 ATAACGCGGT
* *
693406 TCCTACGTGATGAGGACAGCTGGTTATCTAGGGGTGACACGGC
1 TCCTACGTGATGAGGAGATCTGGTTATCTAGGGGTGACACGGC
* ***
693449 TCCTACGTGATGAGGAGATCTGG---TC-GGGGGATGACAATAC
1 TCCTACGTGATGAGGAGATCTGGTTATCTAGGGG-TGACACGGC
* * * * ** *
693489 TCATATGTGATGAAGAGTTCTGGCCATCTTTAGGAATGGTGATAACACGGT
1 TCCTACGTGATGAGGAGATCTGGTTATC--TAGG---GGTG---ACACGGC
* * *
693540 TCCTACGTGATGAGGACAGCTGGTTATCTAGGGGTGACACGAC
1 TCCTACGTGATGAGGAGATCTGGTTATCTAGGGGTGACACGGC
* * * ** * *
693583 TCCTACTTGATGAGGAGATCTAG---TCGAGGAATAACATGGC
1 TCCTACGTGATGAGGAGATCTGGTTATCTAGGGGTGACACGGC
* * * * ** *
693623 TCATACGTGATAAAGAGTTCTGGCCATCTTTAGGAATGGTGATAACACGGT
1 TCCTACGTGATGAGGAGATCTGGTTATC--TAGG---GGTG---ACACGGC
** * * **
693674 TTATACGTGATGAGGACAGCTGGTTATCTAGGGGTGACACAAC
1 TCCTACGTGATGAGGAGATCTGGTTATCTAGGGGTGACACGGC
**
693717 TCCTACGTGATGAGGAGATCTGG---TC-AGAGAATGACACGGC
1 TCCTACGTGATGAGGAGATCTGGTTATCTAG-GGGTGACACGGC
* * * * * *
693757 TCATACGTGATGAAGAGTTCTGGTCATCTTTAGGAATTGTGATAACACGGT
1 TCCTACGTGATGAGGAGATCTGGTTATC--TAGG----G-G-TGACACGGC
693808 TCCTACGTGATGAGGACGA-CTGGTTATCTAGGGGTGACACGGC
1 TCCTACGTGATGAGGA-GATCTGGTTATCTAGGGGTGACACGGC
693851 TCCTACGTGATGAGGAGATCTGGT
1 TCCTACGTGATGAGGAGATCTGGT
693875 CGGGAAATGA
Statistics
Matches: 308, Mismatches: 79, Indels: 78
0.66 0.17 0.17
Matches are distributed among these distances:
39 6 0.02
40 85 0.28
42 2 0.01
43 102 0.33
44 1 0.00
45 5 0.02
46 12 0.04
48 3 0.01
49 14 0.05
51 77 0.25
52 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (43 bp):
TCCTACGTGATGAGGAGATCTGGTTATCTAGGGGTGACACGGC
Found at i:693586 original size:134 final size:134
Alignment explanation
Indices: 693368--693924 Score: 837
Period size: 134 Copynumber: 4.2 Consensus size: 134
693358 TACATAATGT
* * * *
693368 AGAGTTTTGGCCATCTTTAGAAAGGGTGATAACGCGGTTCCTACGTGATGAGGACAGCTGGTTAT
1 AGAGTTCTGGCCATCTTTAGGAATGGTGATAACACGGTTCCTACGTGATGAGGACAGCTGGTTAT
* * * *
693433 CTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACAATACTCATATGTG
66 CTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGAATGACAAGACTCATACGTG
693498 ATGA
131 ATGA
693502 AGAGTTCTGGCCATCTTTAGGAATGGTGATAACACGGTTCCTACGTGATGAGGACAGCTGGTTAT
1 AGAGTTCTGGCCATCTTTAGGAATGGTGATAACACGGTTCCTACGTGATGAGGACAGCTGGTTAT
* * * * * *
693567 CTAGGGGTGACACGACTCCTACTTGATGAGGAGATCTAGTCGAGGAATAACATGGCTCATACGTG
66 CTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGAATGACAAGACTCATACGTG
*
693632 ATAA
131 ATGA
**
693636 AGAGTTCTGGCCATCTTTAGGAATGGTGATAACACGGTTTATACGTGATGAGGACAGCTGGTTAT
1 AGAGTTCTGGCCATCTTTAGGAATGGTGATAACACGGTTCCTACGTGATGAGGACAGCTGGTTAT
* * * * *
693701 CTAGGGGTGACACAACTCCTACGTGATGAGGAGATCTGGTCAGAGAATGACACGGCTCATACGTG
66 CTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGAATGACAAGACTCATACGTG
693766 ATGA
131 ATGA
* *
693770 AGAGTTCTGGTCATCTTTAGGAATTGTGATAACACGGTTCCTACGTGATGAGGAC-GACTGGTTA
1 AGAGTTCTGGCCATCTTTAGGAATGGTGATAACACGGTTCCTACGTGATGAGGACAG-CTGGTTA
* * *
693834 TCTAGGGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCGGGAAATGACACGACTCATACGT
65 TCTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGAATGACAAGACTCATACGT
693899 GATGA
130 GATGA
* *
693904 AGAGTTATGTCCATCTTTAGG
1 AGAGTTCTGGCCATCTTTAGG
693925 GATAATGGTT
Statistics
Matches: 383, Mismatches: 39, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
133 1 0.00
134 382 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.26
Consensus pattern (134 bp):
AGAGTTCTGGCCATCTTTAGGAATGGTGATAACACGGTTCCTACGTGATGAGGACAGCTGGTTAT
CTAGGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGAATGACAAGACTCATACGTG
ATGA
Found at i:694556 original size:36 final size:39
Alignment explanation
Indices: 694476--694564 Score: 107
Period size: 38 Copynumber: 2.4 Consensus size: 39
694466 TTGTGGAAAA
*
694476 TGTCTC-AAGCGAGACATAATTTGTTTTTAAGAGAAAGTT
1 TGTCTCTAA-CGAGACAAAATTTGTTTTTAAGAGAAAGTT
*
694515 T-TCTCTAACGAGATAAAATTTGTTTTT-A-AGAAA-TT
1 TGTCTCTAACGAGACAAAATTTGTTTTTAAGAGAAAGTT
*
694550 TGTCTCTAGCGAGAC
1 TGTCTCTAACGAGAC
694565 GACACTTTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
35 3 0.07
36 16 0.36
37 1 0.02
38 21 0.48
39 3 0.07
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (39 bp):
TGTCTCTAACGAGACAAAATTTGTTTTTAAGAGAAAGTT
Found at i:695894 original size:2 final size:2
Alignment explanation
Indices: 695887--695919 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
695877 AACTTTATTG
695887 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 T
695920 CTGGGTATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:703204 original size:6 final size:5
Alignment explanation
Indices: 703167--703209 Score: 59
Period size: 5 Copynumber: 8.2 Consensus size: 5
703157 TTTTGCAATG
*
703167 ATAAA ATAAA ATAAA ATAAA ACAAA ATAAA AGTAAA AGTAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A-TAAA A-TAAA A
703210 AAGTTGAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
5 24 0.69
6 11 0.31
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:706484 original size:15 final size:16
Alignment explanation
Indices: 706459--706488 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
706449 ATAGGTCACA
706459 TTTATATTTTTAAAAT
1 TTTATATTTTTAAAAT
706475 TTTATA-TTTTAAAA
1 TTTATATTTTTAAAA
706489 AAACTTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATATTTTTAAAAT
Found at i:706489 original size:16 final size:16
Alignment explanation
Indices: 706459--706489 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
706449 ATAGGTCACA
*
706459 TTTATATTTTTAAAAT
1 TTTATATTTTAAAAAT
706475 TTTATATTTTAAAAA
1 TTTATATTTTAAAAA
706490 AACTTATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTATATTTTAAAAAT
Found at i:707283 original size:20 final size:20
Alignment explanation
Indices: 707254--707296 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
707244 CCTAAACTTT
*
707254 AATCTTTAAC-CTAATACTCA
1 AATCTCTAACTCTAAT-CTCA
707274 AATCTCTAACTCTAATCTCA
1 AATCTCTAACTCTAATCTCA
707294 AAT
1 AAT
707297 TTATCATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (20 bp):
AATCTCTAACTCTAATCTCA
Found at i:708681 original size:3 final size:3
Alignment explanation
Indices: 708673--708713 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
708663 TTTCGTCCCG
*
708673 ATT ATT ATT ATT ATT ATT ATT ATT ATA ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
708714 AAAGCTGTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:709542 original size:64 final size:64
Alignment explanation
Indices: 709471--709614 Score: 166
Period size: 64 Copynumber: 2.2 Consensus size: 64
709461 ATGCACCGGA
* * *
709471 AGTGCATCGATGCAC-CCATTAAAAATGGAAACGTCGAATGCAATTAGTGCATCAATGCATAAGG
1 AGTGCATCGATGCACTCCATT-AAAATGAAAACATCGAAGGCAATTAGTGCATCAATGCAT-AGG
709535 -
64 T
* ** * * * *
709535 AGTGCATCGATGCACTCCCTTAAAATGAAAACATCGAAGGTGATTTGTGTATCGATGCATGGGT
1 AGTGCATCGATGCACTCCATTAAAATGAAAACATCGAAGGCAATTAGTGCATCAATGCATAGGT
709599 AGTGCATCGATGCACT
1 AGTGCATCGATGCACT
709615 TCAAGGGAAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
63 2 0.03
64 62 0.91
65 4 0.06
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.25
Consensus pattern (64 bp):
AGTGCATCGATGCACTCCATTAAAATGAAAACATCGAAGGCAATTAGTGCATCAATGCATAGGT
Found at i:710047 original size:20 final size:20
Alignment explanation
Indices: 710018--710055 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
710008 AGTATGCTCG
710018 GAGGGAACCGATTCCCCCCA
1 GAGGGAACCGATTCCCCCCA
*
710038 GAGGGTACCGATTCCCCC
1 GAGGGAACCGATTCCCCC
710056 TTGTATAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.39, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCCA
Found at i:715859 original size:23 final size:20
Alignment explanation
Indices: 715804--715864 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 20
715794 TTTTGGTGCA
*
715804 GAGGGAATCGATTCCCCCTT
1 GAGGGAACCGATTCCCCCTT
*
715824 GAGGGAACTGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
715845 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
715865 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 3 0.09
22 1 0.03
23 15 0.43
ACGTcount: A:0.21, C:0.31, G:0.26, T:0.21
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:715891 original size:20 final size:21
Alignment explanation
Indices: 715847--715886 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
715837 CCCCCTTTGA
*
715847 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
715868 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
715887 TAGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:720277 original size:2 final size:2
Alignment explanation
Indices: 720265--720320 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
720255 GATTATATGA
*
720265 AT AT GT 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
720307 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
720321 GATAATACAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:720745 original size:23 final size:23
Alignment explanation
Indices: 720719--720774 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
720709 TATGGAACTT
*
720719 CGGTGCATTTCTATGCGGCACTA
1 CGGTGCATTTCTATGAGGCACTA
* *
720742 CGGTGCAATTCTATGAGGCACTT
1 CGGTGCATTTCTATGAGGCACTA
720765 CGGTGCATTT
1 CGGTGCATTT
720775 ATACGAGCTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.23, G:0.27, T:0.32
Consensus pattern (23 bp):
CGGTGCATTTCTATGAGGCACTA
Found at i:724329 original size:64 final size:64
Alignment explanation
Indices: 724171--724332 Score: 184
Period size: 64 Copynumber: 2.5 Consensus size: 64
724161 AATTATTCAG
* * * *
724171 TGTGTATCGATGCACAGGAAGTGCATCGATACA-CCCATTAAAAATGGAAACAACGAATGCAATT
1 TGTGTATCGATGCATAGG-AGTGCATCGATGCACCCCATTAAAAATGAAAACAACGAAGGCAATT
* * * * **
724235 AGTGCATCGATGCATAAGGAGTGCATCGATGCACCCCCTT-AAAATGAAAACATCGAAGGTGATT
1 TGTGTATCGATGCAT-AGGAGTGCATCGATGCACCCCATTAAAAATGAAAACAACGAAGGCAATT
*
724299 TGTGTATCGATGCATGGGTAGTGCATCGATGCAC
1 TGTGTATCGATGCATAGG-AGTGCATCGATGCAC
724333 TTCAAGGGAA
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
63 2 0.02
64 72 0.88
65 8 0.10
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.23
Consensus pattern (64 bp):
TGTGTATCGATGCATAGGAGTGCATCGATGCACCCCATTAAAAATGAAAACAACGAAGGCAATT
Found at i:725456 original size:2 final size:2
Alignment explanation
Indices: 725449--725473 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
725439 AGGAAAAATG
725449 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
725474 GAGGAAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:725545 original size:2 final size:2
Alignment explanation
Indices: 725538--725563 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
725528 GAACATGTGA
725538 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
725564 GATAAGACAT
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:725989 original size:23 final size:23
Alignment explanation
Indices: 725963--726016 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
725953 ATGGCACTTT
*
725963 GGTGCATTTCTACGCGGCACTAC
1 GGTGCATTTCTACGAGGCACTAC
* *
725986 GGTGCAATTCTACGAGGCACTTC
1 GGTGCATTTCTACGAGGCACTAC
726009 GGTGCATT
1 GGTGCATT
726017 CACTACAAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.28
Consensus pattern (23 bp):
GGTGCATTTCTACGAGGCACTAC
Found at i:730713 original size:22 final size:23
Alignment explanation
Indices: 730666--730727 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
730656 GATTCCCCTG
*
730666 AGGGGGAATGGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
730689 AGGGGGAATCGGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
730711 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
730728 TCTGCCCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 16 0.44
23 20 0.56
ACGTcount: A:0.19, C:0.24, G:0.34, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:731586 original size:21 final size:21
Alignment explanation
Indices: 731562--731625 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
731552 GCTAGAGTCT
731562 CTAGGATACCAAAGTCCTAAA
1 CTAGGATACCAAAGTCCTAAA
* *
731583 CTA-GA-AGCTAGAGT-CT---
1 CTAGGATA-CCAAAGTCCTAAA
731599 CTAGGATACCAAAGTCCTAAA
1 CTAGGATACCAAAGTCCTAAA
731620 CTAGGA
1 CTAGGA
731626 GTGTCCTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 14
0.64 0.08 0.28
Matches are distributed among these distances:
16 3 0.09
17 7 0.22
18 3 0.09
19 3 0.09
20 7 0.22
21 9 0.28
ACGTcount: A:0.39, C:0.22, G:0.19, T:0.20
Consensus pattern (21 bp):
CTAGGATACCAAAGTCCTAAA
Found at i:731600 original size:37 final size:37
Alignment explanation
Indices: 731550--731623 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
731540 ATGCAAGCTA
731550 AAGCTAGAGTCTCTAGGATACCAAAGTCCTAAACTAG
1 AAGCTAGAGTCTCTAGGATACCAAAGTCCTAAACTAG
731587 AAGCTAGAGTCTCTAGGATACCAAAGTCCTAAACTAG
1 AAGCTAGAGTCTCTAGGATACCAAAGTCCTAAACTAG
731624 GAGTGTCCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.22
Consensus pattern (37 bp):
AAGCTAGAGTCTCTAGGATACCAAAGTCCTAAACTAG
Done.