Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008982.1 Hibiscus syriacus cultivar Beakdansim tig00112344_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: 2253222
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1206738 original size:35 final size:35
Alignment explanation
Indices: 1206690--1206758 Score: 102
Period size: 35 Copynumber: 2.0 Consensus size: 35
1206680 CTTGAGCTCT
* * *
1206690 GATTGATATCAATTAACGCCCTTAGCAGCTTCTCG
1 GATTGATAACAATTAACACCCTTAGCAACTTCTCG
*
1206725 GATTGATAACAATTAACACCCTTAGGAACTTCTC
1 GATTGATAACAATTAACACCCTTAGCAACTTCTC
1206759 TTAGATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (35 bp):
GATTGATAACAATTAACACCCTTAGCAACTTCTCG
Found at i:1216709 original size:17 final size:17
Alignment explanation
Indices: 1216689--1216741 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
1216679 ATTGTTAATA
1216689 AAAATATAAAAATATTT
1 AAAATATAAAAATATTT
*
1216706 AAAATAT-ATAATAATTT
1 AAAATATAAAAAT-ATTT
1216723 AAAAT-TAAAAA-A-TT
1 AAAATATAAAAATATTT
1216737 AAAAT
1 AAAAT
1216742 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 7 0.22
15 1 0.03
16 5 0.16
17 19 0.59
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATATAAAAATATTT
Found at i:1216727 original size:34 final size:34
Alignment explanation
Indices: 1216689--1216756 Score: 88
Period size: 33 Copynumber: 2.0 Consensus size: 34
1216679 ATTGTTAATA
1216689 AAAATATAAAAATATTTAAAA-TATATA-ATA-ATTT
1 AAAAT-TAAAAA-A-TTAAAATTATATATATATATTT
1216723 AAAATTAAAAAATTAAAATTATATATATATATTT
1 AAAATTAAAAAATTAAAATTATATATATATATTT
1216757 TTAAAAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
31 6 0.19
32 7 0.23
33 9 0.29
34 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATTAAAAAATTAAAATTATATATATATATTT
Found at i:1216751 original size:55 final size:50
Alignment explanation
Indices: 1216692--1216800 Score: 141
Period size: 49 Copynumber: 2.1 Consensus size: 50
1216682 GTTAATAAAA
1216692 ATATA-AAAATATTTAAAATATATAATAATTTAAAATTAAAAAATTAAAATTAT
1 ATATATAAAATATTTAAAA-A-AT--TAATTTAAAATTAAAAAATTAAAATTAT
* * *
1216745 ATATAT-ATATTTTTAAAAAATTTATTTAAAATTAAAAAATTAAAATTAT
1 ATATATAAAATATTTAAAAAATTAATTTAAAATTAAAAAATTAAAATTAT
1216794 ATATATA
1 ATATATA
1216801 TATTTAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
49 33 0.65
51 2 0.04
52 1 0.02
53 15 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (50 bp):
ATATATAAAATATTTAAAAAATTAATTTAAAATTAAAAAATTAAAATTAT
Found at i:1217556 original size:24 final size:24
Alignment explanation
Indices: 1217527--1217586 Score: 120
Period size: 24 Copynumber: 2.5 Consensus size: 24
1217517 AGGAAGGAAG
1217527 AAGAAGAAGAAGCACGTGCAGAGA
1 AAGAAGAAGAAGCACGTGCAGAGA
1217551 AAGAAGAAGAAGCACGTGCAGAGA
1 AAGAAGAAGAAGCACGTGCAGAGA
1217575 AAGAAGAAGAAG
1 AAGAAGAAGAAG
1217587 AAAGAATGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.53, C:0.10, G:0.33, T:0.03
Consensus pattern (24 bp):
AAGAAGAAGAAGCACGTGCAGAGA
Found at i:1217857 original size:21 final size:21
Alignment explanation
Indices: 1217831--1217871 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1217821 GACTATCGTA
1217831 TTGCGATTTTCCAAATTCGCG
1 TTGCGATTTTCCAAATTCGCG
*
1217852 TTGCGATTTTCCGAATTCGC
1 TTGCGATTTTCCAAATTCGC
1217872 AATGCGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (21 bp):
TTGCGATTTTCCAAATTCGCG
Found at i:1217877 original size:21 final size:21
Alignment explanation
Indices: 1217832--1217900 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
1217822 ACTATCGTAT
**
1217832 TGCGATTTTCCAAATTCGCGT
1 TGCGATTTTCCAAATTCGCAA
*
1217853 TGCGATTTTCCGAATTCGCAA
1 TGCGATTTTCCAAATTCGCAA
* * **
1217874 TGCGAATATGTAAA-TCGCAA
1 TGCGATTTTCCAAATTCGCAA
1217894 TGCGATT
1 TGCGATT
1217901 ATGACTATCG
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
20 12 0.31
21 27 0.69
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.33
Consensus pattern (21 bp):
TGCGATTTTCCAAATTCGCAA
Found at i:1217893 original size:20 final size:20
Alignment explanation
Indices: 1217868--1217960 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
1217858 TTTTCCGAAT
*
1217868 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTATG-ACAA
*
1217888 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATGACAA
*
1217908 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTATGACAA
* * **
1217928 TCGCAACGCGATTCTGATTA
1 TCGCAATGCGATTATGACAA
*
1217948 TCGCAACGCGATT
1 TCGCAATGCGATT
1217961 CTAACTGTCG
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
19 1 0.01
20 66 0.99
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.28
Consensus pattern (20 bp):
TCGCAATGCGATTATGACAA
Found at i:1217914 original size:40 final size:40
Alignment explanation
Indices: 1217868--1217994 Score: 121
Period size: 40 Copynumber: 3.2 Consensus size: 40
1217858 TTTTCCGAAT
*
1217868 TCGCAATGCGAATATGTA-AATCGCAATGCGATTATGACTA
1 TCGCAATGCGAATATG-ACAATCGCAACGCGATTATGACTA
* * * *
1217908 TCGCAATGCGATTATGACTATCGCAACGCGATTCTGATTA
1 TCGCAATGCGAATATGACAATCGCAACGCGATTATGACTA
* * * * ** **
1217948 TCGCAACGCGATTCTAACTGTCGCAACGCGATGCTGACTA
1 TCGCAATGCGAATATGACAATCGCAACGCGATTATGACTA
1217988 TCGCAAT
1 TCGCAAT
1217995 ACGATTTTCA
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 73 0.99
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (40 bp):
TCGCAATGCGAATATGACAATCGCAACGCGATTATGACTA
Found at i:1217999 original size:20 final size:20
Alignment explanation
Indices: 1217887--1217993 Score: 142
Period size: 20 Copynumber: 5.3 Consensus size: 20
1217877 GAATATGTAA
* *
1217887 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* *
1217907 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
1217927 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
*
1217947 ATCGCAACGCGATTCTAACT
1 ATCGCAACGCGATTCTGACT
* *
1217967 GTCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
1217987 ATCGCAA
1 ATCGCAA
1217994 TACGATTTTC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1218653 original size:20 final size:20
Alignment explanation
Indices: 1218583--1218670 Score: 88
Period size: 20 Copynumber: 4.5 Consensus size: 20
1218573 AGAATCGCAA
*
1218583 TGCGATTTT-AGTTTCGCGT
1 TGCGATTTTCATTTTCGCGT
** **
1218602 TGCGATAGTCAAATTCGCGT
1 TGCGATTTTCATTTTCGCGT
** *
1218622 TGCGATAGTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
*
1218642 TGCGATTTTCATTTTCGTGT
1 TGCGATTTTCATTTTCGCGT
1218662 TGCGATTTT
1 TGCGATTTT
1218671 AAGTTTCAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
19 7 0.12
20 52 0.88
ACGTcount: A:0.15, C:0.16, G:0.24, T:0.45
Consensus pattern (20 bp):
TGCGATTTTCATTTTCGCGT
Found at i:1218677 original size:20 final size:20
Alignment explanation
Indices: 1218634--1218677 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1218624 CGATAGTCAT
* *
1218634 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
1218654 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
1218674 TTTC
1 TTTC
1218678 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:1220690 original size:20 final size:19
Alignment explanation
Indices: 1220638--1220702 Score: 87
Period size: 20 Copynumber: 3.4 Consensus size: 19
1220628 GAAAATCGCA
* *
1220638 TTGCGATAGTCAAATTCGCG
1 TTGCGATAGTC-ATTTCGTG
1220658 TTGCGATAGTCATTTTCGTG
1 TTGCGATAGTCA-TTTCGTG
1220678 TTGCGATAGTCATTT-GTG
1 TTGCGATAGTCATTTCGTG
1220696 TTGCGAT
1 TTGCGAT
1220703 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.24
19 4 0.10
20 28 0.67
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.40
Consensus pattern (19 bp):
TTGCGATAGTCATTTCGTG
Found at i:1221283 original size:21 final size:21
Alignment explanation
Indices: 1221193--1221290 Score: 90
Period size: 21 Copynumber: 4.7 Consensus size: 21
1221183 ACTCACCTGT
*
1221193 CATCGTTCAAGAGG-CCTTCC
1 CATCGTTCAAGAGGCCCCTCC
*
1221213 CTATCGTTCAAGAGGCCCCTAC
1 C-ATCGTTCAAGAGGCCCCTCC
** *
1221235 CATCCCTCAAGAGTCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * **
1221256 CACCGTTCAAGAGGCCACTGT
1 CATCGTTCAAGAGGCCCCTCC
*
1221277 CATCGTTGAAGAGG
1 CATCGTTCAAGAGG
1221291 TCTCTTTCAA
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 1 0.02
21 55 0.90
22 5 0.08
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:1221289 original size:42 final size:42
Alignment explanation
Indices: 1221189--1221289 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
1221179 CCCGACTCAC
* * * *
1221189 CTGTCATCGTTCAAGAGGCCTTCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGAGCCCCTCCCTACCGTTCAAGAGGCCA
** **
1221231 CTACCATCCCTCAAGAGTCCCCTCCC-ACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAG-CCCCTCCCTACCGTTCAAGAGGCCA
*
1221273 CTGTCATCGTTGAAGAG
1 CTGTCATCGTTCAAGAG
1221290 GTCTCTTTCA
Statistics
Matches: 45, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
42 39 0.87
43 6 0.13
ACGTcount: A:0.22, C:0.36, G:0.20, T:0.23
Consensus pattern (42 bp):
CTGTCATCGTTCAAGAGCCCCTCCCTACCGTTCAAGAGGCCA
Found at i:1222710 original size:14 final size:14
Alignment explanation
Indices: 1222691--1222752 Score: 70
Period size: 14 Copynumber: 4.3 Consensus size: 14
1222681 TTGCTTGTTT
1222691 AATTGATTTGTAAA
1 AATTGATTTGTAAA
1222705 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
1222719 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1222734 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1222748 TAATT
1 -AATT
1222753 CTTATTTGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
14 26 0.67
15 13 0.33
ACGTcount: A:0.37, C:0.00, G:0.16, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1222724 original size:28 final size:29
Alignment explanation
Indices: 1222693--1222747 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
1222683 GCTTGTTTAA
*
1222693 TTGATTTG-TAAAAATTGATTTGTAAAAG
1 TTGATTTGTTAAAAATTGATGTGTAAAAG
* *
1222721 TTGATTTGTTTAATATTGATGTGTAAA
1 TTGATTTGTTAAAAATTGATGTGTAAA
1222748 TAATTCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (29 bp):
TTGATTTGTTAAAAATTGATGTGTAAAAG
Found at i:1222892 original size:20 final size:20
Alignment explanation
Indices: 1222867--1222904 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1222857 CGCTAAACTT
*
1222867 AAAATCGCAATGCGAAAGCC
1 AAAATCGCAACGCGAAAGCC
1222887 AAAATCGCAACGCGAAAG
1 AAAATCGCAACGCGAAAG
1222905 TCAATTCGCG
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:0.47, C:0.24, G:0.21, T:0.08
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAGCC
Found at i:1222994 original size:20 final size:20
Alignment explanation
Indices: 1222967--1223103 Score: 229
Period size: 20 Copynumber: 6.8 Consensus size: 20
1222957 GTCGAATACC
* *
1222967 CGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
* *
1222987 CATTGCGATAGTCAAATTCT
1 CGTTGCGATAGTCAAATTCG
1223007 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1223027 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1223047 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1223067 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1223087 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1223104 GAATGTGTAA
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 111 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1223036 original size:60 final size:60
Alignment explanation
Indices: 1222943--1223103 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 60
1222933 CTTTGTGATT
* * * * *
1222943 TTCTCGTTGCAACAGTCGAATACCCGTTGCGATAATCAAATTCACATTGCGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCACATTGCGATAGTCAAA
* * *
1223003 TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAA
1 TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCACATTGCGATAGTCAAA
* *
1223063 TTCGCGTTGCGATAGTCAAATTCGCGTTGCGATATTCAAAT
1 TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAAT
1223104 GAATGTGTAA
Statistics
Matches: 91, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 91 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (60 bp):
TTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAATCAAATTCACATTGCGATAGTCAAA
Found at i:1223289 original size:12 final size:12
Alignment explanation
Indices: 1223271--1223309 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
1223261 GTGAAGCCGG
*
1223271 TTGTGATTGTGA
1 TTGTGATTTTGA
*
1223283 TTTTGATTTTGA
1 TTGTGATTTTGA
*
1223295 TTGCGATTTTGA
1 TTGTGATTTTGA
1223307 TTG
1 TTG
1223310 CCTTTTTCTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.03, G:0.26, T:0.56
Consensus pattern (12 bp):
TTGTGATTTTGA
Found at i:1223295 original size:18 final size:18
Alignment explanation
Indices: 1223274--1223308 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1223264 AAGCCGGTTG
*
1223274 TGATTGTGATTTTGATTT
1 TGATTGCGATTTTGATTT
1223292 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
1223309 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.57
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:1226469 original size:20 final size:20
Alignment explanation
Indices: 1226444--1226551 Score: 180
Period size: 20 Copynumber: 5.4 Consensus size: 20
1226434 GAAATTCAGT
*
1226444 GTTGCGATAGTCAGCATCGC
1 GTTGCGATAGTCAGAATCGC
1226464 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1226484 GTTGCCATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
1226504 GTTGCGATAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1226524 GTTGCGATAGTCATAATCGC
1 GTTGCGATAGTCAGAATCGC
*
1226544 ATTGCGAT
1 GTTGCGAT
1226552 TTAGTTGGTC
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 83 1.00
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1227534 original size:25 final size:25
Alignment explanation
Indices: 1227478--1227537 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
1227468 ATTTTAATTT
*
1227478 ATTTAATTATAATATTTAATTTTAG
1 ATTTAATTATAATATTAAATTTTAG
* *
1227503 ATATAATTATAGTATTAAATTTTA-
1 ATTTAATTATAATATTAAATTTTAG
1227527 ATTTTAATTAT
1 A-TTTAATTAT
1227538 GTCATTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 1 0.03
25 29 0.97
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (25 bp):
ATTTAATTATAATATTAAATTTTAG
Found at i:1227686 original size:5 final size:5
Alignment explanation
Indices: 1227565--1227689 Score: 142
Period size: 5 Copynumber: 25.0 Consensus size: 5
1227555 ATACAAATAG
* * * * * * * * *
1227565 TATAA TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA TGTAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* * *
1227615 TGTAA TGTAA TGTAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
1227665 TATAA TATAA TATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA
1227690 GGGCAGGAAA
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 118 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:1227729 original size:7 final size:7
Alignment explanation
Indices: 1227717--1227746 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
1227707 ATAATTATTT
1227717 TAAAATA
1 TAAAATA
1227724 TAAAATA
1 TAAAATA
1227731 TAAAATA
1 TAAAATA
1227738 TAAAA-A
1 TAAAATA
1227744 TAA
1 TAA
1227747 TTTTATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 19 0.83
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAAATA
Found at i:1229173 original size:69 final size:69
Alignment explanation
Indices: 1229091--1229233 Score: 270
Period size: 69 Copynumber: 2.1 Consensus size: 69
1229081 CTCAGGATAA
1229091 GGTTTTTATGGACAGCTGGTAACCAATTCTTTCATTTTTCCTATCTATTCATTGA-ATCTATTAT
1 GGTTTTTATGGACAGCTGGTAACCAATTCTTTCATTTTTCCTATCTATTCATT-ACATCTATTAT
1229155 TTGCC
65 TTGCC
1229160 GGTTTTTATGGACAGCTGGTAACCAATTCTTTCATTTTTCCTATCTATTCATTACATCTATTATT
1 GGTTTTTATGGACAGCTGGTAACCAATTCTTTCATTTTTCCTATCTATTCATTACATCTATTATT
1229225 TGCC
66 TGCC
1229229 GGTTT
1 GGTTT
1229234 AATATATTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
68 1 0.01
69 72 0.99
ACGTcount: A:0.21, C:0.19, G:0.13, T:0.47
Consensus pattern (69 bp):
GGTTTTTATGGACAGCTGGTAACCAATTCTTTCATTTTTCCTATCTATTCATTACATCTATTATT
TGCC
Found at i:1230498 original size:20 final size:20
Alignment explanation
Indices: 1230473--1230522 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1230463 TCTTGGGGTT
1230473 TTCTTT-TTCGCTGATTGAAG
1 TTCTTTCTT-GCTGATTGAAG
**
1230493 TTCTTTCTTGCTTCTTGAAG
1 TTCTTTCTTGCTGATTGAAG
1230513 TTCTTTCTTG
1 TTCTTTCTTG
1230523 ATGGAGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.10, C:0.18, G:0.16, T:0.56
Consensus pattern (20 bp):
TTCTTTCTTGCTGATTGAAG
Found at i:1238501 original size:14 final size:14
Alignment explanation
Indices: 1238482--1238537 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
1238472 CGTTCGTGAA
1238482 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
1238496 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
1238509 --TT-GTTTATGTT
1 CGTTCGATTATGTT
1238520 CGTTCGATTATGTT
1 CGTTCGATTATGTT
1238534 CGTT
1 CGTT
1238538 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:1238516 original size:24 final size:24
Alignment explanation
Indices: 1238489--1238558 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
1238479 GAACGTTCGA
*
1238489 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
1238513 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
1238537 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
1238559 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:1239297 original size:10 final size:10
Alignment explanation
Indices: 1239282--1239356 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
1239272 GGGTTTCCAA
1239282 CGTTTATGTT
1 CGTTTATGTT
1239292 CGTTTATGTT
1 CGTTTATGTT
1239302 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* ** *
1239313 ATGTTCGTGTC
1 -CGTTTATGTT
1239324 CGTTTATGTT
1 CGTTTATGTT
1239334 CG----TGTT
1 CGTTTATGTT
1239340 CGTTTATGTT
1 CGTTTATGTT
1239350 CGTTTAT
1 CGTTTAT
1239357 TTATTAAATG
Statistics
Matches: 49, Mismatches: 8, Indels: 16
0.67 0.11 0.22
Matches are distributed among these distances:
6 6 0.12
10 33 0.67
11 6 0.12
12 4 0.08
ACGTcount: A:0.09, C:0.13, G:0.21, T:0.56
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:1239313 original size:16 final size:16
Alignment explanation
Indices: 1239288--1239352 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
1239278 CCAACGTTTA
1239288 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1239304 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1239320 TGTCCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1239336 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1239352 T
1 T
1239353 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.14, G:0.23, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1239740 original size:30 final size:30
Alignment explanation
Indices: 1239704--1239774 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
1239694 AAAATTGAAT
*
1239704 TAAACGGGGACGGGGAAAAACCCTTTATGC
1 TAAACGGGGACGGAGAAAAACCCTTTATGC
* *
1239734 TAAACGGGGACGGAGAAAAACCGTTTATGT
1 TAAACGGGGACGGAGAAAAACCCTTTATGC
*
1239764 TAAATGGGGAC
1 TAAACGGGGAC
1239775 TAGTTTAGTA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.18
Consensus pattern (30 bp):
TAAACGGGGACGGAGAAAAACCCTTTATGC
Found at i:1239893 original size:2 final size:2
Alignment explanation
Indices: 1239886--1239936 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
1239876 ATTTAAATTA
* * *
1239886 AT AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1239926 AA AT AT AT AT A
1 AT AT AT AT AT A
1239937 CCCGGCCCGA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.05
2 37 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1239911 original size:46 final size:44
Alignment explanation
Indices: 1239847--1239936 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 44
1239837 AATTATTTTT
1239847 TATATATATATATAATATTAATAAATTTAATTTAAATTAATATATA
1 TATATATATATATAATATTAATAAATTTAATTTAAA-T-ATATATA
* *
1239893 TATATATATATATAATATTTATATATTTAATTTAAATATATATA
1 TATATATATATATAATATTAATAAATTTAATTTAAATATATATA
1239937 CCCGGCCCGA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 7 0.17
45 1 0.02
46 34 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (44 bp):
TATATATATATATAATATTAATAAATTTAATTTAAATATATATA
Found at i:1240618 original size:3 final size:3
Alignment explanation
Indices: 1240610--1240662 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
1240600 TTATTTTAAT
*
1240610 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1240657 TTA TTA
1 TTA TTA
1240663 CAAATTTTGT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1244757 original size:105 final size:103
Alignment explanation
Indices: 1244635--1244957 Score: 388
Period size: 107 Copynumber: 3.1 Consensus size: 103
1244625 TTGTTCTCAT
1244635 TTGAGACATTTTTCCTTTGAGATACAAAATTT-GAATTTGTTTCACATTAAACAAAGTTGATCTC
1 TTGAGACATTTTTCCTTTGAGATAC-AAATTTCGAATTTGTTTCACATTAAACAAAGTTGATCTC
* *
1244699 ATTTGAGATCGTATTTTCTTAAAACAAACTTCGTCTTGC
65 ACTTGAGATCGTATTTTCTTAAAACAAACTTCGTCTCGC
* * * *
1244738 TTGAGACATTTTTTTCCTTTGATATACAAATTTCGAATTTGATTCAC-TTGAAACAAAAATTAAT
1 TTGAGACA--TTTTTCCTTTGAGATACAAATTTCGAATTTGTTTCACATT-AAAC-AAAGTTGAT
* * *
1244802 CTCACTTGAGATTGTTATTCTT-TTCAAAACAAATTTCGTCTCGT
62 CTCACTTGAGATCG-TATT-TTCTT-AAAACAAACTTCGTCTCGC
* *
1244846 TTGAGACATTTTTCCTTTGAGAATACAAATTTCAAATTTGTTTTCATATTAAACAAAGTTGATCT
1 TTGAGACATTTTTCCTTTGAG-ATACAAATTTCGAATTTG-TTTCACATTAAACAAAGTTGATCT
*
1244911 CACTTGAGATCG--TTTTCTCAAAAACAAACGTT-GTCTCGC
64 CACTTGAGATCGTATTTTCT-TAAAACAAAC-TTCGTCTCGC
1244950 TTGAGACA
1 TTGAGACA
1244958 ATTTCTCTAA
Statistics
Matches: 187, Mismatches: 19, Indels: 27
0.80 0.08 0.12
Matches are distributed among these distances:
103 10 0.05
104 33 0.18
105 34 0.18
106 31 0.17
107 43 0.23
108 34 0.18
109 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.40
Consensus pattern (103 bp):
TTGAGACATTTTTCCTTTGAGATACAAATTTCGAATTTGTTTCACATTAAACAAAGTTGATCTCA
CTTGAGATCGTATTTTCTTAAAACAAACTTCGTCTCGC
Found at i:1244937 original size:36 final size:36
Alignment explanation
Indices: 1244896--1245033 Score: 154
Period size: 36 Copynumber: 3.8 Consensus size: 36
1244886 TTTTCATATT
**
1244896 AAACAAA-GTTGATCTCACTTGAGATCGTTTTCTC-AA
1 AAACAAACGTTG-TCTCACTTGAGA-CAATTTCTCTAA
*
1244932 AAACAAACGTTGTCTCGCTTGAGACAATTTCTCTAA
1 AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
*** * **
1244968 AAACAATTTTTGTGTCGTTTGAGACAATTTCTCTAA
1 AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
*
1245004 AAACAAATGTTGTCTCACTTGAGACAATTT
1 AAACAAACGTTGTCTCACTTGAGACAATTT
1245034 TCCAAATTAT
Statistics
Matches: 87, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.08
36 76 0.87
37 4 0.05
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (36 bp):
AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:1245236 original size:99 final size:100
Alignment explanation
Indices: 1245101--1245280 Score: 249
Period size: 99 Copynumber: 1.8 Consensus size: 100
1245091 GAAATAAATG
* *
1245101 ATCTTTGAGTCTATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGACAGATTT-TCTTGAAA-A
1 ATCTTTGAGTATATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGAAAG-TTTCTCTTGAAAGA
* *
1245164 ATCTTTGAGTTTGTTTCACTTAAAACAAAATGAAAA
65 ATCATTGAGTATGTTTCACTTAAAACAAAATGAAAA
* * * *
1245200 ATCTTTGAGTATGTTTC-TTTGATAACAAAATTTTGTCTCTTTTGAGAAAGTTTCTTTTGAAAGA
1 ATCTTTGAGTATATTTCTTTTGA-AACAAAACTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAAGA
1245264 ATCATTGAGTATGTTTC
65 ATCATTGAGTATGTTTC
1245281 TTTGGAAACA
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
98 8 0.11
99 46 0.66
100 16 0.23
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (100 bp):
ATCTTTGAGTATATTTCTTTTGAAACAAAACTTTGTCTCTCTTGAGAAAGTTTCTCTTGAAAGAA
TCATTGAGTATGTTTCACTTAAAACAAAATGAAAA
Found at i:1245365 original size:66 final size:65
Alignment explanation
Indices: 1245195--1245378 Score: 219
Period size: 64 Copynumber: 2.8 Consensus size: 65
1245185 AAAACAAAAT
* * *
1245195 GAAAAATCTTTGAGTATGTTTCTTTGATAACAAAATTTTGTCTCTTTTGAGAAAGTTTCTTTTGA
1 GAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTCCTTTTGA
* * * *
1245260 -AAGAATCATTGAGTATGTTTCTTTGGAAACAAAATTTTGTCACTTTTGAGACAGTTCCTTTTGA
1 GAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTCCTTTTG-
1245324 A
65 A
* * * ** *
1245325 GAAAAATCTTTAAATCTGTTT-TTATGAAAACAAAGGTTTGTCTCTTTTAAGACA
1 GAAAAATCTTTGAGTATGTTTCTT-TGAAAACAAAATTTTGTCTCTTTTGAGACA
1245379 ATTTCTCTTA
Statistics
Matches: 99, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
64 56 0.57
65 3 0.03
66 40 0.40
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (65 bp):
GAAAAATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTGTCTCTTTTGAGACAGTTCCTTTTGA
Found at i:1245467 original size:29 final size:29
Alignment explanation
Indices: 1245397--1245510 Score: 138
Period size: 29 Copynumber: 3.8 Consensus size: 29
1245387 TAAAACAAAC
** *
1245397 ATCTTTGAGATTGTTTCCCTTGAAACAAAA
1 ATCTTTGAG-TTGTTTCTTTTGAAATAAAA
*
1245427 CCTATCTTTGAGTTGTCTCTTTTGAAATAAAA
1 ---ATCTTTGAGTTGTTTCTTTTGAAATAAAA
*
1245459 ATCTGTGAGTTGTTTCTTTTGAAATAAAA
1 ATCTTTGAGTTGTTTCTTTTGAAATAAAA
*
1245488 ATATTTGAGTTGTTTCTTTTGAA
1 ATCTTTGAGTTGTTTCTTTTGAA
1245511 CCAAAGTTTT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
29 48 0.66
32 16 0.22
33 9 0.12
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (29 bp):
ATCTTTGAGTTGTTTCTTTTGAAATAAAA
Found at i:1245626 original size:91 final size:92
Alignment explanation
Indices: 1245455--1245653 Score: 258
Period size: 91 Copynumber: 2.2 Consensus size: 92
1245445 CTTTTGAAAT
* ** * * *
1245455 AAAAATCTGTGAGTTGTTTCTTTTGAAATAAAAATATTTGAGTTGTTTCTTTTGAACCAAAGTTT
1 AAAAATCTTTGAGTCATTTCTTTTAAAACAAAAATATTTGAGTTGTTTCTTTTGAAACAAAGTTT
*
1245520 TGTTTCTCTTAAGACA-ATTTCATGA-
66 TGTCTCTCTTAAGACAGATTTCATGAG
* *
1245545 AAAAATCTTTGAGTCATTTCTTTTAAAACCAAAATTTTTGAGCTTGTTTCTTTTGAAACAAAGTT
1 AAAAATCTTTGAGTCATTTCTTTTAAAACAAAAATATTTGAG-TTGTTTCTTTTGAAACAAAGTT
* * *
1245610 TTGTCTCTCTTGAGACAGTTTTTCTTGAG
65 TTGTCTCTCTTAAGACAG-ATTTCATGAG
1245639 AAAAATCTTTGAGTC
1 AAAAATCTTTGAGTC
1245654 TGTTACTTTT
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
90 35 0.38
91 36 0.39
93 7 0.08
94 15 0.16
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (92 bp):
AAAAATCTTTGAGTCATTTCTTTTAAAACAAAAATATTTGAGTTGTTTCTTTTGAAACAAAGTTT
TGTCTCTCTTAAGACAGATTTCATGAG
Found at i:1245822 original size:29 final size:29
Alignment explanation
Indices: 1245775--1245881 Score: 99
Period size: 29 Copynumber: 3.5 Consensus size: 29
1245765 CCTTTGAGAT
*
1245775 TGTTTCTTTTGAGA-AAAATCCTTGAGTC
1 TGTTTCTTTTGAAACAAAATCCTTGAGTC
*
1245803 TGTTTCTTTGGAAACAAAATTTACAATCTTTGAGTC
1 TGTTTCTTTTGAAACAAAA--T-C---C-TTGAGTC
** *
1245839 TGTTTCTTTTGAAACATCATCTTTGAGTC
1 TGTTTCTTTTGAAACAAAATCCTTGAGTC
1245868 TGTTTCTTTTGAAA
1 TGTTTCTTTTGAAA
1245882 TCATTATCCC
Statistics
Matches: 65, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
28 12 0.18
29 25 0.38
31 1 0.02
32 1 0.02
33 1 0.02
34 1 0.02
35 1 0.02
36 23 0.35
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (29 bp):
TGTTTCTTTTGAAACAAAATCCTTGAGTC
Found at i:1246095 original size:40 final size:40
Alignment explanation
Indices: 1246035--1246182 Score: 154
Period size: 40 Copynumber: 3.6 Consensus size: 40
1246025 CTAAAGATGG
*
1246035 CTAGAACTCTTCATCACGTATGAGCCGTGTCATCCCC-CGA
1 CTAGATCTCTTCATCACGTATGAGCCGTGTCA-CCCCTCGA
*
1246075 CTAGATCTCTTCATCGCGTATGAGCCGTGTCACCCCTCGA
1 CTAGATCTCTTCATCACGTATGAGCCGTGTCACCCCTCGA
* * * * * *
1246115 CCAGATTTCCTCATCACGTAGGAACCGTGTCACCCTTAGACGA
1 CTAGATCTCTTCATCACGTATGAGCCGTGTCACCCCT---CGA
* * *
1246158 CCAGAACTCTTAATCACGTATGAGC
1 CTAGATCTCTTCATCACGTATGAGC
1246183 ATTGTCGTCC
Statistics
Matches: 89, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
39 4 0.04
40 63 0.71
43 22 0.25
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (40 bp):
CTAGATCTCTTCATCACGTATGAGCCGTGTCACCCCTCGA
Found at i:1246369 original size:3 final size:3
Alignment explanation
Indices: 1246361--1246401 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1246351 TTATTTTAAT
*
1246361 TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA ATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1246402 CAAATTTTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1246389 original size:20 final size:20
Alignment explanation
Indices: 1246364--1246401 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1246354 TTTTAATTTA
*
1246364 TTATTATTATTATTATTATT
1 TTATTAATATTATTATTATT
1246384 TTATTAATATTATTATTA
1 TTATTAATATTATTATTA
1246402 CAAATTTTGT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTAATATTATTATTATT
Found at i:1250815 original size:172 final size:167
Alignment explanation
Indices: 1250512--1251011 Score: 673
Period size: 172 Copynumber: 3.0 Consensus size: 167
1250502 AAATTTAATC
* *
1250512 TCCCAAGGTACTGAA-ACGTGTCATCACATGATTAGGAGTTATGTTTTATTTTAATTTATTCAAT
1 TCCCAAGATACT-AACATGTGTCATCACATGATTAGGAGTTATGTTTTATTTTAATTTATTCAAT
* * * *
1250576 TTGTTTTATTATTTACCCACTCAGATTGTGACACATGTCATCATCTGATCGGGTAAAAAATAAAT
65 TTGTTTTATTTTTTACCCACTCAGATTGTGACACATGTCATTATCTGAT-TGGTAGAAAATAAAT
* ***
1250641 TAAAGAATAACATGTTAAAGAAGAATACAGTTGGGGAATTCAA
129 TAAAGAATAGCATGTTAAAGAAGAATACA---ACAG-ATTCAA
* * * ** *
1250684 TCCCACA-ATAGTGACATGTGTCATCACATTATTAAAAGTTATGTTTTATGTTAATTTATTCAAT
1 TCCCA-AGATACTAACATGTGTCATCACATGATTAGGAGTTATGTTTTATTTTAATTTATTCAAT
* * *
1250748 TTGTTTTATTTTTTACCCATTCAAATTGTGTCACATGTCATTATCTGATTAGGTAGAAAATAAAT
65 TTGTTTTATTTTTTACCCACTCAGATTGTGACACATGTCATTATCTGATT-GGTAGAAAATAAAT
* *
1250813 TAAAAGAATAGCATGCTAAAGAAGAATACAACAGATTCGA
129 T-AAAGAATAGCATGTTAAAGAAGAATACAACAGATTCAA
*
1250853 TCCCAAGATACTAACATGTGTCATCACATGCTTAGGAGTTATGTTTTATTTTAATTTATTCAATT
1 TCCCAAGATACTAACATGTGTCATCACATGATTAGGAGTTATGTTTTATTTTAATTTATTCAATT
* *
1250918 TG-TTTATTTTTTACCCACTCAGATTGTGACACATGCCATTATCTGATTGGATAGAAAATAATTT
66 TGTTTTATTTTTTACCCACTCAGATTGTGACACATGTCATTATCTGATTGG-TAGAAAATAAATT
1250982 AAAGAATAGCATGTTAAAGAAGAATACAAC
130 AAAGAATAGCATGTTAAAGAAGAATACAAC
1251012 TAAAGAATCC
Statistics
Matches: 288, Mismatches: 34, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
167 31 0.11
168 55 0.19
169 63 0.22
170 1 0.00
171 1 0.00
172 110 0.38
173 27 0.09
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (167 bp):
TCCCAAGATACTAACATGTGTCATCACATGATTAGGAGTTATGTTTTATTTTAATTTATTCAATT
TGTTTTATTTTTTACCCACTCAGATTGTGACACATGTCATTATCTGATTGGTAGAAAATAAATTA
AAGAATAGCATGTTAAAGAAGAATACAACAGATTCAA
Found at i:1252581 original size:23 final size:23
Alignment explanation
Indices: 1252468--1252573 Score: 167
Period size: 23 Copynumber: 4.6 Consensus size: 23
1252458 CATTTTATAT
* *
1252468 GGCACTTCAGTGCATTTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
1252491 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
* *
1252514 GGCACTTTGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
1252537 GACACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
1252560 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
1252574 TTTATACGAG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 75 1.00
ACGTcount: A:0.18, C:0.28, G:0.25, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:1253929 original size:43 final size:42
Alignment explanation
Indices: 1253849--1254071 Score: 275
Period size: 43 Copynumber: 5.2 Consensus size: 42
1253839 ATGGTAATTA
* *
1253849 GCGGCGTTTGTTCCAAAAACGCCGCTACAGATATGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* ** *
1253891 ACGGCGTTTGTATAAAAAAACGCCGCTATAAATCTGACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCTGACCTTTT
**
1253934 GCGGCGTTTGTTCCAAAAACGTTGCTATAGATCTGACCTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
* *
1253976 GCGGCGTTTGTATTCAAAAACGCCGCTATAGATCTCAACCTTTT
1 GCGGCGTTTGT-TCCAAAAACGCCGCTATAGATCT-GACCTTTT
* * * * *
1254020 GCGGCGTTTGTTTCAAAAACGCTGTTATATATCTTGACTTTTT
1 GCGGCGTTTGTTCCAAAAACGCCGCTATAGATC-TGACCTTTT
1254063 GCGGCGTTT
1 GCGGCGTTT
1254072 TTATTTCAGA
Statistics
Matches: 156, Mismatches: 21, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
42 47 0.30
43 90 0.58
44 19 0.12
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (42 bp):
GCGGCGTTTGTTCCAAAAACGCCGCTATAGATCTGACCTTTT
Found at i:1253995 original size:85 final size:86
Alignment explanation
Indices: 1253849--1254091 Score: 326
Period size: 85 Copynumber: 2.8 Consensus size: 86
1253839 ATGGTAATTA
* * * * **
1253849 GCGGCGTTTGTTCCAAAAACGCCGCTACAGATATGACCTTTTACGGCGTTTGTATAAAAAAACGC
1 GCGGCGTTTGTTCCAAAAACGCTGCTATAGATCTGACCTTTTGCGGCGTTTGTATTCAAAAACGC
*
1253914 CGCTATAAATCT-GACCTTTT
66 CGCTATAAATCTCAACCTTTT
*
1253934 GCGGCGTTTGTTCCAAAAACGTTGCTATAGATCTGACCTTTTGCGGCGTTTGTATTCAAAAACGC
1 GCGGCGTTTGTTCCAAAAACGCTGCTATAGATCTGACCTTTTGCGGCGTTTGTATTCAAAAACGC
*
1253999 CGCTATAGATCTCAACCTTTT
66 CGCTATAAATCTCAACCTTTT
* * * * * *
1254020 GCGGCGTTTGTTTCAAAAACGCTGTTATATATCTTGACTTTTTGCGGCGTTTTTATTTCAGAAAC
1 GCGGCGTTTGTTCCAAAAACGCTGCTATAGATC-TGACCTTTTGCGGCGTTTGTA-TTCAAAAAC
1254085 GCCGCTA
64 GCCGCTA
1254092 ACATTAGCGG
Statistics
Matches: 139, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
85 69 0.50
86 36 0.26
87 19 0.14
88 15 0.11
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (86 bp):
GCGGCGTTTGTTCCAAAAACGCTGCTATAGATCTGACCTTTTGCGGCGTTTGTATTCAAAAACGC
CGCTATAAATCTCAACCTTTT
Found at i:1258982 original size:18 final size:18
Alignment explanation
Indices: 1258955--1258991 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1258945 GAATCATTTA
* *
1258955 ACATATATATGTATATAT
1 ACATACATATATATATAT
1258973 ACATACATATATATATAT
1 ACATACATATATATATAT
1258991 A
1 A
1258992 TATGTGTGTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (18 bp):
ACATACATATATATATAT
Found at i:1259391 original size:9 final size:9
Alignment explanation
Indices: 1259364--1259404 Score: 50
Period size: 9 Copynumber: 4.8 Consensus size: 9
1259354 ATCCTCTTCA
1259364 TTTTT-CTC
1 TTTTTCCTC
*
1259372 TCTTT-CTC
1 TTTTTCCTC
1259380 TTTTTCCTC
1 TTTTTCCTC
*
1259389 TTTTTCCCC
1 TTTTTCCTC
1259398 TTTTTCC
1 TTTTTCC
1259405 CCTCCAAGCT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
8 11 0.38
9 18 0.62
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (9 bp):
TTTTTCCTC
Found at i:1265228 original size:21 final size:19
Alignment explanation
Indices: 1265202--1265259 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 19
1265192 ATTTATTTTA
1265202 ATTTTAAGTTAAATAATAAGT
1 ATTTTAA-TTAAATAA-AAGT
*
1265223 ATTTTAATTTTAATAAAAGT
1 ATTTTAA-TTAAATAAAAGT
* *
1265243 ATATTAATAAAATAAAA
1 ATTTTAATTAAATAAAA
1265260 TTTAAAGATC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
19 8 0.25
20 10 0.31
21 14 0.44
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
ATTTTAATTAAATAAAAGT
Found at i:1265244 original size:20 final size:21
Alignment explanation
Indices: 1265202--1265250 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
1265192 ATTTATTTTA
*
1265202 ATTTTAAGTTAAATAATAAGT
1 ATTTTAATTTAAATAATAAGT
*
1265223 ATTTTAATTTTAATAA-AAGT
1 ATTTTAATTTAAATAATAAGT
*
1265243 ATATTAAT
1 ATTTTAAT
1265251 AAAATAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (21 bp):
ATTTTAATTTAAATAATAAGT
Found at i:1269808 original size:31 final size:31
Alignment explanation
Indices: 1269770--1269831 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
1269760 ACGACTAGAT
*
1269770 TAAAAAATAAATTATGATTTTTCTAATACTA
1 TAAAAAATAAAATATGATTTTTCTAATACTA
1269801 TAAAAAATAAAATATGATTTTTCTAATACTA
1 TAAAAAATAAAATATGATTTTTCTAATACTA
1269832 CTTTTATGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.50, C:0.06, G:0.03, T:0.40
Consensus pattern (31 bp):
TAAAAAATAAAATATGATTTTTCTAATACTA
Found at i:1270304 original size:17 final size:18
Alignment explanation
Indices: 1270265--1270309 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
1270255 TATATAGCTT
*
1270265 TTTAAATTAAATAAATAAT
1 TTTAAATT-AATAAATAAC
*
1270284 TTTAAATTAA-AAATTAC
1 TTTAAATTAATAAATAAC
1270301 TTTAAATTA
1 TTTAAATTA
1270310 GGGTTTGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 14 0.58
18 2 0.08
19 8 0.33
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAATTAATAAATAAC
Found at i:1270424 original size:30 final size:29
Alignment explanation
Indices: 1270351--1270455 Score: 106
Period size: 30 Copynumber: 3.6 Consensus size: 29
1270341 TGGAAAATAA
* * * *
1270351 TTTACATAAAATGGATTTCCATAAATCTGT
1 TTTACGTAAAAT-GAATTGCATAAAACTGT
1270381 TTTACGTAAAATGAATTGCATGAAAACTGT
1 TTTACGTAAAATGAATTGCAT-AAAACTGT
* *
1270411 TTTACGTAAAATGAA-TGACCTAAAA-AGT
1 TTTACGTAAAATGAATTG-CATAAAACTGT
*
1270439 TTTACGTAAAATAAATT
1 TTTACGTAAAATGAATT
1270456 ACATTTTCTA
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
28 16 0.25
29 14 0.22
30 35 0.54
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.35
Consensus pattern (29 bp):
TTTACGTAAAATGAATTGCATAAAACTGT
Found at i:1271658 original size:20 final size:20
Alignment explanation
Indices: 1271635--1271706 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
1271625 ATTGAGCATG
1271635 GTATCGATACTGTGAGGGTA
1 GTATCGATACTGTGAGGGTA
*
1271655 GTATCGATACCTGTTGAGGAG-G
1 GTATCGATA-CTG-TGAGG-GTA
* *
1271677 GTATCGATACTATAAGGGTA
1 GTATCGATACTGTGAGGGTA
* *
1271697 ATATTGATAC
1 GTATCGATAC
1271707 AATGGGGGAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
19 1 0.02
20 21 0.50
21 5 0.12
22 14 0.33
23 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.31
Consensus pattern (20 bp):
GTATCGATACTGTGAGGGTA
Found at i:1271661 original size:42 final size:42
Alignment explanation
Indices: 1271605--1271706 Score: 123
Period size: 42 Copynumber: 2.4 Consensus size: 42
1271595 GTGTATTTCT
* * *
1271605 TAAGAGTAATATCGATACCCATTGAGCATGGTATCGATACTG
1 TAAGGGTAATATCGATACCCATTGAGCAGGGTATCGATACTA
* * ** *
1271647 TGAGGGTAGTATCGATACCTGTTGAGGAGGGTATCGATACTA
1 TAAGGGTAATATCGATACCCATTGAGCAGGGTATCGATACTA
*
1271689 TAAGGGTAATATTGATAC
1 TAAGGGTAATATCGATAC
1271707 AATGGGGGAT
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.31, C:0.13, G:0.26, T:0.29
Consensus pattern (42 bp):
TAAGGGTAATATCGATACCCATTGAGCAGGGTATCGATACTA
Found at i:1271680 original size:22 final size:22
Alignment explanation
Indices: 1271614--1271686 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 22
1271604 TTAAGAGTAA
** * *
1271614 TATCGATACCCATTGAGCATGG
1 TATCGATACCTGTTGAGGAGGG
*
1271636 TATCGATA-CTG-TGAGG-GTAG
1 TATCGATACCTGTTGAGGAG-GG
1271656 TATCGATACCTGTTGAGGAGGG
1 TATCGATACCTGTTGAGGAGGG
1271678 TATCGATAC
1 TATCGATAC
1271687 TATAAGGGTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
20 13 0.32
21 4 0.10
22 23 0.56
23 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (22 bp):
TATCGATACCTGTTGAGGAGGG
Found at i:1272593 original size:21 final size:22
Alignment explanation
Indices: 1272567--1272630 Score: 62
Period size: 21 Copynumber: 2.9 Consensus size: 22
1272557 TCGAGGGTTT
1272567 TATGTGGTCATTCGGGACAAA-
1 TATGTGGTCATTCGGGACAAAC
*
1272588 TATGTGGT-ACTTTGGTG-CAAACC
1 TATGTGGTCA-TTCGG-GACAAA-C
*
1272611 TATGTGGTCCTTCGGGACAA
1 TATGTGGTCATTCGGGACAA
1272631 TTGTGTGGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
20 1 0.03
21 16 0.47
22 2 0.06
23 15 0.44
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (22 bp):
TATGTGGTCATTCGGGACAAAC
Found at i:1272630 original size:44 final size:44
Alignment explanation
Indices: 1272567--1272652 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
1272557 TCGAGGGTTT
* *
1272567 TATGTGGTCATTCGGGACAAATATGTGGTACTTTGGTGCAAACC
1 TATGTGGTCATTCGGGACAAATATGTGGCACTTCGGTGCAAACC
* * *
1272611 TATGTGGTCCTTCGGGACAATTGTGTGGCACTTCGGTGCAAA
1 TATGTGGTCATTCGGGACAAATATGTGGCACTTCGGTGCAAA
1272653 TTACGAGCTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.31
Consensus pattern (44 bp):
TATGTGGTCATTCGGGACAAATATGTGGCACTTCGGTGCAAACC
Found at i:1277615 original size:42 final size:43
Alignment explanation
Indices: 1277568--1277668 Score: 134
Period size: 42 Copynumber: 2.4 Consensus size: 43
1277558 TTTCTTAAGA
* * * *
1277568 GTAGTATCGATACCCT-TTGAGCATGGTATCGATATTGTGAGG
1 GTAGTATCGATACCATGTTGAGCAGGGTATCAATACTGTGAGG
*
1277610 GTAGTATCGATA-CATGTTGAGGAGGGTATCAATACTGTGAGG
1 GTAGTATCGATACCATGTTGAGCAGGGTATCAATACTGTGAGG
*
1277652 GTAGTATCAATACCATG
1 GTAGTATCGATACCATG
1277669 GGGGATGTTA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.04
42 45 0.88
43 4 0.08
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.31
Consensus pattern (43 bp):
GTAGTATCGATACCATGTTGAGCAGGGTATCAATACTGTGAGG
Found at i:1277660 original size:20 final size:20
Alignment explanation
Indices: 1277593--1277664 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1277583 TTTGAGCATG
* *
1277593 GTATCGATATTGTGAGGGTA
1 GTATCAATACTGTGAGGGTA
* *
1277613 GTATCGATACATGTTGAGGAG-G
1 GTATCAATAC-TG-TGAGG-GTA
1277635 GTATCAATACTGTGAGGGTA
1 GTATCAATACTGTGAGGGTA
1277655 GTATCAATAC
1 GTATCAATAC
1277665 CATGGGGGAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 24 0.55
21 4 0.09
22 14 0.32
23 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.31, T:0.31
Consensus pattern (20 bp):
GTATCAATACTGTGAGGGTA
Found at i:1283186 original size:18 final size:19
Alignment explanation
Indices: 1283163--1283205 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
1283153 CATTAATCAT
*
1283163 ATTCCC-TGGTAATCTTAC
1 ATTCCCATGGTAATCTTAA
1283181 ATTCCCATTGGTAATCTTAA
1 ATTCCCA-TGGTAATCTTAA
1283201 ATTCC
1 ATTCC
1283206 GTGAACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.27
20 16 0.73
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.40
Consensus pattern (19 bp):
ATTCCCATGGTAATCTTAA
Found at i:1285785 original size:5 final size:5
Alignment explanation
Indices: 1285775--1285816 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
1285765 TCTTACACTA
*
1285775 ATATT ATATT ATATT ATATC AT-TT CATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT -ATATT ATATT ATATT AT
1285817 TATAAAGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 1 0.03
5 30 0.91
6 2 0.06
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (5 bp):
ATATT
Found at i:1288092 original size:28 final size:27
Alignment explanation
Indices: 1288033--1288095 Score: 119
Period size: 26 Copynumber: 2.4 Consensus size: 27
1288023 ATACATAACA
1288033 TAAAAAATTCAGTGATATATGATATCT
1 TAAAAAATTCAGTGATATATGATATCT
1288060 T-AAAAATTCAGTGATATATGATATCT
1 TAAAAAATTCAGTGATATATGATATCT
1288086 TAAAAAATTC
1 TAAAAAATTC
1288096 GGCAAAAGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 26 0.74
27 9 0.26
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.37
Consensus pattern (27 bp):
TAAAAAATTCAGTGATATATGATATCT
Found at i:1288844 original size:16 final size:16
Alignment explanation
Indices: 1288807--1288850 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
1288797 TATAACTGCA
1288807 AAAAAATAAAAT-ATT
1 AAAAAATAAAATAATT
*
1288822 --TAAATAAAATAATT
1 AAAAAATAAAATAATT
1288836 AAAAAATAAAATAAT
1 AAAAAATAAAATAAT
1288851 ACAATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
13 9 0.38
14 3 0.12
16 12 0.50
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAAAATAAAATAATT
Found at i:1289938 original size:13 final size:13
Alignment explanation
Indices: 1289920--1289944 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1289910 GTCACCTCTT
1289920 CTTCTTCTCCTCA
1 CTTCTTCTCCTCA
1289933 CTTCTTCTCCTC
1 CTTCTTCTCCTC
1289945 CGTCCATTCT
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:0.04, C:0.48, G:0.00, T:0.48
Consensus pattern (13 bp):
CTTCTTCTCCTCA
Found at i:1292093 original size:8 final size:8
Alignment explanation
Indices: 1292078--1292115 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
1292068 TTTCTAAAAA
1292078 TTTTATAT
1 TTTTATAT
*
1292086 TATTATAT
1 TTTTATAT
1292094 ATTTTATA-
1 -TTTTATAT
1292102 TTTTATAT
1 TTTTATAT
1292110 TTTTAT
1 TTTTAT
1292116 TAACAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 7 0.27
8 13 0.50
9 6 0.23
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTATAT
Found at i:1292867 original size:101 final size:101
Alignment explanation
Indices: 1292751--1292936 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 101
1292741 CGTGGACTCT
* *
1292751 TTTTTTTTCAAAGAGAAATTA-TTCATATGACTAGGTCTTGCAATTTTTAAATTTGACAAAGTTG
1 TTTTTTTCCAAAGAGAAATTAGTT-ATATGACTAGGTCTTGCAATTTTTAAATTCGACAAAGTTG
1292815 ACTGTTTAAAGTCGATAAGTAATACACATGTGTGGAC
65 ACTGTTTAAAGTCGATAAGTAATACACATGTGTGGAC
* * * *
1292852 TTTTTTTCCAAAGAGAAATTAGTTATGTGATTAGTTCTTGGAATTTTTAAATTCGACAAAGTTGA
1 TTTTTTTCCAAAGAGAAATTAGTTATATGACTAGGTCTTGCAATTTTTAAATTCGACAAAGTTGA
*
1292917 TTGTTTAAAGTCGATAAGTA
66 CTGTTTAAAGTCGATAAGTA
1292937 TTTCTTTAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 75 0.97
102 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.40
Consensus pattern (101 bp):
TTTTTTTCCAAAGAGAAATTAGTTATATGACTAGGTCTTGCAATTTTTAAATTCGACAAAGTTGA
CTGTTTAAAGTCGATAAGTAATACACATGTGTGGAC
Found at i:1299562 original size:20 final size:20
Alignment explanation
Indices: 1299539--1299576 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1299529 ATTGGTTCAC
1299539 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
1299559 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
1299577 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:1300711 original size:70 final size:69
Alignment explanation
Indices: 1300563--1300712 Score: 169
Period size: 70 Copynumber: 2.1 Consensus size: 69
1300553 TTTGATAATT
* * *
1300563 TTAGTAAAACGTTACTTAAAATATTATTTTTTATATCGAAAATGTTAACATTGGGTGTTACCGAA
1 TTAGTAAAACGTTACTTAAAATATTATTTTTTATACCGAAAATATTAACATTGAGTGTTACCGAA
1300628 AATG
66 AATG
** * * *
1300632 TTAAGGTAAAGTGTTACTTAAAA-ATTATTTTTTCTACCGAAAATATTAATATTGAGT-TATATC
1 TT-A-GTAAAACGTTACTTAAAATATTATTTTTTATACCGAAAATATTAACATTGAGTGT-TACC
1300695 GAAAATTAG
63 GAAAA-T-G
1300704 TTAGTAAAA
1 TTAGTAAAA
1300713 TTAACATTTC
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
69 3 0.04
70 43 0.64
71 18 0.27
72 3 0.04
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.39
Consensus pattern (69 bp):
TTAGTAAAACGTTACTTAAAATATTATTTTTTATACCGAAAATATTAACATTGAGTGTTACCGAA
AATG
Found at i:1304716 original size:3 final size:3
Alignment explanation
Indices: 1304708--1304767 Score: 104
Period size: 3 Copynumber: 20.0 Consensus size: 3
1304698 TATTTATTTG
1304708 TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA
1304753 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
1304768 ACAAAAAAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1304778 original size:18 final size:18
Alignment explanation
Indices: 1304708--1304795 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 18
1304698 TATTTATTTG
* *
1304708 TAATAATAATAATAATAA
1 TAATAAAAAAAATAATAA
*
1304726 TAATAATAAATAAT-ATAA
1 TAATAA-AAAAAATAATAA
* *
1304744 TAATAATAATAATAATAA
1 TAATAAAAAAAATAATAA
1304762 TAATAAACAAAAA-AAT-A
1 TAATAAA-AAAAATAATAA
1304779 TCAATAAAATAAAATAA
1 T-AATAAAA-AAAATAA
1304796 ATGGATGAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
17 9 0.15
18 39 0.65
19 12 0.20
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.28
Consensus pattern (18 bp):
TAATAAAAAAAATAATAA
Found at i:1305146 original size:113 final size:113
Alignment explanation
Indices: 1304948--1305888 Score: 1344
Period size: 113 Copynumber: 8.3 Consensus size: 113
1304938 TTCTCTTCCT
* * *
1304948 GATGAGTTCTTCTCATTATGAACTTC-TCTGGAAAA-ACTGACCCATCAAGTGATGGATTTGAAC
1 GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGA-TAATCCATCAAGTGATGGATTTGAGC
* * * *
1305011 AAAAAGCTGAACAAATTGTTCTCATTATGAACTTCTTCTTCCTTCTTTA
65 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
1305060 AATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAGCA
1305125 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
** *
1305173 GATGAGTTCTTCTCATTATGAAC-TCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAGT
1 GATGAGTTCTTCTCATTATGAACTTC-TTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAGC
1305237 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
65 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
**
1305286 GATGAGTTCTTCTCATTATGAAC-TCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAGC
1 GATGAGTTCTTCTCATTATGAACTTC-TTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAGC
*
1305350 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCCTTCTTCA
65 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
**
1305399 GATGAGTTCTTCTCATTATGAAC-TCGAACTGGAAAAGATAATCCATCAAGTGATGGATTTGAGC
1 GATGAGTTCTTCTCATTATGAACTTC-TTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAGC
**
1305463 AAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
65 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
1305512 GATGAGTTCTTCTTATTATGAACTTCTTCTGGAAAAGATGATCCATCAAGTGATGGATTTGAGCA
1 GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAGCA
* * *
1305577 TAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC-A
* * * *** * **
1305626 GTAATGAATCCTTCTCATTATGAAC-TCTACCTGGAAATTTTAATCCATCACA-TGATGAATTCA
1 G--ATGAGTTCTTCTCATTATGAACTTCT-TCTGGAAAAGATAATCCATCA-AGTGATGGATTTG
* *
1305689 AACAAAAGGTTAAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
62 AGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* * * *
1305741 GATGAGTTCTTCTCATTATGAACTT-TCTCTGGAAAAGCTGATCCATCAAGTGAT-GAATTCAGG
1 GATGAGTTCTTCTCATTATGAACTTCT-TCTGGAAAAGATAATCCATCAAGTGATGGATTTGA-G
*
1305804 CAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
64 CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
1305854 GATGAGTTCTTCTCATTATGAACTT-TCTCTGGAAA
1 GATGAGTTCTTCTCATTATGAACTTCT-TCTGGAAA
1305889 TGTTGATCCA
Statistics
Matches: 758, Mismatches: 59, Indels: 23
0.90 0.07 0.03
Matches are distributed among these distances:
112 31 0.04
113 627 0.83
114 5 0.01
115 5 0.01
116 89 0.12
117 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (113 bp):
GATGAGTTCTTCTCATTATGAACTTCTTCTGGAAAAGATAATCCATCAAGTGATGGATTTGAGCA
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
Found at i:1306826 original size:83 final size:83
Alignment explanation
Indices: 1306729--1307285 Score: 988
Period size: 83 Copynumber: 6.7 Consensus size: 83
1306719 CTGTGGTTCA
* * *
1306729 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATTCTATTAGCAAATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
*
1306794 AAATTCAATGACTGGTTT
66 AAATTCAATAACTGGTTT
*
1306812 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1306877 AAATTCAATAACTGGTTT
66 AAATTCAATAACTGGTTT
1306895 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1306960 AAATTCAATAACTGGTTT
66 AAATTCAATAACTGGTTT
*
1306978 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
* *
1307043 AAATTCAATGATTGGTTTT
66 AAATTCAATAACTGG-TTT
1307062 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
1307127 AAATTCAATAACTGGTTT
66 AAATTCAATAACTGGTTT
* * *
1307145 TACCAAACCAGATCAGATAACTCAAAGAACACTTACAGAAGATGCTATGAGCACATTCCTCTTCC
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
*
1307210 AAATTCAATAATTGGTTTT
66 AAATTCAATAACTGG-TTT
1307229 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1 TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
1307286 ACATTTGTTC
Statistics
Matches: 455, Mismatches: 17, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
83 316 0.69
84 139 0.31
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (83 bp):
TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTC
AAATTCAATAACTGGTTT
Found at i:1307127 original size:250 final size:249
Alignment explanation
Indices: 1306640--1307285 Score: 1069
Period size: 250 Copynumber: 2.6 Consensus size: 249
1306630 GGTTTTATAT
* *
1306640 CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATTCCTC-TTCTAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTC-AA
1306704 ATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
65 ATTCAATAACT-G----GT--TT--TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
* * *
1306769 GATTCTATTAGCAAATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACT
121 GATGCTATGAGCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACT
*
1306834 CAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAATTCAATAACTGGTTTTAC
186 CAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
*
1306898 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
1306963 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
66 TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
* *
1307028 GCACATTTATCTTTCAAATTCAATGATTGGTTTTTACCAAACCAGATCAGATAACTCAAAGAACA
131 GCACATTCATCTTTCAAATTCAATGACTGG-TTTTACCAAACCAGATCAGATAACTCAAAGAACA
1307093 CTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
195 CTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
* *
1307148 CAAACCAGATCAGATAACTCAAAGAACACTTACAGAAGATGCTATGAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
*
1307213 TTCAATAATTGGTTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
66 TTCAATAACTGG-TTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1307278 AGCACATT
130 AGCACATT
1307286 ACATTTGTTC
Statistics
Matches: 372, Mismatches: 13, Indels: 13
0.93 0.03 0.03
Matches are distributed among these distances:
249 75 0.20
250 161 0.43
251 62 0.17
253 2 0.01
257 1 0.00
258 68 0.18
259 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (249 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
TTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGA
GCACATTCATCTTTCAAATTCAATGACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATGAGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
Found at i:1307145 original size:167 final size:167
Alignment explanation
Indices: 1306640--1307285 Score: 1080
Period size: 167 Copynumber: 3.8 Consensus size: 167
1306630 GGTTTTATAT
* *
1306640 CAAACCAAATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGTACATTCCTC-TTCTAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTC-AA
1306704 ATTCAATAACTGGTTCTGTGGTTCATACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
65 ATTCAATAACTGG---T-T--TT--TACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
* * * *
1306769 GATTCTATTAGCAAATTCATCTTTCAAATTCAATGACTGGTTTTAC
122 GATGCTATGAGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
1306815 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
1306880 TTCAATAACTGG-TTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
66 TTCAATAACTGGTTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1306944 AGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
131 AGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
**
1306981 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTTATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
* *
1307046 TTCAATGATTGGTTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
66 TTCAATAACTGGTTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1307111 AGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
131 AGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
* *
1307148 CAAACCAGATCAGATAACTCAAAGAACACTTACAGAAGATGCTATGAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
*
1307213 TTCAATAATTGGTTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
66 TTCAATAACTGGTTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1307278 AGCACATT
131 AGCACATT
1307286 ACATTTGTTC
Statistics
Matches: 454, Mismatches: 15, Indels: 12
0.94 0.03 0.02
Matches are distributed among these distances:
166 155 0.34
167 222 0.49
168 2 0.00
170 1 0.00
175 71 0.16
176 3 0.01
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.27
Consensus pattern (167 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCCTCTTTCAAA
TTCAATAACTGGTTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
AGCACATTCATCTTTCAAATTCAATAACTGGTTTTAC
Found at i:1308460 original size:16 final size:17
Alignment explanation
Indices: 1308434--1308497 Score: 73
Period size: 16 Copynumber: 3.9 Consensus size: 17
1308424 GACCCCCCCT
1308434 TTTTCTTCTTTTTTCTC
1 TTTTCTTCTTTTTTCTC
1308451 TTTT-TTCTTTTTTCT-
1 TTTTCTTCTTTTTTCTC
1308466 TTTTCTCTCTTTTTT-T-
1 TTTTCT-TCTTTTTTCTC
* *
1308482 TCTTCTTTTTTTTTCT
1 TTTTCTTCTTTTTTCT
1308498 TCAAGCATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
15 11 0.26
16 19 0.45
17 12 0.29
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTCTTTTTTCTC
Found at i:1308464 original size:26 final size:23
Alignment explanation
Indices: 1308433--1308498 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 23
1308423 TGACCCCCCC
1308433 TTTTTCTTCTTTTTTCTCTTTTTT
1 TTTTTCTT-TTTTTTCTCTTTTTT
*
1308457 CTTTTT-TCTTTTTCTCTCTTTTTT
1 -TTTTTCT-TTTTTTTCTCTTTTTT
*
1308481 TTCTTCTTTTTTTT-TCTT
1 TTTTTCTTTTTTTTCTCTT
1308499 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
22 4 0.11
23 10 0.28
24 16 0.44
25 6 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTTCTTTTTTTTCTCTTTTTT
Found at i:1308471 original size:22 final size:22
Alignment explanation
Indices: 1308433--1308491 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 22
1308423 TGACCCCCCC
*
1308433 TTTTTCTTCTTTTT-TCTCTTTT
1 TTTTTTTTCTTTTTCTCTC-TTT
1308455 TTCTTTTTTCTTTTTCTCTCTTT
1 TT-TTTTTTCTTTTTCTCTCTTT
*
1308478 TTTTTCTTCTTTTT
1 TTTTTTTTCTTTTT
1308492 TTTTCTTCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 13 0.39
23 16 0.48
24 4 0.12
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTTTCTTTTTCTCTCTTT
Found at i:1308498 original size:22 final size:22
Alignment explanation
Indices: 1308433--1308498 Score: 73
Period size: 22 Copynumber: 3.0 Consensus size: 22
1308423 TGACCCCCCC
1308433 TTTTTCTTCTTTTTTCTCTT-TTT
1 TTTTTCTTCTTTTTT-T-TTCTTT
* *
1308456 TCTTTT-TTCTTTTTCTCTCTTT
1 T-TTTTCTTCTTTTTTTTTCTTT
1308478 TTTTTCTTCTTTTTTTTTCTT
1 TTTTTCTTCTTTTTTTTTCTT
1308499 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 5 0.14
22 18 0.50
23 9 0.25
24 4 0.11
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTCTTCTTTTTTTTTCTTT
Found at i:1308499 original size:13 final size:13
Alignment explanation
Indices: 1308451--1308499 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
1308441 CTTTTTTCTC
1308451 TTTTTTCTT-TTT
1 TTTTTTCTTCTTT
1308463 TCTTTTTC-TCTCTT
1 T-TTTTTCTTCT-TT
1308477 TTTTTTCTTCTTT
1 TTTTTTCTTCTTT
1308490 TTTTTTCTTC
1 TTTTTTCTTC
1308500 AAGCATAATA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
12 2 0.06
13 25 0.76
14 6 0.18
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTTTTCTTCTTT
Found at i:1315787 original size:11 final size:11
Alignment explanation
Indices: 1315773--1315797 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1315763 TTATCTTAAT
1315773 AAATAAAATAA
1 AAATAAAATAA
1315784 AAATAAAATAA
1 AAATAAAATAA
1315795 AAA
1 AAA
1315798 AATATTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (11 bp):
AAATAAAATAA
Found at i:1315853 original size:15 final size:16
Alignment explanation
Indices: 1315833--1315865 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1315823 TGAATGATGA
*
1315833 ATGTATGC-AAAATGT
1 ATGTATGCGAAAAGGT
1315848 ATGTATGCGAAAAGGT
1 ATGTATGCGAAAAGGT
1315864 AT
1 AT
1315866 TGATCCTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.30
Consensus pattern (16 bp):
ATGTATGCGAAAAGGT
Found at i:1321272 original size:3 final size:3
Alignment explanation
Indices: 1321264--1321311 Score: 80
Period size: 3 Copynumber: 16.0 Consensus size: 3
1321254 TATTTATTTG
1321264 TAA TAA TAA TAA TAA TAA TAA TAAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA
1321309 TAA
1 TAA
1321312 ACAAAAAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1321322 original size:24 final size:24
Alignment explanation
Indices: 1321271--1321335 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
1321261 TTGTAATAAT
* * *
1321271 AATAATAATAATAATAAATAATAT
1 AATAATAATAATAATAAACAAAAA
1321295 AATAATAATAATAATAAACAAAAA
1 AATAATAATAATAATAAACAAAAA
1321319 AAT-ATCAATAA-AATAAA
1 AATAAT-AATAATAATAAA
1321336 ATAAATGGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 8 0.22
24 29 0.78
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (24 bp):
AATAATAATAATAATAAACAAAAA
Found at i:1321625 original size:16 final size:17
Alignment explanation
Indices: 1321582--1321634 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
1321572 ACTCACATAC
*
1321582 ATAAAATTTTATATTAA
1 ATAAAATTTTAAATTAA
1321599 AGTAAAA--TTAAATT-A
1 A-TAAAATTTTAAATTAA
1321614 ATAAAATTTTAAA--AA
1 ATAAAATTTTAAATTAA
1321629 ATAAAA
1 ATAAAA
1321635 ATAAATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
14 5 0.16
15 9 0.29
16 11 0.35
17 1 0.03
18 5 0.16
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
ATAAAATTTTAAATTAA
Found at i:1321641 original size:29 final size:31
Alignment explanation
Indices: 1321582--1321641 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 31
1321572 ACTCACATAC
* *
1321582 ATAAAATTTTATATTAAAGTAAAATTAAATTA
1 ATAAAATTTTATA-TAAAATAAAAATAAATTA
1321614 ATAAAATTTTA-A-AAAATAAAAATAAATT
1 ATAAAATTTTATATAAAATAAAAATAAATT
1321642 TATCAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 14 0.54
31 1 0.04
32 11 0.42
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (31 bp):
ATAAAATTTTATATAAAATAAAAATAAATTA
Found at i:1322095 original size:35 final size:35
Alignment explanation
Indices: 1322011--1322085 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
1322001 GTCTTTGTAA
*
1322011 TTTTTTAAAAAATATCAATGCGACCATCGTATTAT
1 TTTTTTAAAAAATATCAATGCGACCATCATATTAT
* *
1322046 TTTTTTAAAAAATATCAATGTGATCATCATATTAT
1 TTTTTTAAAAAATATCAATGCGACCATCATATTAT
1322081 TTTTT
1 TTTTT
1322086 CTCTAAATAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (35 bp):
TTTTTTAAAAAATATCAATGCGACCATCATATTAT
Found at i:1322315 original size:21 final size:21
Alignment explanation
Indices: 1322297--1322352 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
1322287 ATCATGGACT
1322297 GTCACGTCAGCATCGTGGATC
1 GTCACGTCAGCATCGTGGATC
**
1322318 GTCACGTCAGCATCGTAAATC
1 GTCACGTCAGCATCGTGGATC
**
1322339 GTCATTTCAGCATC
1 GTCACGTCAGCATC
1322353 ATAAAGGTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (21 bp):
GTCACGTCAGCATCGTGGATC
Found at i:1322815 original size:22 final size:22
Alignment explanation
Indices: 1322787--1322842 Score: 105
Period size: 22 Copynumber: 2.6 Consensus size: 22
1322777 GTGGCAGTTT
1322787 CTAGAAGGTCCAGTCAGCGGTC
1 CTAGAAGGTCCAGTCAGCGGTC
1322809 CTAGAAGGTCCAGTCAGCGGTC
1 CTAGAAGGTCCAGTCAGCGGTC
1322831 CTAGAAGG-CCAG
1 CTAGAAGGTCCAG
1322843 ATAGATCAGC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.25, C:0.27, G:0.32, T:0.16
Consensus pattern (22 bp):
CTAGAAGGTCCAGTCAGCGGTC
Found at i:1325936 original size:13 final size:13
Alignment explanation
Indices: 1325918--1325942 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1325908 GTTTTATGCA
1325918 TTTTAATTTTATC
1 TTTTAATTTTATC
1325931 TTTTAATTTTAT
1 TTTTAATTTTAT
1325943 TTATTTATAT
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:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTAATTTTATC
Found at i:1327601 original size:20 final size:20
Alignment explanation
Indices: 1327558--1327610 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
1327548 TCAGGCTAGG
*
1327558 AGTATCGATACTTCCATGAG
1 AGTATCGATACTTCCATGAC
*
1327578 AGTATCGATACTTCCCCT-AC
1 AGTATCGATACTT-CCATGAC
*
1327598 AGTATCTATACTT
1 AGTATCGATACTT
1327611 AGGGTGATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTTCCATGAC
Found at i:1330496 original size:36 final size:35
Alignment explanation
Indices: 1330442--1330525 Score: 105
Period size: 36 Copynumber: 2.3 Consensus size: 35
1330432 AGATCTATAA
*
1330442 TTTTCTATTTCAATTCATATCATTGCAAAACTGTAC
1 TTTTCT-TTTCAAATCATATCATTGCAAAACTGTAC
* **
1330478 TTTTCTTTTCGAAATCATATCATTTCAAGTCTGTAC
1 TTTTCTTTTC-AAATCATATCATTGCAAAACTGTAC
1330514 TTTTCTTATTCA
1 TTTTCTT-TTCA
1330526 TATAAAACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
35 4 0.10
36 35 0.83
37 3 0.07
ACGTcount: A:0.26, C:0.19, G:0.06, T:0.49
Consensus pattern (35 bp):
TTTTCTTTTCAAATCATATCATTGCAAAACTGTAC
Found at i:1333374 original size:21 final size:22
Alignment explanation
Indices: 1333348--1333400 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 22
1333338 GCGGCAAACT
1333348 ATATTAA-GATAGAAGACCAAG
1 ATATTAACGATAGAAGACCAAG
*
1333369 ATATTAAATACTATAGAAGACCAAG
1 ATATT--A-ACGATAGAAGACCAAG
1333394 ATATTAA
1 ATATTAA
1333401 ATATGGGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 5 0.19
22 1 0.04
23 2 0.07
24 1 0.04
25 18 0.67
ACGTcount: A:0.53, C:0.09, G:0.13, T:0.25
Consensus pattern (22 bp):
ATATTAACGATAGAAGACCAAG
Found at i:1333390 original size:25 final size:25
Alignment explanation
Indices: 1333356--1333403 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
1333346 CTATATTAAG
1333356 ATAGAAGACCAAGATATTAAATACT
1 ATAGAAGACCAAGATATTAAATACT
1333381 ATAGAAGACCAAGATATTAAATA
1 ATAGAAGACCAAGATATTAAATA
1333404 TGGGTATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.10, G:0.12, T:0.23
Consensus pattern (25 bp):
ATAGAAGACCAAGATATTAAATACT
Found at i:1336598 original size:3 final size:3
Alignment explanation
Indices: 1336590--1336621 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1336580 TTAGATAACA
1336590 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1336622 GCCAATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1336669 original size:33 final size:34
Alignment explanation
Indices: 1336631--1336712 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 34
1336621 AGCCAATATT
* * *
1336631 TAAAAAATAA-TAGTAATAAAATAATAAAAAAAGG
1 TAAAAAATAAGAAATAAAAAAATAAT-AAAAAAGG
1336665 -AAAAAA-AAGAAATAAAAAAATAATAAAAAAGG
1 TAAAAAATAAGAAATAAAAAAATAATAAAAAAGG
1336697 TAAATAAATAAGAAAT
1 TAAA-AAATAAGAAAT
1336713 GGTTAAAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
32 10 0.24
33 21 0.51
34 3 0.07
35 7 0.17
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (34 bp):
TAAAAAATAAGAAATAAAAAAATAATAAAAAAGG
Found at i:1336692 original size:22 final size:24
Alignment explanation
Indices: 1336653--1336704 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
1336643 GTAATAAAAT
1336653 AATAAAAAAAGGAAAAAAAA-G-A
1 AATAAAAAAAGGAAAAAAAAGGTA
*
1336675 AATAAAAAAA-TAATAAAAAAGGTA
1 AATAAAAAAAGGAA-AAAAAAGGTA
1336699 AATAAA
1 AATAAA
1336705 TAAGAAATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 2 0.08
22 16 0.62
23 1 0.04
24 7 0.27
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.12
Consensus pattern (24 bp):
AATAAAAAAAGGAAAAAAAAGGTA
Found at i:1338073 original size:13 final size:13
Alignment explanation
Indices: 1338055--1338080 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1338045 GGTGAATAAT
1338055 AATAAATAAAAAC
1 AATAAATAAAAAC
1338068 AATAAATAAAAAC
1 AATAAATAAAAAC
1338081 TATATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AATAAATAAAAAC
Found at i:1338224 original size:30 final size:31
Alignment explanation
Indices: 1338130--1338229 Score: 107
Period size: 31 Copynumber: 3.2 Consensus size: 31
1338120 CTATATACTA
* *
1338130 TATATAAATTTTCAAAAATGTTTTTCAAAAAAC
1 TATAT-AATTTTTAAAAATGTTTTT-AAAAAAT
*
1338163 TA-A-AATTTTTTAAAAATGTTCTTTTAAAAAT
1 TATATAA-TTTTTAAAAATGTT-TTTAAAAAAT
*
1338194 TATATAATTTTTAAAAAT-ATTTTAAAAAAT
1 TATATAATTTTTAAAAATGTTTTTAAAAAAT
1338224 TATATA
1 TATATA
1338230 TTATATATAA
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
30 17 0.29
31 21 0.36
32 16 0.28
33 4 0.07
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (31 bp):
TATATAATTTTTAAAAATGTTTTTAAAAAAT
Found at i:1338235 original size:37 final size:36
Alignment explanation
Indices: 1338192--1338383 Score: 201
Period size: 36 Copynumber: 5.2 Consensus size: 36
1338182 TCTTTTAAAA
*
1338192 ATTATATAATTTTTAAAAATATTTTAAAAAATTATAT
1 ATTATATAATTTTTAAAAATGTTTT-AAAAATTATAT
* * *
1338229 ATTATATATAAGTTTTCAAAAATGCTCTAAAAATTATAT
1 A-T-TATATAA-TTTTTAAAAATGTTTTAAAAATTATAT
* *
1338268 ATTATAT--GTTTTCAAAATGTTTTTCAAAAATTATAT
1 ATTATATAATTTTTAAAAATG-TTTT-AAAAATTATAT
*
1338304 ATTATAT-ATTTTTAAAAATGTTTTGAAAATATATAT
1 ATTATATAATTTTTAAAAATGTTTTAAAAAT-TATAT
* * * *
1338340 AATATATAGTTTTTAAAAGTGTTTTAAAAATCATAT
1 ATTATATAATTTTTAAAAATGTTTTAAAAATTATAT
1338376 ATTATATA
1 ATTATATA
1338384 TGTATTTTCA
Statistics
Matches: 129, Mismatches: 18, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
34 9 0.07
35 7 0.05
36 44 0.34
37 36 0.28
38 2 0.02
39 19 0.15
40 12 0.09
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (36 bp):
ATTATATAATTTTTAAAAATGTTTTAAAAATTATAT
Found at i:1338376 original size:72 final size:73
Alignment explanation
Indices: 1338194--1338421 Score: 225
Period size: 75 Copynumber: 3.1 Consensus size: 73
1338184 TTTTAAAAAT
* *
1338194 TATATAATTTTTAAAAATATTTTAAAAAATTATATATTATATATAAGTTTTCAAAAATGCTCTAA
1 TATATAGTTTTT-AAAATGTTTTAAAAAATTATATATTATATAT-A-TTTTCAAAAATGCTCTAA
*
1338259 AAATTATATAT
63 AAATTATATAA
* * * * *
1338270 TATAT-GTTTTCAAAATGTTTTTCAAAAATTATATATTATATAT-TTTT-AAAAATGTTTTGAAA
1 TATATAGTTTTTAAAATG-TTTTAAAAAATTATATATTATATATATTTTCAAAAATGCTCTAAAA
1338332 ATATATATAA
65 AT-TATATAA
* ** **
1338342 TATATAGTTTTTAAAAGTGTTTT-AAAAATCATATATTATATATGTATTTTC-AAACCGCT-TGC
1 TATATAGTTTTTAAAA-TGTTTTAAAAAATTATATATTATATA--TATTTTCAAAAATGCTCTAA
1338404 AAATTATATAA
63 AAATTATATAA
1338415 TATATAG
1 TATATAG
1338422 AAATATCCGG
Statistics
Matches: 130, Mismatches: 14, Indels: 19
0.80 0.09 0.12
Matches are distributed among these distances:
71 14 0.11
72 33 0.25
73 27 0.21
74 14 0.11
75 37 0.28
76 5 0.04
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.46
Consensus pattern (73 bp):
TATATAGTTTTTAAAATGTTTTAAAAAATTATATATTATATATATTTTCAAAAATGCTCTAAAAA
TTATATAA
Found at i:1339766 original size:12 final size:12
Alignment explanation
Indices: 1339749--1339773 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1339739 ACTCATAGTT
1339749 TTTTCATTAATC
1 TTTTCATTAATC
1339761 TTTTCATTAATC
1 TTTTCATTAATC
1339773 T
1 T
1339774 AAGTGATTAC
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:0.24, C:0.16, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTCATTAATC
Found at i:1370492 original size:30 final size:30
Alignment explanation
Indices: 1370456--1370524 Score: 138
Period size: 30 Copynumber: 2.3 Consensus size: 30
1370446 ATAAGTAGAG
1370456 AATCTGTTGAACATAGTCCATCAGCTTCCA
1 AATCTGTTGAACATAGTCCATCAGCTTCCA
1370486 AATCTGTTGAACATAGTCCATCAGCTTCCA
1 AATCTGTTGAACATAGTCCATCAGCTTCCA
1370516 AATCTGTTG
1 AATCTGTTG
1370525 TTGATGTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.32
Consensus pattern (30 bp):
AATCTGTTGAACATAGTCCATCAGCTTCCA
Found at i:1376364 original size:17 final size:17
Alignment explanation
Indices: 1376335--1376385 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
1376325 AAAAATAATT
1376335 TTTTAAATT-AATTTAA
1 TTTTAAATTAAATTTAA
*
1376351 TTTTAGATTAAA-TTATA
1 TTTTAAATTAAATTTA-A
1376368 TTTTAAATTAAATTTAA
1 TTTTAAATTAAATTTAA
1376385 T
1 T
1376386 ATTATAGTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 11 0.37
17 16 0.53
18 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTTTAAATTAAATTTAA
Found at i:1378354 original size:20 final size:21
Alignment explanation
Indices: 1378322--1378360 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
1378312 TACTTAATTC
1378322 GTATATAAATAATTTTTTTGA
1 GTATATAAATAATTTTTTTGA
1378343 GTATAT-AATAATTTTTTT
1 GTATATAAATAATTTTTTT
1378361 CATTGAATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (21 bp):
GTATATAAATAATTTTTTTGA
Found at i:1379504 original size:3 final size:3
Alignment explanation
Indices: 1379483--1379524 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
1379473 TAGTTGTTCC
* *
1379483 TGA TGA TGG TGA TGG TGA TGA TGA TGA TGA TGA -GA GTGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA -TGA TGA
1379525 GGAAAAACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.88
4 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.40, T:0.31
Consensus pattern (3 bp):
TGA
Found at i:1385509 original size:14 final size:14
Alignment explanation
Indices: 1385481--1385520 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
1385471 TGTTTTTTGT
1385481 GTTTGTGTT-GTTC
1 GTTTGTGTTCGTTC
*
1385494 GTTTATGTTCGTTC
1 GTTTGTGTTCGTTC
1385508 GTTTGTGTTCGTT
1 GTTTGTGTTCGTT
1385521 TATCATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.03, C:0.10, G:0.28, T:0.60
Consensus pattern (14 bp):
GTTTGTGTTCGTTC
Found at i:1391823 original size:2 final size:2
Alignment explanation
Indices: 1391816--1391904 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
1391806 AGTAATTTTA
1391816 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
1391858 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
1391900 AT AT A
1 AT AT A
1391905 AACTCAAAAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1401207 original size:29 final size:29
Alignment explanation
Indices: 1401175--1401238 Score: 101
Period size: 29 Copynumber: 2.2 Consensus size: 29
1401165 TATGAATTAT
* *
1401175 AAAAAATAGAGGCCCTAATTATAAGTATA
1 AAAAAATAGAGGCCCTAATTATAAATACA
*
1401204 AAAAAATTGAGGCCCTAATTATAAATACA
1 AAAAAATAGAGGCCCTAATTATAAATACA
1401233 AAAAAA
1 AAAAAA
1401239 ATTAGGGCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.56, C:0.11, G:0.11, T:0.22
Consensus pattern (29 bp):
AAAAAATAGAGGCCCTAATTATAAATACA
Found at i:1401237 original size:30 final size:29
Alignment explanation
Indices: 1401175--1401249 Score: 98
Period size: 29 Copynumber: 2.6 Consensus size: 29
1401165 TATGAATTAT
* * *
1401175 AAAAAATAGAGGCCCTAATTATAAGTATA
1 AAAAAATTGAGGCCCTAATTATAAATAAA
1401204 AAAAAATTGAGGCCCTAATTATAAATACAA
1 AAAAAATTGAGGCCCTAATTATAAATA-AA
1401234 AAAAAATT-AGGGCCCT
1 AAAAAATTGA-GGCCCT
1401250 TGAGCAACCG
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
29 26 0.63
30 15 0.37
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.23
Consensus pattern (29 bp):
AAAAAATTGAGGCCCTAATTATAAATAAA
Found at i:1402472 original size:38 final size:38
Alignment explanation
Indices: 1402430--1402505 Score: 116
Period size: 38 Copynumber: 2.0 Consensus size: 38
1402420 GTTGTTTTGT
* * *
1402430 CTTAGATTAGGGTTTGTTTTATGGATAAGAAATATCTC
1 CTTAGATTAGGCTTTGTTTTAGGGATAAAAAATATCTC
*
1402468 CTTAGGTTAGGCTTTGTTTTAGGGATAAAAAATATCTC
1 CTTAGATTAGGCTTTGTTTTAGGGATAAAAAATATCTC
1402506 ATATCTCACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (38 bp):
CTTAGATTAGGCTTTGTTTTAGGGATAAAAAATATCTC
Found at i:1407131 original size:31 final size:31
Alignment explanation
Indices: 1407095--1407154 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1407085 AACTTAAAAG
1407095 AGTTTTACAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
*
1407126 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATACTGAAATTTAAATAATT
1407155 CATACAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:1407202 original size:22 final size:22
Alignment explanation
Indices: 1407177--1407633 Score: 494
Period size: 22 Copynumber: 20.6 Consensus size: 22
1407167 ATAATAAATT
*
1407177 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* **
1407199 TTTTAAAATAAAATATGGAAAT-TTTA
1 TTTTAAAAT--AA-AT--CAATCCATA
*
1407225 TTTTAAAATAAGTCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1407247 TTTTAAAATAAAAT-GTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
*
1407269 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
1407291 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*** *
1407313 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
1407335 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1407357 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATCCATA
1407379 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1407401 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
1407423 TTTTAAAATAAATCAATCCAAA
1 TTTTAAAATAAATCAATCCATA
**
1407445 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
1407467 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1407489 TTTTAAAATAAAAT-TTTACATA
1 TTTTAAAAT-AAATCAATCCATA
1407511 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1407533 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1407555 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATCCATA
** ***
1407577 TTTTAAAATATTTTTTTCCATA
1 TTTTAAAATAAATCAATCCATA
**
1407599 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATCCATA
1407621 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1407634 TTTAAAATAG
Statistics
Matches: 365, Mismatches: 54, Indels: 32
0.81 0.12 0.07
Matches are distributed among these distances:
21 21 0.06
22 304 0.83
23 20 0.05
24 4 0.01
25 2 0.01
26 11 0.03
27 3 0.01
ACGTcount: A:0.48, C:0.09, G:0.01, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1407650 original size:11 final size:12
Alignment explanation
Indices: 1407598--1407647 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
1407588 TTTTTTCCAT
1407598 ATTTTAAAATAA
1 ATTTTAAAATAA
* * *
1407610 A--TCAATATAT
1 ATTTTAAAATAA
1407620 ATTTTAAAATAA
1 ATTTTAAAATAA
*
1407632 ATTTTAAAATAG
1 ATTTTAAAATAA
1407644 ATTT
1 ATTT
1407648 AAATGATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
10 7 0.24
12 22 0.76
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:1409948 original size:24 final size:24
Alignment explanation
Indices: 1409921--1409981 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
1409911 CAAATGAACA
1409921 AACATAAACGAACGAATGTAAACG
1 AACATAAACGAACGAATGTAAACG
* *
1409945 AACATAAACGAATGGATGTAAACG
1 AACATAAACGAACGAATGTAAACG
* *
1409969 AATAGAAACGAAC
1 AACATAAACGAAC
1409982 ACAAACGAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.54, C:0.15, G:0.18, T:0.13
Consensus pattern (24 bp):
AACATAAACGAACGAATGTAAACG
Found at i:1410003 original size:34 final size:34
Alignment explanation
Indices: 1409931--1410004 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
1409921 AACATAAACG
* *
1409931 AACGAATGTAAACGAACATAAACGAATGGATGTA
1 AACGAATGTAAACGAACACAAACGAATCGATGTA
*
1409965 AACGAATAG-AAACGAACACAAACGAA-CGATGGTT
1 AACGAAT-GTAAACGAACACAAACGAATCGAT-GTA
1409999 AACGAA
1 AACGAA
1410005 CATAAACAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
33 3 0.09
34 31 0.89
35 1 0.03
ACGTcount: A:0.51, C:0.15, G:0.20, T:0.14
Consensus pattern (34 bp):
AACGAATGTAAACGAACACAAACGAATCGATGTA
Done.