Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008958.1 Hibiscus syriacus cultivar Beakdansim tig00112289_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: 2490255
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1248135 original size:17 final size:16
Alignment explanation
Indices: 1248093--1248132 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 16
1248083 AAAATAAGTT
1248093 ATAATAATAAATAATA
1 ATAATAATAAATAATA
1248109 ATAATGAATAAATAATA
1 ATAAT-AATAAATAATA
1248126 ATAATAA
1 ATAATAA
1248133 ATATTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
ATAATAATAAATAATA
Found at i:1248144 original size:13 final size:13
Alignment explanation
Indices: 1248093--1248135 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
1248083 AAAATAAGTT
1248093 ATAATAATAA-ATA
1 ATAATAATAATA-A
1248106 ATAATAATGAATAA
1 ATAATAAT-AATAA
1248120 ATAATAATAATAA
1 ATAATAATAATAA
1248133 ATA
1 ATA
1248136 TTTAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 16 0.57
14 11 0.39
15 1 0.04
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (13 bp):
ATAATAATAATAA
Found at i:1248237 original size:38 final size:35
Alignment explanation
Indices: 1248124--1248237 Score: 81
Period size: 38 Copynumber: 3.0 Consensus size: 35
1248114 GAATAAATAA
1248124 TAATAATAAATATTTAAAATATTTTTTTTAAAAACTATA-
1 TAAT-ATAAAT-TTT-AAA-ATTTTTTTT-AAAACTATAT
* *
1248163 TAATATAAATTTTTTAAAA--ATTCTTAAAACTGTATAT
1 TAATATAAA--TTTTAAAATTTTTTTTAAAAC--TATAT
1248200 TATATATAAATTTTCAAAATGTTTTTTTAAAACTATAT
1 TA-ATATAAATTTT-AAAAT-TTTTTTTAAAACTATAT
1248238 AATTTTCAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 21
0.71 0.05 0.24
Matches are distributed among these distances:
34 5 0.08
35 4 0.07
36 8 0.13
37 7 0.11
38 20 0.33
39 7 0.11
40 10 0.16
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.47
Consensus pattern (35 bp):
TAATATAAATTTTAAAATTTTTTTTAAAACTATAT
Found at i:1248260 original size:29 final size:29
Alignment explanation
Indices: 1248202--1248325 Score: 160
Period size: 29 Copynumber: 4.2 Consensus size: 29
1248192 CTGTATATTA
*
1248202 TATATAAATTTTC-AAAATGTTTTTTTAAAAC
1 TATAT-AATTTTCAAAAATG--TTTTAAAAAC
1248233 TATATAATTTTCAAAAATGTTTTAAAAAC
1 TATATAATTTTCAAAAATGTTTTAAAAAC
*
1248262 TATATAATTTTCAAAAATGGTTTAAAAAC
1 TATATAATTTTCAAAAATGTTTTAAAAAC
*** *
1248291 TATATAATTTTCAAAAAAAATTTAAAAAT
1 TATATAATTTTCAAAAATGTTTTAAAAAC
1248320 TATATA
1 TATATA
1248326 TTATATATAA
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
29 68 0.79
30 7 0.08
31 11 0.13
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (29 bp):
TATATAATTTTCAAAAATGTTTTAAAAAC
Found at i:1248332 original size:36 final size:35
Alignment explanation
Indices: 1248291--1248446 Score: 107
Period size: 36 Copynumber: 4.5 Consensus size: 35
1248281 GTTTAAAAAC
*
1248291 TATATAATTTTCAAAAAAAATTTAAAAATTATATATT
1 TATATAATTTTC-AAAAAAATTTAAAAACTATATA-T
1248328 ATATATAAGTTTTC-----AA---AA-AACTATATAT
1 -TATATAA-TTTTCAAAAAAATTTAAAAACTATATAT
* *
1248356 TATATAAGTTTTCAAAATGATTTTAAAAACTATATAT
1 TATATAA-TTTTCAAAA-AAATTTAAAAACTATATAT
** *
1248393 TATATAGA-TTTCAAATCTATTTTAAAAACTATATAT
1 TATATA-ATTTTCAAA-AAAATTTAAAAACTATATAT
1248429 TATATACATTTTCAAAAA
1 TATATA-ATTTTCAAAAA
1248447 CCGTTTGCAA
Statistics
Matches: 97, Mismatches: 7, Indels: 30
0.72 0.05 0.22
Matches are distributed among these distances:
27 13 0.13
28 1 0.01
29 8 0.08
30 2 0.02
33 3 0.03
36 34 0.35
37 23 0.24
38 8 0.08
39 5 0.05
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.42
Consensus pattern (35 bp):
TATATAATTTTCAAAAAAATTTAAAAACTATATAT
Found at i:1248346 original size:29 final size:27
Alignment explanation
Indices: 1248314--1248372 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 27
1248304 AAAAAAATTT
*
1248314 AAAAATTATATATTATATATAAGTTTTCA
1 AAAAACTATATA-T-TATATAAGTTTTCA
1248343 AAAAACTATATATTATATAAGTTTTCA
1 AAAAACTATATATTATATAAGTTTTCA
1248370 AAA
1 AAA
1248373 TGATTTTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 17 0.59
28 1 0.03
29 11 0.38
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (27 bp):
AAAAACTATATATTATATAAGTTTTCA
Found at i:1248387 original size:37 final size:38
Alignment explanation
Indices: 1248343--1248445 Score: 151
Period size: 36 Copynumber: 2.8 Consensus size: 38
1248333 TAAGTTTTCA
1248343 AAAAACTATATATTATATAAGTTTTCAAAAT-GATTTT
1 AAAAACTATATATTATATAAGTTTTCAAAATCGATTTT
* *
1248380 AAAAACTATATATTATAT-AGATTTC-AAATCTATTTT
1 AAAAACTATATATTATATAAGTTTTCAAAATCGATTTT
1248416 AAAAACTATATATTATATACA-TTTTCAAAA
1 AAAAACTATATATTATATA-AGTTTTCAAAA
1248446 ACCGTTTGCA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
35 4 0.07
36 29 0.49
37 22 0.37
38 4 0.07
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.42
Consensus pattern (38 bp):
AAAAACTATATATTATATAAGTTTTCAAAATCGATTTT
Found at i:1250894 original size:19 final size:19
Alignment explanation
Indices: 1250879--1250917 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1250869 TTTAAATTAC
1250879 AAAAATA-AAA-TAAAATA
1 AAAAATATAAATTAAAATA
1250896 AAAAATATAAATTAAAA-A
1 AAAAATATAAATTAAAATA
1250914 AAAA
1 AAAA
1250918 TTAAGTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 8 0.40
19 5 0.25
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAATATAAATTAAAATA
Found at i:1250901 original size:17 final size:17
Alignment explanation
Indices: 1250879--1250918 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1250869 TTTAAATTAC
1250879 AAAAATA-AAATAAAATA
1 AAAAATATAAATAAAA-A
*
1250896 AAAAATATAAATTAAAA
1 AAAAATATAAATAAAAA
1250913 AAAAAT
1 AAAAAT
1250919 TAAGTTGATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAAATATAAATAAAAA
Found at i:1251320 original size:2 final size:2
Alignment explanation
Indices: 1251313--1251338 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1251303 ACAAAATACA
1251313 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
1251339 TCAAAATCGA
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:1251797 original size:22 final size:23
Alignment explanation
Indices: 1251771--1251822 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1251761 TCTCGAGGGA
* *
1251771 CCACATA-GTTTGCACTGAAGTG
1 CCACATAGGGTTGCACCGAAGTG
1251793 CCACATAGGGTTGCACCGAAGTG
1 CCACATAGGGTTGCACCGAAGTG
1251816 CCACATA
1 CCACATA
1251823 TTTATCCCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.26
23 20 0.74
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (23 bp):
CCACATAGGGTTGCACCGAAGTG
Found at i:1251843 original size:21 final size:21
Alignment explanation
Indices: 1251816--1251864 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1251806 CACCGAAGTG
*
1251816 CCACATATTTATCCCAGAGGA
1 CCACATAATTATCCCAGAGGA
* * *
1251837 TCACATAATTGTCCCGGAGGA
1 CCACATAATTATCCCAGAGGA
1251858 CCACATA
1 CCACATA
1251865 GACCGTCAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (21 bp):
CCACATAATTATCCCAGAGGA
Found at i:1253270 original size:28 final size:28
Alignment explanation
Indices: 1253230--1253310 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
1253220 AGAGTCGAGG
*
1253230 GTTCTACGTGGTCATTCGGGATATATGC
1 GTTCTACGTGGTCATTCGGGACATATGC
* *
1253258 GTTCTACGTGGTCCTTCGGGACATATGT
1 GTTCTACGTGGTCATTCGGGACATATGC
* * *
1253286 GTTCTATGTGGTCCTTTGGGACATA
1 GTTCTACGTGGTCATTCGGGACATA
1253311 GTGGTCCTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.37
Consensus pattern (28 bp):
GTTCTACGTGGTCATTCGGGACATATGC
Found at i:1258569 original size:28 final size:28
Alignment explanation
Indices: 1258495--1258569 Score: 114
Period size: 28 Copynumber: 2.7 Consensus size: 28
1258485 TCGAGGGTTC
*
1258495 TATGTGGTCCTTTGGGACATATGTGTTA
1 TATGTGGTCCTTCGGGACATATGTGTTA
* **
1258523 TACGTGGTCCTTCAAGACATATGTGTTA
1 TATGTGGTCCTTCGGGACATATGTGTTA
1258551 TATGTGGTCCTTCGGGACA
1 TATGTGGTCCTTCGGGACA
1258570 AATTTTTACG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (28 bp):
TATGTGGTCCTTCGGGACATATGTGTTA
Found at i:1259929 original size:55 final size:55
Alignment explanation
Indices: 1259836--1259977 Score: 189
Period size: 55 Copynumber: 2.6 Consensus size: 55
1259826 TCATACTTGG
* * *
1259836 GGGTATCAATACACTCCTCAGTGTATCGAGACACAAATAGCACTCGATATTTT-A
1 GGGTATCAATACACTCCTCAGTGTACCGATACAAAAATAGCACTCGATATTTTAA
* * * *
1259890 GGTGTATCGATACACTCCTCAATGTACCGATATAAAAATAGCACTCGATGTTTTAA
1 GG-GTATCAATACACTCCTCAGTGTACCGATACAAAAATAGCACTCGATATTTTAA
*
1259946 GGGTATCAATACACT-CTCAGTATACCGATACA
1 GGGTATCAATACACTCCTCAGTGTACCGATACA
1259978 CACTCATACA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
54 16 0.21
55 56 0.75
56 3 0.04
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (55 bp):
GGGTATCAATACACTCCTCAGTGTACCGATACAAAAATAGCACTCGATATTTTAA
Found at i:1266574 original size:17 final size:17
Alignment explanation
Indices: 1266554--1266593 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1266544 TTACTACACA
1266554 TTTTTTCTTCTTCTTTT
1 TTTTTTCTTCTTCTTTT
** *
1266571 TTTTCACTTTTTCTTTT
1 TTTTTTCTTCTTCTTTT
1266588 TTTTTT
1 TTTTTT
1266594 TCCTTTTTTT
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCTTCTTCTTTT
Found at i:1266599 original size:19 final size:20
Alignment explanation
Indices: 1266561--1266601 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1266551 ACATTTTTTC
1266561 TTCTTCTTTTTTTTCACTTT
1 TTCTTCTTTTTTTTCACTTT
*
1266581 TTCTTTTTTTTTTTC-CTTT
1 TTCTTCTTTTTTTTCACTTT
1266600 TT
1 TT
1266602 TTTACAATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (20 bp):
TTCTTCTTTTTTTTCACTTT
Found at i:1266602 original size:20 final size:21
Alignment explanation
Indices: 1266556--1266602 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1266546 ACTACACATT
1266556 TTTTCTTCTTCTTTTTTTTCAC
1 TTTT-TTCTTCTTTTTTTTCAC
*
1266578 -TTTTTCTTTTTTTTTTTC-C
1 TTTTTTCTTCTTTTTTTTCAC
1266597 TTTTTT
1 TTTTTT
1266603 TTACAATGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 1 0.04
20 19 0.83
21 3 0.13
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTTTTCTTCTTTTTTTTCAC
Found at i:1285608 original size:2 final size:2
Alignment explanation
Indices: 1285603--1285644 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1285593 AAAAAATACA
1285603 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
1285645 TCAAAATCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1286157 original size:21 final size:21
Alignment explanation
Indices: 1286131--1286179 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
1286121 CACCGAAGTG
* *
1286131 CCACATATTTATCCCGGAGAA
1 CCACATAATTATCCCGAAGAA
* *
1286152 CCACATAATTATCCTGAAGGA
1 CCACATAATTATCCCGAAGAA
1286173 CCACATA
1 CCACATA
1286180 GACCCTCGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.29, G:0.12, T:0.22
Consensus pattern (21 bp):
CCACATAATTATCCCGAAGAA
Found at i:1288478 original size:53 final size:52
Alignment explanation
Indices: 1288376--1288505 Score: 197
Period size: 53 Copynumber: 2.4 Consensus size: 52
1288366 TTATACTTAG
*
1288376 GGGTATCGATACATTCCTCAGTGTACCGATACACAAATAGCACTCGATGTTTTA
1 GGGTATCGATACACTCCTCA--GTACCGATACACAAATAGCACTCGATGTTTTA
*
1288430 GGTGTATCGATACACTCCTCAGTATCGATACACAAATAGCACTCGATGTTTTGA
1 GG-GTATCGATACACTCCTCAGTACCGATACACAAATAGCACTCGATGTTTT-A
*
1288484 GGGTATAGATACACTCCTCAGT
1 GGGTATCGATACACTCCTCAGT
1288506 GTACTGATAC
Statistics
Matches: 71, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
53 49 0.69
54 5 0.07
55 17 0.24
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (52 bp):
GGGTATCGATACACTCCTCAGTACCGATACACAAATAGCACTCGATGTTTTA
Found at i:1290603 original size:15 final size:16
Alignment explanation
Indices: 1290585--1290615 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1290575 ATTACTTTGT
1290585 ATTTTTTT-AATTTTA
1 ATTTTTTTAAATTTTA
1290600 ATTTTTTTAAATTTTA
1 ATTTTTTTAAATTTTA
1290616 TTCAGTCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
ATTTTTTTAAATTTTA
Found at i:1293667 original size:27 final size:27
Alignment explanation
Indices: 1293629--1293686 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
1293619 GAAGGTTCAA
1293629 TCAAACTATATGTCCTTGAAATTTAAC
1 TCAAACTATATGTCCTTGAAATTTAAC
1293656 TCAAACTATATGTCCTTGAAATTTAAC
1 TCAAACTATATGTCCTTGAAATTTAAC
1293683 TCAA
1 TCAA
1293687 TGATGACGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (27 bp):
TCAAACTATATGTCCTTGAAATTTAAC
Found at i:1293841 original size:12 final size:12
Alignment explanation
Indices: 1293824--1293861 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
1293814 TGTGTCATTG
*
1293824 ATGACAAGTGTC
1 ATGACATGTGTC
*
1293836 ATGACATGTATC
1 ATGACATGTGTC
1293848 ATGACATGTGTC
1 ATGACATGTGTC
1293860 AT
1 AT
1293862 CATTGAAGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (12 bp):
ATGACATGTGTC
Found at i:1293972 original size:2 final size:2
Alignment explanation
Indices: 1293965--1294024 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1293955 AGAGGGTGTC
1293965 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
1294007 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1294025 CATAAAATAC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1301320 original size:40 final size:40
Alignment explanation
Indices: 1301265--1301386 Score: 217
Period size: 40 Copynumber: 3.0 Consensus size: 40
1301255 TGCAGGTTTA
*
1301265 TAATACACTTCGGTGTATATGGTGGGTACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
* *
1301305 TAATACATTTCGGTGTATATGGTGAGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1301345 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1301385 TA
1 TA
1301387 GCACTACGGT
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 77 1.00
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (40 bp):
TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:1301600 original size:51 final size:48
Alignment explanation
Indices: 1301491--1301720 Score: 267
Period size: 51 Copynumber: 4.8 Consensus size: 48
1301481 GTAAGCATAC
* * **
1301491 AAATAAGCTTACGAGCTTTTGGAA--T-AATGGCAAGTATA-TGGGTA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAAA
1301535 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAAAAA
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGG--AAA
*
1301585 AATATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATAATGGAAAAAA
1 AA-ATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGG---AAA
* *
1301637 AATATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTGG-TA
1 AA-ATAAGCTTACGAGCTTATGGAA-TTTAAATGGTAAGTATATTGGAAA
*
1301686 AAATAAGCTTACGAGCTTATGGGA--TAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAG
1301721 GGATTTTATA
Statistics
Matches: 168, Mismatches: 9, Indels: 17
0.87 0.05 0.09
Matches are distributed among these distances:
44 23 0.14
45 11 0.07
46 1 0.01
47 12 0.07
48 24 0.14
49 3 0.02
50 3 0.02
51 42 0.25
52 30 0.18
53 19 0.11
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (48 bp):
AAATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATATTGGAAA
Found at i:1301645 original size:103 final size:98
Alignment explanation
Indices: 1301491--1301720 Score: 294
Period size: 98 Copynumber: 2.4 Consensus size: 98
1301481 GTAAGCATAC
* * **
1301491 AAATAAGCTTACGAGCTTTTGGAAT-AATGGCAAGTAT-ATGG---GTAAA-ATAAGCTTACGAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAATGGAAAAAAAATATAAGCTTACGAG
1301550 CTTATGGAA-TTTAAATGGTAAGTATATTGGAAAAA
66 CTTATGGAATTTTAAATGGTAAGTATATTGG---AA
1301585 AATATAAGCTTACGAGCTTATGGAATTTAAATGGTAAGTATAATGGAAAAAAAATATAAGCTTAC
1 AA-ATAAGCTTACGAGCTTATGGAA--TAAATGGTAAGTATAATGGAAAAAAAATATAAGCTTAC
* *
1301650 GAGCTTATGGAATTTTAAATGGTAAGTATTTTGGTA
63 GAGCTTATGGAATTTTAAATGGTAAGTATATTGGAA
*
1301686 AAATAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
1301721 GGATTTTATA
Statistics
Matches: 119, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
94 2 0.02
95 21 0.18
97 1 0.01
98 22 0.18
99 4 0.03
100 21 0.18
101 3 0.03
102 3 0.03
103 22 0.18
104 20 0.17
ACGTcount: A:0.40, C:0.07, G:0.22, T:0.31
Consensus pattern (98 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAATGGAAAAAAAATATAAGCTTACGAG
CTTATGGAATTTTAAATGGTAAGTATATTGGAA
Found at i:1303406 original size:22 final size:22
Alignment explanation
Indices: 1303378--1303431 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1303368 GTAGAAAAAA
* *
1303378 CAACTCGCATTTGCCAATTTCG
1 CAACTCGAATTCGCCAATTTCG
1303400 CAACTCGAATTCGCCAATTTCG
1 CAACTCGAATTCGCCAATTTCG
1303422 CAACTC-AATT
1 CAACTCGAATT
1303432 ACCGATATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 4 0.13
22 26 0.87
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (22 bp):
CAACTCGAATTCGCCAATTTCG
Found at i:1303568 original size:42 final size:42
Alignment explanation
Indices: 1303504--1303603 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
1303494 TATCGATAAT
*
1303504 TGAGTTGCAAAATTGGCGAATTCGAATTGCGAATTTGAAAAC
1 TGAGTTGCGAAATTGGCGAATTCGAATTGCGAATTTGAAAAC
* ** *
1303546 TGAGTTGCGAATTTGG-GAAATTCGTGTTGCGAATTTGGAAAC
1 TGAGTTGCGAAATTGGCG-AATTCGAATTGCGAATTTGAAAAC
*
1303588 TGTGTTGCGAAATTGG
1 TGAGTTGCGAAATTGG
1303604 AGTTCGTGTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.32
Consensus pattern (42 bp):
TGAGTTGCGAAATTGGCGAATTCGAATTGCGAATTTGAAAAC
Found at i:1303574 original size:22 final size:21
Alignment explanation
Indices: 1303530--1303639 Score: 104
Period size: 20 Copynumber: 5.4 Consensus size: 21
1303520 CGAATTCGAA
* * *
1303530 TTGCGAATTTGAAAACT-GAG
1 TTGCGAATTTGGAAATTCGTG
1303550 TTGCGAATTTGGGAAATTCGTG
1 TTGCGAATTT-GGAAATTCGTG
*
1303572 TTGCGAATTTGGAAACT-GTG
1 TTGCGAATTTGGAAATTCGTG
* *
1303592 TTGCGAAATTGG-AGTTCGTG
1 TTGCGAATTTGGAAATTCGTG
* *
1303612 TTGCGAATTT-GATA-TCGCG
1 TTGCGAATTTGGAAATTCGTG
1303631 TTGCGAATT
1 TTGCGAATT
1303640 CGTTGGTTAT
Statistics
Matches: 75, Mismatches: 11, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
19 16 0.21
20 36 0.48
21 11 0.15
22 12 0.16
ACGTcount: A:0.25, C:0.11, G:0.29, T:0.35
Consensus pattern (21 bp):
TTGCGAATTTGGAAATTCGTG
Found at i:1306140 original size:3 final size:3
Alignment explanation
Indices: 1306132--1306168 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
1306122 GTAGCATATA
*
1306132 AAT AAT AAT AAT AAT AAT AAT AAC AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1306169 TATTTAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1306581 original size:41 final size:43
Alignment explanation
Indices: 1306524--1306703 Score: 210
Period size: 42 Copynumber: 4.3 Consensus size: 43
1306514 AGGTCGTATG
* *
1306524 GATGGTCCGAAGGACTTA-TCATCTTGCTCGAAAGACTTA-TA
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
* * *
1306565 GATGGCCCGAATGACTTACACATCATGCTCGAAAAACTTACTA
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
* * **
1306608 -ATGGCCTG-AGGAATTAAGCATCATGCTCGAAAGACTTACT-
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
* * *
1306648 GATGGCCTGAAGGACTTACTCATCATGCTCGGAAGACTTA-TT
1 GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
1306690 GATGGCCCGAAGGA
1 GATGGCCCGAAGGA
1306704 TTTATGCTGA
Statistics
Matches: 118, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
41 52 0.44
42 64 0.54
43 2 0.02
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.25
Consensus pattern (43 bp):
GATGGCCCGAAGGACTTACTCATCATGCTCGAAAGACTTACTA
Found at i:1306687 original size:22 final size:22
Alignment explanation
Indices: 1306626--1306687 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 22
1306616 AGGAATTAAG
*
1306626 CATCATGCTCGAAAGACTTACT
1 CATCATGCTCGGAAGACTTACT
* * *
1306648 GAT--GGC-CTGAAGGACTTACT
1 CATCATGCTCGGAA-GACTTACT
1306668 CATCATGCTCGGAAGACTTA
1 CATCATGCTCGGAAGACTTA
1306688 TTGATGGCCC
Statistics
Matches: 29, Mismatches: 7, Indels: 8
0.66 0.16 0.18
Matches are distributed among these distances:
19 3 0.10
20 12 0.41
22 10 0.34
23 4 0.14
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (22 bp):
CATCATGCTCGGAAGACTTACT
Found at i:1306687 original size:83 final size:83
Alignment explanation
Indices: 1306543--1306696 Score: 220
Period size: 83 Copynumber: 1.9 Consensus size: 83
1306533 AAGGACTTAT
* *
1306543 CATCTTGCTCGAAAGACTTATAGATGGCCCGAATGACTTACACATCATGCTCGAAAAACTTACTA
1 CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTACACATCATGCTCGAAAAACTTACTA
1306608 ATGGCCTGAGGAATTAAG
66 ATGGCCTGAGGAATTAAG
* * * * *
1306626 CATCATGCTCGAAAGACTTACT-GATGGCCTGAAGGACTTACTCATCATGCTCGGAAGACTTATT
1 CATCATGCTCGAAAGACTTA-TAGATGGCCCGAAGGACTTACACATCATGCTCGAAAAACTTACT
*
1306690 GATGGCC
65 AATGGCC
1306697 CGAAGGATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
83 61 0.98
84 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.26
Consensus pattern (83 bp):
CATCATGCTCGAAAGACTTATAGATGGCCCGAAGGACTTACACATCATGCTCGAAAAACTTACTA
ATGGCCTGAGGAATTAAG
Found at i:1306809 original size:59 final size:59
Alignment explanation
Indices: 1306739--1306864 Score: 207
Period size: 59 Copynumber: 2.1 Consensus size: 59
1306729 ATCAATTAAT
* *
1306739 AGGAAATGTTAACCCCTCTGGTGGGGTGTTGATGATTCGAAGTGTTTTGAATCGAGAAA
1 AGGAAATGTTAACCCCTCTGGTGGGGCGTTGATGATTCGAAGTGTTGTGAATCGAGAAA
* * *
1306798 AGGAAATGTTAACCCCTCTGGTGGGGCGTTGTTTATTCGAAGTGTTGTGAATCGAGCAA
1 AGGAAATGTTAACCCCTCTGGTGGGGCGTTGATGATTCGAAGTGTTGTGAATCGAGAAA
1306857 AGGAAATG
1 AGGAAATG
1306865 ATGAAAATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 62 1.00
ACGTcount: A:0.27, C:0.13, G:0.31, T:0.29
Consensus pattern (59 bp):
AGGAAATGTTAACCCCTCTGGTGGGGCGTTGATGATTCGAAGTGTTGTGAATCGAGAAA
Found at i:1307042 original size:142 final size:143
Alignment explanation
Indices: 1306771--1307093 Score: 459
Period size: 142 Copynumber: 2.3 Consensus size: 143
1306761 GGGGTGTTGA
* * * *
1306771 TGATTCGAAGTGTTTTGAATCGAGAAAAGGAAATGTTAACCCCTCTGGTGGGGCGTTGTTTATTC
1 TGATTCGAAGTG-TTTGAATCGAGCAAATGAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTC
* * * * *
1306836 GAAGTGTTGTGAATCGAGCAAAGGAAATGATGAAAATAACCTGTCCGAAGGTATTATGGATGGCC
65 AAAGTGTTGTAAATCGAGCAAAGGAAATGATGAAAACAACATGCCCGAAGGTATTATGGATGGCC
*
1306901 CGAAGGACTTAAGT
130 CGAAGGACTTAAGC
* *
1306915 TGATTCGAAGTGCTTGAATTGAGCAAATGAAATGTTAACCCCTCT-GTGGGGCGTTGCTGATTCA
1 TGATTCGAAGTGTTTGAATCGAGCAAATGAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCA
* * * *
1306979 AAGTGTTGTAAATCGAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTATGGATGGCCC
66 AAGTGTTGTAAATCGAGCAAAGGAAATGATGAAAACAACATGCCCGAAGGTATTATGGATGGCCC
*
1307044 GAATGACTTAAGC
131 GAAGGACTTAAGC
*
1307057 TGATTCGAAGTGTTGTGAATCAAGCAAATGAAATGTT
1 TGATTCGAAGTGTT-TGAATCGAGCAAATGAAATGTT
1307094 GGAAACATCT
Statistics
Matches: 158, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
142 97 0.61
143 49 0.31
144 12 0.08
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (143 bp):
TGATTCGAAGTGTTTGAATCGAGCAAATGAAATGTTAACCCCTCTGGTGGGGCGTTGCTGATTCA
AAGTGTTGTAAATCGAGCAAAGGAAATGATGAAAACAACATGCCCGAAGGTATTATGGATGGCCC
GAAGGACTTAAGC
Found at i:1307113 original size:85 final size:85
Alignment explanation
Indices: 1306970--1307141 Score: 272
Period size: 85 Copynumber: 2.0 Consensus size: 85
1306960 GTGGGGCGTT
*
1306970 GCTGATTCAAAGTGTTGTAAATCGAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTAT
1 GCTGATTCAAAGTGTTGTAAATCAAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTAT
* *
1307035 GGATGGCCCGAATGACTTAA
66 GGATGGCCCAAAGGACTTAA
* * * *
1307055 GCTGATTCGAAGTGTTGTGAATCAAGCAAATGAAATGTTGGAAACATCTTGCCCGAAGGTCTTAT
1 GCTGATTCAAAGTGTTGTAAATCAAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTAT
*
1307120 GGATGGCCTAAAGGACTTAA
66 GGATGGCCCAAAGGACTTAA
1307140 GC
1 GC
1307142 ATCATGCTGG
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
85 79 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (85 bp):
GCTGATTCAAAGTGTTGTAAATCAAGCAAATGAAATGTTGAAAACATCATGCCCGAAGGTCTTAT
GGATGGCCCAAAGGACTTAA
Found at i:1308635 original size:14 final size:14
Alignment explanation
Indices: 1308618--1308691 Score: 53
Period size: 14 Copynumber: 5.3 Consensus size: 14
1308608 TGACTTGGGT
1308618 AGGTAATGTGTTTC
1 AGGTAATGTGTTTC
* **
1308632 AGGTTAATTTGGGT-
1 AGG-TAATGTGTTTC
1308646 AGGTAATGTGTTTC
1 AGGTAATGTGTTTC
* ***
1308660 AGGTTAATTTG-GGG
1 AGG-TAATGTGTTTC
1308674 AGGTAATGTGTTTC
1 AGGTAATGTGTTTC
1308688 AGGT
1 AGGT
1308692 TAGCTTCTTG
Statistics
Matches: 42, Mismatches: 14, Indels: 8
0.66 0.22 0.12
Matches are distributed among these distances:
13 13 0.31
14 16 0.38
15 13 0.31
ACGTcount: A:0.22, C:0.04, G:0.34, T:0.41
Consensus pattern (14 bp):
AGGTAATGTGTTTC
Found at i:1308652 original size:28 final size:28
Alignment explanation
Indices: 1308612--1308693 Score: 155
Period size: 28 Copynumber: 2.9 Consensus size: 28
1308602 TTAGGCTGAC
1308612 TTGGGTAGGTAATGTGTTTCAGGTTAAT
1 TTGGGTAGGTAATGTGTTTCAGGTTAAT
1308640 TTGGGTAGGTAATGTGTTTCAGGTTAAT
1 TTGGGTAGGTAATGTGTTTCAGGTTAAT
*
1308668 TTGGGGAGGTAATGTGTTTCAGGTTA
1 TTGGGTAGGTAATGTGTTTCAGGTTA
1308694 GCTTCTTGCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.21, C:0.04, G:0.34, T:0.41
Consensus pattern (28 bp):
TTGGGTAGGTAATGTGTTTCAGGTTAAT
Found at i:1309358 original size:12 final size:12
Alignment explanation
Indices: 1309327--1309412 Score: 68
Period size: 12 Copynumber: 6.8 Consensus size: 12
1309317 TGATCAATTT
1309327 TTTTTCTTCTTTC
1 TTTTTCTT-TTTC
*
1309340 -TTCTCTTTTTC
1 TTTTTCTTTTTC
1309351 TTTTTCTTTTTC
1 TTTTTCTTTTTC
1309363 TCTTTT-TTTTTC
1 T-TTTTCTTTTTC
*
1309375 TTATTTTTTCTTTC
1 TT-TTTCTT-TTTC
*
1309389 TTTTTTCCTTTTTT
1 -TTTTT-CTTTTTC
1309403 TTATTTCTTT
1 TT-TTTCTTT
1309413 CTTTTCTATA
Statistics
Matches: 61, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
11 5 0.08
12 27 0.44
13 12 0.20
14 13 0.21
15 4 0.07
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTCTTTTTC
Found at i:1309363 original size:20 final size:20
Alignment explanation
Indices: 1309324--1309393 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 20
1309314 ATTTGATCAA
1309324 TTTTTTTTCTTCTTTCTTCTC
1 TTTTTTTTCTTCTTT-TTCTC
1309345 TTTTTCTTT-TTCTTTTTCTC
1 TTTTT-TTTCTTCTTTTTCTC
*
1309365 TTTTTTTTTCTTATTTTT-TC
1 -TTTTTTTTCTTCTTTTTCTC
1309385 TTTCTTTTT
1 TTT-TTTTT
1309394 TCCTTTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
19 3 0.07
20 15 0.34
21 23 0.52
22 3 0.07
ACGTcount: A:0.01, C:0.17, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTTCTTCTTTTTCTC
Found at i:1309394 original size:45 final size:41
Alignment explanation
Indices: 1309324--1309428 Score: 106
Period size: 45 Copynumber: 2.4 Consensus size: 41
1309314 ATTTGATCAA
* *
1309324 TTTTTTTTCTTCTTTCTTCTCTTTTT-CTTTTTCTTT-TTCTC
1 TTTTTTTTCTTATTTTTTCTCTTTTTCCTTTTT-TTTATT-TC
1309365 TTTTTTTTTCTTATTTTTTCTTTCTTTTTTCCTTTTTTTTATTTC
1 -TTTTTTTTCTTATTTTTTC--TC-TTTTTCCTTTTTTTTATTTC
*
1309410 TTTCTTTTCTATATTTTTT
1 TTTTTTTTCT-TATTTTTT
1309429 TATGTCTCAT
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
42 17 0.31
44 11 0.20
45 18 0.33
46 8 0.15
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (41 bp):
TTTTTTTTCTTATTTTTTCTCTTTTTCCTTTTTTTTATTTC
Found at i:1309424 original size:17 final size:16
Alignment explanation
Indices: 1309333--1309425 Score: 58
Period size: 14 Copynumber: 6.1 Consensus size: 16
1309323 ATTTTTTTTC
*
1309333 TTCTTTCTTCTCTT-T
1 TTCTTTCTTTTCTTAT
1309348 TTCTTT-TTCTT-TT-T
1 TTCTTTCTT-TTCTTAT
* *
1309362 CTCTTTTTTTTTCTTAT
1 TTC-TTTCTTTTCTTAT
*
1309379 TT-TTTC-TTTCTTTT
1 TTCTTTCTTTTCTTAT
*
1309393 TTCCTT-TTTT-TTAT
1 TTCTTTCTTTTCTTAT
1309407 TTCTTTCTTTTCTATAT
1 TTCTTTCTTTTCT-TAT
1309424 TT
1 TT
1309426 TTTTATGTCT
Statistics
Matches: 60, Mismatches: 8, Indels: 18
0.70 0.09 0.21
Matches are distributed among these distances:
14 24 0.40
15 24 0.40
16 5 0.08
17 7 0.12
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (16 bp):
TTCTTTCTTTTCTTAT
Found at i:1309426 original size:25 final size:25
Alignment explanation
Indices: 1309381--1309431 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1309371 TTTCTTATTT
* *
1309381 TTTCTTTCTTTTTTCCTTTTTTTTA
1 TTTCTTTCTTTTCTCATTTTTTTTA
1309406 TTTCTTTCTTTTCT-ATATTTTTTTA
1 TTTCTTTCTTTTCTCAT-TTTTTTTA
1309431 T
1 T
1309432 GTCTCATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTCTTTCTTTTCTCATTTTTTTTA
Found at i:1309707 original size:2 final size:2
Alignment explanation
Indices: 1309700--1309728 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1309690 ACAACAATGG
1309700 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 A
1309729 AATAAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1310686 original size:2 final size:2
Alignment explanation
Indices: 1310679--1310707 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1310669 ACATTTTCTT
1310679 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1310708 TTCATTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1312511 original size:3 final size:3
Alignment explanation
Indices: 1312503--1312540 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1312493 TCTAGAGTTC
1312503 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1312541 CTTCAGGCGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:1316965 original size:21 final size:21
Alignment explanation
Indices: 1316922--1316965 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1316912 ACATGACAGA
*
1316922 TGGATTGTCATGTCAATATCG
1 TGGATTGTCATGTCAATACCG
*
1316943 TGGATTGTCATGTCAGTACCG
1 TGGATTGTCATGTCAATACCG
1316964 TG
1 TG
1316966 AAGTACCACA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.36
Consensus pattern (21 bp):
TGGATTGTCATGTCAATACCG
Found at i:1318971 original size:19 final size:19
Alignment explanation
Indices: 1318949--1319075 Score: 80
Period size: 19 Copynumber: 6.5 Consensus size: 19
1318939 GGGTCAGACT
* *
1318949 GGTCAAACCGATTCAGATC
1 GGTCAAACCGATTCAAACC
*
1318968 GGTCAAACCGGTTCAAACC
1 GGTCAAACCGATTCAAACC
*
1318987 GGTCGAAACCG-GTCAAACC
1 GGTC-AAACCGATTCAAACC
* * * *
1319006 GGTTCAGATCG-GTCAAATC
1 GG-TCAAACCGATTCAAACC
* *
1319025 GGTTCGAACCG-GTCGAAACC
1 GG-TCAAACCGATTC-AAACC
*
1319045 GGTCAGAACCGATTGAAAACC
1 GGTCA-AACCGATT-CAAACC
1319066 GGTCAAACCG
1 GGTCAAACCG
1319076 GTTTCCAGCC
Statistics
Matches: 88, Mismatches: 14, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
19 53 0.60
20 24 0.27
21 11 0.12
ACGTcount: A:0.31, C:0.28, G:0.25, T:0.17
Consensus pattern (19 bp):
GGTCAAACCGATTCAAACC
Found at i:1318985 original size:10 final size:9
Alignment explanation
Indices: 1318967--1319077 Score: 96
Period size: 10 Copynumber: 11.4 Consensus size: 9
1318957 CGATTCAGAT
1318967 CGGTCAAAC
1 CGGTCAAAC
1318976 CGGTTCAAAC
1 CGG-TCAAAC
1318986 CGGTCGAAAC
1 CGGTC-AAAC
1318996 CGGTCAAAC
1 CGGTCAAAC
* *
1319005 CGGTTCAGAT
1 CGG-TCAAAC
*
1319015 CGGTCAAAT
1 CGGTCAAAC
*
1319024 CGGTTCGAAC
1 CGG-TCAAAC
1319034 CGGTCGAAAC
1 CGGTC-AAAC
1319044 CGGTCAGAAC
1 CGGTCA-AAC
* *
1319054 CGATTGAAAAC
1 CG-GT-CAAAC
1319065 CGGTCAAAC
1 CGGTCAAAC
1319074 CGGT
1 CGGT
1319078 TTCCAGCCCT
Statistics
Matches: 84, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
9 31 0.37
10 46 0.55
11 6 0.07
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:1318999 original size:29 final size:28
Alignment explanation
Indices: 1318967--1319077 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 28
1318957 CGATTCAGAT
1318967 CGGTCAAACCGGTTCAAACCGGTCGAAAC
1 CGGTCAAACCGGTTCAAACCGGTC-AAAC
* * *
1318996 CGGTCAAACCGGTTCAGATCGGTCAAAT
1 CGGTCAAACCGGTTCAAACCGGTCAAAC
*
1319024 CGGTTCGAACCGG-TCGAAACCGGTCAGAAC
1 CGG-TCAAACCGGTTC-AAACCGGTCA-AAC
* *
1319054 CGATTGAAAACCGG-TCAAACCGGT
1 CG-GT-CAAACCGGTTCAAACCGGT
1319078 TTCCAGCCCT
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
28 8 0.12
29 38 0.57
30 13 0.19
31 8 0.12
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (28 bp):
CGGTCAAACCGGTTCAAACCGGTCAAAC
Found at i:1319004 original size:48 final size:48
Alignment explanation
Indices: 1318949--1319078 Score: 188
Period size: 48 Copynumber: 2.7 Consensus size: 48
1318939 GGGTCAGACT
1318949 GGTCAAACCGATTCAGATCGGTCAAACCGGTTCAAACCGGTCGAAACC
1 GGTCAAACCGATTCAGATCGGTCAAACCGGTTCAAACCGGTCGAAACC
* * *
1318997 GGTCAAACCGGTTCAGATCGGTCAAATCGGTTCGAACCGGTCGAAACC
1 GGTCAAACCGATTCAGATCGGTCAAACCGGTTCAAACCGGTCGAAACC
* * *
1319045 GGTCAGAACCGATTGAAAACCGGTCAAACCGGTT
1 GGTCA-AACCGATT-CAGATCGGTCAAACCGGTT
1319079 TCCAGCCCTC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
48 50 0.69
49 7 0.10
50 15 0.21
ACGTcount: A:0.30, C:0.27, G:0.25, T:0.18
Consensus pattern (48 bp):
GGTCAAACCGATTCAGATCGGTCAAACCGGTTCAAACCGGTCGAAACC
Found at i:1326203 original size:5 final size:5
Alignment explanation
Indices: 1326193--1326230 Score: 69
Period size: 5 Copynumber: 7.8 Consensus size: 5
1326183 AAAGGTCAAC
1326193 GGTCG GGTCG GGTCG GGTCG GGTC- GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
1326231 AGACCGGTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.00, C:0.21, G:0.58, T:0.21
Consensus pattern (5 bp):
GGTCG
Found at i:1326238 original size:19 final size:19
Alignment explanation
Indices: 1326198--1326239 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1326188 TCAACGGTCG
* **
1326198 GGTCGGGTCGGGTCGGGTC
1 GGTCGGGTCGGGTCAGACC
1326217 GGTCGGGTCGGGTCAGACC
1 GGTCGGGTCGGGTCAGACC
1326236 GGTC
1 GGTC
1326240 AAACCGGTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.05, C:0.24, G:0.52, T:0.19
Consensus pattern (19 bp):
GGTCGGGTCGGGTCAGACC
Found at i:1326251 original size:19 final size:19
Alignment explanation
Indices: 1326229--1326345 Score: 139
Period size: 19 Copynumber: 6.1 Consensus size: 19
1326219 TCGGGTCGGG
1326229 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
1326248 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
1326267 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
1326286 TC-GAACCGGTCGAAACCGG-
1 TCAG-ACCGGTC-AAACCGGT
* * *
1326305 TCAAACCGATCAGAACCGAT
1 TCAGACCGGTCA-AACCGGT
* *
1326325 TGAAAACCGGTCAAACCGGT
1 T-CAGACCGGTCAAACCGGT
1326345 T
1 T
1326346 TCCAGCCCTC
Statistics
Matches: 86, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
18 2 0.02
19 60 0.70
20 15 0.17
21 9 0.10
ACGTcount: A:0.30, C:0.30, G:0.25, T:0.15
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:1326292 original size:10 final size:9
Alignment explanation
Indices: 1326241--1326295 Score: 51
Period size: 10 Copynumber: 5.8 Consensus size: 9
1326231 AGACCGGTCA
1326241 AACCGGTTC
1 AACCGGTTC
1326250 AGACCGG-TC
1 A-ACCGGTTC
1326259 AAACCGGTTC
1 -AACCGGTTC
1326269 AGACCGG-TC
1 A-ACCGGTTC
1326278 AAACCGGTTC
1 -AACCGGTTC
1326288 GAACCGGT
1 -AACCGGT
1326296 CGAAACCGGT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
9 16 0.41
10 23 0.59
ACGTcount: A:0.25, C:0.31, G:0.27, T:0.16
Consensus pattern (9 bp):
AACCGGTTC
Found at i:1326292 original size:29 final size:27
Alignment explanation
Indices: 1326227--1326344 Score: 110
Period size: 29 Copynumber: 4.1 Consensus size: 27
1326217 GGTCGGGTCG
* *
1326227 GGTCAGACCGGTCAAACCGGTTCAGACC
1 GGTCAAACCGGTCAAACCGG-TCAAACC
*
1326255 GGTCAAACCGGTTCAGACCGGTCAAACC
1 GGTCAAACCGG-TCAAACCGGTCAAACC
*
1326283 GGTTCGAACCGGTCGAAACCGGTCAAACC
1 GG-TCAAACCGGTC-AAACCGGTCAAACC
* * *
1326312 GATCAGAACCGATTGAAAACCGGTCAAACC
1 GGTCA-AACCG-GT-CAAACCGGTCAAACC
1326342 GGT
1 GGT
1326345 TTCCAGCCCT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
28 22 0.30
29 35 0.47
30 17 0.23
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (27 bp):
GGTCAAACCGGTCAAACCGGTCAAACC
Found at i:1326302 original size:10 final size:9
Alignment explanation
Indices: 1326227--1326344 Score: 110
Period size: 9 Copynumber: 12.3 Consensus size: 9
1326217 GGTCGGGTCG
*
1326227 GGTCAGACC
1 GGTCAAACC
1326236 GGTCAAACC
1 GGTCAAACC
*
1326245 GGTTCAGACC
1 GG-TCAAACC
1326255 GGTCAAACC
1 GGTCAAACC
*
1326264 GGTTCAGACC
1 GG-TCAAACC
1326274 GGTCAAACC
1 GGTCAAACC
*
1326283 GGTTCGAACC
1 GG-TCAAACC
1326293 GGTCGAAACC
1 GGTC-AAACC
1326303 GGTCAAACC
1 GGTCAAACC
*
1326312 GATCAGAACC
1 GGTCA-AACC
* *
1326322 GATTGAAAACC
1 G-GT-CAAACC
1326333 GGTCAAACC
1 GGTCAAACC
1326342 GGT
1 GGT
1326345 TTCCAGCCCT
Statistics
Matches: 90, Mismatches: 12, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
9 45 0.50
10 38 0.42
11 6 0.07
12 1 0.01
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:1327578 original size:23 final size:23
Alignment explanation
Indices: 1327542--1327588 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
1327532 TAATTTATGT
*
1327542 AAAAAATAAGTATTTAA-ATTTA
1 AAAAAATAAGTATTAAATATTTA
*
1327564 AAAAAATAATTTATTAAATATTTA
1 AAAAAATAA-GTATTAAATATTTA
1327588 A
1 A
1327589 TTATGTACGG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 9 0.43
23 6 0.29
24 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (23 bp):
AAAAAATAAGTATTAAATATTTA
Found at i:1328689 original size:15 final size:15
Alignment explanation
Indices: 1328669--1328750 Score: 112
Period size: 15 Copynumber: 5.5 Consensus size: 15
1328659 TTCCGGAAAA
*
1328669 TGAATTACTGGAGTT
1 TGAATTACTGGAATT
1328684 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1328699 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
1328714 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
1328729 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
1328743 TGAATTAC
1 TGAATTAC
1328751 ATTTCTGGAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
14 12 0.20
15 47 0.80
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:1328714 original size:45 final size:44
Alignment explanation
Indices: 1328663--1328750 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 44
1328653 TTGGTTTTCC
* **
1328663 GGAAAATGAATTACTGGAGTTTGAATTACTGGAATTTGAATTACT
1 GGAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACT
1328708 GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1328751 ATTTCTGGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.39, C:0.07, G:0.22, T:0.33
Consensus pattern (44 bp):
GGAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACT
Found at i:1328748 original size:29 final size:30
Alignment explanation
Indices: 1328669--1328750 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
1328659 TTCCGGAAAA
***
1328669 TGAATTACTGGAGTTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
1328699 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
1328729 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
1328751 ATTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 16 0.33
30 33 0.67
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:1328756 original size:20 final size:20
Alignment explanation
Indices: 1328733--1328782 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
1328723 GGAATTTGAA
1328733 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1328753 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
1328773 TTCTGGAAAA
1 TTCTGGAAAA
1328783 CATCTGAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:1329034 original size:30 final size:28
Alignment explanation
Indices: 1328978--1329079 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 28
1328968 TTTACTAAAA
*
1328978 TATTATTGAAATATATAAATAA-TATTAT
1 TATTATT-AAATATATAAAAAATTATTAT
1329006 TCATTATTAAATATATAAAAAATTTATTAT
1 T-ATTATTAAATATATAAAAAA-TTATTAT
* *
1329036 ATATTATTAAA-ATAAAATAAAATATCTTA-
1 -TATTATTAAATATATAA-AAAAT-TATTAT
1329065 TATTATTATAATATA
1 TATTATTA-AATATA
1329080 ATTGATTATT
Statistics
Matches: 63, Mismatches: 3, Indels: 14
0.79 0.04 0.17
Matches are distributed among these distances:
28 22 0.35
29 14 0.22
30 26 0.41
31 1 0.02
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (28 bp):
TATTATTAAATATATAAAAAATTATTAT
Found at i:1329093 original size:28 final size:28
Alignment explanation
Indices: 1328977--1329121 Score: 87
Period size: 28 Copynumber: 4.9 Consensus size: 28
1328967 CTTTACTAAA
* * * *
1328977 ATATTATTGAAAT-ATATAAATAATATT
1 ATATTATTAAAATAAAATAAATTATTTT
*
1329004 ATTCATTATTAAATATATAAA-AAATTTATTAT
1 A-T-ATTATTAAA-ATA-AAATAAA-TTATTTT
* *
1329036 ATATTATTAAAATAAAATAAAATATCTT
1 ATATTATTAAAATAAAATAAATTATTTT
* * **
1329064 ATATTATTATAATATAATTGATTATTTT
1 ATATTATTAAAATAAAATAAATTATTTT
*
1329092 ATATAATATTAAAAATATAATATAATTATT
1 ATAT--TATT-AAAATAAAATA-AATTATT
1329122 AAATATTAAT
Statistics
Matches: 90, Mismatches: 17, Indels: 17
0.73 0.14 0.14
Matches are distributed among these distances:
27 1 0.01
28 34 0.38
29 14 0.16
30 15 0.17
31 13 0.14
32 13 0.14
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (28 bp):
ATATTATTAAAATAAAATAAATTATTTT
Found at i:1329116 original size:19 final size:18
Alignment explanation
Indices: 1329092--1329137 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
1329082 TGATTATTTT
1329092 ATATAATATTAAAAATATA
1 ATATAATATTAAAAAT-TA
*
1329111 ATATAATTATTAAATATTA
1 ATATAA-TATTAAAAATTA
1329130 ATA-AATAT
1 ATATAATAT
1329138 ATTTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 3 0.12
18 2 0.08
19 11 0.44
20 9 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAATATTAAAAATTA
Found at i:1329146 original size:21 final size:24
Alignment explanation
Indices: 1329105--1329149 Score: 69
Period size: 21 Copynumber: 2.0 Consensus size: 24
1329095 TAATATTAAA
1329105 AATATAATATAATTATTAAATATT
1 AATATAATATAATTATTAAATATT
1329129 AATA-AATAT-ATT-TTAAATATT
1 AATATAATATAATTATTAAATATT
1329150 TTAATAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.43
22 3 0.14
23 5 0.24
24 4 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
AATATAATATAATTATTAAATATT
Found at i:1329149 original size:28 final size:27
Alignment explanation
Indices: 1329096--1329149 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
1329086 TATTTTATAT
*
1329096 AATATTAAAAATATAATATAATTATTA
1 AATATTAAAAATATAATATAAATATTA
* *
1329123 AATATTAATAAATATATTTTAAATATT
1 AATATTAA-AAATATAATATAAATATT
1329150 TTAATAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
AATATTAAAAATATAATATAAATATTA
Found at i:1329155 original size:19 final size:22
Alignment explanation
Indices: 1329092--1329155 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 22
1329082 TGATTATTTT
*
1329092 ATATAA-TATTAAA-AATA-TA
1 ATATAATTATTAAATATTATTA
*
1329111 ATATAATTATTAAATATTAATA
1 ATATAATTATTAAATATTATTA
1329133 A-ATATATT-TTAAATATT-TTA
1 ATATA-ATTATTAAATATTATTA
1329153 ATA
1 ATA
1329156 ATTAATATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
19 6 0.16
20 10 0.26
21 16 0.42
22 6 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATAATTATTAAATATTATTA
Found at i:1329400 original size:42 final size:42
Alignment explanation
Indices: 1329341--1329452 Score: 206
Period size: 42 Copynumber: 2.7 Consensus size: 42
1329331 AATTACATTC
**
1329341 CGGAAAACGAATTACGTGAAACAAACACGGGAAAATGTTTTT
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTT
1329383 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTT
1 CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTT
1329425 CGGAAAACGAATTACGTGAAACAAACAC
1 CGGAAAACGAATTACGTGAAACAAACAC
1329453 TGAAATTCGG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 68 1.00
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.18
Consensus pattern (42 bp):
CGGAAAACGAATTACGTGAAACAAACACGGGAAAACATTTTT
Found at i:1340353 original size:21 final size:21
Alignment explanation
Indices: 1340324--1340365 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1340314 ATTGCTAACA
*
1340324 TTACTCTCAATATCGATATTG
1 TTACCCTCAATATCGATATTG
*
1340345 TTACCCTCAGTATCGATATTG
1 TTACCCTCAATATCGATATTG
1340366 CTCCTTAGAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.12, T:0.40
Consensus pattern (21 bp):
TTACCCTCAATATCGATATTG
Found at i:1340685 original size:23 final size:23
Alignment explanation
Indices: 1340659--1340712 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
1340649 GTTATAAATT
1340659 TGAATACAATAATAAAGGTCCTA
1 TGAATACAATAATAAAGGTCCTA
*
1340682 TGAATATAATAATAAAGGTCCTA
1 TGAATACAATAATAAAGGTCCTA
1340705 TGAATACA
1 TGAATACA
1340713 TATGCCCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.48, C:0.11, G:0.13, T:0.28
Consensus pattern (23 bp):
TGAATACAATAATAAAGGTCCTA
Found at i:1343034 original size:31 final size:31
Alignment explanation
Indices: 1342996--1343149 Score: 238
Period size: 31 Copynumber: 5.0 Consensus size: 31
1342986 GGGTCGAGGG
1342996 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1343027 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1343058 TTACCTATGTTCTTCGGAACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1343089 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1343120 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1343150 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1347268 original size:31 final size:31
Alignment explanation
Indices: 1347230--1347383 Score: 238
Period size: 31 Copynumber: 5.0 Consensus size: 31
1347220 GGGTCGAGGG
1347230 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
1347261 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1347292 TTACCTATGTTCTTCGGAACATACGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1347323 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
1347354 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
1347384 GTCCTTCGGG
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 112 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:1351884 original size:101 final size:101
Alignment explanation
Indices: 1351708--1351917 Score: 350
Period size: 101 Copynumber: 2.1 Consensus size: 101
1351698 GGGTCTACGC
1351708 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAATCTGGTGAGACACATACTTGATC
1 GGTCCTTCGGGACA-ATATGTATTCTTTGGAACATGTGTGAATCTGGTGAGACACATACTTGATC
* * *
1351773 ATTGGTATATGTATATGATTCTTAATGAATGATATGT
65 ACTAGTATATGTATATGATTCTTAAGGAATGATATGT
1351810 GGTCCTTCGGGAC-ATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GGTCCTTCGGGACAATATGTATTCTTTGGAACATGTGTGAA-TCTGGTGAGACACATACTTGATC
*
1351874 CCTAGTATATGTATATGATTCTTAAGGAATGATATGT
65 ACTAGTATATGTATATGATTCTTAAGGAATGATATGT
*
1351911 GCTCCTT
1 GGTCCTT
1351918 ATGGACATTA
Statistics
Matches: 102, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
100 27 0.26
101 62 0.61
102 13 0.13
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (101 bp):
GGTCCTTCGGGACAATATGTATTCTTTGGAACATGTGTGAATCTGGTGAGACACATACTTGATCA
CTAGTATATGTATATGATTCTTAAGGAATGATATGT
Found at i:1351967 original size:23 final size:23
Alignment explanation
Indices: 1351934--1352001 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
1351924 ATTATTATAT
1351934 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* * *
1351957 GGCACTCCGGTGTAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
1351980 GGAACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1352002 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.22, C:0.25, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1360391 original size:3 final size:3
Alignment explanation
Indices: 1360379--1360427 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
1360369 ACTGAAAGTA
1360379 AAT AAT -AT AAT AAT AAT AAT AAT AAT AA- AAT AAT -AT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1360424 AAT A
1 AAT A
1360428 TAAATAAGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 6 0.14
3 37 0.86
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1360398 original size:14 final size:14
Alignment explanation
Indices: 1360379--1360430 Score: 88
Period size: 14 Copynumber: 3.7 Consensus size: 14
1360369 ACTGAAAGTA
1360379 AATAATATAATAAT
1 AATAATATAATAAT
1360393 AATAATAATAATAA-
1 AATAAT-ATAATAAT
1360407 AATAATATAATAAT
1 AATAATATAATAAT
1360421 AATAATATAA
1 AATAATATAA
1360431 ATAAGTACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.19
14 22 0.61
15 7 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATATAATAAT
Found at i:1360594 original size:2 final size:2
Alignment explanation
Indices: 1360587--1360611 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1360577 TTGAACTTTC
1360587 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
1360612 TAATAATTAA
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:1365780 original size:16 final size:16
Alignment explanation
Indices: 1365759--1365789 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1365749 GTTAGTATAG
*
1365759 TTTTTAATTTATTTTA
1 TTTTTAAGTTATTTTA
1365775 TTTTTAAGTTATTTT
1 TTTTTAAGTTATTTT
1365790 CATGTATGTT
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:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTAAGTTATTTTA
Found at i:1365847 original size:39 final size:40
Alignment explanation
Indices: 1365803--1365880 Score: 133
Period size: 39 Copynumber: 2.0 Consensus size: 40
1365793 GTATGTTTGG
1365803 TTGTTTGGTTAGTGAGAAAGTT-AA-AAACTGATAAGAAAC
1 TTGTTTGGTTAGTGAGAAAGTTGAAGAAA-TGATAAGAAAC
1365842 TTGTTTGGTTAGTGAGAAAGTTGAAGAAATGATAAGAAA
1 TTGTTTGGTTAGTGAGAAAGTTGAAGAAATGATAAGAAA
1365881 ATAAGGGAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
39 22 0.59
40 12 0.32
41 3 0.08
ACGTcount: A:0.41, C:0.03, G:0.26, T:0.31
Consensus pattern (40 bp):
TTGTTTGGTTAGTGAGAAAGTTGAAGAAATGATAAGAAAC
Found at i:1366905 original size:21 final size:21
Alignment explanation
Indices: 1366863--1366905 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1366853 TTTCTGGGCT
* *
1366863 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1366884 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1366905 A
1 A
1366906 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1367582 original size:23 final size:23
Alignment explanation
Indices: 1367556--1367623 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1367546 ATTATTATAT
*
1367556 GGCACTACGGTGCAATTCTATGC
1 GGCACTACGGTGCAATTCTACGC
* *
1367579 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
1367602 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
1367624 AGTTGTGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1373702 original size:21 final size:21
Alignment explanation
Indices: 1373660--1373702 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1373650 ATTTTGGGCT
*
1373660 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
1373681 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
1373702 A
1 A
1373703 ACGAATATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:1374384 original size:23 final size:23
Alignment explanation
Indices: 1374351--1374413 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1374341 ATTATTATAT
1374351 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
1374374 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
1374397 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
1374414 ATAAGAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:1376111 original size:18 final size:18
Alignment explanation
Indices: 1376084--1376174 Score: 119
Period size: 18 Copynumber: 4.9 Consensus size: 18
1376074 ATTGAATATT
*
1376084 TGTCCCGAAGTACCACTA
1 TGTCCCGAAGGACCACTA
*
1376102 TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
1376120 TGTCCCGAAGGACCACTGA
1 TGTCCCGAAGGACCACT-A
* *
1376139 TTGTTCCGAAGAACCACTA
1 -TGTCCCGAAGGACCACTA
*
1376158 TGTCCCAAAGGACCACT
1 TGTCCCGAAGGACCACT
1376175 GATAATCCCT
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
18 46 0.73
19 2 0.03
20 15 0.24
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.21
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1376169 original size:38 final size:38
Alignment explanation
Indices: 1376084--1376177 Score: 131
Period size: 38 Copynumber: 2.5 Consensus size: 38
1376074 ATTGAATATT
* *
1376084 TGTCCCGAAGTACCACT-A-TGTCCTGAAGGACCACTA
1 TGTCCCGAAGGACCACTGATTGTCCTGAAGAACCACTA
1376120 TGTCCCGAAGGACCACTGATTGTTCC-GAAGAACCACTA
1 TGTCCCGAAGGACCACTGATTG-TCCTGAAGAACCACTA
*
1376158 TGTCCCAAAGGACCACTGAT
1 TGTCCCGAAGGACCACTGAT
1376178 AATCCCTTGA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
36 16 0.31
37 1 0.02
38 32 0.62
39 3 0.06
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (38 bp):
TGTCCCGAAGGACCACTGATTGTCCTGAAGAACCACTA
Found at i:1376938 original size:22 final size:22
Alignment explanation
Indices: 1376913--1376958 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1376903 AAAATTTTAT
1376913 GGGATTTTACCTTTGATGCATC
1 GGGATTTTACCTTTGATGCATC
1376935 GGGATTTTACCTTTGATGCATC
1 GGGATTTTACCTTTGATGCATC
1376957 GG
1 GG
1376959 TACACATTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.39
Consensus pattern (22 bp):
GGGATTTTACCTTTGATGCATC
Found at i:1377248 original size:19 final size:18
Alignment explanation
Indices: 1377224--1377265 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1377214 CGATGACAAG
1377224 TCAAAT-TCAACCTCTGATT
1 TCAAATATCAA-CTCT-ATT
*
1377243 TCAAATATGAACTCTATT
1 TCAAATATCAACTCTATT
1377261 TCAAA
1 TCAAA
1377266 ATCCCATTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 8 0.38
19 10 0.48
20 3 0.14
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.36
Consensus pattern (18 bp):
TCAAATATCAACTCTATT
Found at i:1380423 original size:18 final size:18
Alignment explanation
Indices: 1380400--1380454 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 18
1380390 CTTTGTCCAA
1380400 TAATTCTTGTAATTTATT
1 TAATTCTTGTAATTTATT
1380418 TAATTCTTGTAATTCTTTTTATT
1 TAATTCTTGTAA-----TTTATT
1380441 TAATTCTTGTAATT
1 TAATTCTTGTAATT
1380455 CTTTTGGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
18 14 0.44
23 18 0.56
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.62
Consensus pattern (18 bp):
TAATTCTTGTAATTTATT
Found at i:1380430 original size:9 final size:9
Alignment explanation
Indices: 1380400--1380457 Score: 54
Period size: 9 Copynumber: 6.9 Consensus size: 9
1380390 CTTTGTCCAA
1380400 TAATTCTTG
1 TAATTCTTG
*
1380409 TAATT-TATT
1 TAATTCT-TG
1380418 TAATTCTTG
1 TAATTCTTG
1380427 TAATTCTT-
1 TAATTCTTG
*
1380435 T--TTATT-
1 TAATTCTTG
1380441 TAATTCTTG
1 TAATTCTTG
1380450 TAATTCTT
1 TAATTCTT
1380458 TTGGGGTCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
6 5 0.12
8 6 0.15
9 28 0.70
10 1 0.03
ACGTcount: A:0.24, C:0.09, G:0.05, T:0.62
Consensus pattern (9 bp):
TAATTCTTG
Found at i:1380442 original size:23 final size:23
Alignment explanation
Indices: 1380412--1380459 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
1380402 ATTCTTGTAA
1380412 TTTATTTAATTCTTGTAATTCTT
1 TTTATTTAATTCTTGTAATTCTT
1380435 TTTATTTAATTCTTGTAATTCTT
1 TTTATTTAATTCTTGTAATTCTT
1380458 TT
1 TT
1380460 GGGGTCATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.08, G:0.04, T:0.67
Consensus pattern (23 bp):
TTTATTTAATTCTTGTAATTCTT
Found at i:1380469 original size:23 final size:23
Alignment explanation
Indices: 1380418--1380470 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
1380408 GTAATTTATT
* **
1380418 TAATTCTTGTAATTCTTTTTATT
1 TAATTCTTGTAATTCTTTTGAGG
*
1380441 TAATTCTTGTAATTCTTTTGGGG
1 TAATTCTTGTAATTCTTTTGAGG
*
1380464 TCATTCT
1 TAATTCT
1380471 GTATGGTGTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.19, C:0.11, G:0.11, T:0.58
Consensus pattern (23 bp):
TAATTCTTGTAATTCTTTTGAGG
Found at i:1383012 original size:18 final size:18
Alignment explanation
Indices: 1382989--1383060 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
1382979 ACTGAATATT
1382989 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
1383007 TGTCCCGAAAGACCACTGA
1 TGTCCCGAAAGACCACT-A
*
1383026 TTGTTCCG-AAGAACCACTA
1 -TGTCCCGAAAG-ACCACTA
*
1383045 -GTCCCGAAGGACCACT
1 TGTCCCGAAAGACCACT
1383061 GATAATCTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
17 11 0.23
18 19 0.40
19 5 0.11
20 12 0.26
ACGTcount: A:0.31, C:0.32, G:0.19, T:0.18
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:1387207 original size:20 final size:20
Alignment explanation
Indices: 1387182--1387228 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1387172 TTCTTCTGAT
1387182 CTGACCTTTGGTAAGGAGAA
1 CTGACCTTTGGTAAGGAGAA
1387202 CTGACCTTTGGTAAGGAGAA
1 CTGACCTTTGGTAAGGAGAA
1387222 CTGACCT
1 CTGACCT
1387229 GTCTTGCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
CTGACCTTTGGTAAGGAGAA
Found at i:1387767 original size:23 final size:23
Alignment explanation
Indices: 1387741--1387832 Score: 112
Period size: 23 Copynumber: 4.0 Consensus size: 23
1387731 CACCACAGCT
* *
1387741 CGTATAAATGCATCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1387764 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
* *
1387787 CGTAGAAATGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1387810 CGTAGAAATGCACCAAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1387833 TATAAGATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.30, C:0.25, G:0.26, T:0.18
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1395829 original size:63 final size:65
Alignment explanation
Indices: 1395688--1395829 Score: 150
Period size: 64 Copynumber: 2.2 Consensus size: 65
1395678 AATTGTTCAA
* * *
1395688 TGTGTATCGATGCA-CAGGAAGTGCATCGATGCACCCATTAAAAATGGAAACATCGAATGCAGTT
1 TGTGTATCGATGCATAAAGAAGTGCATCGATACACCCATTAAAAATGGAAACATCGAATGCAGTT
* * * ** *
1395752 AGTGCATCGATGCATAAAG-AGTGCATCGATACACCCCTT-AGGATTGAAACATCGAAGGTG-A-
1 TGTGTATCGATGCATAAAGAAGTGCATCGATACACCCATTAAAAATGGAAACATCGAA--TGCAG
1395813 TT
64 TT
1395815 TGTGTATCGATGCAT
1 TGTGTATCGATGCAT
1395830 GGGTAGCGCA
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
63 29 0.45
64 31 0.48
65 4 0.06
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.25
Consensus pattern (65 bp):
TGTGTATCGATGCATAAAGAAGTGCATCGATACACCCATTAAAAATGGAAACATCGAATGCAGTT
Found at i:1396816 original size:23 final size:23
Alignment explanation
Indices: 1396784--1396849 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 23
1396774 CCTTATTTAG
*
1396784 CACTTTGGTGCATTTCTACGCGA
1 CACTTCGGTGCATTTCTACGCGA
* *** * *
1396807 CACTTCGGTGTAAGCCTACGTGG
1 CACTTCGGTGCATTTCTACGCGA
*
1396830 CACTTCGGTGCATTTATACG
1 CACTTCGGTGCATTTCTACG
1396850 AGCTGTGGTG
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.18, C:0.26, G:0.24, T:0.32
Consensus pattern (23 bp):
CACTTCGGTGCATTTCTACGCGA
Found at i:1398801 original size:19 final size:19
Alignment explanation
Indices: 1398739--1398808 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
1398729 ATTTTACGGA
*
1398739 AATAATGTTCATACGGTAT
1 AATACTGTTCATACGGTAT
* *
1398758 AATATTGTTCATATGGTAT
1 AATACTGTTCATACGGTAT
* *
1398777 AGTACTGTTCATACCGTAT
1 AATACTGTTCATACGGTAT
* *
1398796 ATTACTATTCATA
1 AATACTGTTCATA
1398809 AAAATGTTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 43 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (19 bp):
AATACTGTTCATACGGTAT
Found at i:1399054 original size:9 final size:9
Alignment explanation
Indices: 1399042--1399073 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
1399032 TATGAAGGTT
1399042 AGATATAAG
1 AGATATAAG
1399051 AGATATAAG
1 AGATATAAG
1399060 AGATATAAG
1 AGATATAAG
*
1399069 TGATA
1 AGATA
1399074 ACATGAGAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.22, T:0.25
Consensus pattern (9 bp):
AGATATAAG
Found at i:1399386 original size:2 final size:2
Alignment explanation
Indices: 1399381--1399417 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1399371 ATATATTAAT
1399381 TA TA TA TA TA T- 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
1399418 AAAGAGTATG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1399391 original size:15 final size:17
Alignment explanation
Indices: 1399371--1399417 Score: 73
Period size: 16 Copynumber: 2.9 Consensus size: 17
1399361 GATAAGAACA
1399371 ATATATTA-AT-TATAT
1 ATATATTATATATATAT
1399386 ATATATTATATATATAT
1 ATATATTATATATATAT
1399403 ATATA-TATATATATA
1 ATATATTATATATATA
1399418 AAAGAGTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 8 0.27
16 12 0.40
17 10 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATATTATATATATAT
Found at i:1400145 original size:17 final size:17
Alignment explanation
Indices: 1400123--1400156 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1400113 AACCCAACTC
1400123 AAAATAATATATTTATT
1 AAAATAATATATTTATT
* *
1400140 AAAATATTATTTTTATT
1 AAAATAATATATTTATT
1400157 CAATATAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AAAATAATATATTTATT
Found at i:1400553 original size:18 final size:18
Alignment explanation
Indices: 1400503--1400553 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
1400493 TGGTTTAATA
*
1400503 TATCACATTAATATTTTAT
1 TATCA-ATTAATAATTTAT
* * *
1400522 TATAAATGATTAATTTAT
1 TATCAATTAATAATTTAT
1400540 TATCAATTAATAAT
1 TATCAATTAATAAT
1400554 CGCTAATTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
18 21 0.84
19 4 0.16
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (18 bp):
TATCAATTAATAATTTAT
Found at i:1402496 original size:2 final size:2
Alignment explanation
Indices: 1402491--1402519 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1402481 TCGCCCCCCT
1402491 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1402520 AGGGTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1420132 original size:28 final size:28
Alignment explanation
Indices: 1420092--1420149 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
1420082 GATAACTCCT
1420092 TATCATCTGCCTGAAATTAGAGTAGGCA
1 TATCATCTGCCTGAAATTAGAGTAGGCA
1420120 TATCATCTGCCTGAAATTAGAGTAGGCA
1 TATCATCTGCCTGAAATTAGAGTAGGCA
1420148 TA
1 TA
1420150 ATTGTTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (28 bp):
TATCATCTGCCTGAAATTAGAGTAGGCA
Found at i:1421179 original size:90 final size:93
Alignment explanation
Indices: 1421011--1421195 Score: 279
Period size: 90 Copynumber: 2.0 Consensus size: 93
1421001 GTGCATCTAG
1421011 AATTGTTCTGTTCCCTAGAAGATGACATAACCTAATCTGAATCATTTATAGTAATATCACTTTCA
1 AATTGTTCTGTTCCCTAGAAGATGACA-AACCTAATCTGAATCATTTATAGTAATATCACTTTCA
*
1421076 TAATGGATGTTATTGCTGTTTTCATATGT
65 TAATGGATGTTATTACTGTTTTCATATGT
* * *
1421105 AATTGTTCTGTTCCCTTGAA-ATTGAC-AACCTAATCTGAATCATTTCTGGT-A-ATCACTTTCA
1 AATTGTTCTGTTCCCTAGAAGA-TGACAAACCTAATCTGAATCATTTATAGTAATATCACTTTCA
*
1421166 TAATGGATGTTATTACTGTTTTCGTATGT
65 TAATGGATGTTATTACTGTTTTCATATGT
1421195 A
1 A
1421196 TCAGATTGCT
Statistics
Matches: 85, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
90 38 0.45
91 1 0.01
92 22 0.26
93 1 0.01
94 23 0.27
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (93 bp):
AATTGTTCTGTTCCCTAGAAGATGACAAACCTAATCTGAATCATTTATAGTAATATCACTTTCAT
AATGGATGTTATTACTGTTTTCATATGT
Found at i:1423936 original size:23 final size:23
Alignment explanation
Indices: 1423873--1423941 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
1423863 CACCACAGCT
* *
1423873 CGTATAAATGCACCGAAGTTCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
1423896 CGTAGAATTACACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
1423919 CGTAGAAATGCACTGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1423942 TATAAAATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1428305 original size:21 final size:21
Alignment explanation
Indices: 1428265--1428305 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1428255 CTTTCTCTAA
*
1428265 CAATTCTTGCAATTGATTCAT
1 CAATTCTTGCAATTCATTCAT
*
1428286 CAATTCTTGCAATTCTTTCA
1 CAATTCTTGCAATTCATTCA
1428306 GATCCATACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (21 bp):
CAATTCTTGCAATTCATTCAT
Found at i:1429964 original size:65 final size:67
Alignment explanation
Indices: 1429845--1429970 Score: 177
Period size: 65 Copynumber: 1.9 Consensus size: 67
1429835 CTGGTCATAG
* *
1429845 GGTATCGATATCATATGAAGGGGTATCGATACCTCCTCTTAAACGAAAAATTACAGAATGTCAAT
1 GGTATCGATACCATATGAAGGGGTATCGATACCTCCTCTGAAACGAAAAATTACAGAATGTCAAT
1429910 AT
66 AT
* * *
1429912 GGTATCGATACCATAT-AGGGGGTATCGATACC-CC-CTGAAGATGAAAATTTACAGAATGT
1 GGTATCGATACCATATGAAGGGGTATCGATACCTCCTCTGAA-ACGAAAAATTACAGAATGT
1429971 TATCAGGGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
64 4 0.08
65 19 0.36
66 15 0.28
67 15 0.28
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.27
Consensus pattern (67 bp):
GGTATCGATACCATATGAAGGGGTATCGATACCTCCTCTGAAACGAAAAATTACAGAATGTCAAT
AT
Found at i:1429981 original size:65 final size:67
Alignment explanation
Indices: 1429841--1429987 Score: 176
Period size: 65 Copynumber: 2.2 Consensus size: 67
1429831 ATTTCTGGTC
* *
1429841 ATAGGGTATCGATATCATATGAAGGGGTATCGATACCTCCTCTTAAACGAAAAATTACAGAATGT
1 ATAGGGTATCGATACCATATGAAGGGGTATCGATACCTCCTCTGAAACGAAAAATTACAGAATGT
1429906 CA
66 CA
* * * *
1429908 ATATGGTATCGATACCATAT-AGGGGGTATCGATACC-CC-CTGAAGATGAAAATTTACAGAATG
1 ATAGGGTATCGATACCATATGAAGGGGTATCGATACCTCCTCTGAA-ACGAAAAATTACAGAATG
*
1429970 T-T
65 TCA
*
1429972 ATCAGGGTATCTATAC
1 AT-AGGGTATCGATAC
1429988 GATAGGCAGG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
64 6 0.09
65 30 0.43
66 15 0.22
67 18 0.26
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.28
Consensus pattern (67 bp):
ATAGGGTATCGATACCATATGAAGGGGTATCGATACCTCCTCTGAAACGAAAAATTACAGAATGT
CA
Found at i:1429999 original size:20 final size:20
Alignment explanation
Indices: 1429974--1430026 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1429964 AGAATGTTAT
* *
1429974 CAGGGTATCTATACGATAGG
1 CAGGGTATCTATACCATAGA
1429994 CAGGGTATCTATACCATAGA
1 CAGGGTATCTATACCATAGA
1430014 CAGGGTATCTATA
1 CAGGGTATCTATA
1430027 TCTCAGTTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (20 bp):
CAGGGTATCTATACCATAGA
Found at i:1431166 original size:24 final size:24
Alignment explanation
Indices: 1431095--1431174 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
1431085 ACTACGGTGC
* *
1431095 AATTCTAGGTGGCACTTCGATAC-
1 AATTCTACGTGGCACTTCGGTACA
* * * *
1431118 ATTTCTACGCGGTC-CTTTGGGACA
1 AATTCTACGTGG-CACTTCGGTACA
1431142 AATTCTACGTGGCACTTCGGTACA
1 AATTCTACGTGGCACTTCGGTACA
*
1431166 AATTATACG
1 AATTCTACG
1431175 AGTTGTGTTG
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
23 16 0.37
24 27 0.63
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (24 bp):
AATTCTACGTGGCACTTCGGTACA
Found at i:1431885 original size:21 final size:21
Alignment explanation
Indices: 1431861--1431904 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1431851 TACAGAAGTA
*
1431861 CTGTAACAGGGTATCGGTACC
1 CTGTAACAGGGTATCGATACC
*
1431882 CTGTAGCAGGGTATCGATACC
1 CTGTAACAGGGTATCGATACC
1431903 CT
1 CT
1431905 ATTTTTAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (21 bp):
CTGTAACAGGGTATCGATACC
Found at i:1433919 original size:23 final size:23
Alignment explanation
Indices: 1433893--1433936 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1433883 AAAGGGCCAT
*
1433893 GTAGAATTGCACCGAAGTGCCGC
1 GTAGAAATGCACCGAAGTGCCGC
1433916 GTAGAAATGCACCGAAGTGCC
1 GTAGAAATGCACCGAAGTGCC
1433937 ATATAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.25, G:0.30, T:0.16
Consensus pattern (23 bp):
GTAGAAATGCACCGAAGTGCCGC
Found at i:1436608 original size:24 final size:23
Alignment explanation
Indices: 1436568--1436617 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
1436558 GATAATCTGT
* *
1436568 TTTCGCCCCCTAGAATTTTATAA
1 TTTCGCCCCCTAAAATTTTAAAA
1436591 TTTCGTCCCCCTAAAATTTTAAAA
1 TTTCG-CCCCCTAAAATTTTAAAA
1436615 TTT
1 TTT
1436618 GCCTCTAGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 5 0.21
24 19 0.79
ACGTcount: A:0.28, C:0.24, G:0.06, T:0.42
Consensus pattern (23 bp):
TTTCGCCCCCTAAAATTTTAAAA
Found at i:1439720 original size:23 final size:23
Alignment explanation
Indices: 1439694--1439769 Score: 127
Period size: 23 Copynumber: 3.3 Consensus size: 23
1439684 GTTCTATATT
1439694 GTCCTTC-AGGACAAAACTATGTG
1 GTCCTTCGA-GACAAAACTATGTG
1439717 GTCCTTCGAGACAAAACTATGTG
1 GTCCTTCGAGACAAAACTATGTG
*
1439740 GTCCTTCGAGACAAAACTATGGG
1 GTCCTTCGAGACAAAACTATGTG
1439763 GTCCTTC
1 GTCCTTC
1439770 TATTTATATA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
23 50 0.98
24 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (23 bp):
GTCCTTCGAGACAAAACTATGTG
Found at i:1461723 original size:23 final size:23
Alignment explanation
Indices: 1461697--1461765 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
1461687 CACCACAGCT
*
1461697 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
1461720 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
1461743 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1461766 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1462477 original size:63 final size:63
Alignment explanation
Indices: 1462355--1462512 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 63
1462345 TAATGGAGGT
* * *
1462355 ATGCATCGATGCACTACAGCATGCATCGATGCATAAATCCTATTCGATGTTTGTATTT-AATGGG
1 ATGCATCGATGCACTCCA-TATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAAAT-GA
* ** * * * *
1462419 ATGCATCGATGCACTCCTTATGCATCGATGCATTGATGGC-ATTCGATGTTTTTCTTTAAAATTA
1 ATGCATCGATGCACTCCATATGCATCGATGCATAAAT-CCTATTCGATGTTTGTATTT-AAATGA
* *
1462483 ATGCATCGATGCACTTCATGTGCATCGATG
1 ATGCATCGATGCACTCCATATGCATCGATG
1462513 TACCTTAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
63 31 0.40
64 44 0.56
65 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.35
Consensus pattern (63 bp):
ATGCATCGATGCACTCCATATGCATCGATGCATAAATCCTATTCGATGTTTGTATTTAAATGA
Done.